antibody|antibody|NN|_ :|:|:|_ Flag|flag|NN|_
ChIP-Seq|chip-seq|NN|_
Cultures|culture|NNS|_ of|of|IN|_ Caulobacter|caulobacter|NN|_ -LRB-|-lrb-|-LRB-|_ TLS1631-TLS1633|tls1631-tls1633|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30oC|30oC|NNP|_ in|in|IN|_ PYE|PYE|NNP|_ and|and|CC|_ supplemented|supplement|VBN|_ with|with|IN|_ antibiotics|antibiotic|NNS|_ ,|,|,|_ as|as|RB|_ necessary|necessary|JJ|_ ,|,|,|_ at|at|IN|_ appropriate|appropriate|JJ|_ concentrations|concentration|NNS|_ .|.|.|_ To|to|TO|_ deplete|deplete|VB|_ wild-type|wild-type|JJ|_ non-tagged|non-tagged|JJ|_ ParB|parb|NN|_ ,|,|,|_ exponential-phase|exponential-phase|NN|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ off|off|RP|_ xylose|xylose|NN|_ and|and|CC|_ re-introduced|re-introduced|JJ|_ to|to|TO|_ PYE|PYE|NNP|_ +0.2|+0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP for|for|IN|_ an|a|DT|_ additional|additional|JJ|_ 5|5|CD|_ hours|hour|NNS|_ .|.|.|_ After|after|IN|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ vanillate|vanillate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ induce|induce|VB|_ the|the|DT|_ expression|expression|NN|_ of|of|IN|_ flag-parB|flag-parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ flag-parB|flag-parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_
developmental|developmental|JJ|_ stage|stage|NN|_ :|:|:|_ mixed|mixed|JJ|_ population|population|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
DNA|dna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Cell|cell|NN|_ Lysis|lysis|NN|_ and|and|CC|_ Protein|protein|NN|_ Precipitation|precipitation|NN|_ solutions|solution|NNS|_ .|.|.|_ Detailed|detailed|JJ|_ protocols|protocol|NNS|_ are|be|VBP|_ listed|list|VBN|_ in|in|IN|_ the|the|DT|_ Supplementary|Supplementary|NNP|_ Materials|Materials|NNPS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism AB1157|ab1157|NN|_
For|for|IN|_ analysis|analysis|NN|_ of|of|IN|_ ChIP-seq|ChIP-seq|NNP|_ data|datum|NNS|_ ,|,|,|_ Hiseq|Hiseq|NNP|_ 2500|2500|CD|_ Illumina|Illumina|NNP|_ short|short|JJ|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ mapped|map|VBN|_ back|back|RB|_ to|to|TO|_ the|the|DT|_ Caulobacter|Caulobacter|NNP|_ NA1000|na1000|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC-011916.1|nc-011916.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ following|follow|VBG|_ command|command|NN|_ :|:|:|_ bowtie|bowtie|NN|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ -|-|:|_ n|n|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ p|p|NN|_ 4|4|CD|_ --|--|:|_ chunkmbs|chunkmb|NNS|_ 512|512|CD|_ NA1000-bowtie|na1000-bowtie|NN|_ --|--|:|_ sam|sam|NN|_ *|*|NN|_ .|.|.|_ fastq|fastq|NN|_ >|>|JJR|_ output.sam|output.sam|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ the|the|DT|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ at|at|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_ position|position|NN|_ was|be|VBD|_ computed|compute|VBN|_ using|use|VBG|_ BEDTools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Quinlan|Quinlan|NNP|_ and|and|CC|_ Hall|Hall|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ command|command|NN|_ :|:|:|_ bedtools|bedtool|NNS|_ genomecov|genomecov|NN|_ -|-|:|_ d|d|SYM|_ -|-|:|_ ibam|ibam|NN|_ output.sorted.bam|output.sorted.bam|NN|_ -|-|:|_ g|g|NN|_ NA1000.fna|na1000.fna|NN|_ >|>|JJR|_ coverage_output.txt|coverage_output.txt|NN|_ .|.|.|_ For|for|IN|_ analysis|analysis|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ ChIP-seq|ChIP-seq|NNP|_ data|datum|NNS|_ ,|,|,|_ reference|reference|NN|_ genomes|genome|NNS|_ were|be|VBD|_ first|first|JJ|_ reconstructed|reconstruct|VBN|_ in|in|IN|_ silico|silico|NN|_ by|by|IN|_ inserting|insert|VBG|_ the|the|DT|_ nucleotide|nucleotide|NN|_ sequence|sequence|NN|_ of|of|IN|_ parS|pars|NN|_ and|and|CC|_ apramycin|apramycin|NN|_ antibiotic|antibiotic|JJ|_ resistance|resistance|NN|_ cassette|cassette|NN|_ to|to|TO|_ the|the|DT|_ ybbD|ybbd|NN|GEN locus|locus|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ .|.|.|_ Afterwards|afterwards|RB|_ ,|,|,|_ Hiseq|Hiseq|NNP|_ 2500|2500|CD|_ Illumina|Illumina|NNP|_ short|short|JJ|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ back|back|RB|_ to|to|TO|_ these|these|DT|_ reconstructed|reconstruct|VBN|_ reference|reference|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ .|.|.|_ Sequence|sequence|NN|_ coverage|coverage|NN|_ at|at|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_ position|position|NN|_ was|be|VBD|_ also|also|RB|_ computed|compute|VBN|_ using|use|VBG|_ BEDTools|bedtool|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ ChIP-seq|chip-seq|JJ|_ profiles|profile|NNS|_ were|be|VBD|_ plotted|plot|VBN|_ with|with|IN|_ the|the|DT|_ x-axis|x-axis|JJ|_ representing|represent|VBG|_ genomic|genomic|JJ|_ positions|position|NNS|_ and|and|CC|_ the|the|DT|_ y-axis|y-axis|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ base|base|NN|_ pair|pair|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ RPBPM|rpbpm|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ .|.|.|_
For|for|IN|_ analysis|analysis|NN|_ of|of|IN|_ IDAP-seq|idap-seq|JJ|_ data|datum|NNS|_ ,|,|,|_ Hiseq|Hiseq|NNP|_ 2500|2500|CD|_ Illumina|Illumina|NNP|_ short|short|JJ|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ mapped|map|VBN|_ back|back|RB|_ to|to|TO|_ the|the|DT|_ Caulobacter|Caulobacter|NNP|_ NA1000|na1000|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC-011916.1|nc-011916.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ following|follow|VBG|_ command|command|NN|_ :|:|:|_ bowtie|bowtie|NN|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ -|-|:|_ n|n|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ p|p|NN|_ 4|4|CD|_ --|--|:|_ chunkmbs|chunkmb|NNS|_ 512|512|CD|_ NA1000-bowtie|na1000-bowtie|NN|_ --|--|:|_ sam|sam|NN|_ *|*|NN|_ .|.|.|_ fastq|fastq|NN|_ >|>|JJR|_ output.sam|output.sam|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ sorted|sort|VBN|_ to|to|TO|_ either|either|CC|_ being|be|VBG|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ upper|upper|JJ|_ DNA|dna|NN|_ strand|strand|NN|_ or|or|CC|_ to|to|TO|_ the|the|DT|_ lower|lower|JJR|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ ,|,|,|_ as|as|IN|_ suggested|suggest|VBN|_ in|in|IN|_ the|the|DT|_ original|original|JJ|_ IDAP-seq|idap-seq|JJ|_ publication|publication|NN|_ -LRB-|-lrb-|-LRB-|_ Belitsky|Belitsky|NNP|_ and|and|CC|_ Sonenshein|Sonenshein|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ number|number|NN|_ of|of|IN|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ reads|read|VBZ|_ that|that|DT|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ upper|upper|JJ|_ strand|strand|NN|_ was|be|VBD|_ counted|count|VBN|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_ position|position|NN|_ along|along|IN|_ the|the|DT|_ Caulobacter|Caulobacter|NNP|_ genome|genome|NN|_ using|use|VBG|_ BEDTools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Quinlan|Quinlan|NNP|_ &|&|CC|_ Hall|Hall|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ following|follow|VBG|_ command|command|NN|_ :|:|:|_ bedtools|bedtool|NNS|_ genomecov|genomecov|NN|_ -|-|:|_ d|d|NN|_ -5|-5|CD|_ -|-|:|_ strand|strand|NN|_ +|+|CC|_ -|-|:|_ ibam|ibam|NN|_ output.sorted.bam|output.sorted.bam|NN|_ -|-|:|_ g|g|NN|_ NA1000.fna|na1000.fna|NN|_ >|>|JJR|_ upper_strand_output.txt|upper_strand_output.txt|NN|_ .|.|.|_ To|to|TO|_ count|count|VB|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ reads|read|VBZ|_ that|that|DT|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ lower|lower|JJR|_ strand|strand|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ command|command|NN|_ was|be|VBD|_ used|use|VBN|_ instead|instead|RB|_ :|:|:|_ bedtools|bedtool|NNS|_ genomecov|genomecov|NN|_ -|-|:|_ d|d|NN|_ -5|-5|CD|_ -|-|:|_ strand|strand|NN|_ -|-|:|_ -|-|:|_ ibam|ibam|NN|_ output.sorted.bam|output.sorted.bam|NN|_ -|-|:|_ g|g|NN|_ NA1000.fna|na1000.fna|NN|_ >|>|JJR|_ lower_strand_output.txt|lower_strand_output.txt|NN|_ .|.|.|_ The|the|DT|_ IDAP-seq|idap-seq|JJ|_ profile|profile|NN|_ was|be|VBD|_ then|then|RB|_ plotted|plot|VBN|_ using|use|VBG|_ R|r|NN|_ .|.|.|_ The|the|DT|_ sequence|sequence|NN|_ in|in|IN|_ between|between|IN|_ the|the|DT|_ summit|summit|NN|_ of|of|IN|_ upper|upper|JJ|_ strand|strand|NN|_ profile|profile|NN|_ and|and|CC|_ that|that|IN|_ of|of|IN|_ the|the|DT|_ lower|lower|JJR|_ strand|strand|NN|_ profile|profile|NN|_ defines|define|VBZ|_ the|the|DT|_ minimal|minimal|JJ|_ parS|pars|NN|_ sequence|sequence|NN|_ required|require|VBN|_ for|for|IN|_ binding|bind|VBG|_ to|to|TO|_ ParB|parb|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 011916.1|011916.1|CD|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ scrambled|scramble|VBD|_ site|site|NN|_ 3|3|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ scrambled|scramble|VBD|_ site|site|NN|_ 3|3|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 1|1|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 2|2|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 2|2|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 3|3|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 3|3|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 4|4|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 4|4|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 5|5|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 5|5|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 6|6|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 7|7|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ AB1157|ab1157|NN|_ ybbD|ybbd|NN|GEN :|:|:|_ :|:|:|_ parS|pars|NN|_ site|site|NN|_ 7|7|CD|_ pUTC18|putc18|NN|_ :|:|:|_ :|:|:|_ parB|parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
Hiseq|hiseq|JJ|_ 2500|2500|CD|_ Illumina|Illumina|NNP|_ short|short|JJ|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ mapped|map|VBN|_ back|back|RB|_ to|to|TO|_ the|the|DT|_ Caulobacter|Caulobacter|NNP|_ NA1000|na1000|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC-011916.1|nc-011916.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ following|follow|VBG|_ command|command|NN|_ :|:|:|_ bowtie|bowtie|NN|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ -|-|:|_ n|n|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ p|p|NN|_ 4|4|CD|_ --|--|:|_ chunkmbs|chunkmb|NNS|_ 512|512|CD|_ NA1000-bowtie|na1000-bowtie|NN|_ --|--|:|_ sam|sam|NN|_ *|*|NN|_ .|.|.|_ fastq|fastq|NN|_ >|>|JJR|_ output.sam|output.sam|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ the|the|DT|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_ position|position|NN|_ was|be|VBD|_ computed|compute|VBN|_ using|use|VBG|_ BEDTools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Quinlan|Quinlan|NNP|_ &|&|CC|_ Hall|Hall|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ following|follow|VBG|_ command|command|NN|_ :|:|:|_ bedtools|bedtool|NNS|_ genomecov|genomecov|NN|_ -|-|:|_ d|d|SYM|_ -|-|:|_ ibam|ibam|NN|_ output.sorted.bam|output.sorted.bam|NN|_ -|-|:|_ g|g|NN|_ NA1000.fna|na1000.fna|NN|_ >|>|JJR|_ coverage_output.txt|coverage_output.txt|NN|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ ratio|ratio|NN|_ between|between|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ of|of|IN|_ libraries|library|NNS|_ generated|generate|VBN|_ from|from|IN|_ pMCS1-Tn5-ME-R6Kγ-kanR-ME|pmcs1-tn5-me-r6kγ-kanr-me|NN|_ or|or|CC|_ pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME|pmcs1-tn5-me-r6kγ-kanr-pars456-me|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ .|.|.|_ Results|result|NNS|_ were|be|VBD|_ binned|bin|VBN|_ over|over|IN|_ 1|1|CD|_ kb|kb|NN|_ and|and|CC|_ represented|represent|VBN|_ as|as|IN|_ a|a|DT|_ log10|log10|NN|_ scale|scale|NN|_ .|.|.|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1637|tls1637|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1638|tls1638|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1639|tls1639|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1640|tls1640|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1641|tls1641|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1642|tls1642|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELAb|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1643|tls1643|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1644|tls1644|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1645|tls1645|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1646|tls1646|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1647|tls1647|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1648|tls1648|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1649|tls1649|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
LELab|lelab|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|SYM|_ seq|seq|FW|_ _|_|FW|_ TLS1650|tls1650|NN|_ _|_|NN|_ anti|anti|JJ|_ _|_|CD|_ FLAG|flag|NN|_
None|none|NN|_
Standard|Standard|NNP|_ library|library|NN|_ construction|construction|NN|_ for|for|IN|_ Illumina|Illumina|NNP|_ Hiseq2500|hiseq2500|NN|_ sequencing|sequencing|NN|_ platform|platform|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Files|file|NNS|_ ending|end|VBG|_ with|with|IN|_ _|_|CD|_ coverage.txt|coverage.txt|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ of|of|IN|_ nucleotide-resolution|nucleotide-resolution|JJ|_ coverage|coverage|NN|_ from|from|IN|_ RNA-seq|rna-seq|JJ|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ column|column|NN|_ 1|1|CD|_ :|:|:|_ genome|genome|NN|_ ID|id|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ :|:|:|_ nucleotide|nucleotide|NN|_ position|position|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ :|:|:|_ coverage|coverage|NN|_ -RRB-|-rrb-|-RRB-|_
T18-ParB|t18-parb|NN|_ -LRB-|-lrb-|-LRB-|_ G101S|g101s|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ for|for|IN|_ an|a|DT|_ hour|hour|NN|_ before|before|IN|_ formadehyde|formadehyde|NN|_ to|to|TO|_ 1|1|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ fix|fix|VB|_ cells|cell|NNS|_ for|for|IN|_ ChIP-seq|ChIP-seq|NNP|_
T18-ParB|t18-parb|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ for|for|IN|_ an|a|DT|_ hour|hour|NN|_ before|before|IN|_ formadehyde|formadehyde|NN|_ to|to|TO|_ 1|1|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ fix|fix|VB|_ cells|cell|NNS|_ for|for|IN|_ ChIP-seq|ChIP-seq|NNP|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
E.|E.|NNP|_ coli|coli|NN|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ ∆|∆|CD|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MG1693|mg1693|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 1.1.2|1.1.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-2|1-2|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|exponential|JJ|_
Hfq|hfq|NN|_ mut|mut|NN|_ exp|exp|NN|_ mRNA|mrna|NN|_
Hfq|hfq|NN|_ mut|mut|NN|_ exp|exp|NN|_ RPF|rpf|NN|_
Quality|quality|JJ|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Read|read|VBP|_ counting|count|VBG|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ the|the|DT|_ middle|middle|JJ|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_
RNA-Seq|rna-seq|NN|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ CMA540|cma540|NN|_ -LRB-|-lrb-|-LRB-|_ MG1693|mg1693|NN|_ delta|delta|NN|_ _|_|NN|_ hfq|hfq|NN|GEN :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg|µg|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|read|VB|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ unique|unique|JJ|_ CDS|cds|NN|_ per|per|IN|_ kilobase|kilobase|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ enriched|enrich|VBN|_ by|by|IN|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|GeneJET|NNP|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ rRNA|rrna|NN|_ with|with|IN|_ MICROBExpres|microbexpre|NNS|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ fragmented|fragmented|JJ|_ in|in|IN|_ alkaline|alkaline|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ and|and|CC|_ 100|100|CD|_ mM|mm|NN|KWSUPP Na2CO3|na2co3|NN|_ pH|ph|NN|_ 9.2|9.2|CD|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ fragments|fragment|NNS|_ with|with|IN|_ size|size|NN|_ of|of|IN|_ 24-35|24-35|CD|_ nts|nt|NNS|_ .|.|.|_ For|for|IN|_ RPFS|rpf|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ by|by|IN|_ freeze-rupturing|freeze-rupturing|NN|_ -LRB-|-lrb-|-LRB-|_ Retch|Retch|NNP|_ Mill|Mill|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 100|100|CD|_ A260|a260|NN|_ units|unit|NNS|_ of|of|IN|_ ribosome-bound|ribosome-bound|JJ|_ mRNA|mrna|NN|_ fraction|fraction|NN|_ were|be|VBD|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ polysomal|polysomal|JJ|_ analysis|analysis|NN|_ or|or|CC|_ subjected|subject|VBN|_ to|to|TO|_ nucleolytic|nucleolytic|JJ|_ digestion|digestion|NN|_ with|with|IN|_ 10|10|CD|_ units|unit|NNS|_
WT|WT|NNP|_ exp|exp|NN|_ mRNA|mrna|NN|_
WT|wt|JJ|_ exp|exp|NN|_ RPF|rpf|NN|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ well-mixed|well-mixed|JJ|_ minimal|minimal|JJ|_ media|media|NNS|_ modified|modify|VBN|_ with|with|IN|_ M63|m63|NN|_ -LRB-|-lrb-|-LRB-|_ mM63|mm63|NN|_ :|:|:|_ pH|ph|NN|_ 7.0|7.0|CD|_ ,|,|,|_ 62|62|CD|_ mM|mm|NN|KWSUPP K2HPO4|k2hpo4|NN|_ ,|,|,|_ 39|39|CD|_ mM|mm|NN|KWSUPP KH2PO4|kh2po4|NN|_ ,|,|,|_ 15|15|CD|_ mM|mm|NN|KWSUPP ammonium|ammonium|NN|SUPP sulfate|sulfate|NN|SUPP ,|,|,|_ 1.8|1.8|CD|_ µM|µm|NN|_ FeSO4-7H2O|feso4-7h2o|NN|_ ,|,|,|_ 15|15|CD|_ µM|µm|NN|_ thiamine|thiamine|NN|SUPP hydrochloride|hydrochloride|NN|SUPP ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP MgSO4-7H2O|mgso4-7h2o|NN|_ and|and|CC|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ .|.|.|_ One|one|CD|_ amino|amino|NN|_ acid|acid|NN|_ ,|,|,|_ Ile|ile|NN|_ or|or|CC|_ Leu|leu|NN|_ ,|,|,|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ monoculture|monoculture|NN|_ medium|medium|NN|_ when|when|WRB|_ appropriate|appropriate|JJ|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ coculturing|coculturing|NN|_ ,|,|,|_ at|at|IN|_ both|both|CC|_ the|the|DT|_ initial|initial|JJ|_ inoculation|inoculation|NN|_ and|and|CC|_ transfer|transfer|NN|_ ,|,|,|_ we|we|PRP|_ washed|wash|VBD|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ with|with|IN|_ fresh|fresh|JJ|_ mM63|mm63|NN|_ without|without|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP to|to|TO|_ exclude|exclude|VB|_ the|the|DT|_ carry-over|carry-over|NN|_ of|of|IN|_ supplements|supplement|NNS|_ from|from|IN|_ the|the|DT|_ pre-culture|pre-culture|JJ|_ .|.|.|_ For|for|IN|_ coculture|coculture|NN|_ samples|sample|NNS|_ ,|,|,|_ we|we|PRP|_ used|use|VBD|_ cell|cell|NN|_ culture|culture|NN|_ inserts|insert|NNS|_ with|with|IN|_ a|a|DT|_ pore|pore|NN|_ size|size|NN|_ of|of|IN|_ 0.45|0.45|CD|_ µm|µm|NN|_ at|at|IN|_ a|a|DT|_ density|density|NN|_ of|of|IN|_ 10|10|CD|_ ^|^|CD|_ 8|8|CD|_
Ancestral|ancestral|JJ|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ amino|amino|NN|_ acid|acid|NN|_ starvation|starvation|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Ancestral|ancestral|JJ|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Ancestral|ancestral|JJ|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_
Ancestral|ancestral|JJ|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_ ,|,|,|_ a|a|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_
Ancestral|ancestral|JJ|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ amino|amino|NN|_ acid|acid|NN|_ starvation|starvation|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Ancestral|ancestral|JJ|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Ancestral|ancestral|JJ|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_ ,|,|,|_ a|a|DT|_ technical|technical|JJ|_ replicate|replicate|VB|_
Ancestral|ancestral|JJ|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_
Ancestral|ancestral|JJ|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_ ,|,|,|_ a|a|DT|_ biological|biological|JJ|_ replicate|replicate|VBP|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Ancestral|ancestral|JJ|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Ancestral|ancestral|JJ|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Evolved|evolve|VBN|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Evolved|evolve|VBN|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Original|original|JJ|_ prototroph|prototroph|NN|_ DH1|dh1|NN|_ cells|cell|NNS|_
culture|culture|NN|_ type|type|NN|_ :|:|:|_ coculture|coculture|NN|_
culture|culture|NN|_ type|type|NN|_ :|:|:|_ monoculture|monoculture|NN|_
DH1-log|dh1-log|JJ|_
DH1-log-tr|dh1-log-tr|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Evolved|evolve|VBD|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ amino|amino|NN|_ acid|acid|NN|_ starvation|starvation|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Evolved|evolve|VBD|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Evolved|evolve|VBD|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_
Evolved|evolve|VBD|_ I|I|PRP|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_ ,|,|,|_ a|a|DT|_ biological|biological|JJ|_ replicate|replicate|VBP|_
Evolved|evolve|VBD|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ amino|amino|NN|_ acid|acid|NN|_ starvation|starvation|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Evolved|evolve|VBD|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Evolved|evolve|VBD|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_ ,|,|,|_ a|a|DT|_ technical|technical|JJ|_ replicate|replicate|VBP|_
Evolved|evolve|VBD|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_
Evolved|evolve|VBD|_ L|l|NN|_ -|-|:|_ cells|cell|NNS|_ in|in|IN|_ coculture|coculture|NN|_ ,|,|,|_ a|a|DT|_ biological|biological|JJ|_ replicate|replicate|VBP|_
genotype|genotype|NN|_
growth|growth|NN|_ type|type|NN|_ :|:|:|_ amino|amino|NN|_ acid|acid|NN|_ starvation|starvation|NN|_
growth|growth|NN|_ type|type|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
IA-co1|ia-co1|NN|_
IA-co2|ia-co2|NN|_
IA-log|ia-log|JJ|_
IA-starve|ia-starve|JJ|_
IE-co1|ie-co1|NN|_
IE-co2|ie-co2|NN|_
IE-log|ie-log|JJ|_
IE-starve|ie-starve|JJ|_
LA-co1|la-co1|NN|_
LA-co2|la-co2|NN|_
LA-log|la-log|NN|_
LA-log-tr|la-log-tr|NN|_
LA-starve|la-starve|JJ|_
LE-co1|le-co1|NN|_
LE-co2|le-co2|NN|_
LE-log|le-log|JJ|_
LE-log-tr|le-log-tr|NN|_
LE-starve|le-starve|JJ|_
Metabolome|metabolome|NN|_ data|datum|NNS|_ for|for|IN|_ these|these|DT|_ cultures|culture|NNS|_ are|be|VBP|_ also|also|RB|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ \|\|SYM|_ Ecoli|Ecoli|NNP|_ _|_|SYM|_ co|co|FW|_ _|_|FW|_ results.xlsx|results.xlsx|FW|_ \|\|FW|_ ,|,|,|_ just|just|RB|_ for|for|IN|_ information|information|NN|_ .|.|.|_
Microarray|Microarray|NNP|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ a|a|DT|_ custom|custom|NN|_ R|r|NN|_ software|software|NN|_ for|for|IN|_ the|the|DT|_ finite|finite|JJ|_ hybridisation|hybridisation|NN|_ -LRB-|-lrb-|-LRB-|_ FH|fh|NN|_ -RRB-|-rrb-|-RRB-|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Ono|Ono|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2008|2008|CD|_ ,|,|,|_ Bioinformatics|Bioinformatics|NNP|_ 24|24|CD|_ ,|,|,|_ p1278|p1278|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Original|original|JJ|_ prototroph|prototroph|NN|_ DH1|dh1|NN|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_
Original|original|JJ|_ prototroph|prototroph|NN|_ DH1|dh1|NN|_ cells|cell|NNS|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_ in|in|IN|_ monoculture|monoculture|NN|_ ,|,|,|_ a|a|DT|_ technical|technical|JJ|_ replicate|replicate|VBP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
substrain|substrain|NN|_ :|:|:|_ DH1|dh1|NN|_
The|the|DT|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ interrupted|interrupt|VBN|_ by|by|IN|_ placing|place|VBG|_ them|they|PRP|_ directly|directly|RB|_ into|into|IN|_ a|a|DT|_ cold|cold|JJ|_ phenol-ethanol|phenol-ethanol|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1g-phenol|0.1g-phenol|JJ|_
The|the|DT|_ processed|process|VBN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ in|in|IN|_ log10|log10|NN|_ scale|scale|NN|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ \|\|SYM|_ Ecoli|Ecoli|NNP|_ _|_|SYM|_ co|co|FW|_ _|_|FW|_ results.xlsx|results.xlsx|FW|_ \|\|FW|_ .|.|.|_
The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ ,|,|,|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
After|after|IN|_ normalization|normalization|NN|_ ,|,|,|_ the|the|DT|_ read|read|NN|_ counts|count|NNS|_ were|be|VBD|_ estimated|estimate|VBN|_ in|in|IN|_ the|the|DT|_ running|run|VBG|_ windows|window|NNS|_ of|of|IN|_ 35|35|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ ratios|ratio|NNS|_ R|r|NN|_ between|between|IN|_ values|value|NNS|_ obtained|obtain|VBN|_ for|for|IN|_ experimental|experimental|JJ|_ and|and|CC|_ control|control|JJ|_ libraries|library|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ .|.|.|_ Peaks|peak|NNS|_ were|be|VBD|_ localized|localized|JJ|_ requiring|require|VBG|_ R|r|NN|_ ≥|≥|CD|_ 1.5|1.5|CD|_ for|for|IN|_ at|at|IN|_ least|least|JJS|_ 50|50|CD|_ %|%|NN|_ positions|position|NNS|_ of|of|IN|_ at|at|IN|_ least|least|JJS|_ 60|60|CD|_ bp|bp|NN|_ genomic|genomic|JJ|_ region|region|NN|_ in|in|IN|_ length|length|NN|_ .|.|.|_
antibody|antibody|NN|_ :|:|:|_ Anti-Dps|anti-dps|JJ|_ antibodies|antibody|NNS|_
antibody|antibody|NN|_ :|:|:|_ rabbit|rabbit|NN|_ pre-immune|pre-immune|JJ|_ IgG|igg|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 5|5|CD|_ %|%|NN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ under|under|IN|_ constant|constant|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 120|120|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ water|water|NN|_ bath|bath|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ .|.|.|_
ChIP-Seq|chip-seq|NN|_
ChIP-seq|chip-seq|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ duplicate|duplicate|VB|_ using|use|VBG|_ similar|similar|JJ|_ growth|growth|NN|_ condition|condition|NN|_ and|and|CC|_ protocols|protocol|NNS|_ for|for|IN|_ chromatin|chromatin|NN|_ immunoprecipitation|immunoprecipitation|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ experiment|experiment|NN|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ the|the|DT|_ Centre|Centre|NNP|_ for|for|IN|_ Genomic|genomic|JJ|_ Regulation|regulation|NN|_ -LRB-|-lrb-|-LRB-|_ CRG|crg|NN|_ ,|,|,|_ Barcelona|Barcelona|NNP|_ ,|,|,|_ Spain|Spain|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ while|while|IN|_ the|the|DT|_ second|second|JJ|_ one|one|CD|_ in|in|IN|_ the|the|DT|_ Immanuel|Immanuel|NNP|_ Kant|Kant|NNP|_ Baltic|Baltic|NNP|_ Federal|Federal|NNP|_ University|University|NNP|_ -LRB-|-lrb-|-LRB-|_ Kaliningrad|Kaliningrad|NNP|_ ,|,|,|_ Russia|Russia|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ both|both|DT|_ cases|case|NNS|_ ,|,|,|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ formaldehyde|formaldehyde|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ %|%|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ incubation|incubation|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cross-linking|cross-linking|NN|_ was|be|VBD|_ stopped|stop|VBN|_ with|with|IN|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 450|450|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 5|5|CD|_ minutes|minute|NNS|_ of|of|IN|_ incubation|incubation|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ +4|+4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ PBS|PBS|NNP|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 1.3|1.3|CD|_ ml|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ immunoprecipitation|immunoprecipitation|NN|_ buffer|buffer|NN|_ prepared|prepare|VBN|_ from|from|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ buffer|buffer|NN|_ containing|contain|VBG|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.1|8.1|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ NaN3|nan3|NN|_ ,|,|,|_ 0.5|0.5|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ and|and|CC|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ buffer|buffer|NN|_ containing|contain|VBG|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.6|8.6|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ;|;|:|_ 5|5|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 0,2|0,2|CD|_ %|%|NN|_ NaN3|nan3|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ Triton-X-100|triton-x-100|NN|_ .|.|.|_ Then|then|RB|_ phenylmethylsulfonyl|phenylmethylsulfonyl|NN|_ fluoride|fluoride|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ Protease|protease|NN|_ Inhibitor|inhibitor|NN|_ Cocktail|cocktail|NN|_ -LRB-|-lrb-|-LRB-|_ PIC|pic|NN|_ ,|,|,|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ experiment|experiment|NN|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ were|be|VBD|_ added|add|VBN|_ followed|follow|VBN|_ by|by|IN|_ incubation|incubation|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ +4|+4|CD|_ °C|°c|NN|_ .|.|.|_
ChIP-seq|chip-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ 5-10|5-10|CD|_ ng|ng|NN|_ of|of|IN|_ the|the|DT|_ DNA|dna|NN|_ samples|sample|NNS|_ with|with|IN|_ the|the|DT|_ NebNext|NebNext|NNP|_ ®|®|SYM|_ Ultra|ultra|FW|_ ™|™|FW|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ final|final|JJ|_ amplification|amplification|NN|_ of|of|IN|_ the|the|DT|_ library|library|NN|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Size|size|NN|_ distribution|distribution|NN|_ and|and|CC|_ concentration|concentration|NN|_ of|of|IN|_ the|the|DT|_ amplicons|amplicon|NNS|_ was|be|VBD|_ checked|check|VBN|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ first|first|JJ|_ experiment|experiment|NN|_ ,|,|,|_ the|the|DT|_ maximum|maximum|NN|_ was|be|VBD|_ at|at|IN|_ about|about|IN|_ 300|300|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ ChIP|chip|NN|_ libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ 50|50|CD|_ nt|nt|NNS|_ single-end|single-end|JJ|_ read|read|NN|_ protocol|protocol|NN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|hiseq|NN|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ Genomics|Genomics|NNP|_ Facility|Facility|NNP|_ in|in|IN|_ the|the|DT|_ Centre|Centre|NNP|_ for|for|IN|_ Genomic|genomic|JJ|_ Regulation|regulation|NN|_ -LRB-|-lrb-|-LRB-|_ Barcelona|Barcelona|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ second|second|JJ|_ experiment|experiment|NN|_ ,|,|,|_ the|the|DT|_ maximum|maximum|NN|_ was|be|VBD|_ at|at|IN|_ about|about|IN|_ 450|450|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ samples|sample|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ standard|standard|JJ|_ paired-end|paired-end|NN|_ 2|2|CD|_ *|*|SYM|_ 150|150|CD|_ nt|nt|NNS|_ protocol|protocol|NN|_ on|on|IN|_ the|the|DT|_ MiSeq|miseq|NN|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ Immanuel|Immanuel|NNP|_ Kant|Kant|NNP|_ Baltic|Baltic|NNP|_ Federal|Federal|NNP|_ University|University|NNP|_ -LRB-|-lrb-|-LRB-|_ Kaliningrad|Kaliningrad|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Exp|exp|NN|_ 1|1|CD|_ _|_|NN|_ control|control|NN|_
Exp|Exp|NNP|_ 1|1|CD|_ _|_|CD|_ IP|IP|NNP|_ sample|sample|NN|_
Exp|exp|NN|_ 2|2|CD|_ _|_|NN|_ control|control|NN|_
Exp|exp|NN|_ 2|2|CD|_ _|_|CD|_ IP|IP|NNP|_ sample|sample|NN|_
For|for|IN|_ immunoprecipitation|immunoprecipitation|NN|_ ,|,|,|_ 800|800|CD|_ μl|μl|NN|_ of|of|IN|_ collected|collect|VBN|_ chromatin|chromatin|NN|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 1000|1000|CD|_ μg|μg|NN|_ of|of|IN|_ protein|protein|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ incubated|incubate|VBN|_ on|on|IN|_ a|a|DT|_ rotating|rotate|VBG|_ wheel|wheel|NN|_ over|over|IN|_ night|night|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ 10|10|CD|_ μg|μg|NN|_ of|of|IN|_ either|either|CC|_ rabbit|rabbit|NN|_ anti-Dps|anti-dps|JJ|_ antibodies|antibody|NNS|_ -LRB-|-lrb-|-LRB-|_ experimental|experimental|JJ|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ rabbit|rabbit|NN|_ pre-immune|pre-immune|JJ|_ IgG|igg|NN|_ -LRB-|-lrb-|-LRB-|_ negative|negative|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ day|day|NN|_ 30|30|CD|_ μl|μl|NN|_ of|of|IN|_ Ultra|Ultra|NNP|_ Link|Link|NNP|_ Protein|protein|NN|_ A|a|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ log-phase|log-phase|JJ|_
medium|medium|NN|_ :|:|:|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 5|5|CD|_ %|%|NN|_ LB|lb|NN|_
ngs|ng|NNS|_ platform|platform|NN|_ :|:|:|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_
ngs|ng|NNS|_ platform|platform|NN|_ :|:|:|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_
Only|only|RB|_ ideal|ideal|JJ|_ correspondence|correspondence|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ in|in|IN|_ both|both|DT|_ cases|case|NNS|_ was|be|VBD|_ permitted|permit|VBN|_ .|.|.|_ The|the|DT|_ profiles|profile|NNS|_ obtained|obtain|VBN|_ for|for|IN|_ experimental|experimental|JJ|_ and|and|CC|_ control|control|JJ|_ samples|sample|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ scaling|scaling|NN|_ method|method|NN|_ initially|initially|RB|_ offered|offer|VBN|_ by|by|IN|_ Affymetrix|Affymetrix|NNP|_ for|for|IN|_ microarray|microarray|NN|_ data|data|NN|_ analysis|analysis|NN|_ and|and|CC|_ later|later|RB|_ implemented|implement|VBD|_ in|in|IN|_ several|several|JJ|_ other|other|JJ|_ approaches|approach|NNS|_ .|.|.|_ This|this|DT|_ method|method|NN|_ assumes|assume|VBZ|_ unaffected|unaffected|JJ|_ protein|protein|NN|_ occupancy|occupancy|NN|_ at|at|IN|_ most|most|JJS|_ genomic|genomic|JJ|_ positions|position|NNS|_ and|and|CC|_ quantifies|quantify|VBZ|_ the|the|DT|_ scaling|scaling|NN|_ factor|factor|NN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ corrected|correct|VBN|_ mean|mean|NN|_ values|value|NNS|_ obtained|obtain|VBN|_ after|after|IN|_ removal|removal|NN|_ of|of|IN|_ 2|2|CD|_ %|%|NN|_ signals|signal|NNS|_ with|with|IN|_ highest|highest|JJS|_ and|and|CC|_ lowest|lowest|JJS|_ intensities|intensity|NNS|_ from|from|IN|_ both|both|DT|_ control|control|NN|_ and|and|CC|_ experimental|experimental|JJ|_ sets|set|NNS|_ .|.|.|_
Raw|raw|NN|_ data|datum|NNS|_ were|be|VBD|_ quality|quality|JJ|_ filtered|filter|VBN|_ on|on|IN|_ the|the|DT|_ Galaxy|Galaxy|NNP|_ server|server|NN|_ -LRB-|-lrb-|-LRB-|_ Filter|Filter|NNP|_ by|by|IN|_ Quality|Quality|NNP|_ tool|tool|NN|_ ,|,|,|_ Q|Q|NNP|_ ≥|≥|SYM|_ 20|20|CD|_ -RRB-|-rrb-|-RRB-|_ providing|provide|VBG|_ 99|99|CD|_ %|%|NN|_ probability|probability|NN|_ of|of|IN|_ correct|correct|JJ|_ sequencing|sequencing|NN|_ for|for|IN|_ all|all|DT|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ As|as|IN|_ a|a|DT|_ result|result|NN|_ ,|,|,|_ the|the|DT|_ sets|set|NNS|_ contain|contain|VBP|_ 31,656,551|31,656,551|CD|_ and|and|CC|_ 45,396,252|45,396,252|CD|_ sequences|sequence|NNS|_ in|in|IN|_ the|the|DT|_ control|control|NN|_ and|and|CC|_ immunoprecipitated|immunoprecipitate|VBN|_ samples|sample|NNS|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ experiment|experiment|NN|_ ,|,|,|_ and|and|CC|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ 7,493,528|7,493,528|CD|_ and|and|CC|_ 8,214,737|8,214,737|CD|_ reads|read|VBZ|_ for|for|IN|_ the|the|DT|_ second|second|JJ|_ experiment|experiment|NN|_ .|.|.|_
sequencing|sequencing|NN|_ mode|mode|NN|_ :|:|:|_ 50|50|CD|_ nt|nt|NNS|_ single-end|single-end|JJ|_ read|read|NN|_ protocol|protocol|NN|_
sequencing|sequencing|NN|_ mode|mode|NN|_ :|:|:|_ paired-end|paired-end|NN|_ 2|2|CD|_ *|*|SYM|_ 150|150|CD|_ nt|nt|NNS|_ protocol|protocol|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ include|include|VBP|_ read|read|VBN|_ pileups|pileup|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ two|two|CD|_ ChIP-seq|chip-seq|JJ|_ experiments|experiment|NNS|_ by|by|IN|_ two|two|CD|_ different|different|JJ|_ approaches|approach|NNS|_ -LRB-|-lrb-|-LRB-|_ files|file|NNS|_ 1-4|1-4|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ set|set|NN|_ of|of|IN|_ regions|region|NNS|_ bound|bind|VBN|_ by|by|IN|_ Dps|dp|NNS|_ in|in|IN|_ both|both|DT|_ experiments|experiment|NNS|_ -LRB-|-lrb-|-LRB-|_ file|file|NN|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ set|set|NN|_ of|of|IN|_ regions|region|NNS|_ unbound|unbound|JJ|_ by|by|IN|_ Dps|dp|NNS|_ in|in|IN|_ both|both|DT|_ experiments|experiment|NNS|_ -LRB-|-lrb-|-LRB-|_ file|file|NN|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ processed|process|VBN|_ data|datum|NNS|_ are|be|VBP|_ provided|provide|VBN|_ as|as|IN|_ tab-delimited|tab-delimited|JJ|_ .|.|.|_ txt|txt|NN|_ files|file|NNS|_ .|.|.|_
To|to|TO|_ apply|apply|VB|_ the|the|DT|_ second|second|JJ|_ approach|approach|NN|_ variable|variable|NN|_ in|in|IN|_ length|length|NN|_ reads|read|VBZ|_ from|from|IN|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ were|be|VBD|_ first|first|JJ|_ trimmed|trim|VBN|_ from|from|IN|_ both|both|DT|_ sides|side|NNS|_ to|to|TO|_ obtain|obtain|VB|_ a|a|DT|_ set|set|NN|_ of|of|IN|_ standard|standard|JJ|_ 50|50|CD|_ nt|nt|NNS|_ sequences|sequence|NNS|_ taken|take|VBN|_ from|from|IN|_ the|the|DT|_ middle|middle|NN|_ of|of|IN|_ longer|longer|JJR|_ reads|read|VBZ|_ .|.|.|_ Reads|read|NNS|_ shorter|shorter|JJR|_ than|than|IN|_ 50|50|CD|_ nt|nt|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ all|all|DT|_ four|four|CD|_ sets|set|NNS|_ from|from|IN|_ both|both|DT|_ experiments|experiment|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ Matcher|Matcher|NNP|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ available|available|JJ|_ at|at|IN|_ :|:|:|_ http|http|NN|_ :|:|:|_
Two|two|CD|_ different|different|JJ|_ approaches|approach|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ align|align|VB|_ sequence|sequence|NN|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First|first|RB|_ ,|,|,|_ quality|quality|NN|_ controlled|controlled|JJ|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ version|version|NN|_ 7.5.1|7.5.1|CD|_ -LRB-|-lrb-|-LRB-|_ CLC|clc|NN|_ GW|gw|NN|_ ,|,|,|_ Bio-Qiagen|bio-qiagen|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ either|either|CC|_ default|default|NN|_ settings|setting|NNS|_ for|for|IN|_ the|the|DT|_ length|length|NN|_ and|and|CC|_ similarity|similarity|NN|_ fractions|fraction|NNS|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ and|and|CC|_ 0.8|0.8|CD|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ see|see|VB|_ supplemental|supplemental|JJ|_ Table|Table|NNP|_ 2|2|CD|_ of|of|IN|_ the|the|DT|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ stringent|stringent|JJ|_ criteria|criterion|NNS|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ and|and|CC|_ 1.0|1.0|CD|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ deposited|deposit|VBN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reads|read|VBZ|_ with|with|IN|_ sequences|sequence|NNS|_ aligned|align|VBN|_ to|to|TO|_ multiple|multiple|JJ|_ genomic|genomic|JJ|_ regions|region|NNS|_ were|be|VBD|_ ignored|ignore|VBN|_ .|.|.|_
Agilent|Agilent|NNP|_ Scan|scan|VB|_ Control|Control|NNP|_ Software|Software|NNP|_ V.|V.|NNP|_ 8.5|8.5|CD|_ at|at|IN|_ a|a|DT|_ resolution|resolution|NN|_ of|of|IN|_ 3μm|3μm|NN|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ extraction|extraction|NN|_ software|software|NN|_ V|v|NN|_ 10.10|10.10|CD|_
azide|azide|NN|_ treated|treat|VBN|_
Cells|cell|NNS|_ were|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED media|media|NNS|MED
cultures|culture|NNS|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ 10|10|CD|_ ml|ml|NN|_ cultures|culture|NNS|_ .|.|.|_ One|one|CD|_ half|half|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 2|2|CD|_ mM|mm|NN|KWSUPP NaN3|nan3|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ half|half|NN|_ was|be|VBD|_ left|leave|VBN|_ untreated|untreated|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
growth|growth|NN|_ media|media|NNS|_ :|:|:|_ LB|lb|NN|_
od|od|NN|_ :|:|:|_ 0.8|0.8|CD|_
Sample|sample|NN|_ 1|1|CD|_
Sample|sample|NN|_ 2|2|CD|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_
treatment|treatment|NN|_ :|:|:|_ 2|2|CD|_ mM|mm|NN|KWSUPP NaN3|nan3|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
untreated|untreated|JJ|_
Adaptive|adaptive|JJ|_ threshold|threshold|NN|_ -LRB-|-lrb-|-LRB-|_ quantitation|quantitation|NN|_ method|method|NN|_ -RRB-|-rrb-|-RRB-|_ uses|use|VBZ|_ the|the|DT|_ parameters|parameter|NNS|_ of|of|IN|_ the|the|DT|_ spot|spot|NN|_ diameter|diameter|NN|_ and|and|CC|_ background|background|NN|_ inner|inner|JJ|_ and|and|CC|_ outer|outer|JJ|_ dimensions|dimension|NNS|_ to|to|TO|_ create|create|VB|_ a|a|DT|_ spot|spot|NN|_ mask|mask|NN|_ and|and|CC|_ background|background|NN|_ mask|mask|NN|_ ,|,|,|_ then|then|RB|_ refines|refine|VBZ|_ the|the|DT|_ mask|mask|NN|_ on|on|IN|_ a|a|DT|_ pixel-by-pixel|pixel-by-pixel|JJ|_ basis|basis|NN|_ .|.|.|_ Total|total|JJ|_ -LRB-|-lrb-|-LRB-|_ normalization|normalization|NN|_ method|method|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ uses|use|VBZ|_ the|the|DT|_ intensity|intensity|NN|_ of|of|IN|_ each|each|DT|_ spot|spot|NN|_ in|in|IN|_ relation|relation|NN|_ to|to|TO|_ all|all|DT|_ spots|spot|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ ,|,|,|_ 110|110|CD|_ min|min|NN|_ after|after|IN|_ depletion|depletion|NN|_ of|of|IN|_ extracellular|extracellular|JJ|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ ,|,|,|_ 170|170|CD|_ min|min|NN|_ after|after|IN|_ depletion|depletion|NN|_ of|of|IN|_ extracellular|extracellular|JJ|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ ,|,|,|_ 230|230|CD|_ min|min|NN|_ after|after|IN|_ depletion|depletion|NN|_ of|of|IN|_ extracellular|extracellular|JJ|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ depletion|depletion|NN|_ of|of|IN|_ extracellular|extracellular|JJ|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ ,|,|,|_ 350|350|CD|_ min|min|NN|_ after|after|IN|_ depletion|depletion|NN|_ of|of|IN|_ extracellular|extracellular|JJ|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ ,|,|,|_ 50|50|CD|_ min|min|NN|_ after|after|IN|_ depletion|depletion|NN|_ of|of|IN|_ extracellular|extracellular|JJ|_ acetate|acetate|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ ,|,|,|_ acetate|acetate|NN|SUPP concentration|concentration|NN|_ ≤|≤|CD|_ 0.35|0.35|CD|_ gL-1|gl-1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ gL-1|gl-1|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ glucose|glucose|NN|SUPP limitation|limitation|NN|_ -LRB-|-lrb-|-LRB-|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ gL-1|gl-1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fed-batch|fed-batch|JJ|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ -LRB-|-lrb-|-LRB-|_ W3110|w3110|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fed-batch|fed-batch|JJ|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT1|rviat1|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT1|rviat1|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT1|rviat1|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT2|rviat2|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT2|rviat2|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT2|rviat2|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT3|rviat3|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT3|rviat3|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT3|rviat3|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT4|rviat4|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT4|rviat4|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT4|rviat4|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT5|rviat5|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT5|rviat5|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT6|rviat6|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT6|rviat6|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT7|rviat7|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT7|rviat7|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT8|rviat8|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ RviaT8|rviat8|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T1viaR|t1viar|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T1viaR|t1viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T1viaR|t1viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T2viaR|t2viar|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T2viaR|t2viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T2viaR|t2viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T3viaR|t3viar|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T3viaR|t3viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T3viaR|t3viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T4viaR|t4viar|NN|_ _|_|CD|_ SR1|sr1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T4viaR|t4viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T4viaR|t4viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T5viaR|t5viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T5viaR|t5viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T6viaR|t6viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T6viaR|t6viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T7viaR|t7viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T7viaR|t7viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T8viaR|t8viar|NN|_ _|_|CD|_ SR2|sr2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ T8viaR|t8viar|NN|_ _|_|CD|_ SR3|sr3|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ unlimited|unlimited|JJ|_ growth|growth|NN|_ -LRB-|-lrb-|-LRB-|_ batch|batch|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ unlimited|unlimited|JJ|_ growth|growth|NN|_ -LRB-|-lrb-|-LRB-|_ batch|batch|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|NN|_
Raw|raw|NN|_ data|datum|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ analyzing|analyze|VBG|_ 16-bit|16-bit|JJ|_ tiff|tiff|NN|_ files|file|NNS|_ with|with|IN|_ the|the|DT|_ Scan|scan|VB|_ Array|Array|NNP|_ Express|Express|NNP|_ imaging|imaging|NN|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ microarray|microarray|NN|_ analysis|analysis|NN|_ system|system|NN|_ ,|,|,|_ version|version|NN|_ 3.0.0.0016|3.0.0.0016|CD|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Massachusetts|Massachusetts|NNP|_ ,|,|,|_ USA|USA|NNP|_ ;|;|:|_ adaptive|adaptive|JJ|_ treshold|treshold|NN|_ method|method|NN|_ ,|,|,|_ total|total|JJ|_ normalization|normalization|NN|_ method|method|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ directly|directly|RB|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ avoid|avoid|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -|-|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_
The|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ samples|sample|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ with|with|IN|_ a|a|DT|_ capillary|capillary|JJ|_ sampling|sampling|NN|_ probe|probe|NN|_ as|as|IN|_ developed|develop|VBN|_ by|by|IN|_ Theobald|Theobald|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 1997|1997|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ however|however|RB|_ ,|,|,|_ without|without|IN|_ using|use|VBG|_ membrane-covered|membrane-covered|JJ|_ glass|glass|NN|_ tubes|tube|NNS|_ .|.|.|_
The|the|DT|_ fed-batch|fed-batch|JJ|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ strain|strain|NN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ DSM|DSM|NNP|_ 5911|5911|CD|_ ,|,|,|_ German|german|JJ|_ Collection|collection|NN|_ of|of|IN|_ Microorganisms|microorganism|NNS|_ and|and|CC|_ Cell|cell|NN|_ Cultures|culture|NNS|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 30-l|30-l|JJ|_ bioreactor|bioreactor|NN|_ -LRB-|-lrb-|-LRB-|_ Bioengineering|bioengineer|VBG|_ AG|AG|NNP|_ ,|,|,|_ Wald|Wald|NNP|_ ,|,|,|_ Switzerland|Switzerland|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_ The|the|DT|_ batch|batch|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ batch|batch|NN|_ volume|volume|NN|_ VR|vr|NN|_ ,0|,0|NN|_ =|=|JJ|_ 17|17|CD|_ l|l|NN|_ -RRB-|-rrb-|-RRB-|_ consisted|consist|VBD|_ of|of|IN|_ 8.8|8.8|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ glucose|glucose|NN|SUPP •|•|SYM|_ H2O|h2o|NN|_ ,|,|,|_ 2.0|2.0|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ Na2SO4|na2so4|NN|_ •|•|SYM|_ 10H2O|10h2o|CD|_ ,|,|,|_ 2.68|2.68|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 14.6|14.6|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 4.02|4.02|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ NaH2PO4|nah2po4|NN|_ •|•|SYM|_ 2H2O|2h2o|NN|_ ,|,|,|_ 0.01|0.01|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ thiamine|thiamine|NN|SUPP HCl|hcl|NN|_ ;|;|:|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ •|•|SYM|_ 2H2O|2h2o|NN|_ ,|,|,|_ 2mM|2mm|NN|_ MgSO4|mgso4|NN|_ •|•|SYM|_ 7H2O|7h2o|CD|_ ;|;|:|_ 3|3|CD|_ ml|ml|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ of|of|IN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ TES|tes|NN|_ :|:|:|_ 16.7|16.7|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_ FeCl3|fecl3|NN|_ •|•|SYM|_ 6H2O|6h2o|CD|_ ,|,|,|_ 20.1|20.1|CD|_ g|g|NN|_ l|l|NN|_ −|−|CD|_ 1|1|CD|_
Theobald|Theobald|NNP|_ ,|,|,|_ U.|U.|NNP|_ ,|,|,|_ Mailinger|Mailinger|NNP|_ ,|,|,|_ W.|W.|NNP|_ ,|,|,|_ Baltes|Baltes|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ Rizzi|Rizzi|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ Reuss|Reuss|NNP|_ ,|,|,|_ M.|M.|NNP|_ ,|,|,|_ 1997|1997|CD|_ .|.|.|_ In|in|FW|_ vivo|vivo|FW|_ analysis|analysis|NN|_ of|of|IN|_ metabolic|metabolic|JJ|_ dynamics|dynamics|NNS|_ in|in|IN|_ Saccharomyces|saccharomyces|FW|_ cerevisiae|cerevisiae|FW|_ .|.|.|_ 1|1|LS|_ .|.|.|_ Experimental|experimental|JJ|_ observations|observation|NNS|_ .|.|.|_ Biotechnol|Biotechnol|NNP|_ .|.|.|_ Bioeng|Bioeng|NNP|_ .|.|.|_ 55|55|CD|_ ,|,|,|_ 305|305|CD|_ --|--|:|_ 316|316|CD|_ .|.|.|_
The|the|DT|_ VALUE|VALUE|NNP|_ data|datum|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ test|test|NN|_
Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ 8.1|8.1|CD|_ *|*|SYM|_ 10exp9|10exp9|CD|_ cells|cell|NNS|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ On-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ was|be|VBD|_ performed|perform|VBN|_ -LRB-|-lrb-|-LRB-|_ RNase|rnase|NN|_ free|free|JJ|_ DNase|dnase|NN|_ set|set|NN|_ ,|,|,|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ concentration|concentration|NN|_ and|and|CC|_ quality|quality|NN|_ were|be|VBD|_ assessed|assess|VBN|_ photometrically|photometrically|RB|_ -LRB-|-lrb-|-LRB-|_ Nanodrop|nanodrop|JJ|_ ND|nd|NN|_ 1000|1000|CD|_ ,|,|,|_ NanoDrop|NanoDrop|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Delaware|Delaware|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ formaldehyde|formaldehyde|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ bioanalyzer|bioanalyzer|NN|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ LabChip|LabChip|NNP|_ Kit|kit|NN|_ ,|,|,|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ ,|,|,|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ California|California|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Only|only|RB|_ RNA|rna|NN|_ with|with|IN|_ 260|260|CD|_ nm|nm|NN|_
An|a|DT|_ RNeasy|rneasy|NN|_ minikit|minikit|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ prepare|prepare|VB|_ total|total|JJ|_ RNA|rna|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ Ltd.|Ltd.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Any|any|DT|_ contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ a|a|DT|_ DNAase|dnaase|NN|_ column|column|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ Ltd|Ltd|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ MEM-HEPES|mem-hepes|NN|_ +|+|CC|_ 20uM|20um|NN|_ ME0052|me0052|NN|_ -LRB-|-lrb-|-LRB-|_ in|in|IN|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ MEM-HEPES|mem-hepes|NN|_ +|+|CC|_ 20uM|20um|NN|_ ME0053|me0053|NN|_ -LRB-|-lrb-|-LRB-|_ in|in|IN|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ MEM-HEPES|mem-hepes|NN|_ +|+|CC|_ 20uM|20um|NN|_ ME0054|me0054|NN|_ -LRB-|-lrb-|-LRB-|_ in|in|IN|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ MEM-HEPES|mem-hepes|NN|_ +|+|CC|_ 20uM|20um|NN|_ ME0055|me0055|NN|_ -LRB-|-lrb-|-LRB-|_ in|in|IN|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ MEM-HEPES|mem-hepes|NN|_ +|+|CC|_ DMSO|dmso|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ C|c|NN|_ to|to|TO|_ OD|od|NN|_ 0.7|0.7|CD|_ in|in|IN|_ MEM-HEPES|mem-hepes|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ Glucose|glucose|NN|_ and|and|CC|_ 250nM|250nm|NN|_ Fe|Fe|NNP|_ -LRB-|-lrb-|-LRB-|_ NO3|no3|NN|_ -RRB-|-rrb-|-RRB-|_ 2|2|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ C|c|NN|_ to|to|TO|_ OD|od|NN|_ 0.7|0.7|CD|_ in|in|IN|_ MEM-HEPES|mem-hepes|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ Glucose|glucose|NN|_ and|and|CC|_ 250nM|250nm|NN|_ Fe|Fe|NNP|_ -LRB-|-lrb-|-LRB-|_ NO3|no3|NN|_ -RRB-|-rrb-|-RRB-|_ 2|2|CD|_ and|and|CC|_ and|and|CC|_ equivalent|equivalent|JJ|_ volume|volume|NN|_ of|of|IN|_ DMSO|dmso|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20uM|20um|NN|_ ME0052|me0052|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20uM|20um|NN|_ ME0053|me0053|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20uM|20um|NN|_ ME0054|me0054|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20uM|20um|NN|_ ME0055|me0055|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ TUV93-0|tuv93-0|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ DMSO|dmso|NN|_
inhibitor|inhibitor|NN|_ :|:|:|_ 20uM|20um|NN|_ ME0052|me0052|NN|_
inhibitor|inhibitor|NN|_ :|:|:|_ 20uM|20um|NN|_ ME0053|me0053|NN|_
inhibitor|inhibitor|NN|_ :|:|:|_ 20uM|20um|NN|_ ME0054|me0054|NN|_
inhibitor|inhibitor|NN|_ :|:|:|_ 20uM|20um|NN|_ ME0055|me0055|NN|_
LOWESS|lowess|NN|_ normalised|normalised|JJ|_ data|datum|NNS|_ that|that|WDT|_ represents|represent|VBZ|_ the|the|DT|_ average|average|NN|_ of|of|IN|_ the|the|DT|_ three|three|CD|_ replicate|replicate|VBP|_ experiments|experiment|NNS|_
ME0052|me0052|NN|_
ME0053|me0053|NN|_
ME0054|me0054|NN|_
ME0055|me0055|NN|_
media|media|NNS|_ :|:|:|_ MEM-HEPES|mem-hepes|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ Glucose|glucose|NN|_ and|and|CC|_ 250nM|250nm|NN|_ Fe|Fe|NNP|_ -LRB-|-lrb-|-LRB-|_ NO3|no3|NN|_ -RRB-|-rrb-|-RRB-|_ 2|2|CD|_
no|no|DT|_ inhibitor|inhibitor|NN|_ :|:|:|_ equivalent|equivalent|JJ|_ volume|volume|NN|_ of|of|IN|_ DMSO|dmso|NN|_ added|add|VBD|_
od|od|NN|_ :|:|:|_ 0.7|0.7|CD|_
strain|strain|NN|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EHEC|ehec|NN|_ TUV93-0|tuv93-0|NN|_
All|all|DT|_ culture|culture|NN|_ experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 19|19|CD|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP -LRB-|-lrb-|-LRB-|_ without|without|IN|_ methionine|methionine|NN|SUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vitamins|vitamin|NNS|_ ,|,|,|_ bases|basis|NNS|_ and|and|CC|_ micronutrients|micronutrient|NNS|_ -LRB-|-lrb-|-LRB-|_ MOPS|mop|NNS|MED rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ minus|minus|CC|_ methionine|methionine|NN|SUPP ,|,|,|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ an|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD420|od420|NN|_ =|=|JJ|_ .001|.001|CD|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ where|where|WRB|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_ For|for|IN|_ 10|10|CD|_ °C|°c|NN|_ samples|sample|NNS|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD420|od420|NN|_ =|=|JJ|_ 1.1|1.1|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ cold|cold|JJ|_ shock|shock|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ mixing|mix|VBG|_ 70mL|70ml|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ culture|culture|NN|_ with|with|IN|_ 130mL|130ml|NN|_ of|of|IN|_ 0|0|CD|_ °C|°c|NN|_ media|media|NNS|_ pre-chilled|pre-chill|VBN|_ in|in|IN|_ ice-water|ice-water|JJ|_ slurry|slurry|NN|_ ,|,|,|_ with|with|IN|_ continued|continued|JJ|_ growth|growth|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ in|in|IN|_ a|a|DT|_ 10|10|CD|_ °C|°c|NN|_ shaker|shaker|NN|_ .|.|.|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ '|'|''|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ ,|,|,|_ rep1|rep1|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ ,|,|,|_ rep2|rep2|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ ,|,|,|_ rep|rep|NN|GEN 4|4|CD|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ with|with|IN|_ 0.025|0.025|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ with|with|IN|_ 0.05|0.05|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_ ,|,|,|_ rep1|rep1|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_ ,|,|,|_ rep|rep|NN|GEN 4|4|CD|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ rep1|rep1|NN|_
DMS-MaPSeq|dms-mapseq|NN|_ of|of|IN|_ purified|purify|VBN|_ cspA|cspa|NN|GEN mRNA|mrna|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
DMS-seq|dms-seq|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
DMS-seq|dms-seq|NN|_ 6|6|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
DMS-seq|dms-seq|NN|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_ cells|cell|NNS|_
DMS-seq|dms-seq|NN|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ cspBG|cspbg|NN|_ cells|cell|NNS|_
DMS-seq|dms-seq|NN|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
DMS-seq|dms-seq|NN|_ of|of|IN|_ purified|purify|VBN|_ mRNA|mrna|NN|_ in|in|FW|_ vitro|vitro|FW|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ ,|,|,|_ rep1|rep1|NN|_
DMS-seq|dms-seq|NN|_ of|of|IN|_ purified|purify|VBN|_ mRNA|mrna|NN|_ in|in|FW|_ vitro|vitro|FW|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ ,|,|,|_ rep2|rep2|NN|_
DMS-seq|dms-seq|NN|_ of|of|IN|_ WT|wt|JJ|_ cells|cell|NNS|_ after|after|IN|_ kasugamycin|kasugamycin|NN|_ treatment|treatment|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Lysate|lysate|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 750|750|CD|_ U|u|NN|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ ribosome-protected|ribosome-protected|JJ|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ followed|follow|VBN|_ by|by|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_
For|for|IN|_ DMS-MaPSeq|dms-mapseq|NN|_ ,|,|,|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ UTR|utr|NN|_ of|of|IN|_ cspA|cspa|NN|GEN using|use|VBG|_ bowtie2|bowtie2|NN|_ and|and|CC|_ an|a|DT|_ alignment|alignment|NN|_ seed|seed|NN|_ of|of|IN|_ 12nt|12nt|JJ|_ .|.|.|_ Low|low|JJ|_ sequence|sequence|NN|_ quality|quality|NN|_ bases|basis|NNS|_ -LRB-|-lrb-|-LRB-|_ Q|Q|NNP|_ score|score|NN|_ <|<|JJR|_ 20|20|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ missing|miss|VBG|_ bases|basis|NNS|_ due|due|JJ|_ to|to|TO|_ truncated|truncate|VBN|_ reads|read|VBZ|_ were|be|VBD|_ set|set|VBN|_ to|to|TO|_ question|question|VB|_ marks|mark|NNS|_ .|.|.|_ Reads|read|NNS|_ that|that|WDT|_ consisted|consist|VBD|_ of|of|IN|_ more|more|JJR|_ than|than|IN|_ 20|20|CD|_ %|%|NN|_ question|question|NN|_ marks|mark|NNS|_ were|be|VBD|_ filtered|filter|VBN|_ out|out|RP|_ .|.|.|_ Only|only|RB|_ mutations|mutation|NNS|_ that|that|WDT|_ agreed|agree|VBD|_ between|between|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ the|the|DT|_ reverse|reverse|JJ|_ read|read|NN|_ were|be|VBD|_ considered|consider|VBN|_ true|true|JJ|_ mutations|mutation|NNS|_ .|.|.|_ Mutation|mutation|NN|_ rate|rate|NN|_ per|per|IN|_ base|base|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ with|with|IN|_ a|a|DT|_ mutation|mutation|NN|_ at|at|IN|_ the|the|DT|_ base|base|NN|_ divided|divide|VBN|_ by|by|IN|_ total|total|JJ|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ covering|cover|VBG|_ the|the|DT|_ base|base|NN|_ .|.|.|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ .|.|.|_ Incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ or|or|CC|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ .|.|.|_ DMS|dms|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ adding|add|VBG|_ 30|30|CD|_ mL|ml|NN|_ 0|0|CD|_ °C|°c|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ %|%|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ put|put|VBN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ with|with|IN|_ 8|8|CD|_ mL|ml|NN|_ 30|30|CD|_ %|%|NN|_ BME|bme|NN|_ solution|solution|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450|450|CD|_ µL|µl|NN|_ total|total|JJ|_ RNA|rna|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
genotype|genotype|NN|_
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABCEG|cspabceg|NN|_
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_
MG1655|mg1655|NN|_ ∆|∆|CD|_ cspBG|cspbg|NN|_
MG1655|mg1655|NN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ DMS-modified|dms-modified|JJ|_ mRNA|mrna|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ mRNA|mrna|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ '|'|''|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LRB-|-lrb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ ;|;|:|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ ;|;|:|_ Rouskin|Rouskin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
mRNA-seq|mrna-seq|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ 2|2|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ 3|3|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ 4|4|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ 6|6|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ cspABCEG|cspabceg|NN|_ cells|cell|NNS|_
mRNA-seq|mrna-seq|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_ _|_|VBP|_ 1|1|CD|_
mRNA-seq|mrna-seq|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_ _|_|VBP|_ 2|2|CD|_
OTHER|other|JJ|_
Ribosome|ribosome|NN|_ profiling|profile|VBG|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_ _|_|VBP|_ 1|1|CD|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_ _|_|VBP|_ 2|2|CD|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|ribosome|NN|_ profiling|profiling|NN|_ 2|2|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 3|3|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 4|4|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 6|6|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ cspABEG|cspabeg|NN|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ cspABCEG|cspabceg|NN|_ cells|cell|NNS|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_ _|_|VBP|_ 1|1|CD|_
Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_ _|_|VBP|_ 2|2|CD|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Txt|txt|NN|_ files|file|NNS|_ are|be|VBP|_ processed|process|VBN|_ data|datum|NNS|_ for|for|IN|_ DMS-MaPseq|dms-mapseq|NN|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ -LRB-|-lrb-|-LRB-|_ relative|relative|JJ|_ to|to|TO|_ transcription|transcription|NN|_ start|start|NN|_ site|site|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ cspA|cspa|NN|GEN -RRB-|-rrb-|-RRB-|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ mutation|mutation|NN|_ rate|rate|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
temperature|temperature|NN|_ :|:|:|_ 10|10|CD|_ °C|°c|NN|_
temperature|temperature|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Total|Total|NNP|_ RNA-seq|RNA-seq|NNP|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ 4|4|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ 4|4|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ 8|8|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ --|--|:|_ 4|4|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ --|--|:|_ 4|4|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ before|before|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ --|--|:|_ 2|2|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ ∆|∆|CD|_ rnr|rnr|NN|GEN cells|cell|NNS|_
Total|total|JJ|_ RNA-seq|rna-seq|NN|_ before|before|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ --|--|:|_ 2|2|CD|_ hr|hr|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ 10|10|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ cells|cell|NNS|_
treatment|treatment|NN|_ :|:|:|_ 0.025|0.025|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.05|0.05|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CspA|cspa|NN|TF protein|protein|NN|_
treatment|treatment|NN|_ :|:|:|_ After|after|IN|_ 10|10|CD|_ mg|mg|NN|_
treatment|treatment|NN|_ :|:|:|_ After|after|IN|_ 250|250|CD|_ µg|µg|NN|_
treatment|treatment|NN|_ :|:|:|_ Before|before|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
treatment|treatment|NN|_ :|:|:|_ NA|NA|NNP|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
Bicyclomycin|bicyclomycin|NN|_ -LRB-|-lrb-|-LRB-|_ BCM|bcm|NN|_ ,|,|,|_ gift|gift|NN|_ of|of|IN|_ Schering-Plough|Schering-Plough|NNP|_ Animal|Animal|NNP|_ Health|Health|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ dose|dose|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ .|.|.|_ Culture|culture|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacterial|bacterial|JJ|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Coli-MDS42|coli-mds42|NN|_ _|_|CD|_ bcm-100mcg|bcm-100mcg|NN|_
Coli-MDS42|coli-mds42|NN|_ _|_|CD|_ del-nusA|del-nusa|NN|_ _|_|CD|_ rep1|rep1|NN|_
Coli-MDS42|coli-mds42|NN|_ _|_|CD|_ del-nusA|del-nusa|NN|_ _|_|CD|_ rep2|rep2|NN|_
Coli-MDS42|coli-mds42|NN|_ _|_|CD|_ del-nusG|del-nusg|NN|_ _|_|CD|_ rep1|rep1|NN|_
Coli-MDS42|coli-mds42|NN|_ _|_|CD|_ del-nusG|del-nusg|NN|_ _|_|CD|_ rep2|rep2|NN|_
Coli-MDS42|coli-mds42|NN|_ _|_|CD|_ no-drug|no-drug|JJ|_ _|_|NN|_ rep1|rep1|NN|_
Coli-MDS42|coli-mds42|NN|_ _|_|CD|_ no-drug|no-drug|JJ|_ _|_|NN|_ rep2|rep2|NN|_
Coli-MG1655|coli-mg1655|NN|_ _|_|CD|_ bcm-100mcg|bcm-100mcg|NN|_
Coli-MG1655|coli-mg1655|NN|_ _|_|CD|_ bcm-10mcg|bcm-10mcg|NN|_
Coli-MG1655|coli-mg1655|NN|_ _|_|CD|_ bcm-25mcg|bcm-25mcg|NN|_
Coli-MG1655|coli-mg1655|NN|_ _|_|CD|_ no-drug|no-drug|JJ|_ _|_|NN|_ rep1|rep1|NN|_
Coli-MG1655|coli-mg1655|NN|_ _|_|CD|_ no-drug|no-drug|JJ|_ _|_|NN|_ rep2|rep2|NN|_
Coli-O157H7|coli-o157h7|NN|_ _|_|CD|_ bcm-100mcg|bcm-100mcg|NN|_
Coli-O157H7|coli-o157h7|NN|_ _|_|CD|_ no-drug|no-drug|JJ|_ _|_|NN|_ rep1|rep1|NN|_
Coli-O157H7|coli-o157h7|NN|_ _|_|CD|_ no-drug|no-drug|JJ|_ _|_|NN|_ rep2|rep2|NN|_
Culture|culture|NN|_ conditions|condition|NNS|_ :|:|:|_ 37|37|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 220|220|CD|_ RPM|rpm|NN|_
Drug|drug|NN|_ :|:|:|_ bicyclomycin|bicyclomycin|NN|_
Drug|drug|NN|_ :|:|:|_ none|none|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Extraction|extraction|NN|_ :|:|:|_ Rneasy|Rneasy|NNP|_
Extraction|Extraction|NNP|_ :|:|:|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_
Feature|Feature|NNP|_ intensity|intensity|NN|_ was|be|VBD|_ extracted|extract|VBN|_ by|by|IN|_ GeneChip|GeneChip|NNP|_ Operating|Operating|NNP|_ System|System|NNP|_ as|as|IN|_ CEL|CEL|NNP|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ probe-level|probe-level|JJ|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ CEL|CEL|NNP|_ files|file|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ PLIER|plier|NN|_ algorithm|algorithm|NN|_ in|in|IN|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Console|console|NN|_ .|.|.|_ No|no|DT|_ further|further|JJ|_ adjustments|adjustment|NNS|_ were|be|VBD|_ made|make|VBN|_ to|to|TO|_ the|the|DT|_ data|datum|NNS|_ in|in|IN|_ the|the|DT|_ table|table|NN|_ .|.|.|_
Growth|Growth|NNP|_ medium|medium|NN|_ :|:|:|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 0.5|0.5|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP
Growth|Growth|NNP|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
Growth|Growth|NNP|_ phase|phase|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_
Isolate|isolate|VB|_ :|:|:|_ EDL933|edl933|NN|_
Isolate|isolate|VB|_ :|:|:|_ MDS42|mds42|NN|_
Isolate|isolate|VB|_ :|:|:|_ MG1655|mg1655|NN|_
K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ 100|100|CD|_ mcg|mcg|NN|_
K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ 10|10|CD|_ mcg|mcg|NN|_
K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ 25|25|CD|_ mcg|mcg|NN|_
K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ control|control|NN|_ sample|sample|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_ ,|,|,|_ 100|100|CD|_ mcg|mcg|NN|_
O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_ ,|,|,|_ control|control|NN|_ sample|sample|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED was|be|VBD|_ innoculated|innoculate|VBN|_ from|from|IN|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1|1|CD|_
Reduced|reduce|VBN|_ genome|genome|NN|_ strain|strain|NN|_ MDS42|mds42|NN|_ ,|,|,|_ 100|100|CD|_ mcg|mcg|NN|_
Reduced|reduce|VBN|_ genome|genome|NN|_ strain|strain|NN|_ MDS42|mds42|NN|_ ,|,|,|_ control|control|NN|_ sample|sample|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Reduced|reduce|VBN|_ genome|genome|NN|_ strain|strain|NN|_ MDS42|mds42|NN|_ ,|,|,|_ deletion|deletion|NN|_ of|of|IN|_ nusA|nusa|NN|GEN gene|gene|NN|_ ,|,|,|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_
Reduced|reduce|VBN|_ genome|genome|NN|_ strain|strain|NN|_ MDS42|mds42|NN|_ ,|,|,|_ deletion|deletion|NN|_ of|of|IN|_ nusG|nusg|NN|GEN gene|gene|NN|_ ,|,|,|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ overnight|overnight|JJ|_ culture|culture|NN|_
Strain|Strain|NNP|_ :|:|:|_ K-12|k-12|NN|_
Strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ reduced|reduce|VBD|_ genome|genome|NN|_
Strain|Strain|NNP|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ Rneasy|rneasy|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ No|no|DT|_ Rnase|rnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Aligned|Aligned|NNP|_ reads|read|VBZ|_ were|be|VBD|_ designated|designate|VBN|_ to|to|TO|_ top|top|JJ|_ and|and|CC|_ bottom|bottom|JJ|_ strands|strand|NNS|_ using|use|VBG|_ Samtools|Samtools|NNP|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ optical|optical|JJ|_ density|density|NN|_ ,|,|,|_ culture|culture|NN|_ growth|growth|NN|_ was|be|VBD|_ instantaneously|instantaneously|RB|_ arrested|arrest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ chilled|chill|VBN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ until|until|IN|_ they|they|PRP|_ were|be|VBD|_ processed|process|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ ,|,|,|_ after|after|IN|_ chromosomal|chromosomal|JJ|_ DNA|dna|NN|_ has|have|VBZ|_ been|be|VBN|_ digested|digest|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ .|.|.|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
bcl2fastq2|bcl2fastq2|NN|_ v2|v2|NN|_ .15.0|.15.0|CD|_ -LRB-|-lrb-|-LRB-|_ Demultiplexing|demultiplexing|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Fastqc|fastqc|NN|_ 0.11.5|0.11.5|CD|_ -LRB-|-lrb-|-LRB-|_ read|read|VB|_ quality|quality|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Cutadapt-1.9.1|cutadapt-1.9.1|NN|_ -LRB-|-lrb-|-LRB-|_ adaptor|adaptor|NN|_ trimming|trim|VBG|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ nusG|nusg|NN|GEN
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ rho|rho|NN|GEN
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
∆|∆|CD|_ nusG|nusg|NN|GEN UvsW|uvsw|NN|_ _|_|CD|_ replicate1|replicate1|NN|_
∆|∆|CD|_ nusG|nusg|NN|GEN UvsW|uvsw|NN|_ _|_|CD|_ replicate2|replicate2|NN|_
∆|∆|CD|_ nusG|nusg|NN|GEN UvsW|uvsw|NN|_ _|_|CD|_ replicate3|replicate3|NN|_
Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ MG15655|mg15655|NN|_ as|as|IN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ tool|tool|NN|_ .|.|.|_
∆|∆|SYM|_ rho|rho|FW|GEN UvsW|uvsw|NN|_ _|_|CD|_ replicate1|replicate1|NN|_
∆|∆|CD|_ rho|rho|NN|GEN UvsW|uvsw|NN|_ _|_|CD|_ replicate2|replicate2|NN|_
∆|∆|CD|_ rho|rho|NN|GEN UvsW|uvsw|NN|_ _|_|CD|_ replicate3|replicate3|NN|_
ssRNA-seq|ssrna-seq|JJ|_
Starting|start|VBG|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ set|set|VBN|_ up|up|RP|_ in|in|IN|_ triplicate|triplicate|NN|_ for|for|IN|_ overnight|overnight|JJ|_ incubation|incubation|NN|_ :|:|:|_ GJ13507|gj13507|NN|_ ,|,|,|_ GJ13531|gj13531|NN|_ ,|,|,|_ and|and|CC|_ GJ13533|gj13533|NN|_ in|in|IN|_ glucose-minimal|glucose-minimal|JJ|_ A|a|NN|_ ;|;|:|_ and|and|CC|_ GJ13519|gj13519|NN|_ also|also|RB|_ in|in|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol-minimal|glycerol-minimal|JJ|_ A.|a.|NN|_ All|all|PDT|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ of|of|IN|_ GJ13507|gj13507|NN|_ whose|whose|WP$|_ supplementation|supplementation|NN|_ with|with|IN|_ IPTG|iptg|NN|_ was|be|VBD|_ at|at|IN|_ 3|3|CD|_ μM|μm|NN|_ .|.|.|_ The|the|DT|_ overnight-grown|overnight-grown|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ each|each|DT|_ subcultured|subculture|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ composition|composition|NN|_ ,|,|,|_ with|with|IN|_ an|a|DT|_ inoculum|inoculum|NN|_ of|of|IN|_ 1:50|1:50|CD|_ for|for|IN|_ GJ13507|gj13507|NN|_ and|and|CC|_ GJ13531|gj13531|NN|_ and|and|CC|_ of|of|IN|_ 1:100|1:100|CD|_ for|for|IN|_ the|the|DT|_ remainder|remainder|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ to|to|TO|_ 0.45|0.45|CD|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ making|make|VBG|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_
Strand|Strand|NNP|_ specific|specific|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ were|be|VBD|_ determined|determine|VBN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_
Strand-specific|strand-specific|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ generated|generate|VBN|_ ,|,|,|_ following|follow|VBG|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ aid|aid|NN|_ of|of|IN|_ the|the|DT|_ di-tagged|di-tagged|JJ|_ cDNA|cdna|NN|_ strategy|strategy|NN|_ -LRB-|-lrb-|-LRB-|_ ScriptSeq|scriptseq|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ platform|platform|NN|_
substrain|substrain|NN|_ :|:|:|_ GJ13507|gj13507|NN|_
substrain|substrain|NN|_ :|:|:|_ GJ13519|gj13519|NN|_
substrain|substrain|NN|_ :|:|:|_ GJ13531|gj13531|NN|_
substrain|substrain|NN|_ :|:|:|_ GJ13533|gj13533|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ text|text|NN|_ file|file|NN|_ contains|contain|VBZ|_ sense|sense|NN|_ and|and|CC|_ antisense|antisense|JJ|_ raw|raw|JJ|_ base|base|NN|_ read|read|VBD|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4091|4091|CD|_ ORFs|orf|NNS|_ for|for|IN|_ all|all|PDT|_ the|the|DT|_ 15|15|CD|_ samples|sample|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ explanation|explanation|NN|_ key|key|NN|_ is|be|VBZ|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_
Viable|viable|JJ|_ clones|clone|NNS|_ of|of|IN|_ the|the|DT|_ UvsW-expressing|uvsw-expressing|JJ|_ strains|strain|NNS|_ GJ13531|gj13531|NN|_ -LRB-|-lrb-|-LRB-|_ Δrho|δrho|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GJ13507|gj13507|NN|_ -LRB-|-lrb-|-LRB-|_ ΔnusG|δnusg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ white|white|JJ|_ colonies|colony|NNS|_ from|from|IN|_ their|they|PRP$|_ respective|respective|JJ|_ shelter|shelter|NN|_ plasmid-carrying|plasmid-carrying|JJ|_ derivatives|derivative|NNS|_ GJ13531|gj13531|NN|_
WT|wt|JJ|_ glucose|glucose|NN|SUPP _|_|NN|_ replicate1|replicate1|NN|_
WT|wt|JJ|_ glucose|glucose|NN|SUPP _|_|NN|_ replicate2|replicate2|NN|_
WT|wt|JJ|_ glucose|glucose|NN|SUPP _|_|NN|_ replicate3|replicate3|NN|_
WT|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ replicate1|replicate1|NN|_
WT|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ replicate2|replicate2|NN|_
WT|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ replicate3|replicate3|NN|_
WT|wt|JJ|_ UvsW|uvsw|NN|_ _|_|NN|_ replicate1|replicate1|NN|_
WT|wt|JJ|_ UvsW|uvsw|NN|_ _|_|NN|_ replicate2|replicate2|NN|_
WT|wt|JJ|_ UvsW|uvsw|NN|_ _|_|NN|_ replicate3|replicate3|NN|_
cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ grown|grown|JJ|_ culture|culture|NN|_ in|in|IN|_ Lysogeny|Lysogeny|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ harvested|harvest|VBN|_ in|in|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ mid|mid|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_
crpfis.rep1.ee|crpfis.rep1.ee|NN|_
crpfis.rep1.me|crpfis.rep1.me|NN|_
crpfis.rep2.ee|crpfis.rep2.ee|NN|_
crpfis.rep2.me|crpfis.rep2.me|NN|_
crp.rep1.ee|crp.rep1.ee|NN|_
crp.rep1.me|crp.rep1.me|NN|_
crp.rep2.ee|crp.rep2.ee|NN|_
crp.rep2.me|crp.rep2.me|NN|_
cya.rep1.ee|cya.rep1.ee|NN|_
cya.rep1.me|cya.rep1.me|NN|_
cya.rep2.ee|cya.rep2.ee|NN|_
cya.rep2.me|cya.rep2.me|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
fis.rep1.ee|fis.rep1.ee|JJ|_
fis.rep1.me|fis.rep1.me|NN|_
fis.rep2.ee|fis.rep2.ee|JJ|_
fis.rep2.me|fis.rep2.me|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ crpfis|crpfis|NN|_ mutant|mutant|JJ|_ background|background|NN|_
genotype|genotype|NN|_ :|:|:|_ crp|crp|NN|GEN mutant|mutant|JJ|_ background|background|NN|_
genotype|genotype|NN|_ :|:|:|_ cya|cya|NN|_ mutant|mutant|JJ|_ background|background|NN|_
genotype|genotype|NN|_ :|:|:|_ fis|fis|NN|GEN mutant|mutant|JJ|_ background|background|NN|_
genotype|genotype|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Early|early|JJ|_ exponential|exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid|Mid|NNP|_ exponential|exponential|JJ|_
NEXTflexRapid|nextflexrapid|NN|_ Directional|directional|JJ|_ RNA-Seq|rna-seq|NN|_ library|library|NN|_ kit|kit|NN|_
Raw|raw|NN|_ .|.|.|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.7|0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ to|to|TO|_ read|read|VB|_ count|count|NN|_ per|per|IN|_ gene|gene|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ the|the|DT|_ case|case|NN|_ of|of|IN|_ Ion|ion|NN|_ torrent|torrent|NN|_ data|datum|NNS|_ .|.|.|_ bam|bam|NN|_ files|file|NNS|_ were|be|VBD|_ converted|convert|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ .|.|.|_
Resulting|Resulting|NNP|_ read|read|VBD|_ count|count|NN|_ matrix|matrix|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ for|for|IN|_ the|the|DT|_ differntial|differntial|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ in|in|IN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.12.1|3.12.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ .|.|.|_ Depending|depend|VBG|_ upon|upon|IN|_ the|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Dnase|dnase|NN|_ and|and|CC|_ ribocleanup|ribocleanup|NN|_ was|be|VBD|_ given|give|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instruction|instruction|NN|_ manual|manual|NN|_ .|.|.|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1656|mg1656|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1657|mg1657|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1658|mg1658|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1659|mg1659|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1660|mg1660|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1661|mg1661|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1662|mg1662|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1663|mg1663|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1664|mg1664|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1665|mg1665|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1666|mg1666|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1667|mg1667|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1668|mg1668|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1669|mg1669|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1670|mg1670|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1671|mg1671|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1672|mg1672|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1673|mg1673|NN|_
srain|srain|NN|_ :|:|:|_ K12|k12|NN|_ MG1674|mg1674|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ -LRB-|-lrb-|-LRB-|_ log2|log2|NN|_ fold|fold|JJ|_ change|change|NN|_ values|value|NNS|_ ,|,|,|_ p-values|p-value|NNS|_ -RRB-|-rrb-|-RRB-|_
wt.rep1.ee|wt.rep1.ee|NN|_
wt.rep1.me|wt.rep1.me|NN|_
wt.rep2.ee|wt.rep2.ee|NN|_
wt.rep2.me|wt.rep2.me|NN|_
cell|cell|NN|_ pellets|pellet|NNS|_
E.|e.|FW|_ coli|coli|FW|_ 042|042|CD|_ WT|wt|JJ|_
E.|e.|FW|_ coli|coli|FW|_ hhahha2|hhahha2|NN|_
E.|e.|FW|_ coli|coli|FW|_ hns|hns|FW|GEN
E.|e.|FW|_ coli|coli|FW|_ hns2|hns2|NN|_
E.|e.|FW|_ coli|coli|FW|_ hnshns2|hnshns2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 042|042|CD|_
For|for|IN|_ quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ read|read|NN|_ counting|counting|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ alignments|alignment|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Genomics|Genomics|NNP|_ Workbench|Workbench|NNP|_ were|be|VBD|_ exported|export|VBN|_ in|in|IN|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_ Read|Read|NNP|_ counting|counting|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ FeatureCounts|FeatureCounts|NNP|_ v.|v.|CC|_ 1.5.0-p1|1.5.0-p1|CD|_ program|program|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ Level|Level|NNP|_ :|:|:|_ meta-feature|meta-feature|JJ|_ leve|leve|NN|_ .|.|.|_ Paired-end|paired-end|NN|_ :|:|:|_ no|no|DT|_ .|.|.|_ Strand|strand|VB|_ specific|specific|JJ|_ :|:|:|_ yes|yes|UH|_ .|.|.|_ Multimapping|multimapp|VBG|_ reads|read|VBZ|_ :|:|:|_ counted|count|VBN|_ -LRB-|-lrb-|-LRB-|_ as|as|IN|_ fractions|fraction|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Multi-overlapping|multi-overlapping|JJ|_ reads|read|VBZ|_ :|:|:|_ not|not|RB|_ counted|count|VBN|_ .|.|.|_ Overlapping|overlapping|JJ|_ bases|basis|NNS|_ :|:|:|_ 30|30|CD|_ .|.|.|_ Read|Read|NNP|_ orientations|orientation|NNS|_ :|:|:|_ fr|fr|NN|_
From|from|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ first-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ After|after|IN|_ fragmentation|fragmentation|NN|_ ,|,|,|_ the|the|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ in|in|IN|_ a|a|DT|_ strand|strand|NN|_ specific|specific|JJ|_ manner|manner|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ For|for|IN|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ ,|,|,|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ a|a|DT|_ 25:1|25:1|CD|_ ratio|ratio|NN|_ .|.|.|_ The|the|DT|_ library|library|NN|_ pool|pool|NN|_ was|be|VBD|_ fractionated|fractionate|VBN|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ range|range|NN|_ of|of|IN|_ 250-500|250-500|CD|_ bp|bp|NN|_ using|use|VBG|_ a|a|DT|_ differential|differential|JJ|_ clean|clean|JJ|_ -|-|:|_ up|up|RP|_ with|with|IN|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ kit|kit|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ pool|pool|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ using|use|VBG|_ 75|75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 017626.1|017626.1|CD|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hhahha2|hhahha2|NN|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hhs|hh|NNS|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hns2|hns2|NN|_
genotype|genotype|NN|_ :|:|:|_ mutant|mutant|JJ|_ hnshns2|hnshns2|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ instruments|instrument|NNS|_ generate|generate|VBP|_ per-cycle|per-cycle|JJ|_ BCL|BCL|NNP|_ base|base|NN|_ call|call|NN|_ files|file|NNS|_ as|as|IN|_ primary|primary|JJ|_ sequencing|sequencing|NN|_ output|output|NN|_ in|in|IN|_ bcl2|bcl2|NN|_ format|format|NN|_ .|.|.|_ Conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ bcl2|bcl2|NN|_ file|file|NN|_ to|to|TO|_ gzipped|gzipped|JJ|_ fastq|fastq|NN|_ files|file|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ bcl2fastq|bcl2fastq|NN|_ script|script|NN|_ v.|v.|CC|_ 2.18.0.12|2.18.0.12|CD|_ provided|provide|VBN|_ by|by|IN|_ Illumina|Illumina|NNP|_ .|.|.|_
LB|LB|NNP|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ was|be|VBD|_ also|also|RB|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ using|use|VBG|_ the|the|DT|_ `|`|``|_ Map|map|NN|_ Reads|read|VBZ|_ to|to|TO|_ Reference|Reference|NNP|_ '|'|POS|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
Quality|Quality|NNP|_ and|and|CC|_ adapter|adapter|NN|_ trimming|trim|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 9.0|9.0|CD|_ software|software|NN|_ package|package|NN|_ using|use|VBG|_ the|the|DT|_ `|`|``|_ Trim|Trim|NNP|_ Sequences|sequence|NNS|_ '|'|POS|_ tool|tool|NN|_ with|with|IN|_ standard|standard|JJ|_ parameters|parameter|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Strain-expression|strain-expression|NN|_ .|.|.|_ xlsx|xlsx|NN|_ archive|archive|NN|_ contains|contain|VBZ|_ expression|expression|NN|_ values|value|NNS|_ in|in|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Reads|read|NNS|_ Per|per|IN|_ Kb|kb|NN|_ exon|exon|NN|_ -LRB-|-lrb-|-LRB-|_ contig|contig|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ Million|Million|NNP|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ Mortazavi|Mortazavi|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ .|.|.|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 621-8|621-8|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ compared|compare|VBN|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ -RRB-|-rrb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ mill|mill|NN|_ and|and|CC|_ the|the|DT|_ mirVana|mirvana|NN|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ including|include|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
We|we|PRP|_ used|use|VBD|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ system|system|NN|_ and|and|CC|_ a|a|DT|_ MID|mid|NN|_ 150|150|CD|_ Kit|kit|NN|_ with|with|IN|_ 1x75|1x75|CD|_ bp|bp|NN|_ read|read|VBD|_ length|length|NN|_ .|.|.|_ Base-calling|base-calling|NN|_ was|be|VBD|_ perform|perform|VB|_ online|online|NN|_ during|during|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ procedure|procedure|NN|_ with|with|IN|_ the|the|DT|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ version|version|NN|_ 2.4.11|2.4.11|CD|_ and|and|CC|_ System|System|NNP|_ Suite|Suite|NNP|_ Version|Version|NNP|_ 2.1.2.1|2.1.2.1|CD|_ .|.|.|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ∆|∆|SYM|_ ompR|ompr|NN|GEN pH|ph|NN|_ 5.6|5.6|CD|_ A|a|DT|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ∆|∆|SYM|_ ompR|ompr|NN|GEN pH|ph|NN|_ 5.6|5.6|CD|_ B|b|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ∆|∆|SYM|_ ompR|ompr|NN|GEN pH|ph|NN|_ 5.6|5.6|CD|_ C|c|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ∆|∆|SYM|_ ompR|ompr|NN|GEN pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ A|a|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ∆|∆|SYM|_ ompR|ompr|NN|GEN pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ B|b|NN|_
E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MgM|MgM|NNP|_ media|media|NNS|_ at|at|IN|_ pH|ph|NN|_ 5.6|5.6|CD|_ ,|,|,|_ 7.2|7.2|CD|_ and|and|CC|_ 7.2|7.2|CD|_ with|with|IN|_ 15|15|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w|w|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ WT|wt|JJ|_ pH|ph|NN|_ 5.6|5.6|CD|_ A|a|DT|_
E.coli|e.coli|NN|_ _|_|CD|_ WT|WT|NNP|_ pH|ph|NN|_ 5.6|5.6|CD|_ B|b|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ WT|wt|JJ|_ pH|ph|NN|_ 5.6|5.6|CD|_ C|c|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ WT|wt|JJ|_ pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ A|a|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ WT|wt|JJ|_ pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ B|b|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ WT|wt|JJ|_ pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ C|c|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ _|_|CD|_ ompR|ompr|NN|GEN
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|JJ|_
∆|∆|CD|_ ompR|ompr|NN|GEN pH|ph|NN|_ 5.6|5.6|CD|_ A|a|DT|_
∆|∆|CD|_ ompR|ompr|NN|GEN pH|ph|NN|_ 5.6|5.6|CD|_ B|b|NN|_
∆|∆|CD|_ ompR|ompr|NN|GEN pH|ph|NN|_ 5.6|5.6|CD|_ C|c|NN|_
∆|∆|CD|_ ompR|ompr|NN|GEN pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ A|a|NN|_
∆|∆|CD|_ ompR|ompr|NN|GEN pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ B|b|NN|_
ph|ph|NN|_ :|:|:|_ 5.6|5.6|CD|_
ph|ph|NN|_ :|:|:|_ 7.2|7.2|CD|_
Raw|raw|NN|_ signal|signal|NN|_ data|datum|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ TIFF|tiff|NN|_ image|image|NN|_ with|with|IN|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ V10|V10|NNP|_ .7.1.1|.7.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ data|data|NN|_ analysis|analysis|NN|_ is|be|VBZ|_ done|do|VBN|_ using|use|VBG|_ a|a|DT|_ microarray|microarray|NN|_ specialized|specialized|JJ|_ analysis|analysis|NN|_ software|software|NN|_ ,|,|,|_ Genespring|Genespring|NNP|_ GX|GX|NNP|_ .|.|.|_ In|in|IN|_ this|this|DT|_ experiment|experiment|NN|_ ,|,|,|_ the|the|DT|_ microarray|microarray|NN|_ type|type|NN|_ used|use|VBN|_ is|be|VBZ|_ a|a|DT|_ slide|slide|NN|_ having|have|VBG|_ 8|8|CD|_ arrays|array|NNS|_ with|with|IN|_ 60|60|CD|_ thousand|thousand|CD|_ features|feature|NNS|_ per|per|IN|_ array|array|NN|_ .|.|.|_ The|the|DT|_ exact|exact|JJ|_ number|number|NN|_ of|of|IN|_ features|feature|NNS|_ in|in|IN|_ the|the|DT|_ each|each|DT|_ array|array|NN|_ ,|,|,|_ inclusive|inclusive|NN|_ of|of|IN|_ control|control|NN|_ probes|probe|NNS|_ ,|,|,|_ is|be|VBZ|_ 10,751|10,751|CD|_ features|feature|NNS|_ .|.|.|_ The|the|DT|_ microarray|microarray|NN|_ has|have|VBZ|_ a|a|DT|_ specific|specific|JJ|_ Agilent|Agilent|NNP|_ identifier|identifier|NN|_ called|call|VBD|_ an|a|DT|_ AMADID|amadid|NN|_ which|which|WDT|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ identify|identify|VB|_ what|what|WP|_ kind|kind|NN|_ of|of|IN|_ array|array|NN|_ is|be|VBZ|_ being|be|VBG|_ used|use|VBN|_ ;|;|:|_ in|in|IN|_ this|this|DT|_ experiment|experiment|NN|_ the|the|DT|_ AMADID|AMADID|NNP|_ used|use|VBN|_ is|be|VBZ|_ the|the|DT|_ design|design|NN|_ ID|id|NN|_ 020097|020097|CD|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
sucrose|sucrose|NN|_ status|status|NN|_ :|:|:|_ no|no|DT|_ sucrose|sucrose|NN|_
sucrose|sucrose|NN|_ status|status|NN|_ :|:|:|_ with|with|IN|_ 15|15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_
Supplementary|Supplementary|NNP|_ files|file|VBZ|_ contain|contain|VBP|_ the|the|DT|_ following|following|NN|_ :|:|:|_ Raw|raw|NN|_ Signal|signal|NN|_ Values|value|NNS|_ :|:|:|_ The|the|DT|_ term|term|NN|_ ``|``|``|_ raw|raw|JJ|_ ''|''|''|_ signal|signal|NN|_ values|value|NNS|_ refer|refer|VBP|_ to|to|TO|_ the|the|DT|_ linear|linear|JJ|_ data|datum|NNS|_ after|after|IN|_ thresholding|threshold|VBG|_ and|and|CC|_ summarization|summarization|NN|_ Summarization|summarization|NN|_ is|be|VBZ|_ performed|perform|VBN|_ by|by|IN|_ computing|compute|VBG|_ the|the|DT|_ geometric|geometric|JJ|_ mean|mean|NN|_ .|.|.|_ Raw|raw|NN|_ data|datum|NNS|_ filtered|filter|VBN|_ on|on|IN|_ Expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ 20.0|20.0|CD|_ -|-|:|_ 343943.344|343943.344|CD|_ -RRB-|-rrb-|-RRB-|_ •|•|SYM|_ Normalized|normalize|VBN|_ Signal|signal|NN|_ Values|value|NNS|_ :|:|:|_ ``|``|``|_ Normalized|normalize|VBN|_ ''|''|''|_ value|value|NN|_ is|be|VBZ|_ the|the|DT|_ value|value|NN|_ generated|generate|VBN|_ after|after|IN|_ log|log|NN|_ transformation|transformation|NN|_ and|and|CC|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Shift|shift|NN|_ to|to|TO|_ 75|75|CD|_ percentile|percentile|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ baseline|baseline|NN|_ transformation|transformation|NN|_ .|.|.|_
The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WT|WT|NNP|_ pH|ph|NN|_ 5.6|5.6|CD|_ A|a|DT|_
WT|wt|NN|_ pH|ph|NN|_ 5.6|5.6|CD|_ B|b|NN|_
WT|wt|NN|_ pH|ph|NN|_ 5.6|5.6|CD|_ C|c|NN|_
WT|wt|JJ|_ pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ A|a|NN|_
WT|wt|JJ|_ pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ B|b|NN|_
WT|wt|JJ|_ pH|ph|NN|_ 7.2|7.2|CD|_ +15|+15|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ C|c|NN|_
170|170|CD|_ μl|μl|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ four|four|CD|_ wells|well|NNS|_ per|per|IN|_ time|time|NN|_ point|point|NN|_ and|and|CC|_ collected|collect|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ were|be|VBD|_ 1.360|1.360|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protection|protection|NN|_ buffer|buffer|NN|_ had|have|VBD|_ previously|previously|RB|_ been|be|VBN|_ added|add|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ left|leave|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ pellets|pellet|NNS|_ frozen|freeze|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 74104|74104|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ To|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ traces|trace|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ 2|2|CD|_ μg|μg|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ treated|treat|VBN|_ for|for|IN|_ a|a|DT|_ second|second|JJ|_ time|time|NN|_ with|with|IN|_ DNAseI|dnasei|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 79254|79254|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-1511|5067-1511|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ had|have|VBD|_ an|a|DT|_ average|average|JJ|_ RIN|rin|NN|_ of|of|IN|_ 9.5|9.5|CD|_ .|.|.|_ Enrichment|enrichment|NN|_ of|of|IN|_ mRNA|mrna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MicrobExpress|MicrobExpress|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ AM1905|am1905|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Successful|successful|JJ|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ analysis|analysis|NN|_ on|on|IN|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_ Retrotranscription|retrotranscription|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ starting|start|VBG|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ total|total|JJ|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ Tetro|Tetro|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ from|from|IN|_ Bioline|Bioline|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-65043|bio-65043|NN|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ Random|Random|NNP|_ Hexamers|Hexamers|NNPS|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ BIO-38028|bio-38028|NN|_ -RSB-|-rsb-|-RRB-|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Second|second|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ adding|add|VBG|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ mix|mix|NN|_ 5|5|CD|_ μl|μl|NN|_ of|of|IN|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ B6117S|b6117s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 3|3|CD|_ μl|μl|NN|_ of|of|IN|_ dNTPs|dntps|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ N0446S|n0446s|NN|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 2μl|2μl|NN|_ of|of|IN|_ RNAseH|rnaseh|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ M0297L|m0297l|NN|_ -RSB-|-rsb-|-RRB-|_ all|all|DT|_ from|from|IN|_ NEB|NEB|NNP|_ ,|,|,|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ Polymerase|polymerase|NN|_ I|I|PRP|_ from|from|IN|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ 18010025|18010025|CD|_ -RSB-|-rsb-|-RRB-|_ and|and|CC|_ 18|18|CD|_ μl|μl|NN|_ of|of|IN|_ water|water|NN|_ ,|,|,|_ per|per|IN|_ reaction|reaction|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 16|16|CD|_ °C|°c|NN|_ for|for|IN|_ 2.5|2.5|CD|_ h.|h.|NN|_ Purification|purification|NN|_ of|of|IN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 28004|28004|NN|_ -RSB-|-rsb-|-RRB-|_ with|with|IN|_ final|final|JJ|_ elution|elution|NN|_ in|in|IN|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ DEPC-treated|depc-treated|JJ|_ free|free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|qubit|NN|_ fluorometer|fluorometer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
After|after|IN|_ 60|60|CD|_ minutes|minute|NNS|_ into|into|IN|_ the|the|DT|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ plate|plate|NN|_ was|be|VBD|_ briefly|briefly|RB|_ removed|remove|VBN|_ so|so|RB|_ inducer|inducer|NN|_ could|could|MD|_ be|be|VB|_ added|add|VBN|_ to|to|TO|_ wells|well|NNS|_ ,|,|,|_ and|and|CC|_ this|this|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ set|set|VBN|_ as|as|IN|_ time|time|NN|_ 0|0|CD|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ instead|instead|RB|_ removed|remove|VBN|_ from|from|IN|_ wells|well|NNS|_ at|at|IN|_ 15|15|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_
B10|b10|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pSB1C3|psb1c3|NN|_ _|_|NN|_ 2|2|CD|_
B17|b17|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ pSB1C3|psb1c3|NN|_ _|_|NN|_ 2|2|CD|_
B22|b22|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ pSB1C3|psb1c3|NN|_ _|_|CD|_ H3|h3|NN|_ _|_|NN|_ 2|2|CD|_
B26|b26|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ Lux|lux|FW|_ _|_|FW|_ 2|2|CD|_
B3|b3|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pSB1C3|psb1c3|NN|_ _|_|NN|_ 2|2|CD|_
B4|b4|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pLys|ply|VBZ|_ _|_|SYM|_ 2|2|CD|_
B7|b7|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pD864|pd864|NN|_ _|_|NN|_ 2|2|CD|_
B9|b9|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pLys|ply|VBZ|_ _|_|SYM|_ M1|m1|NN|_ _|_|NN|_ 2|2|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ construct|construct|NN|_ and|and|CC|_ control|control|NN|_ plasmids|plasmid|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ defined|define|VBN|_ supplemented|supplement|VBN|_ M9|m9|NN|_ medium|medium|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ antibiotic|antibiotic|JJ|_ .|.|.|_ In|in|IN|_ the|the|DT|_ morning|morning|NN|_ ,|,|,|_ 60|60|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ another|another|DT|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ outgrowth|outgrowth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ in|in|IN|_ 8|8|CD|_ wells|well|NNS|_ of|of|IN|_ a|a|DT|_ 96-well|96-well|JJ|_ plate|plate|NN|_ -LRB-|-lrb-|-LRB-|_ Costar|costar|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ approximately|approximately|RB|_ 0.1|0.1|CD|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ Synergy|synergy|NN|_ HT|ht|NN|_ Microplate|Microplate|NNP|_ Reader|Reader|NNP|_ -LRB-|-lrb-|-LRB-|_ BioTek|BioTek|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 1,000|1,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ performing|perform|VBG|_ measurements|measurement|NNS|_ of|of|IN|_ GFP|gfp|NN|_ -LRB-|-lrb-|-LRB-|_ excitation|excitation|NN|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 485|485|CD|_ nm|nm|NN|_ ;|;|:|_ emission|emission|NN|_ -LRB-|-lrb-|-LRB-|_ em|em|NN|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 528|528|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ every|every|DT|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
G21|g21|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ pD864|pd864|NN|_ _|_|NN|_ 3|3|CD|_
G23|g23|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ pLys|ply|VBZ|_ _|_|SYM|_ M1|m1|NN|_ _|_|NN|_ 3|3|CD|_
G28|g28|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ pD864|pd864|NN|_ _|_|NN|_ 3|3|CD|_
G29|g29|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ None|none|NN|_ _|_|NN|_ 3|3|CD|_
G5|g5|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ Lux|lux|FW|_ _|_|FW|_ 3|3|CD|_
G6|g6|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pD864|pd864|NN|_ _|_|CD|_ LacZ|lacz|NN|_ _|_|SYM|_ 3|3|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ DH10BGFP|dh10bgfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM1942v1|asm1942v1|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Samples|sample|NNS|_ from|from|IN|_ strain|strain|NN|_ MG1655GFP|mg1655gfp|NN|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ geneome|geneome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ .31|.31|CD|_ complemented|complement|VBN|_ with|with|IN|_ the|the|DT|_ GFP|gfp|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sequence|sequence|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ synthetic|synthetic|JJ|_ circuit|circuit|NN|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ FC-131-1096|fc-131-1096|NN|_ -RSB-|-rsb-|-RRB-|_ starting|start|VBG|_ from|from|IN|_ 1|1|CD|_ ng|ng|NN|_ of|of|IN|_ total|total|JJ|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ original|original|JJ|_ protocol|protocol|NN|_ was|be|VBD|_ modified|modify|VBN|_ where|where|WRB|_ 3|3|CD|_ min|min|NN|_ tagmentation|tagmentation|NN|_ and|and|CC|_ 13|13|CD|_ cycles|cycle|NNS|_ of|of|IN|_ step-limited|step-limited|JJ|_ PCR|pcr|NN|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ Ampure|ampure|JJ|_ beads|bead|NNS|_ from|from|IN|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -LSB-|-lsb-|-LRB-|_ Cat|Cat|NNP|_ No|No|NNP|_ A63880|a63880|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ library|library|NN|_ purification|purification|NN|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ assessment|assessment|NN|_ and|and|CC|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ DNA|dna|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ -LSB-|-lsb-|-LRB-|_ Cat|cat|NN|_ No|no|DT|_ 5067-4626|5067-4626|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Finally|finally|RB|_ all|all|DT|_ 90|90|CD|_ samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ reaction|reaction|NN|_ tube|tube|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ nM|nm|NN|_ .|.|.|_
Numer|Numer|NNP|_ of|of|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ Rsubread|Rsubread|NNP|_ package|package|NN|_ v1|v1|NN|_ .12.6|.12.6|CD|_
paired|paired|JJ|_ end|end|NN|_ sequencing|sequencing|NN|_ with|with|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Sequencer|Sequencer|NNP|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PD864|pd864|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PLYS|plys|NN|_
plasmid|plasmid|NN|_ :|:|:|_ PSB1C3|psb1c3|NN|_
R11|r11|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pLys|ply|VBZ|_ _|_|SYM|_ 1|1|CD|_
R16|r16|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ pLys|ply|VBZ|_ _|_|SYM|_ M1|m1|NN|_ _|_|NN|_ 1|1|CD|_
R19|r19|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ Lux|lux|FW|_ _|_|FW|_ 1|1|CD|_
R26|r26|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ Lux|lux|FW|_ _|_|FW|_ 1|1|CD|_
R27|r27|NN|_ MG1655GFP|mg1655gfp|NN|_ _|_|CD|_ pD864|pd864|NN|_ _|_|CD|_ LacZ|lacz|NN|_ _|_|NN|_ 1|1|CD|_
R29|r29|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ None|none|NN|_ _|_|NN|_ 1|1|CD|_
R2|r2|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pLys|ply|VBZ|_ _|_|SYM|_ M1|m1|NN|_ _|_|NN|_ 1|1|CD|_
R3|r3|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pSB1C3|psb1c3|NN|_ _|_|NN|_ 1|1|CD|_
R6|r6|NN|_ DH10BGFP|dh10bgfp|NN|_ _|_|CD|_ pD864|pd864|NN|_ _|_|CD|_ LacZ|lacz|NN|_ _|_|NN|_ 1|1|CD|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ TrimGalore|trimgalore|NN|_ version|version|NN|_ 0.4.1|0.4.1|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ mm8|mm8|VB|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bwa|bwa|NN|_ mem|mem|NN|_ version|version|NN|_ 0.7.12|0.7.12|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
strain|strain|NN|_ :|:|:|_ DH10BGFP|dh10bgfp|NN|_
strain|strain|NN|_ :|:|:|_ MG1655GFP|mg1655gfp|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|VBZ|_ providing|provide|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ gene|gene|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ H3|h3|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ LACZ|lacz|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ Lux|lux|FW|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ M1|m1|NN|_
synthetic|synthetic|JJ|_ circuit|circuit|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ arabinose|arabinose|NN|_
treatment|treatment|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ rhamnose|rhamnose|NN|_
3C-seq|3c-seq|NN|_ :|:|:|_ 5|5|CD|_ µg|µg|NN|_ of|of|IN|_ a|a|DT|_ 3C|3c|NN|_ library|library|NN|_ was|be|VBD|_ suspended|suspend|VBN|_ in|in|IN|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ volume|volume|NN|_ 130|130|CD|_ µL|µl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sheared|shear|VBD|_ using|use|VBG|_ a|a|DT|_ Covaris|Covaris|NNP|_ S220|s220|NN|_ instrument|instrument|NN|_ -LRB-|-lrb-|-LRB-|_ Duty|duty|NN|_ cycle|cycle|NN|_ 5|5|CD|_ ,|,|,|_ Intensity|intensity|NN|_ 5|5|CD|_ ,|,|,|_ cycles|cycle|NNS|_
3C-seq|3c-seq|JJ|_ libraries|library|NNS|_ were|be|VBD|_ proccessed|proccess|VBN|_ using|use|VBG|_ the|the|DT|_ 3C-seq|3c-seq|JJ|_ pipeline|pipeline|NN|_ available|available|JJ|_ at|at|IN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ fis|fis|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ fis|fis|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ hns|hns|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ hns|hns|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ hupAB|hupab|NN|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 37|37|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ hupAB|hupab|NN|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 37|37|CD|_ °C|°c|SYM|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ matP|matp|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 22|22|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ matP|matp|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ matP|matp|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ matPDC20|matpdc20|NN|_ cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2-5xmatS|pgbm2-5xmats|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ matPDC20|matpdc20|NN|_ cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2|pgbm2|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ matPDC20|matpdc20|NN|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ mukB|mukb|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 22|22|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ mukB|mukb|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 22|22|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ mukBmatP|mukbmatp|NN|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 22|22|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2-5xmatS|pgbm2-5xmats|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2-5xmatS|pgbm2-5xmats|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2|pgbm2|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2|pgbm2|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 22|22|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 22|22|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 2|2|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 37|37|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 37|37|CD|_ °C|°c|SYM|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase LB|lb|NN|_ 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase LB|lb|NN|_ 30|30|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ 30h|30h|NN|_ -RRB-|-rrb-|-RRB-|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ 30h|30h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ zapB|zapb|NN|GEN cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2-5xmatS|pgbm2-5xmats|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ zapB|zapb|NN|GEN cells|cell|NNS|_ harbouring|harbour|VBG|_ plasmid|plasmid|NN|_ pGBM2|pgbm2|NN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
3C-seq|3c-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ zapB|zapb|NN|GEN cells|cell|NNS|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_
Assignment|assignment|NN|_ to|to|TO|_ restriction|restriction|NN|_ fragment|fragment|NN|_
Binning|binning|NN|_ at|at|IN|_ 5kb|5kb|JJ|_ .|.|.|_
E|e|NN|_ coli|coli|NN|_ cells|cell|NNS|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 22|22|CD|_ °C|°c|NN|_ ,|,|,|_ 30|30|CD|_ °C|°c|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ either|either|CC|_ Lennox|Lennox|NNP|_ Broth|Broth|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ liquid|liquid|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ A|a|DT|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.12|0.12|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ -LRB-|-lrb-|-LRB-|_ early|early|JJ|_ exponential|exponential|JJ|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Filtering|filter|VBG|_ ,|,|,|_ Mapping|mapping|NN|_ quality|quality|NN|_ =|=|JJ|_ 30|30|CD|_ ,|,|,|_ no|no|DT|_ ambiguous|ambiguous|JJ|_ reads|read|VBZ|_
For|for|IN|_ 3C-seq|3c-seq|NN|_ :|:|:|_ ≈|≈|SYM|_ 1-2|1-2|CD|_ x|x|CC|_ 109|109|CD|_ crosslinked|crosslink|VBN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ ,|,|,|_ unless|unless|IN|_ otherwise|otherwise|RB|_ stated|state|VBN|_ -RRB-|-rrb-|-RRB-|_ are|be|VBP|_ suspended|suspend|VBN|_ in|in|IN|_ 600|600|CD|_ μl|μl|NN|_ Tris|Tris|NNP|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP -LRB-|-lrb-|-LRB-|_ TE|te|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 4|4|CD|_ μl|μl|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 35|35|CD|_ U|U|NNP|_
For|for|IN|_ RNA-seq|RNA-seq|NNP|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Protect|protect|VB|_ Bacteria|bacterium|NNS|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -|-|:|_ #|#|#|_ 74524|74524|CD|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ total|total|JJ|_ length|length|NN|_ :|:|:|_ 4639675|4639675|CD|_ bp|bp|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ fis|fi|VBZ|GEN :|:|:|_ :|:|:|_ frt-kan-frt|frt-kan-frt|JJ|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ hns|hn|NNS|GEN :|:|:|_ :|:|:|_ frt|frt|SYM|_ -|-|:|_ kan|kan|SYM|_ -|-|:|_ frt|frt|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ matP|matp|NN|GEN :|:|:|_ :|:|:|_ frt-cam-frt|frt-cam-frt|JJ|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ mukB|mukb|NN|GEN :|:|:|_ :|:|:|_ frt|frt|SYM|_ -|-|:|_ kan|kan|NN|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ zapB|zapb|NN|GEN :|:|:|_ :|:|:|_ frt-kan-frt|frt-kan-frt|JJ|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ matP|matp|NN|GEN -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ C20|c20|NN|_ :|:|:|_ :|:|:|_ frt-cam-frt|frt-cam-frt|JJ|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ phi80|phi80|NN|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ hupA|hupa|NN|GEN :|:|:|_ :|:|:|_ frt|frt|SYM|_ -|-|:|_ kan|kan|SYM|_ -|-|:|_ frt|frt|NN|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ hupB|hupb|NN|GEN :|:|:|_ :|:|:|_ frt-cam-frt|frt-cam-frt|JJ|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1phi80|rph-1phi80|NN|_ +|+|CC|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ mukB|mukb|NN|GEN :|:|:|_ :|:|:|_ frt|frt|SYM|_ -|-|:|_ apra|apra|NN|_ -LSB-|-lsb-|-LRB-|_ delta|delta|NN|_ -RSB-|-rsb-|-RRB-|_ matP|matp|NN|GEN :|:|:|_ :|:|:|_ frt-cam-frt|frt-cam-frt|JJ|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ MM|mm|NN|_ +|+|CC|_ 0.12|0.12|CD|_ %|%|NN|_ casaminoacids|casaminoacid|NNS|_ +0.4|+0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 22|22|CD|_ °C|°c|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ MM|mm|NN|_ +|+|CC|_ 0.12|0.12|CD|_ %|%|NN|_ casaminoacids|casaminoacid|NNS|_ +0.4|+0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 30|30|CD|_ °C|°c|NN|_
Iterative|iterative|JJ|_ alignment|alignment|NN|_ ,|,|,|_ Min-leght|min-leght|NN|_ =|=|JJ|_ 20|20|CD|_ ,|,|,|_ step|step|NN|_ =|=|JJ|_ 5|5|CD|_ ,|,|,|_ bowtie2|bowtie2|NN|_ --|--|:|_ very-sensitive|very-sensitive|JJ|_
Library|Library|NNP|_ strategy|strategy|NN|_ :|:|:|_ 3C-seq|3c-seq|JJ|_
OTHER|other|JJ|_
Removal|removal|NN|_ of|of|IN|_ PCR|pcr|NN|_ duplicates|duplicate|VBZ|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ 20|20|CD|_ first|first|JJ|_ bp|bp|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ containing|contain|VBG|_ a|a|DT|_ 6|6|CD|_ nt|nt|NN|_ random|random|JJ|_ tag|tag|NN|GEN -LRB-|-lrb-|-LRB-|_ home|home|NN|_ made|make|VBN|_ script|script|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Removal|removal|NN|_ of|of|IN|_ un-informative|un-informative|JJ|_ events|event|NNS|_ -LRB-|-lrb-|-LRB-|_ uncuts|uncut|NNS|_ ,|,|,|_ loops|loop|NNS|_ etc|etc|FW|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Cournac|Cournac|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ BMC|BMC|NNP|_ 2012|2012|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
RNA-seq|rna-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ 30h|30h|NN|_ -RRB-|-rrb-|-RRB-|_
RNA-seq|rna-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ cells|cell|NNS|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 30|30|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ 30h|30h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ rna-seq|rna-seq|NN|_ :|:|:|_ genomic|genomic|JJ|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ middle|middle|NN|_ of|of|IN|_ the|the|DT|_ 5kb-bin|5kb-bin|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ each|each|DT|_ count|count|NN|_ .|.|.|_ 3C|3c|NN|_ seq|seq|NN|_ :|:|:|_ contact|contact|NN|_ maps|map|NNS|_ -LRB-|-lrb-|-LRB-|_ 2D|2d|NN|_ array|array|NN|_ of|of|IN|_ 928|928|CD|_ 5kb-bins|5kb-bin|NNS|_ x|x|CC|_ 928|928|CD|_ 5kb-bins|5kb-bin|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
Counts|Counts|NNPS|_ were|be|VBD|_ depth|depth|NN|_ normalized|normalize|VBD|_ to|to|TO|_ a|a|DT|_ pseudo-reference|pseudo-reference|NN|_ sample|sample|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ using|use|VBG|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ counts|count|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
emptyvec|emptyvec|NN|_ _|_|NN|_ mRNA|mrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep1|rep1|NN|_
emptyvec|emptyvec|NN|_ _|_|NN|_ mRNA|mrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep2|rep2|NN|_
emptyvec|emptyvec|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 30m|30m|FW|_ _|_|FW|_ rep1|rep1|NN|_
emptyvec|emptyvec|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 30m|30m|FW|_ _|_|FW|_ rep2|rep2|NN|_
emptyvec|emptyvec|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep1|rep1|NN|_
emptyvec|emptyvec|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep2|rep2|NN|_
ercc|ercc|NN|_ spike-in|spike-in|NN|_ :|:|:|_ No|no|DT|_
ercc|ercc|NN|_ spike-in|spike-in|NN|_ :|:|:|_ Prior|prior|RB|_ to|to|TO|_ extraction|extraction|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ each|each|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ all|all|DT|_ mapped|map|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ at|at|IN|_ all|all|DT|_ aligned|align|VBN|_ positions|position|NNS|_ a|a|DT|_ count|count|NN|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_
For|for|IN|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ samples|sample|NNS|_ ,|,|,|_ counts|count|VBZ|_ at|at|IN|_ all|all|DT|_ positions|position|NNS|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ a|a|DT|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ MazF|mazf|NN|_ -|-|:|_ empty|empty|JJ|_ vector|vector|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ assessing|assess|VBG|_ MazF|mazf|NN|_ cleavage|cleavage|NN|_ in|in|IN|_ transcripts|transcript|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NCBI|ncbi|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_
MazF|mazf|NN|_ _|_|NN|_ mRNA|mrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep1|rep1|NN|_
MazF|mazf|NN|_ _|_|NN|_ mRNA|mrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep2|rep2|NN|_
MazF|mazf|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 30m|30m|FW|_ _|_|FW|_ rep1|rep1|NN|_
MazF|mazf|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 30m|30m|FW|_ _|_|FW|_ rep2|rep2|NN|_
MazF|mazf|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep1|rep1|NN|_
MazF|mazf|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 5m|5m|FW|_ _|_|FW|_ rep2|rep2|NN|_
MazF|mazf|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 60m|60m|FW|_ _|_|FW|_ rep1|rep1|NN|_
MazF|mazf|NN|_ _|_|CD|_ totalRNA|totalrna|NN|_ _|_|SYM|_ 60m|60m|FW|_ _|_|FW|_ rep2|rep2|NN|_
Paired-end|paired-end|NN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_ Any|any|DT|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ removed|remove|VBN|_ prior|prior|RB|_ to|to|TO|_ mapping|mapping|NN|_ .|.|.|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD30-empty|pbad30-empty|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD30-MazF|pbad30-mazf|NN|_
ribozero|ribozero|NN|_ :|:|:|_ No|no|DT|_
ribozero|ribozero|NN|_ :|:|:|_ Yes|yes|UH|_
RNA-Seq|rna-seq|JJ|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Direct-zol|direct-zol|NN|_ RNA|rna|NN|_ MiniPrep|MiniPrep|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|zymo|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
See|see|VB|_ publication|publication|NN|_ for|for|IN|_ complete|complete|JJ|_ protocol|protocol|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ samples|sample|NNS|_ with|with|IN|_ rRNA|rrna|NN|_ subtraction|subtraction|NN|_ with|with|IN|_ treated|treat|VBN|_ with|with|IN|_ bacterial|bacterial|JJ|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ random|random|JJ|_ primers|primer|NNS|_ and|and|CC|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ enable|enable|VB|_ strand|strand|NN|_ specificity|specificity|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ dUTP|dutp|NN|_ instead|instead|RB|_ of|of|IN|_ dTTP|dttp|NN|_ with|with|IN|_ RNase|rnase|NN|_ H|h|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ ligase|ligase|NN|_ ,|,|,|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Ends|end|NNS|_ were|be|VBD|_ repaired|repair|VBN|_ with|with|IN|_ T4|t4|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ Klenow|Klenow|NNP|_ DNA|DNA|NNP|_ polymerase|polymerase|NN|_ ,|,|,|_ and|and|CC|_ T4|t4|NN|_ PNK|pnk|NN|_ .|.|.|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ the|the|DT|_ Klenow|Klenow|NNP|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ '|'|''|_ >|>|JJR|_ 5|5|CD|_ '|'|''|_ exo|exo|SYM|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Y-shaped|y-shaped|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ and|and|CC|_ 9-12|9-12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ with|with|IN|_ multiplexing|multiplex|VBG|_ indexes|index|NNS|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ an|a|DT|_ acrylamide|acrylamide|NN|_ gel|gel|NN|_ and|and|CC|_ submitted|submit|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ at|at|IN|_ the|the|DT|_ MIT|MIT|NNP|_ BioMicro|BioMicro|NNP|_ Center|Center|NNP|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Separate|separate|JJ|_ E.|e.|FW|_ coli|coli|FW|_ colonies|colony|NNS|_ were|be|VBD|_ picked|pick|VBN|_ from|from|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ for|for|IN|_ each|each|DT|_ replicate|replicate|VBP|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 12-16|12-16|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ and|and|CC|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ 3-4|3-4|CD|_ hours|hour|NNS|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.35|0.35|CD|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ RPM|rpm|NN|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ back|back|RB|_ diluted|dilute|VBN|_ into|into|IN|_ media|media|NNS|_ lacking|lack|VBG|_ glucose|glucose|NN|SUPP .|.|.|_ After|after|IN|_ at|at|IN|_ least|least|JJS|_ 30|30|CD|_ minutes|minute|NNS|_ of|of|IN|_ recovery|recovery|NN|_ Para|para|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ arabinose|arabinose|NN|_ to|to|TO|_ 0.2|0.2|CD|_ %|%|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifuging|centrifuge|VBG|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ maximum|maximum|JJ|_ speed|speed|NN|_ on|on|IN|_ a|a|DT|_ benchtop|benchtop|JJ|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ flash|flash|VB|_ frozen|freeze|VBN|_ in|in|IN|_ lN2|ln2|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ _|_|CD|_ mazF|mazf|NN|GEN
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ 5m_ribozero_counts_cleavage_ratio.csv.gz|5m_ribozero_counts_cleavage_ratio.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ log-transformed|log-transformed|JJ|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strands|strand|NNS|_ for|for|IN|_ each|each|DT|_ ribozero|ribozero|NN|_ treated|treat|VBN|_ sample|sample|NN|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ average|average|JJ|_ cleavage|cleavage|NN|_ ratio|ratio|NN|_ calculated|calculate|VBN|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_ total_RNA_rpm.csv.gz|total_rna_rpm.csv.gz|NN|_ is|be|VBZ|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ depth-normalized|depth-normalized|JJ|_ counts|count|NNS|_ for|for|IN|_ every|every|DT|_ genomic|genomic|JJ|_ position|position|NN|_ at|at|IN|_ both|both|DT|_ strans|stran|NNS|_ for|for|IN|_ all|all|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_
time|time|NN|_ induction|induction|NN|_ :|:|:|_ 30|30|CD|_ minutes|minute|NNS|_
time|time|NN|_ induction|induction|NN|_ :|:|:|_ 5|5|CD|_ minutes|minute|NNS|_
time|time|NN|_ induction|induction|NN|_ :|:|:|_ 60|60|CD|_ minutes|minute|NNS|_
Bacteria|bacterium|NNS|_
Culture|culture|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ strains|strain|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ 20|20|CD|_ min|min|NN|_ at|at|IN|_ 10,000|10,000|CD|_ g|g|NN|_ and|and|CC|_ bacterial|bacterial|JJ|_ pellets|pellet|NNS|_ were|be|VBD|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ 2|2|CD|_ mL|ml|NN|_ of|of|IN|_ phosphate|phosphate|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ -LRB-|-lrb-|-LRB-|_ PBS|PBS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ EasyDNA|easydna|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ instructions|instruction|NNS|_ slightly|slightly|RB|_ modified|modify|VBN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ the|the|DT|_ bacterial|bacterial|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ 5|5|CD|_ min|min|NN|_ in|in|IN|_ 200|200|CD|_ μL|μl|NN|_ of|of|IN|_ PBS|PBS|NNP|_ and|and|CC|_ 1|1|CD|_ μL|μl|NN|_ of|of|IN|_ protéinase|protéinase|NN|_ K|k|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Fluorescence|fluorescence|NN|_ intensities|intensity|NNS|_ of|of|IN|_ oligonucleotide|oligonucleotide|NN|_ spots|spot|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ scanned|scan|VBN|_ images|image|NNS|_ using|use|VBG|_ the|the|DT|_ Feature|Feature|NNP|_ Extraction|extraction|NN|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .0|.0|CD|_ ,|,|,|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ with|with|IN|_ dedicated|dedicated|JJ|_ scripts|script|NNS|_ based|base|VBN|_ on|on|IN|_ C++|C++|NNP|_ and|and|CC|_ Delphi|Delphi|NNP|_ languages|language|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ probe|probe|NN|_ ,|,|,|_ median|median|JJ|_ intensity|intensity|NN|_ value|value|NN|_ of|of|IN|_ the|the|DT|_ 3|3|CD|_ replicates|replicate|VBZ|_ was|be|VBD|_ conserved|conserve|VBN|_ and|and|CC|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ probe|probe|NN|_ signal|signal|NN|_ value|value|NN|_ .|.|.|_ The|the|DT|_ SNR|snr|NN|_ -LRB-|-lrb-|-LRB-|_ Signal-to-Noise|Signal-to-Noise|NNP|_ Ratio|Ratio|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ similar|similar|JJ|_ to|to|TO|_ the|the|DT|_ detection|detection|NN|_ threshold|threshold|NN|_ response|response|NN|_ -LRB-|-lrb-|-LRB-|_ positive|positive|JJ|_ hybridization|hybridization|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ probe|probe|NN|_ signal|signal|NN|_ value|value|NN|_ divided|divide|VBN|_ by|by|IN|_ the|the|DT|_ local|local|JJ|_ background|background|NN|_ intensity|intensity|NN|_ value|value|NN|_ ,|,|,|_ was|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ each|each|DT|_ probe|probe|NN|_ .|.|.|_ The|the|DT|_ SNR|SNR|NNP|_ thresholds|threshold|NNS|_ were|be|VBD|_ set|set|VBN|_ to|to|TO|_ 3|3|CD|_ for|for|IN|_ 25-mer|25-mer|JJ|_ probes|probe|NNS|_ and|and|CC|_ 6|6|CD|_ for|for|IN|_ 54-mer|54-mer|JJ|_ probes|probe|NNS|_ .|.|.|_ Such|such|JJ|_ SNR|snr|NN|_ threshold|threshold|NN|_ values|value|NNS|_ ensured|ensure|VBD|_ a|a|DT|_ very|very|RB|_ specific|specific|JJ|_ response|response|NN|_ of|of|IN|_ the|the|DT|_ FibroChip|FibroChip|NNP|_ ,|,|,|_ except|except|IN|_ for|for|IN|_ genes|gene|NNS|_ belonging|belong|VBG|_ to|to|TO|_ very|very|RB|_ close|close|JJ|_ strains|strain|NNS|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ species|species|NNS|_ .|.|.|_ Results|result|NNS|_ for|for|IN|_ 25|25|CD|_ -|-|:|_ and|and|CC|_ 54-mer|54-mer|JJ|_ probes|probe|NNS|_ were|be|VBD|_ treated|treat|VBN|_ independently|independently|RB|_ and|and|CC|_ for|for|IN|_ each|each|DT|_ probe|probe|NN|_ type|type|NN|_ ,|,|,|_ a|a|DT|_ gene|gene|NN|_ was|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ detected|detect|VBN|_ when|when|WRB|_ 65|65|CD|_ %|%|NN|_ of|of|IN|_ probes|probe|NNS|_ were|be|VBD|_ positive|positive|JJ|_ .|.|.|_ The|the|DT|_ SNR|snr|NN|_ value|value|NN|_ of|of|IN|_ a|a|DT|_ detected|detect|VBN|_ gene|gene|NN|_ was|be|VBD|_ then|then|RB|_ calculated|calculate|VBN|_ by|by|IN|_ the|the|DT|_ mean|mean|NN|_ of|of|IN|_ the|the|DT|_ SNR|snr|NN|_ of|of|IN|_ all|all|DT|_ 25|25|CD|_ -|-|:|_ or|or|CC|_ 54-mer|54-mer|JJ|_ probes|probe|NNS|_ targeting|target|VBG|_ this|this|DT|_ gene|gene|NN|_ ,|,|,|_ meeting|meeting|NN|_ or|or|CC|_ not|not|RB|_ the|the|DT|_ defined|define|VBN|_ SNR|snr|NN|_ threshold|threshold|NN|_ .|.|.|_
gDNA|gdna|NN|_ _|_|CD|_ Ecoli|Ecoli|NNP|_ _|_|SYM|_ K12|k12|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ 4|4|CD|_ bacteria|bacterium|NNS|_ strains|strain|NNS|_ .|.|.|_ Strains|strain|NNS|_ Fibrobacter|fibrobacter|JJ|_ succinogenes|succinogene|NNS|_ S85|s85|NN|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 19169|19169|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Ruminococcus|ruminococcus|NN|_ albus|albus|NN|_ 20|20|CD|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 27211|27211|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Bacteroides|bacteroide|NNS|_ xylanisolvens|xylanisolven|NNS|_ XB1A|xb1a|NN|_ -LRB-|-lrb-|-LRB-|_ DSM|DSM|NNP|_ 18836T|18836T|NNP|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ 15|15|CD|_ h|h|NN|_ under|under|IN|_ strictly|strictly|RB|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ -LRB-|-lrb-|-LRB-|_ Hungate|Hungate|NNP|_ ,|,|,|_ 1950|1950|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ complex|complex|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ 20|20|CD|_ %|%|NN|_ of|of|IN|_ clarified|clarify|VBN|_ rumen|ruman|NNS|_ fluid|fluid|NN|_ -LRB-|-lrb-|-LRB-|_ Béra-Maillet|béra-maillet|JJ|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 0.2|0.2|CD|_ g|g|NN|_ of|of|IN|_ cellobiose|cellobiose|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma-Aldrich|sigma-aldrich|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ ,|,|,|_ at|at|IN|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ the|the|DT|_ two|two|CD|_ first|first|JJ|_ ones|one|NNS|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ the|the|DT|_ third|third|JJ|_ one|one|CD|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 10798|10798|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ cultivated|cultivate|VBN|_ 15|15|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ medium|medium|NN|_ under|under|IN|_ shaking|shake|VBG|_ and|and|CC|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_
gut|gut|NN|_ origin|origin|NN|_ :|:|:|_ Human|human|JJ|_ colon|colon|NN|_
No|no|DT|_ treatment|treatment|NN|_
AcrA-Negative|acra-negative|JJ|_ ,|,|,|_ Multidrug|multidrug|JJ|_ Efflux|Efflux|NNP|_ Mutant|Mutant|NNP|_ Strain|Strain|NNP|_
AcrB|acrb|NN|_ -|-|:|_ and|and|CC|_ EmrAB-Negative|emrab-negative|JJ|_ ,|,|,|_ Multidrug|multidrug|JJ|_ Efflux|Efflux|NNP|_ Mutant|Mutant|NNP|_ Strain|Strain|NNP|_
AcrB-Negative|AcrB-Negative|NNP|_ ,|,|,|_ Multidrug|Multidrug|NNP|_ Efflux|Efflux|NNP|_ Mutant|Mutant|NNP|_ Strain|Strain|NNP|_
AG102MB|ag102mb|NN|_ is|be|VBZ|_ an|a|DT|_ isogenic|isogenic|JJ|_ mutant|mutant|JJ|_ derived|derive|VBN|_ from|from|IN|_ hyper-resistant|hyper-resistant|JJ|_ AG102|ag102|NN|_ -LRB-|-lrb-|-LRB-|_ marR1|marr1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ It|it|PRP|_ contains|contain|VBZ|_ a|a|DT|_ mutation|mutation|NN|_ at|at|IN|_ the|the|DT|_ acrB|acrb|NN|GEN locus|locus|NN|_ -LRB-|-lrb-|-LRB-|_ marR1|marr1|NN|_ ,|,|,|_ acrB|acrb|NN|GEN :|:|:|_ :|:|:|_ kan|kan|NN|_ -RRB-|-rrb-|-RRB-|_ resulting|result|VBG|_ in|in|IN|_ a|a|DT|_ multidrug|multidrug|JJ|_ efflux|efflux|NN|_ negative|negative|JJ|_ phenotype|phenotype|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|JJ|_ medium|medium|NN|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|JJ|_ medium|medium|NN|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ with|with|IN|_ 25|25|CD|_ ug|ug|NN|_
E.|E.|NNP|_ coli|coli|NN|_ AcrA|AcrA|NNP|_ Multidrug|Multidrug|NNP|_ Efflux|Efflux|NNP|_ Mutant|mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ AcrB|acrb|NN|_ and|and|CC|_ EmrAB|EmrAB|NNP|_ Multidrug|Multidrug|NNP|_ Efflux|Efflux|NNP|_ Double|double|JJ|_ Mutant|mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ AcrB|acrb|NN|_ Multidrug|multidrug|JJ|_ Efflux|efflux|NN|_ Mutant|mutant|JJ|_
Efflux|efflux|NN|_ Mutant|mutant|JJ|_ Parent|Parent|NNP|_ Strain|Strain|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
HNCE3|hnce3|NN|_ is|be|VBZ|_ an|a|DT|_ isogenic|isogenic|JJ|_ mutant|mutant|JJ|_ derived|derive|VBN|_ from|from|IN|_ hyper-resistant|hyper-resistant|JJ|_ AG102|ag102|NN|_ -LRB-|-lrb-|-LRB-|_ marR1|marr1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ It|it|PRP|_ contains|contain|VBZ|_ a|a|DT|_ nonpolar|nonpolar|JJ|_ mutation|mutation|NN|_ at|at|IN|_ the|the|DT|_ acrA|acra|NN|GEN locus|locus|NN|_ which|which|WDT|_ allows|allow|VBZ|_ read-through|read-through|NN|_ for|for|IN|_ acrB|acrb|NN|GEN expression|expression|NN|_ and|and|CC|_ results|result|VBZ|_ in|in|IN|_ a|a|DT|_ multidrug|multidrug|JJ|_ efflux|efflux|NN|_ negative|negative|JJ|_ phenotype|phenotype|NN|_ .|.|.|_
HNCE4|hnce4|NN|_ is|be|VBZ|_ an|a|DT|_ isogenic|isogenic|JJ|_ mutant|mutant|JJ|_ derived|derive|VBN|_ from|from|IN|_ drug|drug|NN|_ sensitive|sensitive|JJ|_ AG102MB|ag102mb|NN|_ -LRB-|-lrb-|-LRB-|_ marR1|marr1|NN|_ ,|,|,|_ AcrB|acrb|NN|_ :|:|:|_ :|:|:|_ kan|kan|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ It|it|PRP|_ contains|contain|VBZ|_ an|a|DT|_ additional|additional|JJ|_ mutation|mutation|NN|_ at|at|IN|_ the|the|DT|_ emrAB|emrab|NN|_ locus|locus|NN|_ -LRB-|-lrb-|-LRB-|_ marR1|marr1|NN|_ ,|,|,|_ acrB|acrb|NN|GEN :|:|:|_ :|:|:|_ kan|kan|NN|_ ,|,|,|_ emrAB|emrab|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ -RRB-|-rrb-|-RRB-|_ resulting|result|VBG|_ in|in|IN|_ a|a|DT|_ multidrug|multidrug|JJ|_ efflux|efflux|NN|_ negative|negative|JJ|_ phenotype|phenotype|NN|_ .|.|.|_
The|the|DT|_ analyzed|analyze|VBN|_ data|datum|NNS|_ were|be|VBD|_ imported|import|VBN|_ to|to|TO|_ ArrayTrack|ArrayTrack|NNP|_ -LRB-|-lrb-|-LRB-|_ NCTR|NCTR|NNP|_ Center|Center|NNP|_ for|for|IN|_ Toxicoinformatics|Toxicoinformatics|NNPS|_ ;|;|:|_ http|http|NN|_ :|:|:|_
The|the|DT|_ parent|parent|NN|_ strain|strain|NN|_ ,|,|,|_ AG102|ag102|NN|_ ,|,|,|_ was|be|VBD|_ previously|previously|RB|_ derived|derive|VBN|_ from|from|IN|_ AG100|ag100|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ AG102|ag102|NN|_ is|be|VBZ|_ drug|drug|NN|_ hyper-resistant|hyper-resistant|JJ|_ due|due|JJ|_ to|to|TO|_ a|a|DT|_ mutation|mutation|NN|_ in|in|IN|_ marR|marr|NN|GEN -LRB-|-lrb-|-LRB-|_ marR1|marr1|NN|_ -RRB-|-rrb-|-RRB-|_ which|which|WDT|_ increases|increase|VBZ|_ expression|expression|NN|_ of|of|IN|_ MarA|mara|NN|TF ,|,|,|_ a|a|DT|_ global|global|JJ|_ regulator|regulator|NN|_ ,|,|,|_ which|which|WDT|_ in|in|IN|_ turn|turn|NN|_ results|result|VBZ|_ in|in|IN|_ overexpression|overexpression|NN|_ of|of|IN|_ the|the|DT|_ AcrAB-TolC|acrab-tolc|NN|_ multidrug|multidrug|JJ|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_
Alignment|alignment|NN|_ :|:|:|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ bespoke|bespeak|VB|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ DL4201|dl4201|NN|_ _|_|NN|_ in|in|IN|_ _|_|NN|_ lab|lab|NN|_ _|_|CD|_ reference|reference|NN|_ _|_|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ available|available|JJ|_ on|on|IN|_ series|series|NN|_ record|record|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ parameters|parameter|NNS|_ of|of|IN|_ software|software|NN|_ Bowtie|bowtie|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ ,|,|,|_ B.|B.|NNP|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ S.L.|S.L.|NNP|_ -LRB-|-lrb-|-LRB-|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ Fast|fast|JJ|_ gapped-read|gapped-read|JJ|_ alignment|alignment|NN|_ with|with|IN|_ Bowtie|bowtie|NN|_ 2|2|CD|_ .|.|.|_ Nat|Nat|NNP|_ Methods|method|NNS|_ ,|,|,|_ 9|9|CD|_ ,|,|,|_ 357-359|357-359|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ samples|sample|NNS|_ were|be|VBD|_ processed|process|VBN|_ following|follow|VBG|_ NEB|NEB|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ from|from|IN|_ the|the|DT|_ NEBNext|nebnext|NN|_ ®|®|NN|_ ChIP-Seq|chip-seq|JJ|_ library|library|NN|_ preparation|preparation|NN|_ kit|kit|NN|_ .|.|.|_
background|background|NN|_ strain|strain|NN|_ :|:|:|_ BW27784|bw27784|NN|_
Bacterial|bacterial|JJ|_ Cell|cell|NN|_ Lysates|lysate|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ 1X|1x|NN|_ PBS|PBS|NNP|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ then|then|RB|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 250|250|CD|_ μl|μl|NN|_ ChIP|chip|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 600|600|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ 4|4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X|X|NNP|_ ,|,|,|_ Complete|complete|JJ|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ EDTA-free|edta-free|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Sonication|sonication|NN|_ of|of|IN|_ crosslinked|crosslink|VBN|_ samples|sample|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Diagenode|Diagenode|NNP|_ Bioruptor|Bioruptor|NNP|_ ®|®|NN|_ at|at|IN|_ 30s|30s|CD|_ intervals|interval|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ high|high|JJ|_ amplitude|amplitude|NN|_ .|.|.|_ After|after|IN|_ sonication|sonication|NN|_ ,|,|,|_ 350|350|CD|_ μl|μl|NN|_ of|of|IN|_ ChIP|chip|NN|_ buffer|buffer|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ by|by|IN|_ gentle|gentle|JJ|_ pipetting|pipetting|NN|_ and|and|CC|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ lysate|lysate|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ stored|store|VBN|_ as|as|IN|_ `|`|``|_ input|input|NN|_ '|'|''|_ .|.|.|_ Immunoprecipitation|immunoprecipitation|NN|_ was|be|VBD|_ performed|perform|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ using|use|VBG|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ and|and|CC|_ OD600nm|od600nm|NN|_ of|of|IN|_ 0.2-0.25|0.2-0.25|CD|_
ChIP-Seq|chip-seq|JJ|_
DL4184|dl4184|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 1|1|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_
DL4184|dl4184|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 2|2|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_ _|_|NN|_ reanalyzed|reanalyze|VBN|_
DL4201|dl4201|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 1|1|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_
DL4201|dl4201|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 2|2|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_ _|_|NN|_ reanalyzed|reanalyze|VBN|_
DL5699|dl5699|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 1|1|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_
DL5699|dl5699|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 2|2|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_
DL6204|dl6204|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 1|1|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_
DL6204|dl6204|NN|_ biological|biological|JJ|_ repeat|repeat|NN|_ 2|2|CD|_ RecA|reca|NN|_ ChIP|chip|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ DL4201|dl4201|NN|_ _|_|NN|_ in|in|IN|_ _|_|NN|_ lab|lab|NN|_ _|_|CD|_ reference|reference|NN|_ _|_|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ available|available|JJ|_ on|on|IN|_ series|series|NN|_ record|record|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ BW27784|bw27784|NN|_ delta|delta|NN|_ _|_|CD|_ recD|recd|NN|GEN lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ XXX|xxx|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ XXX|XXX|NNP|_ proA|proA|NNP|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN +|+|CC|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZX|laczx|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ BW27784|bw27784|NN|_ delta|delta|NN|_ _|_|CD|_ recD|recd|NN|GEN lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ XXX|xxx|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ XXX|XXX|NNP|_ proA|proA|NNP|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ pal246|pal246|NN|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZX|laczx|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ BW27784|bw27784|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ XXX|xxx|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ XXX|XXX|NNP|_ proA|proA|NNP|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN +|+|CC|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZX|laczx|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ BW27784|bw27784|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ XXX|xxx|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ XXX|XXX|NNP|_ proA|proA|NNP|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ pal246|pal246|NN|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZX|laczx|NN|_ -|-|:|_
Normalisation|normalisation|NN|_ :|:|:|_ Counts|count|NNS|_ were|be|VBD|_ normalised|normalise|VBN|_ by|by|IN|_ applying|apply|VBG|_ a|a|DT|_ single|single|JJ|_ ,|,|,|_ sample-specific|sample-specific|JJ|_ scaling|scaling|NN|_ factor|factor|NN|_ .|.|.|_ To|to|TO|_ calculate|calculate|VB|_ this|this|DT|_ scaling|scaling|NN|_ factor|factor|NN|_ ,|,|,|_ we|we|PRP|_ implemented|implement|VBD|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ ratios|ratio|NNS|_ normalisation|normalisation|NN|_ of|of|IN|_ DESeq|deseq|NN|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ ,|,|,|_ S.|S.|NNP|_ and|and|CC|_ Huber|Huber|NNP|_ ,|,|,|_ W.|W.|NNP|_ -LRB-|-lrb-|-LRB-|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ for|for|IN|_ sequence|sequence|NN|_ count|count|NN|_ data|datum|NNS|_ .|.|.|_ Genome|Genome|NNP|_ Biol|Biol|NNP|_ ,|,|,|_ 11|11|CD|_ ,|,|,|_ R106|r106|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ R.|R.|NNP|_
Protein|protein|NN|_ DNA|dna|NN|_ interactions|interaction|NNS|_ were|be|VBD|_ crosslinked|crosslink|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 22.5|22.5|CD|_ C|c|NN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ and|and|CC|_ quenched|quench|VBN|_ using|use|VBG|_ glycine|glycine|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ M|m|NN|_
Raw|raw|NN|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ reference|reference|NN|_ base|base|NN|_ pair|pair|NN|_ were|be|VBD|_ then|then|RB|_ calculated|calculate|VBN|_ using|use|VBG|_ SAMtools|samtool|NNS|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ with|with|IN|_ parameter|parameter|NN|_ --|--|:|_ d|d|NN|_ set|set|VBN|_ to|to|TO|_ 10|10|CD|_ ^|^|CD|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ DL4184|dl4184|NN|_
strain|strain|NN|_ :|:|:|_ DL4201|dl4201|NN|_
strain|strain|NN|_ :|:|:|_ DL5966|dl5966|NN|_
strain|strain|NN|_ :|:|:|_ DL6204|dl6204|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ txt|txt|NN|_ files|file|NNS|_ of|of|IN|_ a|a|DT|_ matrix|matrix|NN|_ containing|contain|VBG|_ genome|genome|NN|_ position|position|NN|_ in|in|IN|_ column|column|NN|_ 1|1|CD|_ and|and|CC|_ number|number|NN|_ of|of|IN|_ depth|depth|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ in|in|IN|_ column|column|NN|_ 2|2|CD|_ .|.|.|_ Also|also|RB|_ ,|,|,|_ in|in|IN|_ a|a|DT|_ CSV|CSV|NNP|_ file|file|NN|_ of|of|IN|_ a|a|DT|_ matrix|matrix|NN|_ containing|contain|VBG|_ genome|genome|NN|_ position|position|NN|_ in|in|IN|_ column|column|NN|_ 1|1|CD|_ and|and|CC|_ subsequent|subsequent|JJ|_ coloumns|coloumn|NNS|_ with|with|IN|_ normalised|normalised|JJ|_ number|number|NN|_ of|of|IN|_ depth|depth|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ column|column|NN|_ names|name|NNS|_ have|have|VBP|_ the|the|DT|_ strain|strain|NN|_ number|number|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ CSV|CSV|NNP|_ file|file|NN|_ is|be|VBZ|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ induced|induce|VBN|_ DNA|dna|NN|_ double|double|JJ|_ strand|strand|NN|_ break|break|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
AG102|ag102|NN|_ was|be|VBD|_ previously|previously|RB|_ derived|derive|VBN|_ from|from|IN|_ AG100|ag100|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ AG102|ag102|NN|_ is|be|VBZ|_ drug|drug|NN|_ hyper-resistant|hyper-resistant|JJ|_ due|due|JJ|_ to|to|TO|_ a|a|DT|_ mutation|mutation|NN|_ in|in|IN|_ marR|marr|NN|GEN -LRB-|-lrb-|-LRB-|_ marR1|marr1|NN|_ -RRB-|-rrb-|-RRB-|_ which|which|WDT|_ increases|increase|VBZ|_ expression|expression|NN|_ of|of|IN|_ MarA|mara|NN|TF ,|,|,|_ a|a|DT|_ global|global|JJ|_ regulator|regulator|NN|_ ,|,|,|_ which|which|WDT|_ in|in|IN|_ turn|turn|NN|_ results|result|VBZ|_ in|in|IN|_ overexpression|overexpression|NN|_ of|of|IN|_ the|the|DT|_ AcrAB-TolC|acrab-tolc|NN|_ multidrug|multidrug|JJ|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_
Cholic|cholic|JJ|_ Acid|acid|NN|_ Treatment|treatment|NN|_
DMSO-Only|dmso-only|JJ|_ Treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Cholic|Cholic|NNP|_ Acid|Acid|NNP|_ Treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Estradiol|Estradiol|NNP|_ Treatment|Treatment|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ Hydrocortisone|Hydrocortisone|NNP|_ Treatment|Treatment|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ Progesterone|progesterone|NN|_ Treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|JJ|_ medium|medium|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ dimethyl|dimethyl|JJ|_ sulfoxide|sulfoxide|NN|_ -LRB-|-lrb-|-LRB-|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dissolved|dissolve|VBN|_ cholic|cholic|JJ|_ acid|acid|NN|_ at|at|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ culture|culture|NN|_ concentration|concentration|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|JJ|_ medium|medium|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ dimethyl|dimethyl|JJ|_ sulfoxide|sulfoxide|NN|_ -LRB-|-lrb-|-LRB-|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dissolved|dissolve|VBN|_ estradiol|estradiol|NN|_ at|at|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ culture|culture|NN|_ concentration|concentration|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|JJ|_ medium|medium|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ dimethyl|dimethyl|JJ|_ sulfoxide|sulfoxide|NN|_ -LRB-|-lrb-|-LRB-|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dissolved|dissolve|VBN|_ hydrocortisone|hydrocortisone|NN|_ at|at|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ culture|culture|NN|_ concentration|concentration|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|JJ|_ medium|medium|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ dimethyl|dimethyl|JJ|_ sulfoxide|sulfoxide|NN|_ -LRB-|-lrb-|-LRB-|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dissolved|dissolve|VBN|_ progesterone|progesterone|NN|_ at|at|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ culture|culture|NN|_ concentration|concentration|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|JJ|_ medium|medium|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ dimethyl|dimethyl|JJ|_ sulfoxide|sulfoxide|NN|_ -LRB-|-lrb-|-LRB-|_ DMSO|dmso|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ only|only|RB|_ steroid|steroid|NN|_ carrier|carrier|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Estradiol|estradiol|NN|_ Treatment|treatment|NN|_
Hydrocortisone|hydrocortisone|NN|_ Treatment|treatment|NN|_
Progesterone|progesterone|NN|_ Treatment|treatment|NN|_
The|the|DT|_ analyzed|analyze|VBN|_ data|datum|NNS|_ were|be|VBD|_ imported|import|VBN|_ to|to|TO|_ ArrayTrack|ArrayTrack|NNP|_ -LRB-|-lrb-|-LRB-|_ NCTR|NCTR|NNP|_ Center|Center|NNP|_ for|for|IN|_ Toxicoinformatics|Toxicoinformatics|NNPS|_ .|.|.|_ The|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ using|use|VBG|_ median|median|NN|_ channel|channel|NN|_ -LRB-|-lrb-|-LRB-|_ intensity|intensity|NN|_ -RRB-|-rrb-|-RRB-|_ scaling|scale|VBG|_ with|with|IN|_ no|no|DT|_ background|background|NN|_ subtraction|subtraction|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ batch|batch|NN|_ or|or|CC|_ bioreactor|bioreactor|NN|_ vessels|vessel|NNS|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_
DNA|dna|NN|_ extraction|extraction|NN|_ :|:|:|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ according|accord|VBG|_ to|to|TO|_ standard|standard|JJ|_ procedures|procedure|NNS|_ -LRB-|-lrb-|-LRB-|_ Ausubel|Ausubel|NNP|_ et|et|FW|_ al.|al.|FW|_ 1994|1994|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ nebulization|nebulization|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ Girgis|Girgis|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ 9|9|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e154|e154|NN|_ -LRB-|-lrb-|-LRB-|_ 2007|2007|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ by|by|IN|_ phenol|phenol|NN|_
Elements|element|NNS|_ with|with|IN|_ poor|poor|JJ|_ spot|spot|NN|_ morphology|morphology|NN|_ or|or|CC|_ exhibiting|exhibit|VBG|_ uneven|uneven|JJ|_ hybridization|hybridization|NN|_ caused|cause|VBN|_ by|by|IN|_ dust|dust|NN|_ particles|particle|NNS|_ or|or|CC|_ scratches|scratch|NNS|_ ,|,|,|_ were|be|VBD|_ flagged|flag|VBN|_ manually|manually|RB|_ and|and|CC|_ excluded|exclude|VBN|_ from|from|IN|_ further|further|JJ|_ analyses|analysis|NNS|_ .|.|.|_ After|after|IN|_ local|local|JJ|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ global|global|JJ|_ normalization|normalization|NN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ reference|reference|NN|_ ,|,|,|_ duplicate|duplicate|VB|_ measurements|measurement|NNS|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ array|array|NN|_ were|be|VBD|_ averaged|average|VBN|_ ,|,|,|_ yielding|yield|VBG|_ a|a|DT|_ single|single|JJ|_ vector|vector|NN|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ across|across|IN|_ a|a|DT|_ perturbation|perturbation|NN|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ from|from|IN|_ all|all|DT|_ hybridizations|hybridization|NNS|_ were|be|VBD|_ combined|combine|VBN|_ into|into|IN|_ a|a|DT|_ matrix|matrix|NN|_ and|and|CC|_ scaled|scale|VBD|_ relative|relative|JJ|_ to|to|TO|_ each|each|DT|_ other|other|JJ|_ using|use|VBG|_ quantile-normalization|quantile-normalization|NN|_ as|as|IN|_ implemented|implement|VBN|_ in|in|IN|_ the|the|DT|_ Matlab|Matlab|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ toolbox|toolbox|NN|_ .|.|.|_ Biological|biological|JJ|_ duplicates|duplicate|NNS|_ from|from|IN|_ all|all|DT|_ experiments|experiment|NNS|_ were|be|VBD|_ averaged|average|VBN|_ ,|,|,|_ leading|lead|VBG|_ to|to|TO|_ a|a|DT|_ single|single|JJ|_ set|set|NN|_ of|of|IN|_ time-series|time-series|NNS|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ perturbation|perturbation|NN|_ .|.|.|_ Seven|seven|CD|_ time-points|time-point|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ for|for|IN|_ each|each|DT|_ perturbation|perturbation|NN|_ ,|,|,|_ corresponding|correspond|VBG|_ to|to|TO|_ 0|0|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 12|12|CD|_ ,|,|,|_ 20|20|CD|_ ,|,|,|_ 28|28|CD|_ ,|,|,|_ and|and|CC|_ 44|44|CD|_ minutes|minute|NNS|_ post|post|JJ|_ transition|transition|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
evolved|evolve|VBD|_ _|_|CD|_ temperature|temperature|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 0|0|CD|_ min|min|NN|_
evolved|evolve|VBD|_ _|_|CD|_ temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 16|16|CD|_ min|min|NN|_
evolved|evolve|VBD|_ _|_|CD|_ temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 44|44|CD|_ min|min|NN|_
evolved|evolve|VBD|_ temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ 0|0|CD|_ min|min|NN|_
evolved|evolve|VBD|_ temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ 16|16|CD|_ min|min|NN|_
evolved|evolve|VBD|_ temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ 44|44|CD|_ min|min|NN|_
genomic|genomic|JJ|_ DNA|dna|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ served|serve|VBD|_ as|as|IN|_ a|a|DT|_ universal|universal|JJ|_ reference|reference|NN|_
MG1655|mg1655|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 0|0|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 12|12|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 28|28|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 44|44|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 12|12|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 28|28|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 44|44|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 8|8|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 0|0|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 12|12|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 28|28|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 44|44|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 12|12|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 28|28|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 44|44|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_
oxygen|oxygen|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 8|8|CD|_ min|min|NN|_
parental|parental|JJ|_ _|_|NN|_ temperature|temperature|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 0|0|CD|_ min|min|NN|_
parental|parental|JJ|_ _|_|NN|_ temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 16|16|CD|_ min|min|NN|_
parental|parental|JJ|_ _|_|NN|_ temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 44|44|CD|_ min|min|NN|_
parental|parental|JJ|_ temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ 0|0|CD|_ min|min|NN|_
parental|parental|JJ|_ temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ 16|16|CD|_ min|min|NN|_
parental|parental|JJ|_ temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ 44|44|CD|_ min|min|NN|_
Physiological|physiological|JJ|_ perturbations|perturbation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ under|under|IN|_ a|a|DT|_ controlled|controlled|JJ|_ environment|environment|NN|_ in|in|IN|_ the|the|DT|_ context|context|NN|_ of|of|IN|_ bioreactor|bioreactor|NN|_ -LRB-|-lrb-|-LRB-|_ Bioflo|bioflo|NN|_ 110|110|CD|_ ,|,|,|_ New|New|NNP|_ Brunswick|Brunswick|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ growth|growth|NN|_ .|.|.|_ Thermoelectric|Thermoelectric|NNP|_ sensors|sensor|NNS|_ and|and|CC|_ heaters|heater|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ shift|shift|VB|_ temperature|temperature|NN|_ profiles|profile|NNS|_ between|between|IN|_ 250|250|CD|_ C|c|NN|_ and|and|CC|_ 370|370|CD|_ C|c|NN|_ ,|,|,|_ and|and|CC|_ polarographic|polarographic|JJ|_ dissolved|dissolve|VBN|_ oxygen|oxygen|NN|_ sensors|sensor|NNS|_ -LRB-|-lrb-|-LRB-|_ Mettler|Mettler|NNP|_ Toledo|Toledo|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ nitrogen|nitrogen|NN|_ gas|gas|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ rapidly|rapidly|RB|_ change|change|VB|_ oxygen|oxygen|NN|_ saturation|saturation|NN|_ between|between|IN|_ anaerobic|anaerobic|JJ|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ %|%|NN|_ dissolved|dissolve|VBN|_ oxygen|oxygen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ aerobic|aerobic|JJ|_ -LRB-|-lrb-|-LRB-|_ 16-21|16-21|CD|_ %|%|NN|_ dissolved|dissolve|VBN|_ oxygen|oxygen|NN|_ -RRB-|-rrb-|-RRB-|_ condition|condition|NN|_ .|.|.|_
RNA|rna|NN|_ extraction|extraction|NN|_ :|:|:|_ A|a|DT|_ hot-phenol|hot-phenol|NN|_ procedure|procedure|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 500|500|CD|_ μl|μl|NN|_ TE|te|NN|_ -LRB-|-lrb-|-LRB-|_ pH8|ph8|NN|_ .0|.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 50|50|CD|_ μl|μl|NN|_ 10|10|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mg|mg|NN|_
temperature|temperature|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 0|0|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 12|12|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 28|28|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 44|44|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|CD|_ down|down|IN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
temperature|temperature|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
temperature|temperature|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 12|12|CD|_ min|min|NN|_
temperature|temperature|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_
temperature|temperature|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 28|28|CD|_ min|min|NN|_
temperature|temperature|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 44|44|CD|_ min|min|NN|_
temperature|temperature|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_
temperature|temperature|NN|_ down|down|IN|_ shift|shift|NN|_ ,|,|,|_ 8|8|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|CD|_ Up|up|IN|_ _|_|CD|_ 0|0|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 12|12|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 20|20|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 28|28|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 44|44|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 4|4|CD|_ min|min|NN|_
temperature|temperature|NN|_ _|_|VBD|_ Up|up|RP|_ _|_|SYM|_ 8|8|CD|_ min|min|NN|_
temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 12|12|CD|_ min|min|NN|_
temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_
temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 28|28|CD|_ min|min|NN|_
temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 44|44|CD|_ min|min|NN|_
temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_
temperature|temperature|NN|_ up|up|IN|_ shift|shift|NN|_ ,|,|,|_ 8|8|CD|_ min|min|NN|_
Basecalling|basecalling|NN|_ performed|perform|VBN|_ by|by|IN|_ MiSeq|miseq|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glucose|glucose|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ Glycerol|glycerol|NN|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ barcoded|barcode|VBN|_ with|with|IN|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ MiSeq|MiSeq|NNP|_ to|to|TO|_ produce|produce|VB|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ reads|read|VBZ|_ .|.|.|_ All|all|DT|_ steps|step|NNS|_ in|in|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ were|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standards|standard|NNS|_ .|.|.|_
CF104|cf104|NN|_ .3.3|.3.3|CD|_ _|_|NN|_ u1|u1|NN|_
CF104|cf104|NN|_ .3.3|.3.3|CD|_ _|_|NN|_ u7|u7|NN|_
CF104|cf104|NN|_ .3.3|.3.3|CD|_ _|_|NN|_ y2|y2|NN|_
CF104|cf104|NN|_ .3.3|.3.3|CD|_ _|_|NN|_ y9|y9|NN|_
CF108|cf108|NN|_ .4|.4|NN|_ B|b|NN|_ _|_|CD|_ u1|u1|NN|_
CF108|cf108|NN|_ .4|.4|NN|_ B|b|NN|_ _|_|CD|_ u2|u2|NN|_
CF108|cf108|NN|_ .4|.4|NN|_ B|b|NN|_ _|_|CD|_ y3|y3|NN|_
CF108|cf108|NN|_ .4|.4|NN|_ B|b|NN|_ _|_|CD|_ y8|y8|NN|_
Compile|compile|VB|_ annotated|annotated|JJ|_ counts|count|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ ExtractMapCounts|extractmapcount|NNS|_ from|from|IN|_ http|http|NN|_ :|:|:|_
CON206|con206|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ u1|u1|NN|_
CON206|con206|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ u2|u2|NN|_
CON206|con206|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ y1|y1|NN|_
CON206|con206|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ y2|y2|NN|_
CON208|con208|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ u1|u1|NN|_
CON208|con208|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ u8|u8|NN|_
CON208|con208|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ y2|y2|NN|_
CON208|con208|NN|_ .3|.3|NN|_ A|a|NN|_ _|_|NN|_ y6|y6|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ control|control|NN|_
disease|disease|NN|_ state|state|NN|_ :|:|:|_ cystic|cystic|JJ|_ fibrosis|fibrosis|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ CF|cf|NN|_ patient|patient|NN|_ stool|stool|VBP|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ isolated|isolate|VBN|_ from|from|IN|_ healthy|healthy|JJ|_ child|child|NN|_ stool|stool|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Experiments|experiment|NNS|_ were|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ followed|follow|VBD|_ three|three|CD|_ steps|step|NNS|_ :|:|:|_ seed|seed|NN|_ culture|culture|NN|_ ,|,|,|_ pre-culture|pre-culture|JJ|_ and|and|CC|_ experimental|experimental|JJ|_ culture|culture|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ seed|seed|NN|_ culture|culture|NN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ ,|,|,|_ then|then|RB|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ either|either|CC|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glycerol|glycerol|NN|SUPP or|or|CC|_ glucose|glucose|NN|SUPP for|for|IN|_ the|the|DT|_ pre-cultures|pre-culture|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ experimental|experimental|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ started|start|VBN|_ from|from|IN|_ the|the|DT|_ overnight|overnight|JJ|_ grown|grown|JJ|_ pre-cultures|pre-culture|NNS|_ containing|contain|VBG|_ the|the|DT|_ same|same|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ a|a|DT|_ normalized|normalize|VBN|_ optical|optical|JJ|_ density|density|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.05|0.05|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ spun|spin|VBN|_ down|down|RP|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processed|process|VBN|_ .|.|.|_
Filter|Filter|NNP|_ for|for|IN|_ map|map|NN|GEN quality|quality|NN|_ >|>|JJR|_ =|=|JJ|_ 20|20|CD|_ using|use|VBG|_ Samtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_
Filter|Filter|NNP|_ out|out|IN|_ rRNA|rrna|NN|_ reads|read|VBZ|_ ,|,|,|_ multi-mapped|multi-mapped|JJ|_ reads|read|VBZ|_ ,|,|,|_ >|>|JJR|_ 3|3|CD|_ mismatches|mismatch|NNS|_ ,|,|,|_ and|and|CC|_ gapped|gap|VBD|_ mappings|mapping|NNS|_ using|use|VBG|_ custom|custom|NN|_ Python|Python|NNP|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ FilterBAM2BAM|filterbam2bam|NN|_ from|from|IN|_ http|http|NN|_ :|:|:|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_
individual|individual|NN|_ :|:|:|_ CF|cf|NN|_ patient|patient|NN|_
individual|individual|JJ|_ :|:|:|_ healthy|healthy|JJ|_ child|child|NN|_
Map|map|NN|_ to|to|TO|_ MG1655|mg1655|NN|_ reference|reference|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.4|0.7.4|CD|_ -LRB-|-lrb-|-LRB-|_ bwa|bwa|NN|_ mem|mem|NN|_ ,|,|,|_ default|default|NN|_ parameters|parameter|NNS|_ -RRB-|-rrb-|-RRB-|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ and|and|CC|_ chloroform|chloroform|NN|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ A.|a.|NN|_ Untergasser|Untergasser|NNP|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ level|level|NN|_ files|file|NNS|_ are|be|VBP|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ with|with|IN|_ columns|column|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ index|index|NN|_ ,|,|,|_ hits|hit|VBZ|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ RPM|RPM|NNP|_ ,|,|,|_ start|start|VB|_ _|_|SYM|_ position|position|NN|_ ,|,|,|_ end|end|NN|_ _|_|NN|_ position|position|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ feature|feature|NN|_ _|_|CD|_ type|type|NN|_ ,|,|,|_ reference|reference|NN|_ _|_|NN|_ replicon|replicon|NN|_ -LRB-|-lrb-|-LRB-|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ locus|locus|NN|_ _|_|NN|_ tag|tag|NN|GEN ,|,|,|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ ,|,|,|_ product|product|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ dYT|dyt|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ ,|,|,|_ JH|JH|NNP|_ -LRB-|-lrb-|-LRB-|_ 1972|1972|CD|_ -RRB-|-rrb-|-RRB-|_ Experiments|experiment|NNS|_ in|in|IN|_ Molecular|molecular|JJ|_ Genetics|Genetics|NNP|_ -LRB-|-lrb-|-LRB-|_ Cold|Cold|NNP|_ Spring|Spring|NNP|_ Harbor|Harbor|NNP|_ Laboratory|Laboratory|NNP|_ ,|,|,|_ Cold|Cold|NNP|_ Spring|Spring|NNP|_ Harbor|Harbor|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ kanamycin|kanamycin|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mg|mg|NN|_
E.coli|e.coli|JJ|_
E.|e.|FW|_ coli|coli|FW|_ B178|b178|NN|_ groESL|groesl|NN|_ -LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ expressing|express|VBG|_ human|human|JJ|_ Hsp60|hsp60|NN|_ and|and|CC|_ Hsp10|hsp10|NN|_
E.|e.|FW|_ coli|coli|FW|_ B178|b178|NN|_ groESL|groesl|NN|_ -LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ expressing|express|VBG|_ human|human|JJ|_ wt|wt|JJ|_ and|and|CC|_ Val98Ile|val98ile|NN|_ Hsp60|hsp60|NN|_ and|and|CC|_ Hsp10|hsp10|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ B178|b178|NN|_ -LRB-|-lrb-|-LRB-|_ Georgopoulos|Georgopoulos|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 1973|1973|CD|_ -RRB-|-rrb-|-RRB-|_ J|J|NNP|_ Mol|Mol|NNP|_ Biol|Biol|NNP|_ 76|76|CD|_ :|:|:|_ 45-60|45-60|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ which|which|WDT|_ the|the|DT|_ endogenous|endogenous|JJ|_ groES|groes|NN|_ and|and|CC|_ groEL|groel|NN|_ genes|gene|NNS|_ have|have|VBP|_ been|be|VBN|_ deleted|delete|VBN|_ and|and|CC|_ that|that|DT|_ is|be|VBZ|_ maintained|maintain|VBN|_ alive|alive|JJ|_ by|by|IN|_ the|the|DT|_ pOFX-tac1-derived|pofx-tac1-derived|JJ|_ plasmid|plasmid|NN|_ carrying|carry|VBG|_ an|a|DT|_ IPTG-inducible|iptg-inducible|JJ|_ operon|operon|NN|_ with|with|IN|_ cDNA|cdna|NN|_ encoding|encode|VBG|_ human|human|JJ|_ Hsp10|hsp10|NN|_ and|and|CC|_ the|the|DT|_ mature|mature|JJ|_ part|part|NN|_ of|of|IN|_ human|human|JJ|_ wild|wild|JJ|_ type|type|NN|_ Hsp60|hsp60|NN|_ -LRB-|-lrb-|-LRB-|_ Hansen|Hansen|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2002|2002|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ These|these|DT|_ cells|cell|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ transformed|transform|VBN|_ by|by|IN|_ electroporation|electroporation|NN|_ with|with|IN|_ a|a|DT|_ second|second|JJ|_ plasmid|plasmid|NN|_ ,|,|,|_ derivative|derivative|NN|_ of|of|IN|_ pBAD|pbad|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS5|mas5|NN|_ .0|.0|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ RNAeasy|rnaeasy|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Data|Data|NNP|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ custom|custom|NN|_ software|software|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ R|r|NN|_ programming|programming|NN|_ environment|environment|NN|_ and|and|CC|_ BioConductor|BioConductor|NNP|_ packages|package|NNS|_ .|.|.|_ Each|each|DT|_ probe|probe|NN|_ was|be|VBD|_ randomly|randomly|RB|_ spotted|spot|VBN|_ in|in|IN|_ three|three|CD|_ to|to|TO|_ five|five|CD|_ replicates|replicate|VBZ|_ to|to|TO|_ control|control|VB|_ for|for|IN|_ positional|positional|JJ|_ effects|effect|NNS|_ on|on|IN|_ the|the|DT|_ array|array|NN|_ .|.|.|_ Data|datum|NNS|_ from|from|IN|_ replicate|replicate|VBP|_ probes|probe|NNS|_ were|be|VBD|_ summarized|summarize|VBN|_ by|by|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ the|the|DT|_ log2-transformed|log2-transformed|JJ|_ intensities|intensity|NNS|_ .|.|.|_ No|no|DT|_ normalization|normalization|NN|_ or|or|CC|_ background|background|NN|_ correction|correction|NN|_ was|be|VBD|_ performed|perform|VBN|_ .|.|.|_
E.coli|e.coli|NN|_ CFT073|cft073|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
E.coli|e.coli|NN|_ CFT073|cft073|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ hybridization|hybridization|NN|_ to|to|TO|_ LLNL|llnl|NN|_ virulence|virulence|NN|_ mechanism|mechanism|NN|_ array|array|NN|_ v2A|v2a|NN|_
E.coli|e.coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL|edl|NN|_ 933|933|CD|_ genomic|genomic|JJ|_ DNA|dna|NN|_
E.coli|e.coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL|edl|NN|_ 933|933|CD|_ genomic|genomic|JJ|_ DNA|dna|NN|_ hybridization|hybridization|NN|_ to|to|TO|_ LLNL|llnl|NN|_ virulence|virulence|NN|_ mechanism|mechanism|NN|_ array|array|NN|_ v2A|v2a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CFT073|cft073|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Epicentre|Epicentre|NNP|_ DNA|dna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocols|protocol|NNS|_ .|.|.|_
serovar|serovar|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_ ;|;|:|_ GenBank|genbank|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|CD|_ 002655.2|002655.2|CD|_
strain|strain|NN|_ CFT073|cft073|NN|_ ;|;|:|_ GenBank|genbank|NN|_ accession|accession|NN|_ AE014075|ae014075|NN|_ .1|.1|CD|_
The|the|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ grown|grow|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ from|from|IN|_ ATCC|atcc|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Functional|functional|JJ|_ annotation|annotation|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ Database|database|NN|_ for|for|IN|_ Annotation|Annotation|NNP|_ ,|,|,|_ Visualization|visualization|NN|_ and|and|CC|_ Integrated|Integrated|NNP|_ Discovery|Discovery|NNP|_ -LRB-|-lrb-|-LRB-|_ DAVID|DAVID|NNP|_ -RRB-|-rrb-|-RRB-|_ Bioinformatics|Bioinformatics|NNP|_ Resources|Resources|NNP|_ 6.7|6.7|CD|_ ,|,|,|_ NIAID|NIAID|NNP|_ ,|,|,|_ NIH|NIH|NNP|_ -LRB-|-lrb-|-LRB-|_ http|http|JJ|_ :|:|:|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ 5|5|CD|_ hr|hr|NN|_
Next|Next|NNP|_ ,|,|,|_ a|a|DT|_ linear|linear|JJ|_ model|model|NN|_ was|be|VBD|_ built|build|VBN|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ using|use|VBG|_ the|the|DT|_ R|r|NN|_ LIMMA|limma|NN|_ package|package|NN|_ and|and|CC|_ statistics|statistics|NNS|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ were|be|VBD|_ computed|compute|VBN|_ .|.|.|_ To|to|TO|_ filter|filter|NN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ ,|,|,|_ two|two|CD|_ fold|fold|JJ|_ or|or|CC|_ three-fold|three-fold|JJ|_ change|change|NN|_ with|with|IN|_ a|a|DT|_ FDR|FDR|NNP|_ ≤|≤|SYM|_ 0.05|0.05|CD|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ threshold|threshold|NN|_ .|.|.|_
PA20|pa20|NN|_ cultures|culture|NNS|_
PA20|pa20|NN|_ cultures|culture|NNS|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ T-agar|t-agar|JJ|_ with|with|IN|_ and|and|CC|_ without|without|IN|_ added|add|VBN|_ Sulfamethoxazole|Sulfamethoxazole|NNP|_ -|-|:|_ Trimethoprim|Trimethoprim|NNP|_ at|at|IN|_ designated|designate|VBN|_ levels|level|NNS|_ for|for|IN|_ the|the|DT|_ indicated|indicated|JJ|_ times|time|NNS|_ and|and|CC|_ temperatures|temperature|NNS|_ .|.|.|_ Working|work|VBG|_ stocks|stock|NNS|_ were|be|VBD|_ tested|test|VBN|_ and|and|CC|_ maintained|maintain|VBN|_ using|use|VBG|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ LB|lb|NN|_ agar|agar|NN|_ .|.|.|_ Plasmid|plasmid|NN|_ pSE380|pse380|NN|_ derivatives|derivative|NNS|_ were|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ IPTG|iptg|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ ;|;|:|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Ribozero|ribozero|NN|_ -LRB-|-lrb-|-LRB-|_ gram|gram|NN|_ negative|negative|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ protocol|protocol|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
RNA-seq|rna-seq|NN|_ data|datum|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ Sakai|Sakai|NNP|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ Subjunc|subjunc|NN|_ aligner|aligner|NN|_ program|program|NN|_ from|from|IN|_ the|the|DT|_ Subread|Subread|NNP|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .4.6|.4.6|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
T5|t5|NN|_ _|_|SYM|_ 1x|1x|FW|_ _|_|FW|_ 4|4|CD|_
T5|t5|NN|_ _|_|CD|_ 27x|27x|CD|_ _|_|NN|_ 1|1|CD|_
The|the|DT|_ alignment|alignment|NN|_ Bam|bam|UH|_ files|file|NNS|_ were|be|VBD|_ compared|compare|VBN|_ against|against|IN|_ the|the|DT|_ gene|gene|NN|_ annotation|annotation|NN|_ general|general|JJ|_ feature|feature|NN|_ format|format|NN|_ -LRB-|-lrb-|-LRB-|_ GFF|gff|NN|_ -RRB-|-rrb-|-RRB-|_ file|file|NN|_ ,|,|,|_ and|and|CC|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ featureCounts|featureCounts|NNPS|_ tool|tool|NN|_ from|from|IN|_ Subread|Subread|NNP|_ .|.|.|_ The|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ data|datum|NNS|_ of|of|IN|_ the|the|DT|_ expressed|express|VBN|_ genes|gene|NNS|_ was|be|VBD|_ normalized|normalize|VBN|_ for|for|IN|_ RNA|rna|NN|_ composition|composition|NN|_ using|use|VBG|_ the|the|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M|m|NN|_ values|value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ RNAzol|rnazol|NN|_ RT|rt|NN|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Research|Research|NNP|_ Center|Center|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ following|follow|VBG|_ manufature|manufature|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ by|by|IN|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ using|use|VBG|_ the|the|DT|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
15degrees|15degree|NNS|_ replicate|replicate|VBP|_ 1|1|CD|_
15degrees|15degree|NNS|_ replicate|replicate|VBP|_ 2|2|CD|_
15degrees|15degree|NNS|_ replicate|replicate|VBP|_ 3|3|CD|_
46degrees|46degree|NNS|_ replicate|replicate|VBP|_ 1|1|CD|_
46degrees|46degree|NNS|_ replicate|replicate|VBP|_ 2|2|CD|_
46degrees|46degree|NNS|_ replicate|replicate|VBP|_ 3|3|CD|_
BC-7ppm|bc-7ppm|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
BC-7ppm|bc-7ppm|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
BC-7ppm|bc-7ppm|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
BC-9ppm|bc-9ppm|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
BC-9ppm|bc-9ppm|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
BC-9ppm|bc-9ppm|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
CH3COOH|ch3cooh|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.9|5.9|CD|_ ±|±|SYM|_ 0.05|0.05|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ HCl|hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.75|4.75|CD|_ ±|±|SYM|_ 0.05|0.05|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ NaOH|naoh|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 9.6|9.6|CD|_ ±|±|SYM|_ 0.05|0.05|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ EtOH|etoh|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ 4.5|4.5|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ Glycerol|glycerol|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ BC|bc|NN|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ and|and|CC|_ 9|9|CD|_ mg|mg|NN|_
CH3COOH|ch3cooh|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
CH3COOH|ch3cooh|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
CH3COOH|ch3cooh|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
Control|Control|NNP|_ replicate|replicate|VB|_ 1|1|CD|_
Control|Control|NNP|_ replicate|replicate|VB|_ 2|2|CD|_
Control|Control|NNP|_ replicate|replicate|VB|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
EtBr|etbr|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
EtBr|etbr|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
EtBr|etbr|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
EtOH|etoh|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
EtOH|etoh|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
EtOH|etoh|NN|_ replicate|replicate|VB|_ 3|3|CD|_
Glycerol|Glycerol|NNP|_ replicate|replicate|VB|_ 1|1|CD|_
Glycerol|Glycerol|NNP|_ replicate|replicate|VB|_ 2|2|CD|_
Glycerol|Glycerol|NNP|_ replicate|replicate|VB|_ 3|3|CD|_
HCl|hcl|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
HCl|hcl|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
NaCl|nacl|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
NaCl|nacl|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
NaCl|nacl|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
NaOH|naoh|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
NaOH|naoh|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
pooled|pool|VBD|_ RNA|rna|NN|_ from|from|IN|_ all|all|DT|_ conditions|condition|NNS|_ including|include|VBG|_ the|the|DT|_ control|control|NN|_ ,|,|,|_ reference|reference|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ inoculating|inoculate|VBG|_ one|one|CD|_ colony|colony|NN|_ from|from|IN|_ tryptone|tryptone|NN|SUPP soya|soya|NN|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ TSA|tsa|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Oxoid|Oxoid|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ overnight|overnight|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ 5|5|CD|_ ml|ml|NN|_ TSB|tsb|NN|_ and|and|CC|_ incubating|incubate|VBG|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ This|this|DT|_ culture|culture|NN|_ was|be|VBD|_ initially|initially|RB|_ diluted|dilute|VBN|_ 1:10|1:10|CD|_ in|in|IN|_ medium|medium|NN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ room-temperature|room-temperature|JJ|_ TSB|tsb|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ different|different|JJ|_ stress|stress|NN|_ factors|factor|NNS|_ -LRB-|-lrb-|-LRB-|_ 40|40|CD|_ ml|ml|NN|_ total|total|JJ|_ volume|volume|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ approx.|approx.|RB|_ 1|1|CD|_ '|'|''|_ 107|107|CD|_ CFU|CFU|NNP|_
The|the|DT|_ fluorescent|fluorescent|JJ|_ spot|spot|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ ImaGeneÔ|imageneô|NN|_ 5.6.1|5.6.1|CD|_ -LRB-|-lrb-|-LRB-|_ BioDiscovery|BioDiscovery|NNP|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ Background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ LOWESS|lowess|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ GeneSpringä|GeneSpringä|NNP|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ Silicon|Silicon|NNP|_ Genetics|Genetics|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ A|a|DT|_ lowess|lowess|NN|_ curve|curve|NN|_ was|be|VBD|_ fit|fit|VBN|_ to|to|TO|_ the|the|DT|_ log-intensity|log-intensity|JJ|_ versus|versus|CC|_ log-ratio|log-ratio|JJ|_ plot|plot|NN|_ .|.|.|_ 20|20|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ the|the|DT|_ lowess|lowess|NN|_ fit|fit|NN|_ at|at|IN|_ each|each|DT|_ point|point|NN|_ .|.|.|_ The|the|DT|_ curve|curve|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ adjust|adjust|VB|_ the|the|DT|_ control|control|NN|_ value|value|NN|_ for|for|IN|_ each|each|DT|_ measurement|measurement|NN|_ .|.|.|_ If|if|IN|_ the|the|DT|_ control|control|NN|_ channel|channel|NN|_ was|be|VBD|_ lower|lower|JJR|_ than|than|IN|_ 10|10|CD|_ then|then|RB|_ the|the|DT|_ value|value|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ 10|10|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Only|only|RB|_ data|datum|NNS|_ from|from|IN|_ spots|spot|NNS|_ representing|represent|VBG|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ genes|gene|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ our|we|PRP$|_ studies|study|NNS|_ .|.|.|_ All|all|DT|_ analyses|analysis|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ 3|3|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ with|with|IN|_ the|the|DT|_ exception|exception|NN|_ of|of|IN|_ the|the|DT|_ second|second|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ from|from|IN|_ conditions|condition|NNS|_ HCl|hcl|NN|_ and|and|CC|_ NaOH|naoh|NN|_ .|.|.|_ These|these|DT|_ two|two|CD|_ observations|observation|NNS|_ were|be|VBD|_ removed|remove|VBN|_ due|due|JJ|_ to|to|TO|_ bad|bad|JJ|_ hybridization|hybridization|NN|_ giving|give|VBG|_ a|a|DT|_ total|total|NN|_ of|of|IN|_ 34|34|CD|_ array|array|NN|_ hybridizations|hybridization|NNS|_ -LRB-|-lrb-|-LRB-|_ observations|observation|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Genes|gene|NNS|_ not|not|RB|_ present|present|VB|_ in|in|IN|_ any|any|DT|_ of|of|IN|_ the|the|DT|_ 34|34|CD|_ observations|observation|NNS|_ were|be|VBD|_ filtered|filter|VBN|_ out|out|RP|_ ,|,|,|_ resulting|result|VBG|_ in|in|IN|_ the|the|DT|_ analysis|analysis|NN|_ of|of|IN|_ 4279|4279|CD|_ out|out|IN|_ of|of|IN|_ 4289|4289|CD|_ MG1655|mg1655|NN|_ genes|gene|NNS|_ on|on|IN|_ the|the|DT|_ array|array|NN|_ .|.|.|_ Missing|miss|VBG|_ values|value|NNS|_ -LRB-|-lrb-|-LRB-|_ data|datum|NNS|_ points|point|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ replaced|replace|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ KNNimpute|knnimpute|NN|_ procedure|procedure|NN|_ -LRB-|-lrb-|-LRB-|_ k|k|NN|_ =|=|JJ|_ 10|10|CD|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ log2|log2|NN|_ transformed|transform|VBN|_ data|datum|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ 1|1|CD|_ ml|ml|NN|_ cells|cell|NNS|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Protect|Protect|NNP|_ Bacteria|bacterium|NNS|_ Mini|Mini|NNP|_ Prep|Prep|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ recommended|recommend|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ including|include|VBG|_ the|the|DT|_ ``|``|``|_ on-column|on-column|JJ|_ ''|''|''|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
accession|accession|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_ +|+|CC|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
After|after|IN|_ 0.5|0.5|CD|_ M|m|NN|_ NaCl|nacl|NN|_ treatment|treatment|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ of|of|IN|_ the|the|DT|_ early-exponential|early-exponential|JJ|_ phase|phase|NN|_ cells|cell|NNS|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_
After|after|IN|_ 0.5|0.5|CD|_ M|m|NN|_ NaCl|nacl|NN|_ treatment|treatment|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ of|of|IN|_ the|the|DT|_ early-exponential|early-exponential|JJ|_ phase|phase|NN|_ cells|cell|NNS|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_
After|after|IN|_ 0.5|0.5|CD|_ M|m|NN|_ NaCl|nacl|NN|_ treatment|treatment|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ of|of|IN|_ the|the|DT|_ early-exponential|early-exponential|JJ|_ phase|phase|NN|_ cells|cell|NNS|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ .|.|.|_
Arrays|array|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Nimblegen|Nimblegen|NNP|_ 's|'s|POS|_ standard|standard|JJ|_ protocol|protocol|NN|_ for|for|IN|_ Nimblescan|Nimblescan|NNP|_ ChIP|ChIP|NNP|_ data|datum|NNS|_ extraction|extraction|NN|_ .|.|.|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ none|none|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ antibody|antibody|NN|_
E.|e.|FW|_ coli|coli|FW|_ CC72|cc72|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ water|water|NN|_ bath|bath|NN|_ to|to|TO|_ early-exponential|early-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.2|0.2|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_
E.coli|e.coli|NNS|_ _|_|VBP|_ LB|lb|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ LB|lb|NN|_ _|_|CD|_ rep3|rep3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na10|na10|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na10|na10|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na10|na10|NN|_ _|_|CD|_ rep3|rep3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na20|na20|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na20|na20|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na20|na20|NN|_ _|_|CD|_ rep3|rep3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na45|na45|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na45|na45|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ Na45|na45|NN|_ _|_|CD|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ Fusion|fusion|NN|_ of|of|IN|_ venus|venus|NN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ rpoC|rpoc|NN|GEN in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ wild-type|wild-type|JJ|_ MG1655|mg1655|NN|_
RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ CC72|cc72|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ osmotic|osmotic|JJ|_ stress|stress|NN|_
RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ CC72|cc72|NN|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ osmotic|osmotic|JJ|_ stress|stress|NN|_
RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ CC72|cc72|NN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ osmotic|osmotic|JJ|_ stress|stress|NN|_
RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ CC72|cc72|NN|_ at|at|IN|_ early-exponential|early-exponential|JJ|_ phase|phase|NN|_
The|the|DT|_ ChIP|chip|NN|_ experiment|experiment|NN|_ was|be|VBD|_ performed|perform|VBN|_ essentially|essentially|RB|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Herring|Herring|NNP|_ ,|,|,|_ Raffaelle|Raffaelle|NNP|_ et|et|FW|_ al.|al.|FW|_ 2005|2005|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ the|the|DT|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ by|by|IN|_ a|a|DT|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ and|and|CC|_ 10|10|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.6|7.6|CD|_ -RRB-|-rrb-|-RRB-|_ solution|solution|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ After|after|IN|_ cell|cell|NN|_ lysis|lysis|NN|_ ,|,|,|_ RNase|rnase|NN|_ A|a|NN|_ treatment|treatment|NN|_ and|and|CC|_ sonication|sonication|NN|_ ,|,|,|_ the|the|DT|_ chromosome|chromosome|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ to|to|TO|_ 100-1200|100-1200|CD|_ bp|bp|NN|_ .|.|.|_ RNAP|rnap|NN|_ binding|binding|NN|_ DNA|dna|NN|_ -LRB-|-lrb-|-LRB-|_ IP|IP|NNP|_ DNA|dna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ with|with|IN|_ RNAP|rnap|NN|_ using|use|VBG|_ an|a|DT|_ antibody|antibody|NN|_ against|against|IN|_ the|the|DT|_ RNAP|rnap|NN|_ β|β|NN|_ '|'|''|_ subunit|subunit|NN|_ and|and|CC|_ pan|pan|NN|_ mouse|mouse|NN|_ magnetic|magnetic|JJ|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ same|same|JJ|_ sample|sample|NN|_ without|without|IN|_ the|the|DT|_ β|β|NN|_ '|'|''|_ antibody|antibody|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ mock|mock|JJ|_ immunoprecipitation|immunoprecipitation|NN|_ DNA|dna|NN|_ -LRB-|-lrb-|-LRB-|_ mock|mock|JJ|_ IP|IP|NNP|_ DNA|dna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ washing|wash|VBG|_ and|and|CC|_ de-crosslinking|de-crosslinking|NN|_ ,|,|,|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ early-exponential|early-exponential|JJ|_ phase|phase|NN|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ without|without|IN|_ NaCl|nacl|NN|_ treatment|treatment|NN|_ .|.|.|_
A|a|NN|_ culture|culture|NN|_ volume|volume|NN|_ of|of|IN|_ 7|7|CD|_ ml|ml|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ volume|volume|NN|_ of|of|IN|_ boiling|boil|VBG|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 4mM|4mm|NN|_ EDTA|edta|NN|_ and|and|CC|_ heated|heat|VBN|_ at|at|IN|_ 100|100|CD|_ °C|°c|NN|_ for|for|IN|_ 3|3|CD|_ to|to|TO|_ 5|5|CD|_ minutes|minute|NNS|_ then|then|RB|_ vortexed|vortex|VBD|_ .|.|.|_ At|at|IN|_ this|this|DT|_ stage|stage|NN|_ ,|,|,|_ the|the|DT|_ extract|extract|NN|_ was|be|VBD|_ either|either|CC|_ processed|process|VBN|_ further|further|JJ|_ or|or|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
Affymetrix|Affymetrix|NNP|_ .|.|.|_ CEL|CEL|NNP|_ files|file|VBZ|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ with|with|IN|_ dChip|dchip|NN|_ using|use|VBG|_ the|the|DT|_ array|array|NN|_ of|of|IN|_ median|median|JJ|_ brightness|brightness|NN|_ -LRB-|-lrb-|-LRB-|_ BS|bs|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Model|Model|NNP|_ method|method|NN|_ :|:|:|_ model-base|model-base|NN|_ expression|expression|NN|_ ;|;|:|_ background|background|NN|_ substraction|substraction|NN|_ :|:|:|_ Mismatch|Mismatch|NNP|_ Probe|Probe|NNP|_ -LRB-|-lrb-|-LRB-|_ PM|PM|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|min|NN|_ Glucose|glucose|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ Min|Min|NNP|_ Glucose|Glucose|NNP|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|min|NN|_ Glucose|glucose|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ Min|Min|NNP|_ Glucose|Glucose|NNP|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ WT|WT|NNP|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO2057|jo2057|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
JO2081|jo2081|NN|_ -LRB-|-lrb-|-LRB-|_ hupA|hupa|NN|GEN -RRB-|-rrb-|-RRB-|_
JO2081|jo2081|NN|_ -LRB-|-lrb-|-LRB-|_ hupA|hupa|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2081|jo2081|NN|_ hupA|hupa|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2081|jo2081|NN|_ hupA|hupa|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2081|jo2081|NN|_ hupA|hupa|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
JO2081|jo2081|NN|_ -LRB-|-lrb-|-LRB-|_ hupA|hupa|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2081|jo2081|NN|_ -LRB-|-lrb-|-LRB-|_ hupA|hupa|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
JO2083|jo2083|NN|_ -LRB-|-lrb-|-LRB-|_ hupB|hupb|NN|GEN -RRB-|-rrb-|-RRB-|_
JO2083|jo2083|NN|_ -LRB-|-lrb-|-LRB-|_ hupB|hupb|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2083|jo2083|NN|_ hupB|hupb|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2083|jo2083|NN|_ hupB|hupb|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2083|jo2083|NN|_ hupB|hupb|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
JO2083|jo2083|NN|_ -LRB-|-lrb-|-LRB-|_ hupB|hupb|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO2083|jo2083|NN|_ -LRB-|-lrb-|-LRB-|_ hupB|hupb|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|min|NN|_ Glucose|glucose|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ Min|min|NN|_ Glucose|glucose|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|min|NN|_ Glucose|glucose|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ Min|min|NN|_ Glucose|glucose|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ hupAB|hupab|NN|_ ,|,|,|_ Min|Min|NNP|_ Glycerol|Glycerol|NNP|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition1|repetition1|NN|_
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ repetition2|repetition2|NN|_
JO3020|jo3020|NN|_ -LRB-|-lrb-|-LRB-|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ phase|phase|NN|_
MW30|mw30|NN|_ -LRB-|-lrb-|-LRB-|_ rpoS|rpos|NN|GEN -RRB-|-rrb-|-RRB-|_
MW30|mw30|NN|_ -LRB-|-lrb-|-LRB-|_ rpoS|rpos|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
MW30|mw30|NN|_ rpoS|rpos|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase
MW30|mw30|NN|_ -LRB-|-lrb-|-LRB-|_ rpoS|rpos|NN|GEN -RRB-|-rrb-|-RRB-|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
MW30|mw30|NN|_ rpoS|rpos|NN|GEN ,|,|,|_ LB|lb|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Seven|seven|CD|_ mililiter|mililiter|NN|_ of|of|IN|_ phenol|phenol|NN|_
stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
The|the|DT|_ five|five|CD|_ bacterial|bacterial|JJ|_ strains|strain|NNS|_ -LRB-|-lrb-|-LRB-|_ JO2057|jo2057|NN|_ ,|,|,|_ JO2081|jo2081|NN|_ ,|,|,|_ JO2083|jo2083|NN|_ ,|,|,|_ JO3020|jo3020|NN|_ and|and|CC|_ MW30|mw30|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|_ 0.5|0.5|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ M9|m9|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP or|or|CC|_ M9|m9|NN|_ minimal|minimal|JJ|_ glycerol|glycerol|NN|SUPP at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ New|New|NNP|_ Brunswick|Brunswick|NNP|_ laboratory|laboratory|NN|_ shaker|shaker|NN|_ in|in|IN|_ 2liter|2liter|JJ|_ flasks|flask|NNS|_ .|.|.|_ The|the|DT|_ typical|typical|JJ|_ doubling|doubling|NN|_ time|time|NN|_ ,|,|,|_ observed|observe|VBN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ was|be|VBD|_ 40|40|CD|_ min|min|NN|_ for|for|IN|_ JO2057|jo2057|NN|_ ,|,|,|_ JO2081|jo2081|NN|_ ,|,|,|_ JO2083|jo2083|NN|_ ,|,|,|_ MW30|mw30|NN|_ and|and|CC|_ 75|75|CD|_ min|min|NN|_ for|for|IN|_ JO3020|jo3020|NN|_ .|.|.|_ After|after|IN|_ growth|growth|NN|_ curve|curve|NN|_ calibration|calibration|NN|_ ,|,|,|_ the|the|DT|_ various|various|JJ|_ growth|growth|NN|_ phase|phase|NN|_ sample|sample|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ the|the|DT|_ following|following|JJ|_ cell|cell|NN|_ densities|density|NNS|_ :|:|:|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase :|:|:|_ OD600|od600|NN|_ 0.6-0.7|0.6-0.7|CD|_ ;|;|:|_ transition|transition|NN|_ :|:|:|_ 2.2-2.5|2.2-2.5|CD|_ and|and|CC|_ stationary|stationary|JJ|_ :|:|:|_ 4.6-4.8|4.6-4.8|CD|_ -LRB-|-lrb-|-LRB-|_ 3.0|3.0|CD|_ for|for|IN|_ hupAB|hupab|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
transition|transition|NN|_ phase|phase|NN|_
Anaerobic|anaerobic|JJ|_ ,|,|,|_ minus|minus|CC|_ nitrate|nitrate|NN|SUPP ,|,|,|_ IP|IP|NNP|_
Anaerobic|Anaerobic|NNP|_ ,|,|,|_ plus|plus|CC|_ nitrate|nitrate|NN|SUPP ,|,|,|_ IP|IP|NNP|_
Chromatin|Chromatin|NNP|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ Oxford|Oxford|NNP|_ Gene|Gene|NNP|_ Technology|Technology|NNP|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ www.ogt.co.uk|www.ogt.co.uk|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ expressing|express|VBG|_ NsrR|nsrr|NN|TF with|with|IN|_ a|a|DT|_ C-terminal|c-terminal|JJ|_ Flag-tag|flag-tag|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ L|l|NN|_ broth|broth|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ expressing|express|VBG|_ NsrR|nsrr|NN|TF with|with|IN|_ a|a|DT|_ C-terminal|c-terminal|JJ|_ Flag-tag|flag-tag|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ L|l|NN|_ broth|broth|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ expressing|express|VBG|_ NsrR|nsrr|NN|TF with|with|IN|_ a|a|DT|_ C-terminal|c-terminal|JJ|_ Flag-tag|flag-tag|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ L|l|NN|_ broth|broth|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ expressing|express|VBG|_ NsrR|nsrr|NN|TF with|with|IN|_ a|a|DT|_ C-terminal|c-terminal|JJ|_ Flag-tag|flag-tag|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ L|l|NN|_ broth|broth|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP and|and|CC|_ nitrate|nitrate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ expressing|express|VBG|_ NsrR|nsrr|NN|TF with|with|IN|_ a|a|DT|_ C-terminal|c-terminal|JJ|_ Flag-tag|flag-tag|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ L|l|NN|_ broth|broth|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP and|and|CC|_ nitrate|nitrate|NN|SUPP .|.|.|_
NsrR|nsrr|NN|TF _|_|CD|_ Flagtag|Flagtag|NNP|_ _|_|CD|_ rep1|rep1|NN|_
NsrR|nsrr|NN|TF _|_|CD|_ Flagtag|Flagtag|NNP|_ _|_|CD|_ rep2|rep2|NN|_
NsrR|nsrr|NN|TF _|_|CD|_ Flagtag|Flagtag|NNP|_ _|_|CD|_ rep3|rep3|NN|_
The|the|DT|_ value|value|NN|_ is|be|VBZ|_ the|the|DT|_ simple|simple|JJ|_ linear|linear|JJ|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ processed|process|VBN|_ Cy3|cy3|NN|_ and|and|CC|_ Cy5|cy5|NN|_ signals|signal|NNS|_ .|.|.|_
The|the|DT|_ value|value|NN|_ is|be|VBZ|_ the|the|DT|_ simple|simple|JJ|_ linear|linear|JJ|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ processed|process|VBN|_ Cy5|cy5|NN|_ and|and|CC|_ Cy3|cy3|NN|_ signals|signal|NNS|_ .|.|.|_
bacteria|bacterium|NNS|_ harvested|harvest|VBN|_ from|from|IN|_ blood|blood|NN|_ of|of|IN|_ chickens|chicken|NNS|_
condition|condition|NN|_ :|:|:|_ in|in|FW|_ vivo|vivo|FW|_
Data|Data|NNP|_ were|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ Feature|feature|NN|_ Extraction|extraction|NN|_ software|software|NN|_ 10.7|10.7|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|JJ|_ technologies|technology|NNS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ US|US|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Raw|raw|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ Quantile|quantile|JJ|_ algorithm|algorithm|NN|_ ,|,|,|_ GeneSpring|GeneSpring|NNP|_ Software|Software|NNP|_ 11.0|11.0|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|JJ|_ technologies|technology|NNS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ US|US|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E058|e058|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E058|e058|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E058|e058|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
E058ΔrstAB|e058δrstab|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E058ΔrstAB|e058δrstab|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E058ΔrstAB|e058δrstab|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism APEC|apec|NN|_ O2|o2|CD|_
genotype|genotype|NN|_
strain|strain|NN|_ :|:|:|_ E058|e058|NN|_
The|the|DT|_ in|in|FW|_ vivo|vivo|FW|_ bacterial|bacterial|JJ|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ two-step|two-step|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ We|we|PRP|_ first|first|RB|_ centrifuged|centrifuge|VBD|_ the|the|DT|_ collected|collect|VBN|_ anticoagulated|anticoagulated|JJ|_ blood|blood|NN|_ samples|sample|NNS|_ at|at|IN|_ low|low|JJ|_ speed|speed|NN|_ to|to|TO|_ remove|remove|VB|_ the|the|DT|_ abundant|abundant|JJ|_ red|red|JJ|_ and|and|CC|_ white|white|JJ|_ blood|blood|NN|_ cells|cell|NNS|_ and|and|CC|_ collected|collect|VBN|_ the|the|DT|_ upper|upper|JJ|_ serum|serum|NN|_ layer|layer|NN|_ .|.|.|_ We|we|PRP|_ then|then|RB|_ used|use|VBD|_ high-speed|high-speed|JJ|_ centrifugation|centrifugation|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ bacteria|bacterium|NNS|_ from|from|IN|_ the|the|DT|_ serum|serum|NN|_ .|.|.|_
To|to|TO|_ prepare|prepare|VB|_ the|the|DT|_ in|in|FW|_ vivo|vivo|FW|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ bacteria|bacterium|NNS|_ was|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ cardiac|cardiac|JJ|_ blood|blood|NN|_ in|in|IN|_ 1-day-old|1-day-old|JJ|_ chickens|chicken|NNS|_ at|at|IN|_ 5|5|CD|_ hours|hour|NNS|_ post|post|NN|_ infection|infection|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ from|from|IN|_ in|in|FW|_ vivo|vivo|FW|_ samples|sample|NNS|_ of|of|IN|_ APEC|APEC|NNP|_ E058|e058|NN|_ and|and|CC|_ E058ΔrstAB|e058δrstab|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74106|74106|CD|_ ,|,|,|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ GmBH|GmBH|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
10|10|CD|_ .|.|.|_ FHI9.IND.HUS|fhi9.ind.hus|NN|_
11|11|CD|_ .|.|.|_ FHI12.nIND.HUS|fhi12.nind.hus|NN|_
12|12|CD|_ .|.|.|_ FHI12.IND.HUS|fhi12.ind.hus|NN|_
13|13|CD|_ .|.|.|_ FHI24.nIND.HUS|fhi24.nind.hus|NN|_
15|15|CD|_ .|.|.|_ FHI25.nIND.HUS|fhi25.nind.hus|NN|_
16|16|CD|_ .|.|.|_ FHI25.IND.HUS|fhi25.ind.hus|NN|_
17|17|CD|_ .|.|.|_ FHI27.nIND.HUS|fhi27.nind.hus|NN|_
18|18|CD|_ .|.|.|_ FHI27.IND.HUS|fhi27.ind.hus|NN|_
19|19|CD|_ .|.|.|_ FHI36.nIND.nHUS|fhi36.nind.nhus|NN|_
1|1|CD|_ .|.|.|_ FHI4.nIND.HUS|fhi4.nind.hus|NN|_
20|20|CD|_ .|.|.|_ FHI36.IND.nHUS|fhi36.ind.nhus|NN|_
21|21|CD|_ .|.|.|_ FHI43.nIND.nHUS|fhi43.nind.nhus|NN|_
22|22|CD|_ .|.|.|_ FHI43.IND.nHUS|fhi43.ind.nhus|NN|_
23|23|CD|_ .|.|.|_ FHI48.nIND.HUS|fhi48.nind.hus|NN|_
25|25|CD|_ .|.|.|_ FHI79.nIND.HUS|fhi79.nind.hus|NN|_
26|26|CD|_ .|.|.|_ FHI79.IND.HUS|fhi79.ind.hus|NN|_
27|27|CD|_ .|.|.|_ FHI95.nIND.nHUS|fhi95.nind.nhus|NN|_
28|28|CD|_ .|.|.|_ FHI95.IND.nHUS|fhi95.ind.nhus|NN|_
29|29|CD|_ .|.|.|_ St.|St.|NNP|_ Olav40.nIND.nHUS|olav40.nind.nhus|JJ|_
2|2|CD|_ .|.|.|_ FHI4.IND.HUS|fhi4.ind.hus|NN|_
31|31|CD|_ .|.|.|_ St.|St.|NNP|_ Olav104.nIND.nHUS|Olav104.nIND.nHUS|NNP|_
32|32|CD|_ .|.|.|_ St.|St.|NNP|_ Olav104.IND.nHUS|Olav104.IND.nHUS|NNP|_
33|33|CD|_ .|.|.|_ St.|St.|NNP|_ Olav157.nIND.nHUS|Olav157.nIND.nHUS|NNP|_
34|34|CD|_ .|.|.|_ St.|St.|NNP|_ Olav157.IND.nHUS|Olav157.IND.nHUS|NNP|_
35|35|CD|_ .|.|.|_ St.|St.|NNP|_ Olav172.nIND.nHUS|Olav172.nIND.nHUS|NNP|_
37|37|CD|_ .|.|.|_ St.|St.|NNP|_ Olav174.nIND.nHUS|Olav174.nIND.nHUS|NNP|_
38|38|CD|_ .|.|.|_ St.|St.|NNP|_ Olav174.IND.nHUS|Olav174.IND.nHUS|NNP|_
39|39|CD|_ .|.|.|_ St.|St.|NNP|_ Olav178.nIND.nHUS|Olav178.nIND.nHUS|NNP|_
3|3|CD|_ .|.|.|_ FHI6.nIND.HUS|fhi6.nind.hus|NN|_
40|40|CD|_ .|.|.|_ St.|St.|NNP|_ Olav178.IND.nHUS|Olav178.IND.nHUS|NNP|_
41|41|CD|_ .|.|.|_ St.|St.|NNP|_ Olav179.nIND.nHUS|Olav179.nIND.nHUS|NNP|_
42|42|CD|_ .|.|.|_ St.|St.|NNP|_ Olav179.IND.nHUS|Olav179.IND.nHUS|NNP|_
43|43|CD|_ .|.|.|_ FHI63.nIND.HUS|fhi63.nind.hus|NN|_
44|44|CD|_ .|.|.|_ FHI63.IND.HUS|fhi63.ind.hus|NN|_
45|45|CD|_ .|.|.|_ FHI66.nIND.nHUS|fhi66.nind.nhus|NN|_
46|46|CD|_ .|.|.|_ FHI66.IND.nHUS|fhi66.ind.nhus|NN|_
47|47|CD|_ .|.|.|_ FHI83.nIND.HUS|fhi83.nind.hus|NN|_
48|48|CD|_ .|.|.|_ FHI83.IND.HUS|fhi83.ind.hus|NN|_
49|49|CD|_ .|.|.|_ St.|St.|NNP|_ Olav17.nIND.nHUS|Olav17.nIND.nHUS|NNP|_
4|4|CD|_ .|.|.|_ FHI6.IND.HUS|fhi6.ind.hus|NN|_
50|50|CD|_ .|.|.|_ St.|St.|NNP|_ Olav17.IND.nHUS|Olav17.IND.nHUS|NNP|_
51|51|CD|_ .|.|.|_ St.|St.|NNP|_ Olav39.IND.nHUS|Olav39.IND.nHUS|NNP|_
52|52|CD|_ .|.|.|_ St.|St.|NNP|_ Olav63.nIND.nHUS|Olav63.nIND.nHUS|NNP|_
53|53|CD|_ .|.|.|_ St.|St.|NNP|_ Olav63.IND.nHUS|Olav63.IND.nHUS|NNP|_
54|54|CD|_ .|.|.|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_ .|.|.|_ nIND.HUS|nind.hus|NN|_
55|55|CD|_ .|.|.|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_ .|.|.|_ IND.HUS|ind.hus|NN|_
56|56|CD|_ .|.|.|_ St.|St.|NNP|_ Olav176.IND.HUS|Olav176.IND.HUS|NNP|_
57|57|CD|_ .|.|.|_ St.|St.|NNP|_ Olav39.nIND.nHUS|Olav39.nIND.nHUS|NNP|_
59|59|CD|_ .|.|.|_ St.|St.|NNP|_ Olav173.IND.nHUS|Olav173.IND.nHUS|NNP|_
5|5|CD|_ .|.|.|_ FHI7.nIND.HUS|fhi7.nind.hus|NN|_
60|60|CD|_ .|.|.|_ St.|St.|NNP|_ Olav176.nIND.HUS|Olav176.nIND.HUS|NNP|_
6|6|CD|_ .|.|.|_ FHI7.IND.HUS|fhi7.ind.hus|NN|_
7|7|CD|_ .|.|.|_ FHI8.nIND.HUS|fhi8.nind.hus|NN|_
8|8|CD|_ .|.|.|_ FHI8.IND.HUS|fhi8.ind.hus|NN|_
9|9|CD|_ .|.|.|_ FHI9.nIND.HUS|fhi9.nind.hus|NN|_
A|a|NN|_ generalized|generalize|VBN|_ linear|linear|JJ|_ model|model|NN|_ likelihood|likelihood|NN|_ ratio|ratio|NN|_ test|test|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ test|test|VB|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NNS|_ vs.|vs.|CC|_ non-HUS|non-hus|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ condition|condition|NN|_ -LRB-|-lrb-|-LRB-|_ induced|induce|VBN|_ vs.|vs.|CC|_ non-induced|non-induced|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ FDR-adjusted|fdr-adjusted|JJ|_ p-values|p-values|NN|_ <|<|JJR|_ 0.05|0.05|CD|_ regarded|regard|VBN|_ as|as|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ SILAC|silac|NN|_ -LRB-|-lrb-|-LRB-|_ stable|stable|JJ|_ isotope|isotope|NN|_ labeling|labeling|NN|_ with|with|IN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ optimized|optimize|VBN|_ for|for|IN|_ non-auxotrophic|non-auxotrophic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ Ping|ping|VB|_ LY|LY|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|J|NNP|_ Proteome|Proteome|NNP|_ Res.|Res.|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ before|before|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ agitation|agitation|NN|_ until|until|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.3|0.3|CD|_ .|.|.|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.1|3.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.8.5|3.8.5|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ FHI12|fhi12|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI24|fhi24|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI25|fhi25|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI27|fhi27|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI36|fhi36|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI4|fhi4|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI43|fhi43|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI48|fhi48|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI6|fhi6|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI63|fhi63|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI66|fhi66|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI7|fhi7|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI79|fhi79|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI8|fhi8|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI83|fhi83|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI9|fhi9|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ FHI95|fhi95|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav172|Olav172|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav173|Olav173|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav40|Olav40|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000752975|000752975|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000753215|000753215|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000753275|000753275|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936225|000936225|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936245|000936245|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000936475|000936475|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000937275|000937275|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000938695|000938695|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000938995|000938995|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939195|000939195|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939755|000939755|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000939955|000939955|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000941395|000941395|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000941895|000941895|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000946755|000946755|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000947315|000947315|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951835|000951835|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951875|000951875|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000951915|000951915|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965545|000965545|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965555|000965555|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965575|000965575|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965625|000965625|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965635|000965635|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965655|000965655|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965665|000965665|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965705|000965705|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000965715|000965715|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ GCA|gca|NN|_ _|_|SYM|_ 000966935|000966935|CD|_
genome|genome|NN|_ accession|accession|NN|_ :|:|:|_ PVRW00000000|pvrw00000000|NN|_
group|group|NN|_ -LRB-|-lrb-|-LRB-|_ hus|hus|NN|_
induced|induce|VBD|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ HT|ht|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ with|with|IN|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ read|read|NN|_ configuration|configuration|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Lowly|Lowly|NNP|_ expressed|express|VBD|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 1|1|CD|_ read|read|NN|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_
Normalization|normalization|NN|_ factors|factor|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ non-linear|non-linear|JJ|_ Loess|loess|JJ|_ model|model|NN|_ using|use|VBG|_ csaw|csaw|NN|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_
Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ each|each|DT|_ protein-encoding|protein-encoding|JJ|_ gene|gene|NN|_ family|family|NN|_ with|with|IN|_ strand-specific|strand-specific|JJ|_ mapping|mapping|NN|_ quality|quality|NN|_ above|above|IN|_ 23|23|CD|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq-count|htseq-count|JJ|_
Reads|read|NNS|_ were|be|VBD|_ end-to-end|end-to-end|JJ|_ aligned|align|VBN|_ ,|,|,|_ with|with|IN|_ no|no|DT|_ mismatches|mismatch|NNS|_ allowed|allow|VBN|_ ,|,|,|_ to|to|TO|_ the|the|DT|_ respective|respective|JJ|_ draft|draft|NN|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ FHI12|fhi12|NN|_
strain|strain|NN|_ :|:|:|_ FHI24|fhi24|NN|_
strain|strain|NN|_ :|:|:|_ FHI25|fhi25|CD|_
strain|strain|NN|_ :|:|:|_ FHI27|fhi27|NN|_
strain|strain|NN|_ :|:|:|_ FHI36|fhi36|NN|_
strain|strain|NN|_ :|:|:|_ FHI4|fhi4|NN|_
strain|strain|NN|_ :|:|:|_ FHI43|fhi43|NN|_
strain|strain|NN|_ :|:|:|_ FHI48|fhi48|NN|_
strain|strain|NN|_ :|:|:|_ FHI6|fhi6|NN|_
strain|strain|NN|_ :|:|:|_ FHI63|fhi63|NN|_
strain|strain|NN|_ :|:|:|_ FHI66|fhi66|NN|_
strain|strain|NN|_ :|:|:|_ FHI7|fhi7|NN|_
strain|strain|NN|_ :|:|:|_ FHI79|fhi79|NN|_
strain|strain|NN|_ :|:|:|_ FHI8|fhi8|NN|_
strain|strain|NN|_ :|:|:|_ FHI83|fhi83|NN|_
strain|strain|NN|_ :|:|:|_ FHI9|fhi9|NN|_
strain|strain|NN|_ :|:|:|_ FHI95|fhi95|NN|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav104|Olav104|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav157|Olav157|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav164|Olav164|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav17|Olav17|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav172|Olav172|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav173|Olav173|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav174|Olav174|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav176|Olav176|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav178|Olav178|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav179|Olav179|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav39|Olav39|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav40|Olav40|NNP|_
strain|strain|NN|_ :|:|:|_ St.|St.|NNP|_ Olav63|Olav63|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ CDS|cd|NNS|_ genomic|genomic|JJ|_ features|feature|NNS|_ ,|,|,|_ locations|location|NNS|_ of|of|IN|_ genomic|genomic|JJ|_ features|feature|NNS|_ are|be|VBP|_ provided|provide|VBN|_ in|in|IN|_ associated|associate|VBN|_ .|.|.|_ gtf|gtf|NN|_ files|file|NNS|_
Tagwise|Tagwise|NNP|_ dispersion|dispersion|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ using|use|VBG|_ the|the|DT|_ weighted|weighted|JJ|_ likelihood|likelihood|NN|_ empirical|empirical|JJ|_ Bayes|baye|NNS|_ method|method|NN|_
The|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase culture|culture|NN|_ was|be|VBD|_ split|split|VBN|_ in|in|IN|_ two|two|CD|_ ,|,|,|_ and|and|CC|_ one|one|CD|_ part|part|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.25|0.25|CD|_ μg|μg|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ Aurum|Aurum|NNP|_ total|total|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bio-Rad|Bio-Rad|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ controlled|control|VBN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ kit|kit|NN|_ and|and|CC|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Alignment|alignment|NN|_ ,|,|,|_ Quantiatino|quantiatino|NN|_ and|and|CC|_ Normalization|normalization|NN|_ ,|,|,|_ Differential|differential|JJ|_ Expression|expression|NN|_ :|:|:|_ We|we|PRP|_ used|use|VBD|_ the|the|DT|_ SPARTA|SPARTA|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ package|package|NN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ ,|,|,|_ and|and|CC|_ post-analysis|post-analysis|JJ|_ diagnostics|diagnostic|NNS|_ .|.|.|_ SPARTA|SPARTA|NNP|_ is|be|VBZ|_ an|a|DT|_ RNA-Seq|rna-seq|NN|_ package|package|NN|_ specifically|specifically|RB|_ designed|design|VBN|_ for|for|IN|_ bacterial|bacterial|JJ|_ studies|study|NNS|_ .|.|.|_ It|it|PRP|_ uses|use|VBZ|_ the|the|DT|_ Bowtie|Bowtie|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1.1.1|1.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ short|short|JJ|_ read|read|NN|_ aligner|aligner|NN|_ ,|,|,|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ count|count|VB|_ gene|gene|NN|_ features|feature|NNS|_ ,|,|,|_ and|and|CC|_ edgeR|edger|NN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ .|.|.|_
Annotation|Annotation|NNP|_ :|:|:|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ cft073.ASM744v1.dna.chromosome.Chromosome.fa|cft073.asm744v1.dna.chromosome.chromosome.fa|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ annotations|annotation|NNS|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ cft073.ASM744v1|cft073.asm744v1|NN|_ .32|.32|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ EnsemblBacteria|EnsemblBacteria|NNP|_
Bacteria|bacterium|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ lysed|lyse|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ µM|µm|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ in|in|IN|_ TE|TE|NNP|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-Cl|tris-cl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ eliminated|eliminate|VBN|_ by|by|IN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Depletion|depletion|NN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ accomplished|accomplish|VBN|_ with|with|IN|_ the|the|DT|_ Ribominus|Ribominus|NNP|_ Transcriptome|Transcriptome|NNP|_ Isolation|isolation|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_
CFT073|cft073|NN|_ +|+|CC|_ pBAD|pbad|NN|_ rep|rep|NN|GEN 1|1|CD|_
CFT073|cft073|NN|_ +|+|CC|_ pBAD|pbad|NN|_ rep|rep|NN|GEN 2|2|CD|_
CFT073|cft073|NN|_ +|+|CC|_ pBAD|pbad|NN|_ rep|rep|NN|GEN 3|3|CD|_
CFT073|cft073|NN|_ +|+|CC|_ pBAD-tosR|pbad-tosr|NN|_ rep|rep|NN|GEN 1|1|CD|_
CFT073|cft073|NN|_ +|+|CC|_ pBAD-tosR|pbad-tosr|NN|_ rep|rep|NN|GEN 2|2|CD|_
CFT073|cft073|NN|_ +|+|CC|_ pBAD-tosR|pbad-tosr|NN|_ rep|rep|NN|GEN 3|3|CD|_
Depletion|depletion|NN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ accomplished|accomplish|VBN|_ with|with|IN|_ the|the|DT|_ Ribominus|Ribominus|NNP|_ Transcriptome|Transcriptome|NNP|_ Isolation|isolation|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ A|a|DT|_ stranded|stranded|JJ|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ a|a|DT|_ ScriptSeq|ScriptSeq|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommended|recommend|VBN|_ protocols|protocol|NNS|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ tagged|tag|VBN|_ with|with|IN|_ a|a|DT|_ six|six|CD|_ nucleotide|nucleotide|NN|_ barcode|barcode|NN|_ unique|unique|JJ|_ to|to|TO|_ each|each|DT|_ sample|sample|NN|_ to|to|TO|_ allow|allow|VB|_ multiplexing|multiplexing|NN|_ .|.|.|_ The|the|DT|_ products|product|NNS|_ are|be|VBP|_ purified|purify|VBN|_ and|and|CC|_ enriched|enrich|VBN|_ by|by|IN|_ PCR|pcr|NN|_ to|to|TO|_ create|create|VB|_ the|the|DT|_ final|final|JJ|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Final|final|JJ|_ libraries|library|NNS|_ were|be|VBD|_ checked|check|VBN|_ for|for|IN|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ by|by|IN|_ TapeStation|TapeStation|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ qPCR|qpcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ 's|'s|POS|_ library|library|NN|_ quantification|quantification|NN|_ kit|kit|NN|_ for|for|IN|_ Illumina|Illumina|NNP|_ Sequencing|sequencing|NN|_ platforms|platform|NNS|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommended|recommend|VBN|_ protocols|protocol|NNS|_ .|.|.|_ Six|six|CD|_ samples|sample|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ per|per|IN|_ lane|lane|NN|_ on|on|IN|_ a|a|DT|_ 50|50|CD|_ cycle|cycle|NN|_ single|single|JJ|_ end|end|NN|_ run|run|NN|_ on|on|IN|_ a|a|DT|_ HiSeq|hiseq|JJ|_ 2500|2500|CD|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ high|high|JJ|_ output|output|NN|_ mode|mode|NN|_ using|use|VBG|_ version|version|NN|_ 4|4|CD|_ reagents|reagent|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ CFT073|cft073|NN|_ carrying|carry|VBG|_ either|either|CC|_ pBAD|pbad|NN|_ or|or|CC|_ pBAD-tosR-his6|pbad-tosr-his6|NN|_ were|be|VBD|_ cultured|culture|VBN|_ overnight|overnight|JJ|_ in|in|IN|_ biological|biological|JJ|_ triplicates|triplicate|NNS|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ µg|µg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CFT073|CFT073|NNP|_ E.|E.|NNP|_ coli|coli|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD|pbad|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD-tosR|pbad-tosr|NN|_
qC|qc|NN|_ :|:|:|_ We|we|PRP|_ checked|check|VBD|_ the|the|DT|_ quality|quality|NN|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ reads|read|VBZ|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.11.3|0.11.3|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ identify|identify|VB|_ features|feature|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ that|that|WDT|_ may|may|MD|_ indicate|indicate|VB|_ quality|quality|NN|_ problems|problem|NNS|_ -LRB-|-lrb-|-LRB-|_ e.g.|e.g.|FW|_ low|low|JJ|_ quality|quality|NN|_ scores|score|NNS|_ ,|,|,|_ over-represented|over-represented|JJ|_ sequences|sequence|NNS|_ ,|,|,|_ inappropriate|inappropriate|JJ|_ GC|gc|NN|_ content|content|NN|_ ,|,|,|_ etc.|etc.|FW|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CFT073|cft073|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ xls|xl|NNS|_ ,|,|,|_ spreadsheet|spreadsheet|NN|_ of|of|IN|_ normalized|normalize|VBN|_ read|read|NN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ differential|differential|JJ|_ expression|expression|NN|_ data|datum|NNS|_ ,|,|,|_ and|and|CC|_ annotation|annotation|NN|_
After|after|IN|_ chilling|chill|VBG|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ each|each|DT|_ 100-ml|100-ml|JJ|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 25|25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ ethanol|ethanol|NN|_
Bacterial|bacterial|JJ|_ cultures|culture|NNS|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
dnaB-Ts|dnab-t|NNS|_ _|_|VBP|_ 30|30|CD|_ °C|°c|NN|_
dnaB-Ts|dnab-t|NNS|_ _|_|VBP|_ 42|42|CD|_ °C|°c|NN|_
dnaB-Ts|dnab-t|NNS|_ Î|î|NN|_ ''|''|''|_ ahpC|ahpc|NN|GEN _|_|CD|_ 30|30|CD|_ °C|°c|NN|_
dnaB-Ts|dnab-t|NNS|_ Î|î|NN|_ ''|''|''|_ ahpC|ahpc|NN|GEN _|_|CD|_ 42|42|CD|_ °C|°c|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.coli|e.coli|NN|_ K12|k12|NN|_ BW25113|bw25113|NN|_
Illumina|Illumina|NNP|_ Casava1|Casava1|NNP|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
medium|medium|NN|_ :|:|:|_ SB|sb|NN|_ broth|broth|NN|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ of|of|IN|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ single|single|JJ|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 2429|2429|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ dnaB-Ts|dnab-ts|JJ|_ ΔahpC|δahpc|NN|_ double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 3780|3780|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ diluted|dilute|VBN|_ 100-fold|100-fold|RB|_ into|into|IN|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2|3.2|CD|_ %|%|NN|_ peptone|peptone|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 1|1|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ then|then|RB|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ early-log|early-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|JJ|_ these|these|DT|_ log-phase|log-phase|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 20-fold|20-fold|RB|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ pre-warmed|pre-warmed|JJ|_ ,|,|,|_ fresh|fresh|JJ|_ SB|sb|NN|_ medium|medium|NN|_ ,|,|,|_ and|and|CC|_ they|they|PRP|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ and|and|CC|_ cDNA|cdna|NN|_ amplification|amplification|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ SMART-Seq|smart-seq|NN|_ v4|v4|NN|_ Ultra|Ultra|NNP|_ Low|Low|NNP|_ Input|Input|NNP|_ RNA|rna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Clontech|clontech|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ kit|kit|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ for|for|IN|_ concentration|concentration|NN|_ ,|,|,|_ size|size|NN|_ distribution|distribution|NN|_ and|and|CC|_ quantification|quantification|NN|_ of|of|IN|_ viable|viable|JJ|_ sequencing|sequencing|NN|_ templates|template|NNS|_ via|via|IN|_ qPCR|qpcr|NN|_ .|.|.|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-ml|200-ml|JJ|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ cultures|culture|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ 100|100|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ aliquots|aliquot|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ or|or|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ another|another|DT|_ 60|60|CD|_ min|min|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.coli|e.coli|VB|_ K2|k2|NN|_ BW25113|bw25113|NN|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.2|.12.2|CD|_
strain|strain|NN|_ :|:|:|_ 2429|2429|CD|_
strain|strain|NN|_ :|:|:|_ 3780|3780|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
To|to|TO|_ generate|generate|VB|_ Illumina-compatible|illumina-compatible|JJ|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ molecular|molecular|JJ|_ indexes|index|NNS|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ library|library|NN|_ ,|,|,|_ allowing|allow|VBG|_ samples|sample|NNS|_ to|to|TO|_ be|be|VB|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ with|with|IN|_ a|a|DT|_ 1|1|CD|_ x|x|CC|_ 50|50|CD|_ bp|bp|NN|_ single-end|single-end|JJ|_ configuration|configuration|NN|_ .|.|.|_ More|more|JJR|_ than|than|IN|_ 250|250|CD|_ million|million|CD|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ per|per|IN|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ at|at|IN|_ least|least|JJS|_ 80|80|CD|_ %|%|NN|_ bases|basis|NNS|_ had|have|VBD|_ quality|quality|NN|_ scores|score|NNS|_ above|above|IN|_ Q30|q30|NN|_ .|.|.|_
1|1|CD|_ ml|ml|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ pressure|pressure|VB|_ vessel|vessel|NN|_ and|and|CC|_ pressurized|pressurize|VBD|_ at|at|IN|_ 1MPa|1mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG|mg|NN|_ 1655|1655|CD|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB-Miller|lb-miller|NN|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,160|,160|CD|_ rpm|rpm|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Gene|gene|NN|_ annotation|annotation|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ EcoCyc|EcoCyc|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Database|database|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_
MiSeq|miseq|NN|_ for|for|IN|_ base|base|NN|_ calling|call|VBG|_
RNA-Seq|rna-seq|NN|_
stimulus|stimulus|NN|_ :|:|:|_ 1|1|CD|_ MPa|mpa|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
stimulus|stimulus|NN|_ :|:|:|_ Control|Control|NNP|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Table|Table|NNP|_ of|of|IN|_ read|read|VBN|_ counts|count|NNS|_ with|with|IN|_ genes|gene|NNS|_ as|as|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ as|as|IN|_ columns|column|NNS|_ .|.|.|_
The|the|DT|_ counts|count|NNS|_ of|of|IN|_ reads|read|VBZ|_ 150|150|CD|_ aligning|align|VBG|_ to|to|TO|_ genomic|genomic|JJ|_ features|feature|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ `|`|``|_ feaureCounts|feaurecount|NNS|_ '|'|POS|_ function|function|NN|_ from|from|IN|_ the|the|DT|_ R|r|NN|_ package|package|NN|_ `|`|``|_ Rsubread|Rsubread|NNP|_ '|'|''|_
The|The|NNP|_ lysates|lysate|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ gDNA|gdna|NN|_ removal|removal|NN|_ columns|column|NNS|_ and|and|CC|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ for|for|IN|_ Gram-positive|gram-positive|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ The|the|DT|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ the|the|DT|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ RNA|rna|NN|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ independently|independently|RB|_ indexed|index|VBN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ multi-plex|multi-plex|JJ|_ oligos|oligo|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ NEB|NEB|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ at|at|IN|_ equimolar|equimolar|JJ|_ ratios|ratio|NNS|_ before|before|IN|_ they|they|PRP|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reagent|Reagent|NNP|_ Kit|kit|NN|_ v3|v3|NN|_ 600|600|CD|_ cycles|cycle|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ data|datum|NNS|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ V11|v11|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ V0|v0|NN|_ .33|.33|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ `|`|``|_ DESeq2|deseq2|NN|_ '|'|''|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 1.12.4|1.12.4|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ LP|lp|NN|_ group|group|NN|_ and|and|CC|_ the|the|DT|_ HP|HP|NNP|_ group|group|NN|_ .|.|.|_
The|the|DT|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ against|against|IN|_ E.|E.|NNP|_ 149|149|CD|_ coli|coli|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 2.2.4|2.2.4|CD|_ -RRB-|-rrb-|-RRB-|_
tissue|tissue|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
Total|total|JJ|_ RNAs|rna|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ each|each|DT|_ with|with|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Total|total|JJ|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Norgen|Norgen|NNP|_ Biotek|Biotek|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ with|with|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mg|mg|NN|_
all|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED at|at|IN|_ 37C|37c|NN|_
bacterial|bacterial|JJ|_ pellet|pellet|NN|_
Control|Control|NNP|_ _|_|NNP|_ 1|1|CD|_
Control|Control|NNP|_ _|_|NNP|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
media|media|NNS|_ :|:|:|_ LB|lb|NN|MED broth|broth|NN|MED
NN2|nn2|NN|_ _|_|CD|_ 0018|0018|CD|_ _|_|NN|_ 1|1|CD|_
NN2|nn2|NN|_ _|_|CD|_ 0018|0018|CD|_ _|_|NN|_ 2|2|CD|_
Omega17|omega17|NN|_ _|_|NN|_ 1|1|CD|_
Omega17|omega17|NN|_ _|_|NN|_ 2|2|CD|_
Omega76|omega76|NN|_ _|_|NN|_ 1|1|CD|_
Omega76|omega76|NN|_ _|_|NN|_ 2|2|CD|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|rneasy|NN|_ minikit|minikit|NN|_ Cat|cat|NN|_ #|#|#|_ 74106|74106|CD|_
Samples|sample|NNS|_ were|be|VBD|_ background|background|NN|_ corrected|correct|VBN|_ using|use|VBG|_ the|the|DT|_ normexp|normexp|NN|_ -LRB-|-lrb-|-LRB-|_ -RRB-|-rrb-|-RRB-|_ function|function|NN|_ in|in|IN|_ the|the|DT|_ Limma|Limma|NNP|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ quantile|quantile|NN|_ normalization|normalization|NN|_ and|and|CC|_ log2|log2|NN|_ transformation|transformation|NN|_ .|.|.|_
1|1|CD|_ ml|ml|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ DY|dy|NN|_ 330|330|CD|_ GyrA-SPA|gyra-spa|NN|_ or|or|CC|_ E.|e.|FW|_ coli|coli|FW|_ DY|dy|NN|_ 330|330|CD|_ GyrA-SPA|gyra-spa|NN|_ MuSGS|musgs|NN|_ by|by|IN|_ seeding|seed|VBG|_ 2YT|2yt|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ antibiotics|antibiotic|NNS|_ -LRB-|-lrb-|-LRB-|_ kanamycin|kanamycin|NN|_ 50|50|CD|_ µg|µg|NN|_
Cfx|Cfx|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 3|3|CD|_
Cfx|Cfx|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 10mkM|10mkm|NN|_ _|_|NN|_ 1|1|CD|_
Cfx|Cfx|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 10mkM|10mkm|NN|_ _|_|NN|_ 2|2|CD|_
Cfx|Cfx|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|NNP|_ 10mkM|10mkM|NNP|_ _|_|SYM|_ 3|3|CD|_
Cfx|Cfx|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 10mkM|10mkm|NN|_ _|_|NN|_ 1|1|CD|_
Cfx|Cfx|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 10mkM|10mkm|NN|_ _|_|NN|_ 2|2|CD|_
ChIP-Seq|chip-seq|NN|_
Ciprofloxacin|ciprofloxacin|NN|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Ciprofloxacin|ciprofloxacin|NN|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Ciprofloxacin|ciprofloxacin|NN|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Ciprofloxacin|ciprofloxacin|NN|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A+IP|a+ip|NN|_
Cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ A|a|DT|_ and|and|CC|_ -|-|:|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 32|32|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ additional|additional|JJ|_ 15|15|CD|_ min|min|NN|_ ,|,|,|_ then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 10|10|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ 4500xg|4500xg|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ of|of|IN|_ TES|tes|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-Cl|tris-cl|NN|_ pH7|ph7|NN|_ .5|.5|CD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 250|250|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Washing|wash|VBG|_ procedure|procedure|NN|_ was|be|VBD|_ repeated|repeat|VBN|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ culture|culture|NN|_ liquid|liquid|NN|_ and|and|CC|_ excess|excess|NN|_ of|of|IN|_ gyrase|gyrase|NN|_ poison|poison|NN|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ resulting|result|VBG|_ supernatant|supernatant|JJ|_ with|with|IN|_ phenol|phenol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ proteolysis|proteolysis|NN|_ ,|,|,|_ affinity|affinity|NN|_ gel|gel|NN|_ obtained|obtain|VBN|_ after|after|IN|_ the|the|DT|_ last|last|JJ|_ centrifugation|centrifugation|NN|_ step|step|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ with|with|IN|_ TES|tes|NN|_ buffer|buffer|NN|_ up|up|IN|_ to|to|TO|_ final|final|JJ|_ volume|volume|NN|_ 200|200|CD|_ μl|μl|NN|_ ,|,|,|_ proteinase|proteinase|NN|_ K|k|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma-Aldrich|sigma-aldrich|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ mg|mg|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110|w3110|NN|_ MuSGS|musgs|NN|_ -LRB-|-lrb-|-LRB-|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ NC|NC|NNP|_ _|_|SYM|_ 007779.1|007779.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ FASTA|fasta|NN|_ and|and|CC|_ GFF|gff|NN|_ are|be|VBP|_ included|include|VBN|_ on|on|IN|_ series|series|NN|_ record|record|NN|_ .|.|.|_
Gyrase|gyrase|NN|_ Cleavage|cleavage|NN|_ Sites|site|NNS|_ -LRB-|-lrb-|-LRB-|_ GCSs|gcss|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ called|call|VBN|_ using|use|VBG|_ custom|custom|NN|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ GCSs_calling.py|gcss_calling.py|NN|_ ,|,|,|_ github|github|NN|_ :|:|:|_ https|http|NNS|_ :|:|:|_
Lysates|lysate|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TES|tes|NN|_ buffer|buffer|NN|_ and|and|CC|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ ANTI-FLAG|anti-flag|NN|_ ®|®|CD|_ M2|m2|NN|_ affinity|affinity|NN|_ gel|gel|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma-Aldrich|sigma-aldrich|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_ Immunoprecipitation|immunoprecipitation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 1.5-2|1.5-2|CD|_ hours|hour|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ with|with|IN|_ moderate|moderate|JJ|_ mixing|mix|VBG|_ ,|,|,|_ then|then|RB|_ affinity|affinity|NN|_ gel|gel|NN|_ was|be|VBD|_ washed|wash|VBN|_ 4|4|CD|_ times|time|NNS|_ by|by|IN|_ repeating|repeat|VBG|_ steps|step|NNS|_ of|of|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 1.5|1.5|CD|_ minute|minute|NN|_ ,|,|,|_ 1000xg|1000xg|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ resuspention|resuspention|NN|_ -LRB-|-lrb-|-LRB-|_ x2|x2|NN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TESS|TESS|NNP|_ buffer|buffer|NN|_ ,|,|,|_ x1|x1|NN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TES|tes|NN|_ buffer|buffer|NN|_ ,|,|,|_ x1|x1|NN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Microcin|microcin|NN|_ B17|b17|NN|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Microcin|microcin|NN|_ B17|b17|NN|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Microcin|Microcin|NNP|_ B17|B17|NNP|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Microcin|microcin|NN|_ B17|b17|NN|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Microcin|Microcin|NNP|_ B17|B17|NNP|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Microcin|microcin|NN|_ B17|b17|NN|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Microcin|Microcin|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|CD|_ 50mkM|50mkm|NN|_ _|_|NN|_ 3|3|CD|_
Microcin|microcin|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 1|1|CD|_
Microcin|microcin|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|NN|_ 10mkM|10mkm|NN|_ _|_|NN|_ 2|2|CD|_
Microcin|microcin|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|NNP|_ 50mkM|50mkM|NNP|_ _|_|SYM|_ 3|3|CD|_
MIcrocin|microcin|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 10mkM|10mkm|NN|_ _|_|NN|_ 1|1|CD|_
Microcin|microcin|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 10mkM|10mkm|NN|_ _|_|NN|_ 2|2|CD|_
musgs|musg|NNS|_ presence|presence|NN|_ :|:|:|_ -|-|:|_
musgs|musg|NNS|_ presence|presence|NN|_ :|:|:|_ MuSGS|musgs|NN|_
Oxo|Oxo|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|CD|_ 120mkM|120mkm|NN|_ _|_|NN|_ 3|3|CD|_
Oxo|Oxo|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 120mkM|120mkm|NN|_ _|_|NN|_ 1|1|CD|_
Oxo|Oxo|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 120mkM|120mkm|NN|_ _|_|NN|_ 2|2|CD|_
Oxo|Oxo|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|SYM|_ 120mkM|120mkm|NN|_ _|_|NN|_ 3|3|CD|_
Oxo|Oxo|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 120mkM|120mkm|NN|_ _|_|NN|_ 1|1|CD|_
Oxo|Oxo|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 120mkM|120mkm|NN|_ _|_|NN|_ 2|2|CD|_
Oxolinic|oxolinic|JJ|_ acid|acid|NN|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Oxolinic|oxolinic|JJ|_ acid|acid|NN|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Oxolinic|oxolinic|JJ|_ acid|acid|NN|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Oxolinic|oxolinic|JJ|_ acid|acid|NN|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Oxolinic|oxolinic|JJ|_ acid|acid|NN|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Oxolinic|oxolinic|JJ|_ acid|acid|NN|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ w3110|w3110|NN|_ MuSGS|musgs|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ containing|contain|VBG|_ a|a|DT|_ strong|strong|JJ|_ gyrase|gyrase|NN|_ binding|binding|NN|_ site|site|NN|_ from|from|IN|_ bacteriophage|bacteriophage|NN|_ Mu|mu|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ BWA|bwa|NN|_ MEM|mem|NN|_ -LRB-|-lrb-|-LRB-|_ default|default|NN|_ settings|setting|NNS|_ -RRB-|-rrb-|-RRB-|_
Resulting|result|VBG|_ SAM|SAM|NNP|_ files|file|NNS|_ were|be|VBD|_ processed|process|VBN|_ with|with|IN|_ custom|custom|NN|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ SAM_to_coverage_and_N5E_N3E.py|sam_to_coverage_and_n5e_n3e.py|NN|_ ,|,|,|_ github|github|NN|_ :|:|:|_ https|http|NNS|_ :|:|:|_
Rifampicine|Rifampicine|NNP|_ Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 1|1|LS|_ -|-|:|_ A-IP|a-ip|NN|_
Rifampicine|Rifampicine|NNP|_ Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Rifampicine|Rifampicine|NNP|_ Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 1|1|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Rifampicine|Rifampicine|NNP|_ Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Rifampicine|Rifampicine|NNP|_ Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 2|2|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
Rifampicine|Rifampicine|NNP|_ Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A-IP|a-ip|JJ|_
Rifampicine|Rifampicine|NNP|_ Ciprofloxacin|Ciprofloxacin|NNP|_ Rep|Rep|NNP|_ 3|3|CD|_ +|+|CC|_ A+IP|A+IP|NNP|_
RifCfx|RifCfx|NNP|_ _|_|NNP|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|NN|_ 122mkM|122mkm|NN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 1|1|CD|_
RifCfx|rifcfx|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|NN|_ 122mkM|122mkm|NN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 2|2|CD|_
RifCfx|rifcfx|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|NN|_ 122mkM|122mkm|NN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 3|3|CD|_
RifCfx|rifcfx|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 122mkM|122mkm|NN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 1|1|CD|_
RifCfx|rifcfx|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 122mkM|122mkm|NN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 2|2|CD|_
RifCfx|rifcfx|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 122mkM|122mkm|NN|_ _|_|CD|_ 10mkM|10mkm|NN|_ _|_|NN|_ 3|3|CD|_
Rif|rif|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|CD|_ 122mkM|122mkm|NN|_ _|_|NN|_ 1|1|CD|_
Sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ Accel|Accel|NNP|_ NGS|NGS|NNP|_ 1S|1s|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Swift|Swift|NNP|_ Bioscience|Bioscience|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordanse|accordanse|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
Starter|Starter|NNP|_ was|be|VBD|_ cultivated|cultivate|VBN|_ at|at|IN|_ 32|32|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ 2YT|2yt|NN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ and|and|CC|_ cultivation|cultivation|NN|_ was|be|VBD|_ proceeded|proceed|VBN|_ under|under|IN|_ the|the|DT|_ same|same|JJ|_ conditions|condition|NNS|_ until|until|IN|_ culture|culture|NN|_ reaching|reach|VBG|_ mid-logphase|mid-logphase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.6-0.8|0.6-0.8|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ DY330|dy330|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tar|tar|NN|GEN archives|archive|NNS|_ contain|contain|VBP|_ the|the|DT|_ following|following|NN|_ :|:|:|_
tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ with|with|IN|_ GCSs|gcss|NNS|_ coordinates|coordinate|VBZ|_ ,|,|,|_ N3E|n3e|NN|_ values|value|NNS|_ -LRB-|-lrb-|-LRB-|_ \|\|CD|_ height|height|NN|_ of|of|IN|_ the|the|DT|_ peak|peak|NN|_ \|\|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ GCSs|gcss|NNS|_ scores|score|NNS|_ -LRB-|-lrb-|-LRB-|_ score|score|NN|_ of|of|IN|_ the|the|DT|_ sequence|sequence|NN|_ under|under|IN|_ the|the|DT|_ GCS|gc|NNS|_ obtained|obtain|VBN|_ after|after|IN|_ scanning|scan|VBG|_ the|the|DT|_ genome|genome|NN|_ with|with|IN|_ DNA-gyrase|dna-gyrase|NN|_ binding|binding|NN|_ motif|motif|NN|_ -RRB-|-rrb-|-RRB-|_
tagged|tag|VBD|_ gyrase|gyrase|NN|_ subunit|subunit|NN|_ :|:|:|_ GyrA-SPA|gyra-spa|JJ|_
text|text|NN|_ wig|wig|NN|_ files|file|NNS|_ contain|contain|VBP|_ coverage|coverage|NN|_ depth|depth|NN|_ data|datum|NNS|_
text|text|NN|_ wig|wig|NN|_ files|file|NNS|_ contain|contain|VBP|_ N3E|n3e|NN|_ values|value|NNS|_ -LRB-|-lrb-|-LRB-|_ number|number|NN|_ of|of|IN|_ DNA|dna|NN|_ fragments|fragment|NNS|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ for|for|IN|_ each|each|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ -RRB-|-rrb-|-RRB-|_
Un|un|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ 3|3|CD|_
Un|un|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|NN|_ 1|1|CD|_
Un|un|NN|_ _|_|CD|_ IN|in|IN|_ _|_|CD|_ Mu|mu|NN|_ _|_|NN|_ 2|2|CD|_
Un|un|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ 3|3|CD|_
Un|un|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 1|1|CD|_
Un|un|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ Mu|mu|FW|_ _|_|FW|_ 2|2|CD|_
Untreated|untreated|JJ|_ Rep|Rep|NNP|_ 1|1|LS|_ -|-|:|_ A-IP|a-ip|NN|_
Untreated|untreated|JJ|_ Rep|Rep|NNP|_ 1|1|LS|_ -|-|:|_ A+IP|a+ip|NN|_
Untreated|untreated|JJ|_ Rep|Rep|NNP|_ 2|2|LS|_ -|-|:|_ A-IP|a-ip|NN|_
Untreated|untreated|JJ|_ Rep|Rep|NNP|_ 2|2|LS|_ -|-|:|_ A+IP|a+ip|NN|_
Untreated|untreated|JJ|_ Rep|Rep|NNP|_ 3|3|LS|_ -|-|:|_ A-IP|a-ip|NN|_
Untreated|untreated|JJ|_ Rep|Rep|NNP|_ 3|3|LS|_ -|-|:|_ A+IP|a+ip|NN|_
Washed|wash|VBD|_ pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TESS|TESS|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-Cl|tris-cl|NN|_ pH7|ph7|NN|_ .5|.5|CD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 250|250|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 0.02|0.02|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tween-20|tween-20|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ addition|addition|NN|_ of|of|IN|_ proteases|protease|NNS|_ inhibitors|inhibitor|NNS|_ cocktail|cocktail|NN|_ -LRB-|-lrb-|-LRB-|_ cOmplete|complete|JJ|_ ultra|ultra|NNS|_ EDTA|edta|NN|_ free|free|JJ|_ ,|,|,|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNAse|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Resulting|result|VBG|_ suspensions|suspension|NNS|_ were|be|VBD|_ sonicated|sonicate|VBN|_ with|with|IN|_ parameters|parameter|NNS|_ optimized|optimize|VBN|_ to|to|TO|_ obtain|obtain|VB|_ DNA|dna|NN|_ fragments|fragment|NNS|_ between|between|IN|_ 200|200|CD|_ and|and|CC|_ 700|700|CD|_ bp|bp|NN|_ -LRB-|-lrb-|-LRB-|_ SONOPULS|sonopuls|NN|_ HD|hd|NN|_ 3100|3100|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Lysates|lysate|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TES|tes|NN|_ buffer|buffer|NN|_ and|and|CC|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ ANTI-FLAG|anti-flag|NN|_ ®|®|CD|_ M2|m2|NN|_ affinity|affinity|NN|_ gel|gel|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma-Aldrich|sigma-aldrich|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_ Immunoprecipitation|immunoprecipitation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 1.5-2|1.5-2|CD|_ hours|hour|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ with|with|IN|_ moderate|moderate|JJ|_ mixing|mix|VBG|_ ,|,|,|_ then|then|RB|_ affinity|affinity|NN|_ gel|gel|NN|_ was|be|VBD|_ washed|wash|VBN|_ 4|4|CD|_ times|time|NNS|_ by|by|IN|_ repeating|repeat|VBG|_ steps|step|NNS|_ of|of|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 1.5|1.5|CD|_ minute|minute|NN|_ ,|,|,|_ 1000xg|1000xg|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ resuspention|resuspention|NN|_ -LRB-|-lrb-|-LRB-|_ x2|x2|NN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TESS|TESS|NNP|_ buffer|buffer|NN|_ ,|,|,|_ x1|x1|NN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TES|tes|NN|_ buffer|buffer|NN|_ ,|,|,|_ x1|x1|NN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
When|when|WRB|_ reaching|reach|VBG|_ the|the|DT|_ optical|optical|JJ|_ density|density|NN|_ indicated|indicate|VBD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.6-0.8|0.6-0.8|CD|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ bisected|bisect|VBN|_ and|and|CC|_ DNA|dna|NN|_ gyrase|gyrase|NN|_ poison|poison|NN|_ -LRB-|-lrb-|-LRB-|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ oxolinic|oxolinic|JJ|_ acid|acid|NN|_ or|or|CC|_ microcin|microcin|NN|_ B17|b17|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ half|half|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ A|a|DT|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ while|while|IN|_ second|second|JJ|_ served|serve|VBD|_ as|as|IN|_ a|a|DT|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ -|-|:|_ A|a|NN|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
After|after|IN|_ exposed|expose|VBN|_ under|under|IN|_ the|the|DT|_ red|red|JJ|_ light|light|NN|_ with|with|IN|_ a|a|DT|_ specific|specific|JJ|_ ON|ON|NNP|_
BW25113|bw25113|NN|_
envz3600|envz3600|NN|_
envz600|envz600|NN|_
envz900|envz900|NN|_
envzM1200|envzm1200|NN|_
envzM2400|envzm2400|NN|_
envzM3600|envzm3600|NN|_
envzM600|envzm600|NN|_
envzM900|envzm900|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
input|input|NN|_ signal|signal|NN|_ frequency|frequency|NN|_ :|:|:|_ 1|1|CD|_
In|in|IN|_ the|the|DT|_ 15|15|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tube|tube|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ ,|,|,|_ 430791|430791|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng|ng|NN|_
PCA|pca|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ top|top|JJ|_ 500|500|CD|_ genes|gene|NNS|_ with|with|IN|_ the|the|DT|_ most|most|RBS|_ variations|variation|NNS|_ .|.|.|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZM|plcenvzm|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_
Plasmid|plasmid|NN|_ pLCenvZ|plcenvz|NN|_ or|or|CC|_ pLCenvZM|plcenvzm|NN|_ was|be|VBD|_ co-transformed|co-transform|VBN|_ with|with|IN|_ pPCB|ppcb|NN|_ into|into|IN|_ the|the|DT|_ competent|competent|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ JW3367|jw3367|NN|_ and|and|CC|_ spread|spread|NN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ng|ng|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLCenvZ|plcenvz|NN|_ ,|,|,|_ pPCB|ppcb|NN|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ -RRB-|-rrb-|-RRB-|_
Read|read|VB|_ counts|count|NNS|_ per|per|IN|_ gene|gene|NN|_ determined|determine|VBN|_ using|use|VBG|_ HTseq|htseq|NN|_ count|count|NN|_ before|before|IN|_ normalized|normalize|VBN|_ using|use|VBG|_ DESeq2|deseq2|NN|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|RNA-Seq|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ with|with|IN|_ bowtie2|bowtie2|NN|_
strain|strain|NN|_ :|:|:|_ JW3367|jw3367|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ txt|txt|NN|_ file|file|NN|_ includes|include|VBZ|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ profiles|profile|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ The|the|DT|_ xlsx|xlsx|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ PC1|pc1|NN|_ and|and|CC|_ PC2|pc2|NN|_ values|value|NNS|_ of|of|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
BW25113|bw25113|NN|_ sdiA-empty|sdia-empty|JJ|_ vector|vector|NN|_ 12h|12h|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ at|at|IN|_ 30oC|30oC|NNP|_
BW25113|bw25113|NN|_ sdiA-SdiA1E11|sdia-sdia1e11|NN|_ 12h|12h|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ at|at|IN|_ 30oC|30oC|NNP|_
BW25113|bw25113|NN|_ sdiA-WTSdiA|sdia-wtsdia|NN|_ 12h|12h|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ at|at|IN|_ 30oC|30oC|NNP|_
Channel|Channel|NNP|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
mutant|mutant|JJ|_ SdiA1E11|sdia1e11|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ K-12|k-12|NN|_ sdiA-no|sdia-no|JJ|_ SdiA|sdia|NN|TF 1|1|CD|_ after|after|IN|_ 12h|12h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ 1|1|CD|_ mMIPTG|mmiptg|NN|_ and|and|CC|_ 30|30|CD|_ microM|microm|NN|_ Cm|cm|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_ at|at|IN|_ 30oC|30oC|NNP|_
RNA|RNA|NNP|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ K-12|k-12|NN|_ sdiA-SdiA1E11|sdia-sdia1e11|NN|_ after|after|IN|_ 12h|12h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ 1|1|CD|_ mMIPTG|mmiptg|NN|_ and|and|CC|_ 30|30|CD|_ microM|microm|NN|_ Cm|cm|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_ at|at|IN|_ 30oC|30oC|NNP|_
RNA|RNA|NNP|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ K-12|k-12|NN|_ sdiA-WTSdiA|sdia-wtsdia|NN|_ after|after|IN|_ 12h|12h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ 1|1|CD|_ mMIPTG|mmiptg|NN|_ and|and|CC|_ 30|30|CD|_ microM|microm|NN|_ Cm|cm|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_ at|at|IN|_ 30oC|30oC|NNP|_
To|to|TO|_ lyse|lyse|VB|_ the|the|DT|_ cells|cell|NNS|_ ,|,|,|_ 1.0|1.0|CD|_ mL|ml|NN|_ RLT|rlt|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 0.2|0.2|CD|_ mL|ml|NN|_ 0.1|0.1|CD|_ mm|mm|NN|_ zirconia|zirconia|NN|_
wild|wild|JJ|_ type|type|NN|_ SdiA|sdia|NN|TF
After|after|IN|_ 50|50|CD|_ hours|hour|NNS|_ ,|,|,|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ harvested|harvest|VBN|_ directly|directly|RB|_ into|into|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ as|as|IN|_ recommended|recommend|VBN|_ by|by|IN|_ the|the|DT|_ suppliers|supplier|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ BioPhotometer|biophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Spots|spot|NNS|_ automatically|automatically|RB|_ flagged|flag|VBD|_ as|as|IN|_ bad|bad|JJ|_ ,|,|,|_ negative|negative|JJ|_ or|or|CC|_ poor|poor|JJ|_ in|in|IN|_ the|the|DT|_ Imagene|imagene|NN|_ software|software|NN|_ were|be|VBD|_ removed|remove|VBN|_ before|before|IN|_ the|the|DT|_ statistical|statistical|JJ|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ GeneSight|GeneSight|NNP|_ .|.|.|_ The|the|DT|_ mean|mean|NN|_ values|value|NNS|_ from|from|IN|_ each|each|DT|_ channel|channel|NN|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ normalised|normalise|VBN|_ using|use|VBG|_ the|the|DT|_ Lowess|lowess|NN|_ method|method|NN|_ to|to|TO|_ remove|remove|VB|_ intensity-dependent|intensity-dependent|JJ|_ effects|effect|NNS|_ in|in|IN|_ the|the|DT|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ ratios|ratio|NNS|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ .|.|.|_ The|the|DT|_ Cy3|cy3|NN|_
Steady-state|steady-state|JJ|_ continuously-cultured|continuously-cultured|JJ|_ control|control|NN|_ samples|sample|NNS|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ adequate|adequate|JJ|_ Zn|zn|NN|_
Steady-state|steady-state|JJ|_ continuously-cultured|continuously-cultured|JJ|_ experiment|experiment|NN|_ samples|sample|NNS|_ in|in|IN|_ the|the|DT|_ total|total|JJ|_ absence|absence|NN|_ of|of|IN|_ Zn|zn|NN|_
Steady-state|steady-state|JJ|_ continuously-cultured|continuously-cultured|JJ|_ experiment|experiment|NN|_ samples|sample|NNS|_ in|in|IN|_ total|total|JJ|_ absence|absence|NN|_ of|of|IN|_ Zn|zn|NN|_
Steady-state|steady-state|JJ|_ continuously-cultured|continuously-cultured|JJ|_ MG1655|mg1655|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ adequate|adequate|JJ|_ Zn|zn|NN|_
Steady-state|steady-state|JJ|_ continuously-cultured|continuously-cultured|JJ|_ MG1655|mg1655|NN|_ in|in|IN|_ the|the|DT|_ total|total|JJ|_ absence|absence|NN|_ of|of|IN|_ Zn|zn|NN|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cultured|culture|VBN|_ under|under|IN|_ severe|severe|JJ|_ zinc|zinc|NN|_ limitation|limitation|NN|_ Chemostat|Chemostat|NNP|_ 1A|1a|NN|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cultured|culture|VBN|_ under|under|IN|_ severe|severe|JJ|_ zinc|zinc|NN|_ limitation|limitation|NN|_ Chemostat|chemostat|NN|_ 1B|1b|NN|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cultured|culture|VBN|_ under|under|IN|_ severe|severe|JJ|_ zinc|zinc|NN|_ limitation|limitation|NN|_ Chemostat|Chemostat|NNP|_ 2A|2a|NN|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cultured|culture|VBN|_ under|under|IN|_ severe|severe|JJ|_ zinc|zinc|NN|_ limitation|limitation|NN|_ Chemostat|Chemostat|NNP|_ 2B|2b|NN|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cultured|culture|VBN|_ under|under|IN|_ severe|severe|JJ|_ zinc|zinc|NN|_ limitation|limitation|NN|_ Chemostat|Chemostat|NNP|_ 3A|3a|NN|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cultured|culture|VBN|_ under|under|IN|_ severe|severe|JJ|_ zinc|zinc|NN|_ limitation|limitation|NN|_ Chemostat|Chemostat|NNP|_ 3B|3b|NN|_
1|1|CD|_ .|.|.|_ Holme|Holme|NNP|_ T|t|NN|_ ,|,|,|_ Arvidson|Arvidson|NNP|_ S|S|NNP|_ ,|,|,|_ Lindholm|Lindholm|NNP|_ B|B|NNP|_ ,|,|,|_ and|and|CC|_ Pavlu|Pavlu|NNP|_ B.|B.|NNP|_ 1970|1970|CD|_ .|.|.|_ Enzymes|enzyme|NNS|_ :|:|:|_ Laboratory-scale|laboratory-scale|JJ|_ production|production|NN|_ .|.|.|_ Process|process|VB|_ Biochemistry|Biochemistry|NNP|_ 62-66|62-66|CD|_ .|.|.|_
1|1|CD|_ .|.|.|_ Neubauer|Neubauer|NNP|_ ,|,|,|_ A.|a.|NN|_ ,|,|,|_ J.|J.|NNP|_ Soini|Soini|NNP|_ ,|,|,|_ M.|M.|NNP|_ Bollok|Bollok|NNP|_ ,|,|,|_ M.|M.|NNP|_ Zenker|Zenker|NNP|_ ,|,|,|_ J.|J.|NNP|_ Sandqvist|Sandqvist|NNP|_ ,|,|,|_ J.|J.|NNP|_ Myllyharju|Myllyharju|NNP|_ ,|,|,|_ and|and|CC|_ P.|P.|NNP|_ Neubauer|Neubauer|NNP|_ .|.|.|_ 2007|2007|CD|_ .|.|.|_ Fermentation|fermentation|NN|_ process|process|NN|_ for|for|IN|_ tetrameric|tetrameric|JJ|_ human|human|JJ|_ collagen|collagen|NN|_ prolyl|prolyl|JJ|_ 4-hydroxylase|4-hydroxylase|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism :|:|:|_ improvement|improvement|NN|_ by|by|IN|_ gene|gene|NN|_ optimisation|optimisation|NN|_ of|of|IN|_ the|the|DT|_ PDI|PDI|NNP|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_ after|after|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_ ,|,|,|_ sample|sample|NN|_ S2|s2|NN|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_ ,|,|,|_ sample|sample|NN|_ S1|s1|NN|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ 45|45|CD|_ minutes|minute|NNS|_ after|after|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_ ,|,|,|_ sample|sample|NN|_ S3|s3|NN|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ 75|75|CD|_ minutes|minute|NNS|_ after|after|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_ ,|,|,|_ sample|sample|NN|_ S4|s4|NN|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ fermentation|fermentation|NN|_ sample|sample|NN|_ taken|take|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ after|after|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ fermentation|fermentation|NN|_ sample|sample|NN|_ taken|take|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ fermentation|fermentation|NN|_ sample|sample|NN|_ taken|take|VBN|_ 45|45|CD|_ minutes|minute|NNS|_ after|after|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_
E.coli|e.coli|NN|_ W3110|w3110|NN|_ ,|,|,|_ fermentation|fermentation|NN|_ sample|sample|NN|_ taken|take|VBN|_ 75|75|CD|_ minutes|minute|NNS|_ after|after|IN|_ oxygen|oxygen|NN|_ downshift|downshift|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
GCOS|gcos|NN|_ 1.0|1.0|CD|_
References|References|NNPS|_
References|References|NNPS|_ :|:|:|_
Samples|sample|NNS|_ for|for|IN|_ microarray|microarray|NN|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ described|describe|VBN|_ earlier|earlier|JJR|_ -LSB-|-lsb-|-LRB-|_ 1|1|CD|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ Samples|sample|NNS|_ were|be|VBD|_ shortly|shortly|RB|_ mixed|mix|VBN|_ by|by|IN|_ vortexing|vortex|VBG|_ ,|,|,|_ divided|divide|VBN|_ in|in|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ 1|1|CD|_ .|.|.|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 16,100|16,100|CD|_ ×|×|CD|_ g|g|NN|_ and|and|CC|_ +4|+4|NN|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250|250|CD|_ µL|µl|NN|_ of|of|IN|_ RNALater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ analysis|analysis|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ A&A|A&A|NNP|_ Biotechnology|Biotechnology|NNP|_ ,|,|,|_ Poland|Poland|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Strain|Strain|NNP|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110|w3110|NN|_ -LSB-|-lsb-|-LRB-|_ F|f|NN|_ --|--|:|_ IN|in|IN|_ -LRB-|-lrb-|-LRB-|_ rrnD-rrnE|rrnd-rrne|NN|_ -RRB-|-rrb-|-RRB-|_ 1|1|CD|_ -RSB-|-rsb-|-RRB-|_
The|the|DT|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ a|a|DT|_ Biostat|biostat|NN|_ C|c|NN|_ 15|15|CD|_ L|l|NN|_ bioreactor|bioreactor|NN|_ with|with|IN|_ the|the|DT|_ DCU-3|dcu-3|NN|_ controlling|control|VBG|_ unit|unit|NN|_ and|and|CC|_ MFCS-win|mfcs-win|NN|_ supervisory|supervisory|JJ|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Sartorius|sartorius|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ working|work|VBG|_ volume|volume|NN|_ of|of|IN|_ 8|8|CD|_ L|l|NN|_ .|.|.|_ The|the|DT|_ mineral|mineral|NN|_ salt|salt|NN|_ medium|medium|NN|_ contained|contain|VBD|_ per|per|IN|_ liter|liter|NN|_ :|:|:|_ 14.6|14.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.6|3.6|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ ×|×|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.0|2.0|CD|_ g|g|NN|_ Na2SO4|na2so4|NN|_ ,|,|,|_ 2.47|2.47|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ 0.5|0.5|CD|_ g|g|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2-H-citrate|2-h-citrate|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ thiamine|thiamine|NN|SUPP hydrochloride|hydrochloride|NN|SUPP ,|,|,|_ 0.1|0.1|CD|_ mL|ml|NN|_ antifoam|antifoam|NN|_ 204|204|CD|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ mL|ml|NN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ initial|initial|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ was|be|VBD|_ 40|40|CD|_ g|g|NN|_ L-1|l-1|NN|_ .|.|.|_ The|the|DT|_ feed|feed|NN|_ solution|solution|NN|_ contained|contain|VBD|_ 650|650|CD|_ g|g|NN|_ L-1|l-1|NN|_ glucose|glucose|NN|SUPP .|.|.|_ 2|2|CD|_ mL|ml|NN|_ L-1|l-1|NN|_ of|of|IN|_ sterile|sterile|JJ|_ filtered|filter|VBN|_ 1M|1m|NN|_ MgSO4|mgso4|NN|_ were|be|VBD|_ added|add|VBN|_ regularly|regularly|RB|_ per|per|IN|_ OD600|od600|NN|_ =|=|JJ|_ 10|10|CD|_ increase|increase|NN|_ .|.|.|_
Two|two|CD|_ precultures|preculture|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ mineral|mineral|NN|_ salt|salt|NN|_ medium|medium|NN|_ with|with|IN|_ 10|10|CD|_ g|g|NN|_ L|l|NN|_ 1|1|CD|_ of|of|IN|_ glucose|glucose|NN|SUPP without|without|IN|_ antifoam|antifoam|JJ|_ agent|agent|NN|_ consecutively|consecutively|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ at|at|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ at|at|IN|_ 180|180|CD|_ rpm|rpm|NN|_ .|.|.|_ Main|Main|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ started|start|VBN|_ as|as|IN|_ batch|batch|NN|_ cultures|culture|NNS|_ at|at|IN|_ a|a|DT|_ temperature|temperature|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ pH|ph|NN|_ was|be|VBD|_ kept|keep|VBN|_ at|at|IN|_ 7.0|7.0|CD|_ by|by|IN|_ controlled|controlled|JJ|_ addition|addition|NN|_ of|of|IN|_ 25|25|CD|_ %|%|NN|_ ammonia|ammonia|NN|_ solution|solution|NN|_ .|.|.|_ At|at|IN|_ the|the|DT|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ cell|cell|NN|_ dry|dry|JJ|_ weight|weight|NN|_ about|about|IN|_ 16|16|CD|_ g|g|NN|_ L-1|l-1|NN|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ stirrer|stirrer|NN|_ rate|rate|NN|_ was|be|VBD|_ lowered|lower|VBN|_ from|from|IN|_ 1000|1000|CD|_ rpm|rpm|NN|_ to|to|TO|_ 500|500|CD|_ rpm|rpm|NN|_ ,|,|,|_ to|to|TO|_ provoke|provoke|VB|_ oxygen|oxygen|NN|_ limitation|limitation|NN|_ by|by|IN|_ decreased|decrease|VBN|_ oxygen|oxygen|NN|_ transfer|transfer|NN|_ .|.|.|_ Constant|constant|JJ|_ glucose|glucose|NN|SUPP feed|feed|NN|_ of|of|IN|_ 100|100|CD|_ g|g|NN|_ L-1|l-1|NN|_ h-1|h-1|NN|_ was|be|VBD|_ started|start|VBN|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ the|the|DT|_ oxygen|oxygen|NN|_ drop|drop|NN|_ which|which|WDT|_ was|be|VBD|_ enough|enough|RB|_ to|to|TO|_ ensure|ensure|VB|_ glucose|glucose|NN|SUPP excess|excess|NN|_ during|during|IN|_ the|the|DT|_ whole|whole|JJ|_ cultivation|cultivation|NN|_ .|.|.|_
Background|background|NN|_ correction|correction|NN|_ ,|,|,|_ normalization|normalization|NN|_ and|and|CC|_ calculation|calculation|NN|_ of|of|IN|_ the|the|DT|_ expression|expression|NN|_ measures|measure|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RMA|RMA|NNP|_ procedure|procedure|NN|_ with|with|IN|_ the|the|DT|_ WebArray|WebArray|NNP|_ platform|platform|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ ammended|ammend|VBN|_ with|with|IN|_ 1.25|1.25|CD|_ M|m|NN|_ sucrose|sucrose|NN|_ to|to|TO|_ an|a|DT|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ of|of|IN|_ 2.7|2.7|CD|_ Os|os|NNS|_ kg-1|kg-1|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ biomass|biomass|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ rpm|rpm|NN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ treated|treat|VBN|_ with|with|IN|_ RNAProtect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
Cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ ammended|ammend|VBN|_ with|with|IN|_ 1.37|1.37|CD|_ M|m|NN|_ NaCl|nacl|NN|_ to|to|TO|_ obtain|obtain|VB|_ an|a|DT|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ of|of|IN|_ 2.7|2.7|CD|_ Os|os|NNS|_ kg-1|kg-1|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ biomass|biomass|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ rpm|rpm|NN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ treated|treat|VBN|_ with|with|IN|_ RNAProtect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ Frag1|frag1|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ Frag1|frag1|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ sample|sample|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ Frag1|frag1|NN|_ ,|,|,|_ hyperosmotic|hyperosmotic|JJ|_ NaCl|nacl|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ Frag1|frag1|NN|_ ,|,|,|_ NaCl|nacl|NN|_ hyperosmotic|hyperosmotic|JJ|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
E.coli|e.coli|NN|_ Frag1|frag1|NN|_ ,|,|,|_ sucrose|sucrose|NN|_ hyperosmotic|hyperosmotic|JJ|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ Frag1|frag1|NN|_ ,|,|,|_ sucrose|sucrose|NN|_ hyperosmotic|hyperosmotic|JJ|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ NaCl|nacl|NN|_ hyperosmotic|hyperosmotic|JJ|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ NaCl|nacl|NN|_ hyperosmotic|hyperosmotic|JJ|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ strain|strain|NN|_ Frag1|frag1|NN|_
E.|e.|FW|_ coli|coli|FW|_ sucrose|sucrose|NN|_ hyperosmotic|hyperosmotic|JJ|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ sucrose|sucrose|NN|_ hyperosmotic|hyperosmotic|JJ|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Grown|grow|VBN|_ in|in|IN|_ Davis|Davis|NNP|_ 's|'s|POS|_ Mineral|Mineral|NNP|_ Salts|salt|NNS|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Gibco|Gibco|NNP|_ BRL|brl|NN|_ Life|Life|NNP|_ Technologies|Technologies|NNP|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.1|0.1|CD|_ %|%|NN|_ D-glucose|d-glucose|NN|_ at|at|IN|_ 25|25|CD|_ C|c|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ r.p.m.|r.p.m.|NN|_ shaking|shake|VBG|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 550|550|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.6|0.6|CD|_ .|.|.|_
No|no|DT|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ RNAeasy|rnaeasy|NN|_ MIDI|midi|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ lysis|lysis|NN|_ buffer|buffer|NN|_ containing|contain|VBG|_ 0.1|0.1|CD|_ %|%|NN|_ beta-mercaptoethanol|beta-mercaptoethanol|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ lysates|lysate|NNS|_ and|and|CC|_ purified|purify|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ standard|standard|JJ|_ protocol|protocol|NN|_ and|and|CC|_ subsequently|subsequently|RB|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ electrophoresis|electrophoresis|NN|_ using|use|VBG|_ a|a|DT|_ RNA|rna|NN|_ bioanalyser|bioanalyser|NN|_ 2100|2100|CD|_ and|and|CC|_ Lab|lab|NN|_ RNAChip|rnachip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ progression|progression|NN|_ to|to|TO|_ microarray|microarray|NN|_ hybridization|hybridization|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ 15|15|CD|_ minute|minute|NN|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ dye|dye|VB|_ swap|swap|NN|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 15|15|CD|_ minute|minute|NN|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 15|15|CD|_ minute|minute|NN|_ pH|ph|NN|_ only|only|RB|_ dye|dye|VB|_ swap|swap|NN|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 15|15|CD|_ minute|minute|NN|_ pH|ph|NN|_ only|only|RB|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_ ,|,|,|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_ ,|,|,|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 7|7|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_ ,|,|,|_ no|no|DT|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_ ,|,|,|_ no|no|DT|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 7|7|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 5|5|CD|_ minute|minute|NN|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ dye|dye|VB|_ swap|swap|NN|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 5|5|CD|_ minute|minute|NN|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 5|5|CD|_ minute|minute|NN|_ pH|ph|NN|_ only|only|RB|_ dye|dye|VB|_ swap|swap|NN|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 5|5|CD|_ minute|minute|NN|_ pH|ph|NN|_ only|only|RB|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ 5|5|CD|_ µM|µm|NN|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 7|7|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ no|no|DT|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ no|no|DT|_ cadmium|cadmium|NN|_ ,|,|,|_ pH|ph|NN|_ 7|7|CD|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 7|7|CD|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 5.4|5.4|CD|_ µM|µm|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ µg|µg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 7|7|CD|_ .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ with|with|IN|_ manual|manual|JJ|_ rotations|rotation|NNS|_ of|of|IN|_ the|the|DT|_ flasks|flask|NNS|_ once|once|RB|_ per|per|IN|_ minute|minute|NN|_ to|to|TO|_ resuspend|resuspend|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 7|7|CD|_ .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ with|with|IN|_ manual|manual|JJ|_ rotations|rotation|NNS|_ of|of|IN|_ the|the|DT|_ flasks|flask|NNS|_ once|once|RB|_ per|per|IN|_ minute|minute|NN|_ to|to|TO|_ resuspend|resuspend|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ four|four|CD|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 5|5|CD|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 5.4|5.4|CD|_ µM|µm|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ µg|µg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ four|four|CD|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 5|5|CD|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 5.4|5.4|CD|_ µM|µm|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ µg|µg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ four|four|CD|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 5|5|CD|_ .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ with|with|IN|_ manual|manual|JJ|_ rotations|rotation|NNS|_ of|of|IN|_ the|the|DT|_ flasks|flask|NNS|_ once|once|RB|_ per|per|IN|_ minute|minute|NN|_ to|to|TO|_ resuspend|resuspend|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ four|four|CD|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 5|5|CD|_ .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ with|with|IN|_ manual|manual|JJ|_ rotations|rotation|NNS|_ of|of|IN|_ the|the|DT|_ flasks|flask|NNS|_ once|once|RB|_ per|per|IN|_ minute|minute|NN|_ to|to|TO|_ resuspend|resuspend|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ four|four|CD|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 7|7|CD|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 5.4|5.4|CD|_ µM|µm|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ µg|µg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ until|until|IN|_ the|the|DT|_ contents|contents|NNS|_ of|of|IN|_ the|the|DT|_ flask|flask|NN|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 25|25|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ ,|,|,|_ transferred|transfer|VBN|_ to|to|TO|_ four|four|CD|_ 50|50|CD|_ mL|ml|NN|_ conical|conical|JJ|_ tubes|tube|NNS|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 2540|2540|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 12|12|CD|_ minutes|minute|NNS|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ at|at|IN|_ pH|ph|NN|_ 7|7|CD|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 5.4|5.4|CD|_ µM|µm|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ µg|µg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ strain|strain|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ Masterpure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ Masterpure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Spot|Spot|NNP|_ intensities|intensity|NNS|_ and|and|CC|_ locations|location|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ TIGR|TIGR|NNP|_ Spotfinder|Spotfinder|NNP|_ ,|,|,|_ Version|Version|NNP|_ 3.1.1|3.1.1|CD|_ .|.|.|_ All|all|DT|_ subsequent|subsequent|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ ma-anova|ma-anova|JJ|_ package|package|NN|_ in|in|IN|_ the|the|DT|_ open-source|open-source|JJ|_ statistical|statistical|JJ|_ software|software|NN|_ package|package|NN|_ ,|,|,|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ www.r-project.org|www.r-project.org|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Version|Version|NNP|_ 2.4.1|2.4.1|CD|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ regional|regional|JJ|_ lowess|lowess|NN|_ method|method|NN|_ .|.|.|_
Spot|Spot|NNP|_ intensities|intensity|NNS|_ and|and|CC|_ locations|location|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ TIGR|TIGR|NNP|_ Spotfinder|Spotfinder|NNP|_ ,|,|,|_ Version|Version|NNP|_ 3.1.1|3.1.1|CD|_ .|.|.|_ All|all|DT|_ subsequent|subsequent|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ ma-anova|ma-anova|JJ|_ package|package|NN|_ in|in|IN|_ the|the|DT|_ open-source|open-source|JJ|_ statistical|statistical|JJ|_ software|software|NN|_ package|package|NN|_ ,|,|,|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ www.r-project.org|www.r-project.org|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Version|Version|NNP|_ 2.4.1|2.4.1|CD|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ regional|regional|JJ|_ lowess|lowess|NN|_ method|method|NN|_ .|.|.|_
Cells|cell|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ 10|10|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ 0|0|CD|_ hrs|hr|NNS|_ using|use|VBG|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ immediately|immediately|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processing|processing|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ cold|cold|JJ|_ phosphate-buffered|phosphate-buffered|JJ|_ saline|saline|NN|_ to|to|TO|_ remove|remove|VB|_ RNAlater|rnalater|NN|_ .|.|.|_
Cells|cell|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ 10|10|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ using|use|VBG|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ immediately|immediately|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processing|processing|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ cold|cold|JJ|_ phosphate-buffered|phosphate-buffered|JJ|_ saline|saline|NN|_ to|to|TO|_ remove|remove|VB|_ RNAlater|rnalater|NN|_ .|.|.|_
Cells|cell|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ 10|10|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0|0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ using|use|VBG|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ immediately|immediately|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processing|processing|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ cold|cold|JJ|_ phosphate-buffered|phosphate-buffered|JJ|_ saline|saline|NN|_ to|to|TO|_ remove|remove|VB|_ RNAlater|rnalater|NN|_ .|.|.|_
Cells|cell|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ 10|10|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ using|use|VBG|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ immediately|immediately|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processing|processing|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ cold|cold|JJ|_ phosphate-buffered|phosphate-buffered|JJ|_ saline|saline|NN|_ to|to|TO|_ remove|remove|VB|_ RNAlater|rnalater|NN|_ .|.|.|_
Cells|cell|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ 10|10|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ using|use|VBG|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ immediately|immediately|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processing|processing|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ cold|cold|JJ|_ phosphate-buffered|phosphate-buffered|JJ|_ saline|saline|NN|_ to|to|TO|_ remove|remove|VB|_ RNAlater|rnalater|NN|_ .|.|.|_
Cells|cell|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ 10|10|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0|0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ using|use|VBG|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ immediately|immediately|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processing|processing|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ cold|cold|JJ|_ phosphate-buffered|phosphate-buffered|JJ|_ saline|saline|NN|_ to|to|TO|_ remove|remove|VB|_ RNAlater|rnalater|NN|_ .|.|.|_
Cells|cell|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ 10|10|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ using|use|VBG|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ immediately|immediately|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processing|processing|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ cold|cold|JJ|_ phosphate-buffered|phosphate-buffered|JJ|_ saline|saline|NN|_ to|to|TO|_ remove|remove|VB|_ RNAlater|rnalater|NN|_ .|.|.|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0|0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 1.5|1.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ high|high|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ low|low|JJ|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ no|no|DT|_ IPTG|iptg|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 0|0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ 3.5|3.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_ with|with|IN|_ 1.0|1.0|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ IPTG|iptg|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ IPTG|iptg|NN|_ induction|induction|NN|_ -LRB-|-lrb-|-LRB-|_ T|t|NN|_ =|=|JJ|_ 0|0|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ IPTG|iptg|NN|_ induction|induction|NN|_ -LRB-|-lrb-|-LRB-|_ T|t|NN|_ =|=|JJ|_ 0|0|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ IPTG|iptg|NN|_ induction|induction|NN|_ -LRB-|-lrb-|-LRB-|_ T|t|NN|_ =|=|JJ|_ 0|0|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep|rep|NN|GEN 1|1|CD|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ IPTG|iptg|NN|_ induction|induction|NN|_ -LRB-|-lrb-|-LRB-|_ T|t|NN|_ =|=|JJ|_ 0|0|CD|_ hrs|hr|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ ,|,|,|_ technical|technical|JJ|_ rep2|rep2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
The|the|DT|_ probe|probe|NN|_ intensity|intensity|NN|_ data|datum|NNS|_ was|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ Genetraffic|genetraffic|JJ|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Iobion|Iobion|NNP|_ Informatics|Informatics|NNPS|_ LLC|LLC|NNP|_ ,|,|,|_ La|La|NNP|_ Jolla|Jolla|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ probe|probe|NN|_ intensity|intensity|NN|_ data|datum|NNS|_ was|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ GC-RMA|gc-rma|NN|_ algorithm|algorithm|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_
Acidic|Acidic|NNP|_ Hot|Hot|NNP|_ Phenol|Phenol|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ minimal|minimal|JJ|_ media|media|NNS|_ at|at|IN|_ 37oC|37oc|NN|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ with|with|IN|_ single|single|JJ|_ ,|,|,|_ independent|independent|JJ|_ colonies|colony|NNS|_ in|in|IN|_ triplicate|triplicate|NN|_ ,|,|,|_ incubated|incubate|VBN|_ aerobically|aerobically|RB|_ overnight|overnight|JJ|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ and|and|CC|_ sub-cultured|sub-cultured|JJ|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.0001|0.0001|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ after|after|IN|_ being|be|VBG|_ maintained|maintain|VBN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase for|for|IN|_ at|at|IN|_ least|least|JJS|_ eight|eight|CD|_ generations|generation|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ minimal|minimal|JJ|_ media|media|NNS|_ at|at|IN|_ 37oC|37oc|NN|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ with|with|IN|_ single|single|JJ|_ ,|,|,|_ independent|independent|JJ|_ colonies|colony|NNS|_ in|in|IN|_ triplicate|triplicate|NN|_ ,|,|,|_ incubated|incubate|VBN|_ aerobically|aerobically|RB|_ overnight|overnight|JJ|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ and|and|CC|_ sub-cultured|sub-cultured|JJ|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.0001|0.0001|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 1.5|1.5|CD|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ sampled|sample|VBN|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ sampled|sample|VBN|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase OD600|od600|NN|_ =|=|JJ|_ 1.5|1.5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Exp-rpoS-Rep1|exp-rpos-rep1|NN|_
Exp-rpoS-Rep2|exp-rpos-rep2|NN|_
Exp-rpoS-Rep3|exp-rpos-rep3|NN|_
Exp-WT-Rep1|exp-wt-rep1|NN|_
Exp-WT-Rep2|exp-wt-rep2|NN|_
Exp-WT-Rep3|exp-wt-rep3|NN|_
GCRMA|gcrma|NN|_ normalized|normalize|VBD|_
MG1655|MG1655|NNP|_ rpoS|rpos|NN|GEN mutants|mutant|NNS|_
MG1655|mg1655|NN|_ wild|wild|JJ|_ type|type|NN|_
Stat-rpoS-Rep1|stat-rpos-rep1|NN|_
Stat-rpoS-Rep2|stat-rpos-rep2|NN|_
Stat-rpoS-Rep3|stat-rpos-rep3|NN|_
Stat-WT-Rep1|stat-wt-rep1|NN|_
Stat-WT-Rep2|stat-wt-rep2|NN|_
Stat-WT-Rep3|stat-wt-rep3|NN|_
Ambion|Ambion|NNP|_ RiboPure|RiboPure|NNP|_ RNA|rna|NN|_ Isolation|isolation|NN|_
Ambion|Ambion|NNP|_ RiboPure|RiboPure|NNP|_ RNA|rna|NN|_ Isolation|isolation|NN|_
Data|Data|NNP|_ has|have|VBZ|_ not|not|RB|_ been|be|VBN|_ processed|process|VBN|_ other|other|JJ|_ than|than|IN|_ those|those|DT|_ protocols|protocol|NNS|_ within|within|IN|_ GCOSv1|gcosv1|NN|_ .4|.4|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 8624|8624|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 8624|8624|CD|_ qseF|qsef|NN|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ 8624|8624|CD|_ WT|WT|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseF|qsef|NN|_ deletion|deletion|NN|_ mutant|mutant|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseF|qsef|NN|_ deletion|deletion|NN|_ mutant|mutant|JJ|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ media|media|NNS|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_
Aerobic|Aerobic|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_
Aerobic|Aerobic|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ not|not|RB|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ cells|cell|NNS|_ -RRB-|-rrb-|-RRB-|_
Aerobic|aerobic|JJ|_ MG1655|mg1655|NN|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_
Aerobic|aerobic|JJ|_ MG1655|mg1655|NN|_ not|not|RB|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ cells|cell|NNS|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 1a|1a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 1b|1b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 2a|2a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 2b|2b|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 3a|3a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 3b|3b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 4a|4a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ aerobically|aerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 4b|4b|NN|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ harvested|harvest|VBN|_ directly|directly|RB|_ into|into|IN|_ cold|cold|JJ|_ phenol|phenol|NN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 187|187|CD|_ µl|µl|NN|_ phenol|phenol|NN|_ ,|,|,|_ 3.56|3.56|CD|_ ml|ml|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ as|as|IN|_ recommended|recommend|VBN|_ by|by|IN|_ suppliers|supplier|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ BioPhotometer|biophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Spots|spot|NNS|_ automatically|automatically|RB|_ flagged|flag|VBD|_ as|as|IN|_ bad|bad|JJ|_ ,|,|,|_ negative|negative|JJ|_ or|or|CC|_ poor|poor|JJ|_ in|in|IN|_ the|the|DT|_ Imagene|imagene|NN|_ software|software|NN|_ were|be|VBD|_ removed|remove|VBN|_ before|before|IN|_ the|the|DT|_ statistical|statistical|JJ|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ GeneSight|GeneSight|NNP|_ .|.|.|_ The|the|DT|_ mean|mean|NN|_ values|value|NNS|_ from|from|IN|_ each|each|DT|_ channel|channel|NN|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ normalised|normalise|VBN|_ using|use|VBG|_ the|the|DT|_ Lowess|lowess|NN|_ method|method|NN|_ to|to|TO|_ remove|remove|VB|_ intensity-dependent|intensity-dependent|JJ|_ effects|effect|NNS|_ in|in|IN|_ the|the|DT|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ ratios|ratio|NNS|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ .|.|.|_ The|the|DT|_ Cy3|cy3|NN|_
Anaerobic|anaerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_
Anaerobic|anaerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ not|not|RB|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ cells|cell|NNS|_ -RRB-|-rrb-|-RRB-|_
Anaerobic|anaerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_
Anaerobic|anaerobic|JJ|_ MG1655|mg1655|NN|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_
Anaerobic|anaerobic|JJ|_ MG1655|mg1655|NN|_ not|not|RB|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ cells|cell|NNS|_ -RRB-|-rrb-|-RRB-|_
Anaerobic|anaerobic|JJ|_ MG1655|mg1655|NN|_ were|be|VBD|_ exposed|expose|VBN|_ to|to|TO|_ CO-RMs|co-rm|NNS|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 1a|1a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 1b|1b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 2a|2a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 2b|2b|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 3a|3a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 3b|3b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 4a|4a|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism after|after|IN|_ addition|addition|NN|_ of|of|IN|_ CO-RMs|co-rm|NNS|_ to|to|TO|_ anaerobically|anaerobically|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ -|-|:|_ Sample|sample|NN|_ 4b|4b|NN|_
Samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ harvested|harvest|VBN|_ directly|directly|RB|_ into|into|IN|_ cold|cold|JJ|_ phenol|phenol|NN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 187|187|CD|_ µl|µl|NN|_ phenol|phenol|NN|_ ,|,|,|_ 3.56|3.56|CD|_ ml|ml|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ as|as|IN|_ recommended|recommend|VBN|_ by|by|IN|_ suppliers|supplier|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ BioPhotometer|biophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Spots|spot|NNS|_ automatically|automatically|RB|_ flagged|flag|VBD|_ as|as|IN|_ bad|bad|JJ|_ ,|,|,|_ negative|negative|JJ|_ or|or|CC|_ poor|poor|JJ|_ in|in|IN|_ the|the|DT|_ Imagene|imagene|NN|_ software|software|NN|_ were|be|VBD|_ removed|remove|VBN|_ before|before|IN|_ the|the|DT|_ statistical|statistical|JJ|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ GeneSight|GeneSight|NNP|_ .|.|.|_ The|the|DT|_ mean|mean|NN|_ values|value|NNS|_ from|from|IN|_ each|each|DT|_ channel|channel|NN|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ normalised|normalise|VBN|_ using|use|VBG|_ the|the|DT|_ Lowess|lowess|NN|_ method|method|NN|_ to|to|TO|_ remove|remove|VB|_ intensity-dependent|intensity-dependent|JJ|_ effects|effect|NNS|_ in|in|IN|_ the|the|DT|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ ratios|ratio|NNS|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ .|.|.|_ The|the|DT|_ Cy3|cy3|NN|_
Bexp|bexp|NN|_ _|_|CD|_ Bstat|Bstat|NNP|_ _|_|SYM|_ dyeswap1|dyeswap1|CD|_
Bexp|bexp|NN|_ _|_|CD|_ Bstat|Bstat|NNP|_ _|_|SYM|_ dyeswap2|dyeswap2|CD|_
Bexp|bexp|NN|_ _|_|CD|_ Bstat|Bstat|NNP|_ _|_|CD|_ rep1|rep1|NN|_
Bexp|bexp|NN|_ _|_|CD|_ Bstat|Bstat|NNP|_ _|_|CD|_ rep2|rep2|NN|_
Bexp|bexp|NN|_ _|_|CD|_ Kexp|Kexp|NNP|_ _|_|SYM|_ dyeswap1|dyeswap1|CD|_
Bexp|bexp|NN|_ _|_|CD|_ Kexp|Kexp|NNP|_ _|_|SYM|_ dyeswap2|dyeswap2|CD|_
Bexp|bexp|NN|_ _|_|CD|_ Kexp|Kexp|NNP|_ _|_|CD|_ rep1|rep1|NN|_
Bexp|bexp|NN|_ _|_|CD|_ Kexp|Kexp|NNP|_ _|_|CD|_ rep2|rep2|NN|_
Bexp|bexp|NN|_ _|_|CD|_ Kstat|Kstat|NNP|_ _|_|SYM|_ dyeswap1|dyeswap1|CD|_
Bexp|bexp|NN|_ _|_|CD|_ Kstat|Kstat|NNP|_ _|_|SYM|_ dyeswap2|dyeswap2|CD|_
Bexp|bexp|NN|_ _|_|CD|_ Kstat|Kstat|NNP|_ _|_|CD|_ rep1|rep1|NN|_
Bexp|bexp|NN|_ _|_|CD|_ Kstat|Kstat|NNP|_ _|_|SYM|_ rep2|rep2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Following|follow|VBG|_ background|background|NN|_ subtraction|subtraction|NN|_ ,|,|,|_ spot|spot|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ percentages|percentage|NNS|_ of|of|IN|_ total|total|JJ|_ signal|signal|NN|_ intensities|intensity|NNS|_ of|of|IN|_ Cy-3|cy-3|NN|_ or|or|CC|_ Cy-5|cy-5|NN|_ signals|signal|NNS|_ on|on|IN|_ each|each|DT|_ microarray|microarray|NN|_ ,|,|,|_ as|as|IN|_ a|a|DT|_ means|means|NN|_ of|of|IN|_ normalization|normalization|NN|_ .|.|.|_ Spots|spot|NNS|_ with|with|IN|_ low|low|JJ|_ intensities|intensity|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ .|.|.|_
MG1655|mg1655|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ LB|lb|NN|_
MG1655|mg1655|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ LB|lb|NN|_
REL606|rel606|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ LB|lb|NN|_
REL606|rel606|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ LB|lb|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cells|cell|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ column|column|NN|_ .|.|.|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample3|sample3|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample3|sample3|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ arcA|arca|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecoli|JJ|_ ko-arcA|ko-arca|NN|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED
Ecoli|Ecoli|NNP|_ ko-arcA|ko-arcA|NNP|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ fur|fur|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecoli|JJ|_ ko-fur|ko-fur|JJ|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED
Ecoli|Ecoli|NNP|_ ko-fur|ko-fur|JJ|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ ko-furgrown|ko-furgrown|NN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample3|sample3|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample3|sample3|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ihfA|ihfa|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecoli|JJ|_ ko-ihfA|ko-ihfa|NN|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED
Ecoli|Ecoli|NNP|_ ko-ihfA|ko-ihfA|NNP|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample3|sample3|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample3|sample3|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ phoB|phob|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecoli|JJ|_ ko-phoB|ko-phob|NN|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED
Ecoli|Ecoli|NNP|_ ko-phoB|ko-phob|NN|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ubiE|ubie|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ubiE|ubie|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ ko|ko|FW|_ _|_|FW|_ ubiE|ubie|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ ko|ko|NN|_ _|_|NN|_ ubiE|ubie|NN|GEN _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecoli|JJ|_ ko-ubiE|ko-ubie|NN|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED
Ecoli|Ecoli|NNP|_ ko-ubiE|ko-ubiE|NNP|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample1|sample1|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample1|sample1|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample4|sample4|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|SYM|_ Sample4|sample4|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample2|sample2|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|NN|_ Sample4|sample4|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample5|sample5|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 1|1|CD|_ %|%|NN|_ _|_|CD|_ isobutanol|isobutanol|NN|_ _|_|SYM|_ Sample5|sample5|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|SYM|_ Sample1|sample1|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|NN|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|SYM|_ Sample4|sample4|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ 3|3|CD|_ %|%|NN|_ _|_|CD|_ ethanol|ethanol|NN|_ _|_|SYM|_ Sample4|sample4|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ calibration|calibration|NN|_ _|_|CD|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ calibration|calibration|NN|_ _|_|CD|_ Sample1|sample1|NN|_ _|_|CD|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ calibration|calibration|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wildtype|wildtype|JJ|_ _|_|NN|_ calibration|calibration|NN|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecoli|JJ|_ wildtype|wildtype|JJ|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED
Ecoli|Ecoli|NNP|_ wildtype|wildtype|JJ|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ butanol|butanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ wildtype|wildtype|JJ|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treatment|treatment|NN|_
Ecoli|Ecoli|NNP|_ wildtype|wildtype|JJ|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED ,|,|,|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ 3|3|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Midikit|Midikit|NNP|_
Quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ scans|scan|NNS|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ ImaGene|imagene|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 6.0.1|6.0.1|CD|_ ;|;|:|_ BioDiscovery|BioDiscovery|NNP|_ ;|;|:|_ El|El|NNP|_ Segundo|Segundo|NNP|_ ,|,|,|_ CA|CA|NNP|_ ;|;|:|_ www.biodiscovery.com|www.biodiscovery.com|NNP|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ with|with|IN|_ the|the|DT|_ results|result|NNS|_ presented|present|VBN|_ in|in|IN|_ the|the|DT|_ associated|associate|VBN|_ text|text|NN|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ normalized|normalize|VBN|_ data|datum|NNS|_ VALUE|value|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ LOWESS|LOWESS|NNP|_ normalization|normalization|NN|_ with|with|IN|_ rank|rank|NN|_ invariant|invariant|JJ|_ selection|selection|NN|_ ,|,|,|_ as|as|IN|_ implemented|implement|VBN|_ in|in|IN|_ lcDNA|lcdna|NN|_ -LRB-|-lrb-|-LRB-|_ receptor.seas.ucla.edu|receptor.seas.ucla.edu|JJ|_
RNA|rna|NN|_ from|from|IN|_ 1|1|CD|_ %|%|NN|_ isobutanol|isobutanol|NN|_ treated|treat|VBN|_ sample|sample|NN|_ and|and|CC|_ untreated|untreated|JJ|_ sample|sample|NN|_ were|be|VBD|_ mixed|mix|VBN|_ after|after|IN|_ RNA|rna|NN|_ purification|purification|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ vol|vol|NN|_
Treated|treat|VBN|_ with|with|IN|_ 3|3|CD|_ %|%|NN|_ vol|vol|NN|_
BW25113|bw25113|NN|_ ,|,|,|_ H2O2|h2o2|NN|_
BW25113|bw25113|NN|_ ,|,|,|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ negative|negative|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
BW25113|bw25113|NN|_ ychH|ychh|NN|GEN ,|,|,|_ H2O2|h2o2|NN|_
BW25113|bw25113|NN|_ ychH|ychh|NN|GEN ,|,|,|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ negative|negative|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
BW25113|bw25113|NN|_ ygiW|ygiw|NN|GEN ,|,|,|_ H2O2|h2o2|NN|_
BW25113|bw25113|NN|_ ygiW|ygiw|NN|GEN ,|,|,|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ negative|negative|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
Channel|Channel|NNP|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_ after|after|IN|_ contacting|contact|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ with|with|IN|_ 2|2|CD|_ mM|mm|NN|KWSUPP H2O2|h2o2|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_ after|after|IN|_ contacting|contact|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ with|with|IN|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ negative|negative|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ ychH|ychh|NN|GEN at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_ after|after|IN|_ contacting|contact|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ with|with|IN|_ 2|2|CD|_ mM|mm|NN|KWSUPP H2O2|h2o2|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ ychH|ychh|NN|GEN at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_ after|after|IN|_ contacting|contact|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ with|with|IN|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ negative|negative|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ ygiW|ygiw|NN|GEN at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_ after|after|IN|_ contacting|contact|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ with|with|IN|_ 2|2|CD|_ mM|mm|NN|KWSUPP H2O2|h2o2|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ ygiW|ygiw|NN|GEN at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_ after|after|IN|_ contacting|contact|VBG|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ with|with|IN|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ negative|negative|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ TG1|tg1|NN|_
To|to|TO|_ lyse|lyse|VB|_ the|the|DT|_ cells|cell|NNS|_ ,|,|,|_ 1.0|1.0|CD|_ mL|ml|NN|_ RLT|rlt|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 0.2|0.2|CD|_ mL|ml|NN|_ 0.1|0.1|CD|_ mm|mm|NN|_ zirconia|zirconia|NN|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250ul|250ul|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ with|with|IN|_ vigorous|vigorous|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|NN|_ -LRB-|-lrb-|-LRB-|_ light|light|JJ|_ scattering|scattering|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ equivalent|equivalent|NN|_ to|to|TO|_ 0.4|0.4|CD|_ OD|od|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 100ug|100ug|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ HA3|ha3|NN|_ :|:|:|_ :|:|:|_ nusG|nusg|NN|GEN cells|cell|NNS|_
Monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ HA|HA|NNP|_ -LRB-|-lrb-|-LRB-|_ 12CA5|12ca5|NN|_ -RRB-|-rrb-|-RRB-|_
Monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ NusA|nusa|NN|_ -LRB-|-lrb-|-LRB-|_ 1NA1|1na1|NN|_ -RRB-|-rrb-|-RRB-|_
Monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ Beta|beta|NN|_ '|'|''|_ subunit|subunit|NN|_ -LRB-|-lrb-|-LRB-|_ NT73|nt73|NN|_ -RRB-|-rrb-|-RRB-|_
Monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ Sigma70|sigma70|NN|_ -LRB-|-lrb-|-LRB-|_ 2G10|2g10|NN|_ -RRB-|-rrb-|-RRB-|_
NusA|nusa|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 56226|56226|CD|_ -RRB-|-rrb-|-RRB-|_
NusA|nusa|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 61392|61392|CD|_ -RRB-|-rrb-|-RRB-|_
NusA|nusa|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 64131|64131|CD|_ -RRB-|-rrb-|-RRB-|_
NusA|nusa|NN|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
NusG|nusg|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 70568|70568|CD|_ -RRB-|-rrb-|-RRB-|_
NusG|nusg|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ HA3|ha3|NN|_ :|:|:|_ :|:|:|_ nusG|nusg|NN|GEN cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 62261|62261|CD|_ -RRB-|-rrb-|-RRB-|_
NusG|nusg|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ HA3|ha3|NN|_ :|:|:|_ :|:|:|_ nusG|nusg|NN|GEN cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 62263|62263|CD|_ -RRB-|-rrb-|-RRB-|_
NusG|nusg|NN|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
NusG|nusg|NN|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ HA3|ha3|NN|_ :|:|:|_ :|:|:|_ nusG|nusg|NN|GEN cells|cell|NNS|_
Polyclonal|polyclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ NusG|nusg|NN|_ -LRB-|-lrb-|-LRB-|_ raised|raise|VBN|_ for|for|IN|_ this|this|DT|_ study|study|NN|_ -RRB-|-rrb-|-RRB-|_
Polyclonal|polyclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ Rho|rho|NN|_ -LRB-|-lrb-|-LRB-|_ gift|gift|NN|_ from|from|IN|_ Jeff|Jeff|NNP|_ Roberts|Roberts|NNP|_ -RRB-|-rrb-|-RRB-|_
Rho|rho|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 3421602|3421602|CD|_ -RRB-|-rrb-|-RRB-|_
Rho|rho|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 70261|70261|CD|_ -RRB-|-rrb-|-RRB-|_
Rho|rho|NN|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 100040|100040|CD|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 56706|56706|CD|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 62215|62215|CD|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 100ug|100ug|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 100ug|100ug|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
Sigma70|sigma70|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 56859|56859|CD|_ -RRB-|-rrb-|-RRB-|_
Sigma70|sigma70|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 62214|62214|CD|_ -RRB-|-rrb-|-RRB-|_
Sigma70|sigma70|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 64194|64194|CD|_ -RRB-|-rrb-|-RRB-|_
Sigma70|sigma70|NN|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 100ug|100ug|JJ|_
Sigma70|sigma70|NN|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
Sigma70|sigma70|NN|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 100ug|100ug|JJ|_
Strain|strain|NN|_ MG1655|mg1655|NN|_ or|or|CC|_ isogenic|isogenic|JJ|_ strain|strain|NN|_ MG1655|mg1655|NN|_ HA3|ha3|NN|_ :|:|:|_ :|:|:|_ nusG|nusg|NN|GEN cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ www.genome.wisc.edu|www.genome.wisc.edu|NN|_
VALUE|value|NN|_ =|=|JJ|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ Cy3|cy3|NN|_ _|_|NN|_ signal|signal|NN|_
VALUE|value|NN|_ =|=|JJ|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ Cy5|cy5|NN|_ _|_|NN|_ signal|signal|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ AE|ae|NN|_ _|_|NN|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ AE|ae|NN|_ _|_|NN|_ 2|2|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|NN|_ aerobic|aerobic|JJ|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ ANA|ANA|NNP|_ _|_|SYM|_ 1|1|CD|_
E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ ANA|ANA|NNP|_ _|_|NN|_ 2|2|CD|_
E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ 15|15|CD|_ min|min|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ CORM-2|corm-2|NN|_ treated|treat|VBN|_ _|_|SYM|_ aerobic|aerobic|JJ|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ CORM-2|corm-2|NN|_ treated|treat|VBN|_ _|_|SYM|_ anaerobic|anaerobic|JJ|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ CORM|CORM|NNP|_ _|_|CD|_ AE|AE|NNP|_ _|_|SYM|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ CORM|CORM|NNP|_ _|_|CD|_ AE|AE|NNP|_ _|_|NN|_ 2|2|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ CORM|CORM|NNP|_ _|_|NNP|_ ANA|ANA|NNP|_ _|_|SYM|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ CORM|CORM|NNP|_ _|_|NNP|_ ANA|ANA|NNP|_ _|_|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Scanned|scan|VBD|_ arrays|array|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Affymetrix|Affymetrix|NNP|_ GCOS|GCOS|NNP|_ 1.4|1.4|CD|_ software|software|NN|_ to|to|TO|_ obtain|obtain|VB|_ Detection|detection|NN|_ calls|call|NNS|_ and|and|CC|_ Expression|expression|NN|_ values|value|NNS|_ based|base|VBN|_ on|on|IN|_ MAS|MAS|NNP|_ 5.0|5.0|CD|_ algorithms|algorithm|NNS|_ .|.|.|_ All|all|DT|_ arrays|array|NNS|_ were|be|VBD|_ scaled|scale|VBN|_ to|to|TO|_ a|a|DT|_ target|target|NN|_ value|value|NN|_ of|of|IN|_ 500|500|CD|_ .|.|.|_
The|the|DT|_ hot-phenol|hot-phenol|NN|_ method|method|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ two|two|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_ of|of|IN|_ cells|cell|NNS|_ grown|grow|VBN|_ aerobically|aerobically|RB|_
The|the|DT|_ hot-phenol|hot-phenol|NN|_ method|method|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ two|two|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_ of|of|IN|_ cells|cell|NNS|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ μM|μm|NN|_ CORM-2|corm-2|NN|_ during|during|IN|_ 15|15|CD|_ min|min|NN|_ .|.|.|_
The|the|DT|_ hot-phenol|hot-phenol|NN|_ method|method|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ two|two|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_ of|of|IN|_ cells|cell|NNS|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_
The|the|DT|_ hot-phenol|hot-phenol|NN|_ method|method|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ two|two|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_ of|of|IN|_ cells|cell|NNS|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ μM|μm|NN|_ CORM-2|corm-2|NN|_ during|during|IN|_ 15|15|CD|_ min|min|NN|_ .|.|.|_
Acid|acid|NN|_ adaptation|adaptation|NN|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ at|at|IN|_ pH|ph|NN|_ 5.0|5.0|CD|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ acid-stress|acid-stress|NN|_ at|at|IN|_ pH|ph|NN|_ 3.0|3.0|CD|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_
Acid|acid|NN|_ shocking|shocking|JJ|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ at|at|IN|_ pH|ph|NN|_ 3.0|3.0|CD|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_
Acid|acid|NN|_ shocking|shocking|JJ|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ at|at|IN|_ pH|ph|NN|_ 3.0|3.0|CD|_ -LRB-|-lrb-|-LRB-|_ unbuffered|unbuffered|JJ|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED overnight|overnight|JJ|_ and|and|CC|_ subcultured|subculture|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED overnight|overnight|JJ|_ and|and|CC|_ subcultured|subculture|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ prior|prior|RB|_ to|to|TO|_ acid|acid|NN|_ stress|stress|NN|_
Control|Control|NNP|_ treatment|treatment|NN|_ .|.|.|_ Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 7.4|7.4|CD|_ -LRB-|-lrb-|-LRB-|_ unstressed|unstressed|JJ|_ -RRB-|-rrb-|-RRB-|_
Cy3|cy3|NN|_ labeled|label|VBN|_ EHEC|EHEC|NNP|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 7.4|7.4|CD|_
Cy3|cy3|NN|_ labeled|label|VBN|_ EHEC|EHEC|NNP|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 7.4|7.4|CD|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_
Cy5|cy5|NN|_ labeled|label|VBN|_ EHEC|ehec|NN|_ acid-adapted|acid-adapted|JJ|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 5|5|CD|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ 30|30|CD|_ minutes|minute|NNS|_ pH|ph|NN|_ 3|3|CD|_
Cy5|cy5|NN|_ labeled|label|VBN|_ EHEC|EHEC|NNP|_ acid-stressed|acid-stressed|JJ|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 3|3|CD|_ ,|,|,|_ 15|15|CD|_ minutes|minute|NNS|_
Cy5|cy5|NN|_ labeled|label|VBN|_ EHEC|EHEC|NNP|_ acid-stressed|acid-stressed|JJ|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 3|3|CD|_ ,|,|,|_ 30minutes|30minutes|CD|_
EHEC|ehec|NN|_ strain|strain|NN|_ 86-24|86-24|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_
Signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ averaged|average|VBN|_ among|among|IN|_ the|the|DT|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_ Two|two|CD|_ types|type|NNS|_ of|of|IN|_ data|data|NN|_ analysis|analysis|NN|_ were|be|VBD|_ performed|perform|VBN|_ :|:|:|_ to|to|TO|_ indentify|indentify|VB|_ density-dependent|density-dependent|JJ|_ changes|change|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ ,|,|,|_ single|single|JJ|_ averaged|average|VBD|_ normalized|normalize|VBN|_ signal|signal|NN|_ intensities|intensity|NNS|_ for|for|IN|_ each|each|DT|_ treatment|treatment|NN|_ point|point|NN|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ the|the|DT|_ average|average|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ unstressed|unstressed|JJ|_ control|control|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ .|.|.|_ Genes|gene|NNS|_ which|which|WDT|_ showed|show|VBD|_ a|a|DT|_ relative|relative|JJ|_ signal|signal|NN|_ log2ratio|log2ratio|NN|_ -LRB-|-lrb-|-LRB-|_ SLR|slr|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ above|above|IN|_ 1.0|1.0|CD|_ or|or|CC|_ below|below|IN|_ -1.0|-1.0|CD|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
Signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ averaged|average|VBN|_ among|among|IN|_ the|the|DT|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_ Two|two|CD|_ types|type|NNS|_ of|of|IN|_ data|data|NN|_ analysis|analysis|NN|_ were|be|VBD|_ performed|perform|VBN|_ :|:|:|_ to|to|TO|_ indentify|indentify|VB|_ density-dependent|density-dependent|JJ|_ changes|change|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ ,|,|,|_ single|single|JJ|_ averaged|average|VBD|_ normalized|normalize|VBN|_ signal|signal|NN|_ intensities|intensity|NNS|_ for|for|IN|_ each|each|DT|_ treatment|treatment|NN|_ point|point|NN|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ the|the|DT|_ average|average|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ unstressed|unstressed|JJ|_ control|control|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ .|.|.|_ Genes|gene|NNS|_ which|which|WDT|_ showed|show|VBD|_ a|a|DT|_ relative|relative|JJ|_ signal|signal|NN|_ log2ratio|log2ratio|NN|_ -LRB-|-lrb-|-LRB-|_ SLR|slr|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ above|above|IN|_ 1.0|1.0|CD|_ or|or|CC|_ below|below|IN|_ -1.0|-1.0|CD|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
Treatment|treatment|NN|_ 1|1|CD|_ :|:|:|_ UA30|ua30|NN|_ -LRB-|-lrb-|-LRB-|_ EHEC|ehec|NN|_ 86-24|86-24|CD|_ exposed|expose|VBN|_ to|to|TO|_ pH|ph|NN|_ 3|3|CD|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Treatment|treatment|NN|_ 2|2|CD|_ :|:|:|_ AA30|aa30|NN|_ -LRB-|-lrb-|-LRB-|_ EHEC|ehec|NN|_ 86-24|86-24|CD|_ pH|ph|NN|_ 5.0|5.0|CD|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ 30|30|CD|_ min|min|NN|_ pH|ph|NN|_ 3.0|3.0|CD|_ -RRB-|-rrb-|-RRB-|_
Treatment|treatment|NN|_ 3|3|CD|_ :|:|:|_ UA15|ua15|NN|_ -LRB-|-lrb-|-LRB-|_ EHEC|ehec|NN|_ 86-24|86-24|CD|_ exposed|expose|VBN|_ to|to|TO|_ pH|ph|NN|_ 3|3|CD|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
BW25113|bw25113|NN|_
BW25113|bw25113|NN|_ mqsR|mqsr|NN|GEN mutant|mutant|NN|_ at|at|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ LB|lb|NN|_ 37C|37c|NN|_ suspension|suspension|NN|_ cell|cell|NN|_
BW25113|bw25113|NN|_ wt|wt|JJ|_ at|at|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ LB|lb|NN|_ 37C|37c|NN|_ suspension|suspension|NN|_ cell|cell|NN|_
Chipchip|chipchip|NN|_ BW25113|bw25113|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ mqsR|mqsr|NN|GEN mutant|mutant|NN|_ at|at|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ LB|lb|NN|_ 37C|37c|NN|_ suspension|suspension|NN|_ cell|cell|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ wt|wt|JJ|_ at|at|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ LB|lb|NN|_ 37C|37c|NN|_ suspension|suspension|NN|_ cell|cell|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
His-tagged|his-tagged|JJ|_ DNA|dna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ wild|wild|JJ|_ type|type|NN|_ BW25113|bw25113|NN|_
His-tagged|his-tagged|JJ|_ DNA|dna|NN|_ extracted|extract|VBN|_ from|from|IN|_ planktonic|planktonic|JJ|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ wild|wild|JJ|_ type|type|NN|_ BW25113|bw25113|NN|_
MAS|mas|NN|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ suspension|suspension|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ suspension|suspension|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ mqsR|mqsr|NN|GEN deleted|delete|VBN|_ mutant|mutant|JJ|_ after|after|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ suspension|suspension|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 24|24|CD|_ h|h|NN|_ at|at|IN|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0oC|0oc|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0oC|0oc|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ at|at|IN|_ 37oC|37oc|NN|_ under|under|IN|_ 2|2|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ planktonic|planktonic|JJ|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ at|at|IN|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ planktonic|planktonic|JJ|_ cells|cell|NNS|_ were|be|VBD|_ quickly|quickly|RB|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ at|at|IN|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ adding|add|VBG|_ 0.5|0.5|CD|_ %|%|NN|_ L-arabinose|l-arabinose|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 24|24|CD|_ h|h|NN|_
10,000|10,000|CD|_ U|U|NNP|_ Pencillin|Pencillin|NNP|_ G|G|NNP|_ in|in|IN|_ media|media|NNS|_
72|72|CD|_ hr|hr|NN|_ colony|colony|NN|_ growth|growth|NN|_ equiv|equiv|NN|_ .|.|.|_ to|to|TO|_ wildtype|wildtype|JJ|_ colony|colony|NN|_ size|size|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
L-form|l-form|NN|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ +|+|CC|_ Sucrose|sucrose|NN|_ +|+|CC|_ MgSO4|mgso4|NN|_ +|+|CC|_ Pen|pen|NN|_ G|g|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
L-form|l-form|NN|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ +|+|CC|_ Sucrose|sucrose|NN|_ +|+|CC|_ MgSO4|mgso4|NN|_ +|+|CC|_ Pen|pen|NN|_ G|g|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
L-form|l-form|NN|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ +|+|CC|_ Sucrose|sucrose|NN|_ +|+|CC|_ MgSO4|mgso4|NN|_ +|+|CC|_ Pen|pen|NN|_ G|g|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
L-form|l-form|JJ|_ colony|colony|NN|_ morphology|morphology|NN|_
MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ Kit|kit|NN|_
overnight|overnight|JJ|_ colony|colony|NN|_ growth|growth|NN|_
strain|strain|NN|_ :|:|:|_ L-form|l-form|JJ|_
strain|strain|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ GCOS|gcos|NN|_ 1.4|1.4|CD|_ software|software|NN|_ .|.|.|_ All|all|DT|_ probe|probe|NN|_ sets|set|VBZ|_ scaling|scale|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ a|a|DT|_ target|target|NN|_ signal|signal|NN|_ value|value|NN|_ of|of|IN|_ 500|500|CD|_ .|.|.|_ No|no|DT|_ normalization|normalization|NN|_ was|be|VBD|_ performed|perform|VBN|_ .|.|.|_
wildtype|wildtype|JJ|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
wildtype|wildtype|JJ|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
wildtype|wildtype|JJ|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
wildtype|wildtype|JJ|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ +|+|CC|_ Sucrose|sucrose|NN|_ +|+|CC|_ MgSO4|mgso4|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
wildtype|wildtype|JJ|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ +|+|CC|_ Sucrose|sucrose|NN|_ +|+|CC|_ MgSO4|mgso4|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
wildtype|wildtype|JJ|_ ,|,|,|_ brain|brain|NN|_ heart|heart|NN|_ infusion|infusion|NN|_ agar|agar|NN|_ +|+|CC|_ Sucrose|sucrose|NN|_ +|+|CC|_ MgSO4|mgso4|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
wildtype|wildtype|JJ|_ colony|colony|NN|_ morphology|morphology|NN|_
Ambion|Ambion|NNP|_ RiboPure|RiboPure|NNP|_ RNA|rna|NN|_ Isolation|isolation|NN|_
Data|Data|NNP|_ included|include|VBD|_ in|in|IN|_ file|file|NN|_ has|have|VBZ|_ not|not|RB|_ been|be|VBN|_ processed|process|VBN|_ other|other|JJ|_ than|than|IN|_ those|those|DT|_ protocols|protocol|NNS|_ within|within|IN|_ GCOSv1|gcosv1|NN|_ .4|.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ AI3|ai3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ Epinephrine|epinephrine|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ grown|grow|VBN|_ in|in|IN|_ LB|LB|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ in|in|IN|_ LB|LB|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ kdpE|kdpe|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ kdpE|kdpe|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseB|qseb|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseB|qseb|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_ grown|grow|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ AI3|ai3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_ grown|grow|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ Epinephrine|epinephrine|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN mutant|mutant|JJ|_ grown|grow|VBN|_ in|in|IN|_ LB|LB|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN mutant|mutant|NN|_ in|in|IN|_ DMEM|DMEM|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN mutant|mutant|NN|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ AI3|ai3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN mutant|mutant|NN|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ epinephrine|epinephrine|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_ qseC|qsec|NN|GEN mutant|mutant|NN|_ in|in|IN|_ LB|LB|NNP|_
grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ in|in|IN|_ DMEM|DMEM|NNP|_
grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ 50|50|CD|_ uM|um|NN|_ epinephrine|epinephrine|NN|_
grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ AI3|ai3|NN|_
grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ AI3|ai3|NN|_ signaling|signaling|NN|_ molecule|molecule|NN|_
grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ in|in|IN|_ DMEM|dmem|NN|_ with|with|IN|_ Epinephrine|epinephrine|NN|_
grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ in|in|IN|_ LB|LB|NNP|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 8624|8624|CD|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ 8624|8624|CD|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ 8624|8624|CD|_ kdpE|kdpe|NN|GEN mutant|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ 8624|8624|CD|_ qseB|qseb|NN|GEN mutant|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ 8624|8624|CD|_ qseC|qseC|NNP|GEN
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ 8624|8624|CD|_ qseC|qsec|NN|GEN mutant|mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ B-a|b-a|JJ|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ B-b|b-b|JJ|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ B|b|NN|_ DNA|dna|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12-a|k12-a|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12-b|k12-b|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12-c|k12-c|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12-d|k12-d|JJ|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_ DNA|dna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Genomic|genomic|JJ|_ bacterial|bacterial|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ following|follow|VBG|_ the|the|DT|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Maniatis|Maniatis|NNP|_ Sambrook|Sambrook|NNP|_ -LRB-|-lrb-|-LRB-|_ Sambrook|Sambrook|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1989|1989|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ sonicated|sonicate|VBN|_ in|in|IN|_ a|a|DT|_ Bioruptor|Bioruptor|NNP|_ -LRB-|-lrb-|-LRB-|_ Diagenode|Diagenode|NNP|_ ,|,|,|_ Liege|Liege|NNP|_ ,|,|,|_ Belgium|Belgium|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ fragments|fragment|NNS|_ of|of|IN|_ approximately|approximately|RB|_ 500|500|CD|_ bp|bp|NN|_ .|.|.|_
Signals|signal|NNS|_ of|of|IN|_ each|each|DT|_ slide|slide|NN|_ were|be|VBD|_ smoothed|smooth|VBN|_ using|use|VBG|_ the|the|DT|_ NMPP|nmpp|NN|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ Wang|Wang|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2006|2006|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Normalisation|Normalisation|NNP|_ per|per|IN|_ chip|chip|NN|_ to|to|TO|_ 50th|50th|JJ|_ percentile|percentile|NN|_ and|and|CC|_ further|further|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ v7|v7|NN|_ .3.1|.3.1|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Basel|Basel|NNP|_ ,|,|,|_ Switzerland|Switzerland|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ B|b|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Adenosine|adenosine|NN|_ addition|addition|NN|_
Alanine|Alanine|NNP|_ addition|addition|NN|_
Amino|amino|NN|_ acid|acid|NN|_ or|or|CC|_ nucleotide|nucleotide|NN|_ added|add|VBD|_ to|to|TO|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP not|not|RB|_ exceeding|exceed|VBG|_ 1|1|CD|_
Arginine|arginine|NN|_ addition|addition|NN|_
Aspartate|aspartate|NN|_ addition|addition|NN|_
Cysteine|cysteine|NN|_ addition|addition|NN|_
Cytidine|cytidine|NN|_ addition|addition|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ perturbation|perturbation|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ specific|specific|JJ|_ perturbation|perturbation|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ after|after|IN|_ 6-8|6-8|CD|_ generations|generation|NNS|_ after|after|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Glutamate|glutamate|JJ|_ addition|addition|NN|_
Glutamine|Glutamine|NNP|_ addition|addition|NN|_
Glycine|Glycine|NNP|_ addition|addition|NN|_
Guanosine|Guanosine|NNP|_ addition|addition|NN|_
Histidine|Histidine|NNP|_ addition|addition|NN|_
Images|image|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ software|software|NN|_
Isoleucine|isoleucine|NN|_ addition|addition|NN|_
Lysine|Lysine|NNP|_ addition|addition|NN|_
Median|median|JJ|_ of|of|IN|_ intensity|intensity|NN|_ data|datum|NNS|_ was|be|VBD|_ extracted|extract|VBN|_ ,|,|,|_ LOESS|LOESS|NNP|_ normalized|normalize|VBD|_ and|and|CC|_ an|a|DT|_ ANOVA|ANOVA|NNP|_ model|model|NN|_ was|be|VBD|_ fit|fit|VBN|_ using|use|VBG|_ the|the|DT|_ MAANOVA|MAANOVA|NNP|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ .|.|.|_ The|the|DT|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ Cy5|cy5|NN|_
Methionine|methionine|NN|_ addition|addition|NN|_
Phenylalanine|Phenylalanine|NNP|_ addition|addition|NN|_
Proline|Proline|NNP|_ addition|addition|NN|_
Serine|serine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Adenosine|Adenosine|NNP|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Alanine|alanine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Arginine|arginine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Aspartate|Aspartate|NNP|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ before|before|IN|_ perturbation|perturbation|NN|_ -RRB-|-rrb-|-RRB-|_
stress|stress|NN|_ :|:|:|_ Cysteine|cysteine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Cytidine|cytidine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Glutamate|glutamate|JJ|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Glutamine|glutamine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Glycine|glycine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Guanosine|Guanosine|NNP|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Histidine|histidine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Isoleucine|isoleucine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Lysine|lysine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Methionine|methionine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Phenylalanine|phenylalanine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Proline|Proline|NNP|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Serine|serine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Threonine|threonine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Thymidine|Thymidine|NNP|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Tryptophan|tryptophan|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Uridine|uridine|NN|_ addition|addition|NN|_
stress|stress|NN|_ :|:|:|_ Valine|Valine|NNP|_ addition|addition|NN|_
Threonine|threonine|NN|_ addition|addition|NN|_
Thymidine|Thymidine|NNP|_ addition|addition|NN|_
Total|Total|NNP|_ RNA|RNA|NNP|_ extracted|extract|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNEASY|RNEASY|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ directions|direction|NNS|_
Tryptophan|Tryptophan|NNP|_ addition|addition|NN|_
Uridine|uridine|NN|_ addition|addition|NN|_
Valine|Valine|NNP|_ addition|addition|NN|_
antibody|antibody|NN|_ :|:|:|_ IgG|igg|NN|_
antibody|antibody|NN|_ :|:|:|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ -LRB-|-lrb-|-LRB-|_ NT63|nt63|NN|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ at|at|IN|_ appropriate|appropriate|JJ|_ cell|cell|NN|_ density|density|NN|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ by|by|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 25|25|CD|_ min|min|NN|_ .|.|.|_ Following|follow|VBG|_ quenching|quench|VBG|_ the|the|DT|_ unused|unused|JJ|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 125|125|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ Buffered|buffer|VBN|_ Saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ washed|wash|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ composed|compose|VBN|_ of|of|IN|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ ug|ug|NN|_
condition|condition|NN|_ :|:|:|_ heat-shocked|heat-shocked|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
condition|condition|NN|_ :|:|:|_ mid-exponential|mid-exponential|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
condition|condition|NN|_ :|:|:|_ mid-exponential|mid-exponential|JJ|_ condition|condition|NN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
condition|condition|NN|_ :|:|:|_ nitrogen-limiting|nitrogen-limiting|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
condition|condition|NN|_ :|:|:|_ stationary|stationary|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ RNAP|rnap|NN|_ beta-subunit|beta-subunit|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ -LRB-|-lrb-|-LRB-|_ Upstate|upstate|JJ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ mock-IP|mock-ip|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ RNAP|rnap|NN|_ beta-subunit|beta-subunit|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ NT63|nt63|NN|_ mouse|mouse|NN|_ antibody|antibody|NN|_ .|.|.|_
E.coli|e.coli|NNS|_ _|_|VBP|_ heat|heat|NN|_ _|_|NN|_ dynamic|dynamic|JJ|_ _|_|NN|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ heat|heat|NN|_ _|_|NN|_ dynamic|dynamic|JJ|_ _|_|NN|_ 2|2|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ log|log|NN|_ _|_|NN|_ dynamic|dynamic|JJ|_ _|_|NN|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ log|log|NN|_ _|_|NN|_ dynamic|dynamic|JJ|_ _|_|NN|_ 2|2|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ log|log|NN|_ _|_|NN|_ dynamic|dynamic|JJ|_ _|_|NN|_ 3|3|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ log|log|NN|_ _|_|SYM|_ rif|rif|FW|_ _|_|FW|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ log|log|NN|_ _|_|CD|_ rif|rif|NN|_ _|_|NN|_ 2|2|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ log|log|NN|_ _|_|SYM|_ rif|rif|FW|_ _|_|FW|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|_ complete|complete|JJ|_ medium|medium|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|_ complete|complete|JJ|_ medium|medium|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ ~|~|NN|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|_ complete|complete|JJ|_ medium|medium|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ .|.|.|_ For|for|IN|_ heat-shock|heat-shock|NN|_ ,|,|,|_ culture|culture|NN|_ was|be|VBD|_ mix|mix|NN|_ with|with|IN|_ pre-warmed|pre-warmed|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 45|45|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ W2|w2|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ nitrogen-limiting|nitrogen-limiting|JJ|_ condition|condition|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Powell|Powell|NNP|_ ,|,|,|_ B.|B.|NNP|_ S.|S.|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ J|j|NN|_ of|of|IN|_ Biol|Biol|NNP|_ .|.|.|_ Chem|Chem|NNP|_ .270|.270|CD|_ -LRB-|-lrb-|-LRB-|_ 9|9|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 4822|4822|CD|_ -RRB-|-rrb-|-RRB-|_
E.coli|e.coli|NNS|_ _|_|VBP|_ nitrogen|nitrogen|NN|_ _|_|NN|_ dynamic|dynamic|JJ|_ _|_|NN|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ nitrogen|nitrogen|NN|_ _|_|NN|_ dynamic|dynamic|JJ|_ _|_|NN|_ 2|2|CD|_
E.coli|e.coli|NNS|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ heat-shocked|heat-shocked|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
E.coli|e.coli|NNS|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ mid-exponential|mid-exponential|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
E.coli|e.coli|NNS|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ mid-exponential|mid-exponential|JJ|_ condition|condition|NN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
E.coli|e.coli|NNS|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ nitrogen-limiting|nitrogen-limiting|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
E.coli|e.coli|NNS|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ stationary|stationary|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ stat|stat|NN|_ _|_|CD|_ dynamic|dynamic|JJ|_ _|_|NN|_ 1|1|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ stat|stat|NN|_ _|_|CD|_ dynamic|dynamic|JJ|_ _|_|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Input|input|NN|_ DNA|dna|NN|_ from|from|IN|_ heat-shocked|heat-shocked|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ mid-exponential|mid-exponential|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ mid-exponential|mid-exponential|JJ|_ condition|condition|NN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ nitrogen-limiting|nitrogen-limiting|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ stationary|stationary|JJ|_ condition|condition|NN|_ without|without|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_
reference|reference|NN|_ :|:|:|_ Input|input|NN|_ DNA|dna|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
test|test|NN|_ :|:|:|_ ChIP|chip|NN|_ DNA|dna|NN|_
The|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ per|per|IN|_ channel|channel|NN|_ quantile|quantile|NN|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 19|19|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 185|185|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ IP|IP|NNP|_
5|5|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 1|1|CD|_
bovine-biased-1|bovine-biased-1|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
bovine-biased-2|bovine-biased-2|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
bovine-biased-3|bovine-biased-3|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
bovine-biased-4|bovine-biased-4|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
clinical-1|clinical-1|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
Clinical-1|clinical-1|NN|_ vs|vs|CC|_ Bovine-biased-1|bovine-biased-1|NN|_
Clinical-1|clinical-1|NN|_ vs|vs|CC|_ Bovine-biased-2|bovine-biased-2|NN|_
Clinical-1|clinical-1|NN|_ vs|vs|CC|_ Bovine-biased-3|bovine-biased-3|NN|_
Clinical-1|clinical-1|NN|_ vs|vs|CC|_ Bovine-biased-4|bovine-biased-4|NN|_
clinical-2|clinical-2|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
Clinical-2|clinical-2|NN|_ vs|vs|CC|_ Bovine-biased-1|bovine-biased-1|NN|_
Clinical-2|clinical-2|NN|_ vs|vs|CC|_ Bovine-biased-2|bovine-biased-2|NN|_
Clinical-2|clinical-2|NN|_ vs|vs|CC|_ Bovine-biased-3|bovine-biased-3|NN|_
Clinical-2|clinical-2|NN|_ vs|vs|CC|_ Bovine-biased-4|bovine-biased-4|NN|_
clinical-3|clinical-3|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
Clinical-3|clinical-3|NN|_ vs|vs|CC|_ Bovine-biased-1|bovine-biased-1|NN|_
Clinical-3|clinical-3|NN|_ vs|vs|CC|_ Bovine-biased-2|bovine-biased-2|NN|_
Clinical-3|clinical-3|NN|_ vs|vs|CC|_ Bovine-biased-3|bovine-biased-3|NN|_
Clinical-3|clinical-3|NN|_ vs|vs|CC|_ Bovine-biased-4|bovine-biased-4|NN|_
clinical-4|clinical-4|NN|_ strain|strain|NN|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ growth|growth|NN|_
Clinical-4|clinical-4|NN|_ vs|vs|CC|_ Bovine-biased-1|bovine-biased-1|NN|_
Clinical-4|clinical-4|NN|_ vs|vs|CC|_ Bovine-biased-2|bovine-biased-2|NN|_
Clinical-4|clinical-4|NN|_ vs|vs|CC|_ Bovine-biased-3|bovine-biased-3|NN|_
Clinical-4|clinical-4|NN|_ vs|vs|CC|_ Bovine-biased-4|bovine-biased-4|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
replicate|replicate|VBP|_ :|:|:|_ 3|3|CD|_
replicate|replicate|VB|_ :|:|:|_ 4|4|CD|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10915|tw10915|NN|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10916|tw10916|NN|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10917|tw10917|NN|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10938|tw10938|NN|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10948|tw10948|NN|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10950|tw10950|NN|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10957|tw10957|NN|_
strain|strain|NN|_ :|:|:|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|FW|_ H7|h7|NN|_ strain|strain|NN|_ TW10967|tw10967|NN|_
The|the|DT|_ microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 2.2.1|2.2.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ MAANOVA|MAANOVA|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.98.8|0.98.8|CD|_ -RRB-|-rrb-|-RRB-|_ package|package|NN|_ .|.|.|_ Raw|raw|NN|_ intensity|intensity|NN|_ values|value|NNS|_ from|from|IN|_ replicate|replicate|VBP|_ probes|probe|NNS|_ were|be|VBD|_ averaged|average|VBN|_ and|and|CC|_ log2|log2|NN|_ transformed|transform|VBN|_ after|after|IN|_ normalization|normalization|NN|_ with|with|IN|_ the|the|DT|_ pin-tip|pin-tip|JJ|_ LOWESS|lowess|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ normalized|normalize|VBN|_ intensity|intensity|NN|_ values|value|NNS|_ were|be|VBD|_ fitted|fit|VBN|_ to|to|TO|_ a|a|DT|_ mixed|mixed|JJ|_ model|model|NN|_ ANOVA|ANOVA|NNP|_ considering|consider|VBG|_ array|array|NN|_ and|and|CC|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ as|as|IN|_ random|random|JJ|_ factors|factor|NNS|_ and|and|CC|_ dye|dye|VB|_ ,|,|,|_ strain|strain|NN|_ as|as|IN|_ fixed|fixed|JJ|_ factors|factor|NNS|_ .|.|.|_ The|the|DT|_ linear|linear|JJ|_ model|model|NN|_ tested|test|VBN|_ was|be|VBD|_ Y|y|NN|_ -LRB-|-lrb-|-LRB-|_ intensity|intensity|NN|_ -RRB-|-rrb-|-RRB-|_ =|=|JJ|_ array|array|NN|_ +|+|CC|_ dye|dye|VB|_ +|+|CC|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ clinical|clinical|JJ|_ or|or|CC|_ bovine-biased|bovine-biased|JJ|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ error|error|NN|_ .|.|.|_ Significant|significant|JJ|_ differences|difference|NNS|_ in|in|IN|_ expression|expression|NN|_ due|due|JJ|_ to|to|TO|_ strain|strain|NN|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ Fs|f|NNS|_ test|test|NN|_ in|in|IN|_ MAANOVA|MAANOVA|NNP|_ which|which|WDT|_ uses|use|VBZ|_ a|a|DT|_ shrinkage|shrinkage|NN|_ estimator|estimator|NN|_ for|for|IN|_ gene-specific|gene-specific|JJ|_ variance|variance|NN|_ components|component|NNS|_ that|that|WDT|_ makes|make|VBZ|_ no|no|DT|_ assumption|assumption|NN|_ about|about|IN|_ the|the|DT|_ variances|variance|NNS|_ across|across|IN|_ genes|gene|NNS|_ with|with|IN|_ 500|500|CD|_ random|random|JJ|_ permutations|permutation|NNS|_ to|to|TO|_ estimate|estimate|VB|_ the|the|DT|_ p-values|p-value|NNS|_ .|.|.|_ The|the|DT|_ q-value|q-value|JJ|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ determining|determine|VBG|_ the|the|DT|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAM|SAM|NNP|_ provided|provide|VBN|_ by|by|IN|_ TMEV|tmev|NN|_ was|be|VBD|_ also|also|RB|_ used|use|VBN|_ for|for|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
The|the|DT|_ microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 2.2.1|2.2.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ MAANOVA|MAANOVA|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.98.8|0.98.8|CD|_ -RRB-|-rrb-|-RRB-|_ package|package|NN|_ .|.|.|_ Raw|raw|NN|_ intensity|intensity|NN|_ values|value|NNS|_ from|from|IN|_ replicate|replicate|VBP|_ probes|probe|NNS|_ were|be|VBD|_ averaged|average|VBN|_ and|and|CC|_ log2|log2|NN|_ transformed|transform|VBN|_ after|after|IN|_ normalization|normalization|NN|_ with|with|IN|_ the|the|DT|_ pin-tip|pin-tip|JJ|_ LOWESS|lowess|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ normalized|normalize|VBN|_ intensity|intensity|NN|_ values|value|NNS|_ were|be|VBD|_ fitted|fit|VBN|_ to|to|TO|_ a|a|DT|_ mixed|mixed|JJ|_ model|model|NN|_ ANOVA|ANOVA|NNP|_ considering|consider|VBG|_ array|array|NN|_ and|and|CC|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ as|as|IN|_ random|random|JJ|_ factors|factor|NNS|_ and|and|CC|_ dye|dye|VB|_ ,|,|,|_ strain|strain|NN|_ as|as|IN|_ fixed|fixed|JJ|_ factor|factor|NN|_ .|.|.|_ The|the|DT|_ linear|linear|JJ|_ model|model|NN|_ tested|test|VBN|_ was|be|VBD|_ Y|y|NN|_ -LRB-|-lrb-|-LRB-|_ intensity|intensity|NN|_ -RRB-|-rrb-|-RRB-|_ =|=|JJ|_ array|array|NN|_ +|+|CC|_ dye|dye|VB|_ +|+|CC|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ clinical|clinical|JJ|_ or|or|CC|_ bovine-biased|bovine-biased|JJ|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ error|error|NN|_ .|.|.|_ Significant|significant|JJ|_ differences|difference|NNS|_ in|in|IN|_ expression|expression|NN|_ due|due|JJ|_ to|to|TO|_ strain|strain|NN|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ Fs|f|NNS|_ test|test|NN|_ in|in|IN|_ MAANOVA|MAANOVA|NNP|_ which|which|WDT|_ uses|use|VBZ|_ a|a|DT|_ shrinkage|shrinkage|NN|_ estimator|estimator|NN|_ for|for|IN|_ gene-specific|gene-specific|JJ|_ variance|variance|NN|_ components|component|NNS|_ that|that|WDT|_ makes|make|VBZ|_ no|no|DT|_ assumption|assumption|NN|_ about|about|IN|_ the|the|DT|_ variances|variance|NNS|_ across|across|IN|_ genes|gene|NNS|_ with|with|IN|_ 500|500|CD|_ random|random|JJ|_ permutations|permutation|NNS|_ to|to|TO|_ estimate|estimate|VB|_ the|the|DT|_ p-values|p-value|NNS|_ .|.|.|_ The|the|DT|_ q-value|q-value|JJ|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ determining|determine|VBG|_ the|the|DT|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAM|SAM|NNP|_ provided|provide|VBN|_ by|by|IN|_ TMEV|tmev|NN|_ was|be|VBD|_ also|also|RB|_ used|use|VBN|_ for|for|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
TW10915|tw10915|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
TW10916|tw10916|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
TW10917|tw10917|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
TW10938|tw10938|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
TW10948|tw10948|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
TW10950|tw10950|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
TW10957|tw10957|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
TW10967|tw10967|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ upto|upto|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.5|0.5|CD|_ ,|,|,|_ 2.5|2.5|CD|_ h|h|NN|_ after|after|IN|_ inoclulation|inoclulation|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_
Batch|batch|NN|_ cultures|culture|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ %|%|NN|_ Bacto|bacto|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 0.05|0.05|CD|_ %|%|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP ,|,|,|_ 0.05|0.05|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ cross-linking|cross-linking|NN|_ ,|,|,|_ 30|30|CD|_ mL|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 300|300|CD|_ uL|ul|NN|_ 1M|1m|NN|_ sodium|sodium|NN|_ phosphates|phosphate|NNS|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.6|7.6|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 810|810|CD|_ uL|ul|NN|_ 37|37|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ .|.|.|_ Cross-linking|cross-linking|NN|_ was|be|VBD|_ quenched|quench|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 2|2|CD|_ mL|ml|NN|_ 2M|2m|NN|_ glycine|glycine|NN|_ .|.|.|_ Protein-DNA|protein-dna|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cells|cell|NNS|_ grown|grow|VBN|_ to|to|TO|_ early|early|JJ|_ -LRB-|-lrb-|-LRB-|_ 2.4|2.4|CD|_ x|x|CC|_ 10|10|CD|_ ^|^|NN|_ 7|7|CD|_ CFU|CFU|NNP|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ Extraction|extraction|NN|_ :|:|:|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ according|accord|VBG|_ to|to|TO|_ Current|current|JJ|_ Protocols|protocol|NNS|_ in|in|IN|_ Molecular|molecular|JJ|_ Biology|biology|NN|_ .|.|.|_ Protein-DNA|protein-dna|JJ|_ complex|complex|NN|_ isolation|isolation|NN|_ :|:|:|_ Protein-DNA|protein-dna|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ phenol|phenol|NN|_ extraction|extraction|NN|_ with|with|IN|_ 150|150|CD|_ μL|μl|NN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ and|and|CC|_ 500|500|CD|_ μL|μl|NN|_ 25:24:1|25:24:1|CD|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ .|.|.|_ A|a|DT|_ white|white|JJ|_ disk|disk|NN|_ was|be|VBD|_ readily|readily|RB|_ discernible|discernible|JJ|_ at|at|IN|_ the|the|DT|_ aqueous|aqueous|JJ|_
genomic|genomic|JJ|_ _|_|NN|_ ref1|ref1|NN|_
genomic|genomic|JJ|_ _|_|NN|_ ref2|ref2|NN|_
genomic|genomic|JJ|_ _|_|NN|_ ref3|ref3|NN|_
genomic|genomic|JJ|_ _|_|NN|_ ref4|ref4|NN|_
genomic|genomic|JJ|_ _|_|NN|_ ref5|ref5|NN|_
genomic|genomic|JJ|_ _|_|NN|_ ref6|ref6|NN|_
IPOD|ipod|VBD|_ _|_|RB|_ early|early|JJ|_ _|_|NN|_ log|log|NN|_ _|_|NN|_ 1|1|CD|_
IPOD|ipod|NN|_ _|_|RB|_ early|early|JJ|_ _|_|NN|_ log|log|NN|_ _|_|NN|_ 2|2|CD|_
IPOD|ipod|VBD|_ _|_|RB|_ late|late|JJ|_ _|_|NN|_ log|log|NN|_ _|_|NN|_ 1|1|CD|_
IPOD|ipod|NN|_ _|_|CD|_ late|late|JJ|_ _|_|NN|_ log|log|NN|_ _|_|NN|_ 2|2|CD|_
IPOD|ipod|VBD|_ _|_|SYM|_ MDS42|mds42|NN|_
MDS42|mds42|NN|_ DNA|dna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ early-phase|early-phase|JJ|_ DNA-protein|dna-protein|JJ|_ complexes|complex|NNS|_
MG1655|mg1655|NN|_ DNA|dna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ early-phase|early-phase|JJ|_ DNA-protein|dna-protein|JJ|_ complexes|complex|NNS|_
MG1655|mg1655|NN|_ DNA|dna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ late-phase|late-phase|JJ|_ DNA-protein|dna-protein|JJ|_ complexes|complex|NNS|_
MG1655|mg1655|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
MG1655|mg1655|NN|_ RNA|rna|NN|_
RNA|rna|NN|_ _|_|NN|_ 1|1|CD|_
RNA|rna|NN|_ _|_|NN|_ 2|2|CD|_
strain|strain|NN|_ :|:|:|_ MDS42|mds42|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
We|we|PRP|_ developed|develop|VBD|_ in-house|in-house|JJ|_ computational|computational|JJ|_ and|and|CC|_ statistical|statistical|JJ|_ analysis|analysis|NN|_ tools|tool|NNS|_ for|for|IN|_ use|use|NN|_ with|with|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ tiling|tiling|NN|_ array|array|NN|_ .|.|.|_ We|we|PRP|_ used|use|VBD|_ a|a|DT|_ previous|previous|JJ|_ study|study|NN|_ -LRB-|-lrb-|-LRB-|_ Choe|Choe|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2005|2005|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ a|a|DT|_ model|model|NN|_ for|for|IN|_ perfect|perfect|JJ|_ match|match|NN|_ adjustment|adjustment|NN|_ on|on|IN|_ single|single|JJ|_ arrays|array|NNS|_ .|.|.|_ Analysis|analysis|NN|_ scripts|script|NNS|_ were|be|VBD|_ written|write|VBN|_ in|in|IN|_ Perl|Perl|NNP|_ ,|,|,|_ MatLab|MatLab|NNP|_ ,|,|,|_ and|and|CC|_ R|r|NN|_ to|to|TO|_ standardize|standardize|VB|_ the|the|DT|_ statistical|statistical|JJ|_ manipulations|manipulation|NNS|_ across|across|IN|_ all|all|DT|_ data|datum|NNS|_ sets|set|NNS|_ .|.|.|_ The|the|DT|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ the|the|DT|_ scanning|scanning|NN|_ process|process|NN|_ is|be|VBZ|_ a|a|DT|_ CEL|cel|NN|_ file|file|NN|_ .|.|.|_ The|the|DT|_ raw|raw|JJ|_ CEL|cel|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ basis|basis|NN|_ for|for|IN|_ the|the|DT|_ manuscript|manuscript|NN|_ ;|;|:|_ no|no|DT|_ processed|process|VBN|_ data|datum|NNS|_ are|be|VBP|_ available|available|JJ|_ .|.|.|_
antibody|antibody|NN|_ :|:|:|_ Monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ Beta|beta|NN|_ '|'|''|_ subunit|subunit|NN|_ -LRB-|-lrb-|-LRB-|_ NT73|nt73|NN|_ -RRB-|-rrb-|-RRB-|_
antibody|antibody|NN|_ :|:|:|_ Monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ for|for|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ Beta|beta|NN|_ subunit|subunit|NN|_ -LRB-|-lrb-|-LRB-|_ W0002|w0002|NN|_ -RRB-|-rrb-|-RRB-|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250ul|250ul|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ with|with|IN|_ vigorous|vigorous|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|NN|_ -LRB-|-lrb-|-LRB-|_ light|light|JJ|_ scattering|scattering|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ equivalent|equivalent|NN|_ to|to|TO|_ 0.4|0.4|CD|_ OD|od|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ ,|,|,|_ untreated|untreated|JJ|_
reference|reference|NN|_ :|:|:|_ input|input|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ control|control|NN|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 100040|100040|CD|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ Dataset|Dataset|NNP|_ 3427302|3427302|CD|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ -RRB-|-rrb-|-RRB-|_ ChIP-chip|chip-chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ 20ug|20ug|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ ,|,|,|_ untreated|untreated|JJ|_
RNA|rna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Beta|beta|NN|_ -RRB-|-rrb-|-RRB-|_ ChIP|chip|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ ,|,|,|_ untreated|untreated|JJ|_
Strain|strain|NN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ www.genome.wisc.edu|www.genome.wisc.edu|NN|_
The|the|DT|_ log2-ratio|log2-ratio|NN|_ is|be|VBZ|_ computed|compute|VBN|_ and|and|CC|_ scaled|scale|VBN|_ to|to|TO|_ center|center|VB|_ the|the|DT|_ ratio|ratio|NN|_ data|datum|NNS|_ around|around|IN|_ zero|zero|CD|_ .|.|.|_ Scaling|scaling|NN|_ is|be|VBZ|_ performed|perform|VBN|_ by|by|IN|_ subtracting|subtract|VBG|_ the|the|DT|_ bi-weight|bi-weight|JJ|_ mean|mean|NN|_ for|for|IN|_ the|the|DT|_ log2-ratio|log2-ratio|JJ|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ features|feature|NNS|_ on|on|IN|_ the|the|DT|_ array|array|NN|_ from|from|IN|_ each|each|DT|_ log2-ratio|log2-ratio|JJ|_ value|value|NN|_ .|.|.|_
VALUE|value|NN|_ =|=|JJ|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ Cy5|cy5|NN|_ _|_|NN|_ signal|signal|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 4|4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 5|5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 6|6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 7|7|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 8|8|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_ vs.|vs.|CC|_ Control|control|NN|_ Slide|slide|NN|_ 9|9|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ Outside|outside|JJ|_ Control|control|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Inside|inside|IN|_ Acanthamoeba|acanthamoeba|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Outside|outside|JJ|_ Control|control|NN|_
Mixed|Mixed|NNP|_ model|model|NN|_ analysis|analysis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Madsen|Madsen|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2006|2006|CD|_ -RRB-|-rrb-|-RRB-|_ excluding|exclude|VBG|_ slide|slide|NN|_ region|region|NN|_ and|and|CC|_ slide-by-region|slide-by-region|NN|_ interaction|interaction|NN|_ effects|effect|NNS|_ .|.|.|_ The|the|DT|_ value|value|NN|_ column|column|NN|_ was|be|VBD|_ not|not|RB|_ used|use|VBN|_ for|for|IN|_ analysis|analysis|NN|_ or|or|CC|_ in|in|IN|_ publication|publication|NN|_ .|.|.|_ The|the|DT|_ normalized|normalize|VBN|_ values|value|NNS|_ for|for|IN|_ duplicate|duplicate|VBP|_ spots|spot|NNS|_ were|be|VBD|_ averaged|average|VBN|_ within|within|IN|_ each|each|DT|_ array|array|NN|_ to|to|TO|_ produce|produce|VB|_ one|one|CD|_ normalized|normalize|VBD|_ measure|measure|NN|_ of|of|IN|_ expression|expression|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ probe|probe|NN|_ sequences|sequence|NNS|_ and|and|CC|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ -LSB-|-lsb-|-LRB-|_ mean|mean|VB|_ log|log|NN|_ transformed|transform|VBN|_ median|median|JJ|_ centered|centered|JJ|_ lowess|lowess|NN|_ normalized|normalize|VBD|_ signal|signal|NN|_ intensity|intensity|NN|_ -RSB-|-rsb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ lysis|lysis|NN|_ all|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ in|in|IN|_ RNA|rna|NN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Acidic|acidic|JJ|_ phenol|phenol|NN|_ ,|,|,|_ 19|19|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ ice|ice|NN|_ cold|cold|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ lysis|lysis|NN|_ and|and|CC|_ digestion|digestion|NN|_ protocol|protocol|NN|_ was|be|VBD|_ followed|follow|VBN|_ with|with|IN|_ two|two|CD|_ 50|50|CD|_ μl|μl|NN|_ ddH20|ddh20|NN|_ elutions|elution|NNS|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 2|2|CD|_ μl|μl|NN|_ of|of|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ using|use|VBG|_ Microcon|Microcon|NNP|_ YM-30|ym-30|NN|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Millipore|Millipore|NNP|_ ,|,|,|_ Billerica|Billerica|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ quantity|quantity|NN|_ and|and|CC|_ purity|purity|NN|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ an|a|DT|_ ND-1000|nd-1000|NN|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Nanodrop|Nanodrop|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ to|to|TO|_ be|be|VB|_ free|free|JJ|_ of|of|IN|_ contaminating|contaminate|VBG|_ genomic|genomic|JJ|_ DNA|dna|NN|_ by|by|IN|_ absence|absence|NN|_ of|of|IN|_ a|a|DT|_ band|band|NN|_ on|on|IN|_ a|a|DT|_ DNA|dna|NN|_ electrophoresis|electrophoresis|NN|_ gel|gel|NN|_ after|after|IN|_ 30|30|CD|_ rounds|round|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_
BRP|BRP|NNP|_ Induction|induction|NN|_ 10|10|CD|_ Minutes|Minutes|NNPS|_ against|against|IN|_ 5|5|CD|_ Minutes|Minutes|NNPS|_
BRP|BRP|NNP|_ Induction|induction|NN|_ -10|-10|CD|_ minutes|minute|NNS|_ against|against|IN|_ 60|60|CD|_ minutes|minute|NNS|_
BRP|BRP|NNP|_ Induction|induction|NN|_ 20|20|CD|_ minutes|minute|NNS|_ against|against|IN|_ 10|10|CD|_ minutes|minute|NNS|_
BRP|BRP|NNP|_ Induction|induction|NN|_ 30|30|CD|_ minutes|minute|NNS|_ against|against|IN|_ 20|20|CD|_ minutes|minute|NNS|_
BRP|BRP|NNP|_ Induction|induction|NN|_ 45|45|CD|_ minutes|minute|NNS|_ against|against|IN|_ 30|30|CD|_ minutes|minute|NNS|_
BRP|BRP|NNP|_ Induction|induction|NN|_ 5|5|CD|_ minutes|minute|NNS|_ against|against|IN|_ 2|2|CD|_ minutes|minute|NNS|_
BRP|BRP|NNP|_ Induction|induction|NN|_ 60|60|CD|_ minutes|minute|NNS|_ against|against|IN|_ 45|45|CD|_ minutes|minute|NNS|_
E.coli|e.coli|NN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ -10|-10|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ 10|10|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ 2|2|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ 30|30|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ 45|45|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NNS|_ 5|5|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|brp|NN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ BRP|BRP|NNP|_ induction|induction|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ response|response|NN|_ analysis|analysis|NN|_ of|of|IN|_ E.coli|e.coli|NN|_ during|during|IN|_ coexpression|coexpression|NN|_ of|of|IN|_ a|a|DT|_ bacteriocin|bacteriocin|NN|_ release|release|NN|_ protein|protein|NN|_
The|the|DT|_ scanning|scanning|NN|_ process|process|NN|_ of|of|IN|_ the|the|DT|_ hybridized|hybridize|VBN|_ chips|chip|NNS|_ included|include|VBD|_ a|a|DT|_ fourteen-fold|fourteen-fold|JJ|_ scan|scan|VB|_ of|of|IN|_ each|each|DT|_ chip|chip|NN|_ at|at|IN|_ different|different|JJ|_ settings|setting|NNS|_ ,|,|,|_ altering|alter|VBG|_ both|both|CC|_ PMT|PMT|NNP|_ and|and|CC|_ laser|laser|NN|_ power|power|NN|_ settings|setting|NNS|_ .|.|.|_ The|the|DT|_ following|follow|VBG|_ primary|primary|JJ|_ analysis|analysis|NN|_ served|serve|VBD|_ as|as|IN|_ a|a|DT|_ quantification|quantification|NN|_ method|method|NN|_ and|and|CC|_ is|be|VBZ|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Gene|Gene|NNP|_ Pix|Pix|NNP|_ Pro|pro|FW|_ 6.0|6.0|CD|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ ,|,|,|_ Sunnyvale|Sunnyvale|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ tool|tool|NN|_ .|.|.|_
The|the|DT|_ secondary|secondary|JJ|_ analysis|analysis|NN|_ is|be|VBZ|_ subsequently|subsequently|RB|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ data|datum|NNS|_ from|from|IN|_ the|the|DT|_ primary|primary|JJ|_ analysis|analysis|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ data|datum|NNS|_ from|from|IN|_ different|different|JJ|_ scans|scan|NNS|_ is|be|VBZ|_ first|first|JJ|_ searched|search|VBD|_ for|for|IN|_ saturation|saturation|NN|_ effects|effect|NNS|_ ,|,|,|_ which|which|WDT|_ are|be|VBP|_ eliminated|eliminate|VBN|_ .|.|.|_ A|a|DT|_ locally|locally|RB|_ weighted|weighted|JJ|_ linear|linear|JJ|_ regression|regression|NN|_ -LRB-|-lrb-|-LRB-|_ Lowess|lowess|NN|_ -RRB-|-rrb-|-RRB-|_ has|have|VBZ|_ been|be|VBN|_ employed|employ|VBN|_ as|as|IN|_ a|a|DT|_ normalization|normalization|NN|_ method|method|NN|_ in|in|IN|_ order|order|NN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ intensity-dependent|intensity-dependent|JJ|_ effects|effect|NNS|_ .|.|.|_ Due|due|JJ|_ to|to|TO|_ the|the|DT|_ lacking|lack|VBG|_ gene|gene|NN|_ replicates|replicate|VBZ|_ on|on|IN|_ the|the|DT|_ commercial|commercial|JJ|_ whole|whole|JJ|_ genome|genome|NN|_ array|array|NN|_ ,|,|,|_ a|a|DT|_ t-test|t-test|NN|_ could|could|MD|_ not|not|RB|_ be|be|VB|_ applied|apply|VBN|_ .|.|.|_ Instead|instead|RB|_ ,|,|,|_ the|the|DT|_ quotients|quotient|NNS|_ of|of|IN|_ respectively|respectively|RB|_ two|two|CD|_ states|state|NNS|_ have|have|VBP|_ been|be|VBN|_ calculated|calculate|VBN|_ for|for|IN|_ the|the|DT|_ assessment|assessment|NN|_ of|of|IN|_ the|the|DT|_ regulation|regulation|NN|_ .|.|.|_ A|a|DT|_ absolute|absolute|JJ|_ value|value|NN|_ of|of|IN|_ log-ratio|log-ratio|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ base2|base2|NN|_ -RRB-|-rrb-|-RRB-|_ higher|higher|JJR|_ than|than|IN|_ 1|1|CD|_ is|be|VBZ|_ used|use|VBN|_ as|as|IN|_ criteria|criterion|NNS|_ for|for|IN|_ a|a|DT|_ regulated|regulate|VBN|_ gene|gene|NN|_ .|.|.|_
The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 5L|5l|NN|_ defined|define|VBN|_ medium|medium|NN|_ with|with|IN|_ glycerol|glycerol|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ in|in|IN|_ a|a|DT|_ 7L|7l|NN|_ -LRB-|-lrb-|-LRB-|_ total|total|NN|_ -RRB-|-rrb-|-RRB-|_ MBR-bioreactor|mbr-bioreactor|NN|_ .|.|.|_ When|when|WRB|_ the|the|DT|_ OD|od|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ reached|reach|VBD|_ a|a|DT|_ value|value|NN|_ of|of|IN|_ around|around|IN|_ 5|5|CD|_ ,|,|,|_ the|the|DT|_ BAD|BAD|NNP|_ --|--|:|_ promoter|promoter|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ adding|add|VBG|_ 1g|1g|NN|_ per|per|IN|_ litre|litre|NN|_ and|and|CC|_ OD|od|NN|_ arabinose|arabinose|NN|_ to|to|TO|_ the|the|DT|_ medium|medium|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ --|--|:|_ 10|10|CD|_ ,|,|,|_ 0|0|CD|_ ,|,|,|_ 2|2|CD|_ ,|,|,|_ 5|5|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 20|20|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 45|45|CD|_ and|and|CC|_ 60|60|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ induction|induction|NN|_ .|.|.|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ -10|-10|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 30|30|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 45|45|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 5|5|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|brp|NN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 60|60|CD|_ minutes|minute|NNS|_ related|related|JJ|_ to|to|TO|_ point|point|NN|_ of|of|IN|_ BRP|BRP|NNP|_ induction|induction|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ is|be|VBZ|_ extracted|extract|VBN|_ from|from|IN|_ 10|10|CD|_ ^|^|CD|_ 9|9|CD|_ cells|cell|NNS|_ by|by|IN|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ according|accord|VBG|_ to|to|TO|_ Sambrook|Sambrook|NNP|_ et|et|FW|_ al.|al.|FW|_ and|and|CC|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ with|with|IN|_ 5M|5m|NN|_ NaCl|nacl|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ a|a|DT|_ DNAse|dnase|NN|_ I|I|PRP|_ digest|digest|VBP|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ and|and|CC|_ an|a|DT|_ additional|additional|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ step|step|NN|_ is|be|VBZ|_ performed|perform|VBN|_ .|.|.|_ Integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ is|be|VBZ|_ electrophoretically|electrophoretically|RB|_ confirmed|confirm|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ is|be|VBZ|_ extracted|extract|VBN|_ from|from|IN|_ 10|10|CD|_ ^|^|CD|_ 9|9|CD|_ cells|cell|NNS|_ by|by|IN|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ and|and|CC|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ with|with|IN|_ 5M|5m|NN|_ NaCl|nacl|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ a|a|DT|_ DNAse|dnase|NN|_ I|I|PRP|_ digest|digest|VBP|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ minutes|minute|NNS|_ and|and|CC|_ an|a|DT|_ additional|additional|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ step|step|NN|_ is|be|VBZ|_ performed|perform|VBN|_ .|.|.|_ Integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ is|be|VBZ|_ electrophoretically|electrophoretically|RB|_ confirmed|confirm|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
0|0|CD|_ min|min|NN|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_
0min-1|0min-1|NN|_
0min-2|0min-2|JJ|_
0min-3|0min-3|NN|_
0|0|CD|_ min|min|NN|_ ,|,|,|_ unstressed|unstressed|JJ|_
195|195|CD|_ min|min|NN|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_
195min-1|195min-1|CD|_
195min-2|195min-2|JJ|_
195min-3|195min-3|JJ|_
195|195|CD|_ min|min|NN|_ ,|,|,|_ unstressed|unstressed|JJ|_
30|30|CD|_ min|min|NN|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_
30min-1|30min-1|JJ|_
30min-2|30min-2|JJ|_
30min-3|30min-3|JJ|_
30|30|CD|_ min|min|NN|_ ,|,|,|_ unstressed|unstressed|JJ|_
80|80|CD|_ min|min|NN|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_
80min-1|80min-1|CD|_
80min-2|80min-2|CD|_
80min-3|80min-3|CD|_
80|80|CD|_ min|min|NN|_ ,|,|,|_ unstressed|unstressed|JJ|_
Biomass|Biomass|NNP|_ was|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ C|c|NN|_ prior|prior|JJ|_ to|to|TO|_ extraction|extraction|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Midi|Midi|NNP|_ kits|kit|NNS|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ verified|verify|VBN|_ with|with|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Feature|feature|NN|_ fluorescence|fluorescence|NN|_ intensities|intensity|NNS|_ -LSB-|-lsb-|-LRB-|_ F532|f532|NN|_ media-B532|media-b532|NN|_ and|and|CC|_ F635media-B635|f635media-b635|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 6.0|6.0|CD|_ .|.|.|_ Local|local|JJ|_ hybridization|hybridization|NN|_ and|and|CC|_ intensity-dependent|intensity-dependent|JJ|_ artifacts|artifact|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Lowess|lowess|NN|_ normalization|normalization|NN|_ using|use|VBG|_ Standardization|standardization|NN|_ and|and|CC|_ Normalization|normalization|NN|_ of|of|IN|_ Microarray|Microarray|NNP|_ Data|Data|NNP|_ -LRB-|-lrb-|-LRB-|_ SNOMAD|SNOMAD|NNP|_ ,|,|,|_ http|http|NN|_ :|:|:|_
Individual|Individual|NNP|_ clones|clone|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ DH1|dh1|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|M9|NNP|_ MOPS|MOPS|NNP|MED media|media|NNS|_ in|in|IN|_ 300|300|CD|_ mL|ml|NN|_ media|media|NNS|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ baffled|baffle|VBD|_ flasks|flask|NNS|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ DH1|dh1|NN|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 195|195|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 80|80|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ 0.8|0.8|CD|_ %|%|NN|_ n-butanol|n-butanol|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ time|time|NN|_ 0|0|CD|_
81-4420|81-4420|CD|_
83-2315|83-2315|CD|_
86-1390|86-1390|CD|_
86-4220|86-4220|CD|_
87-4725|87-4725|CD|_
88-1861|88-1861|CD|_
88-4299|88-4299|CD|_
89-56-196|89-56-196|CD|_
91-19-172|91-19-172|CD|_
Data|Data|NNP|_ obtained|obtain|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ microarrays|microarray|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ Ratio-based|ratio-based|JJ|_ and|and|CC|_ Lowess|lowess|JJ|_ methods|method|NNS|_ in|in|IN|_ Acuity|acuity|NN|_ 3.1|3.1|CD|_ -LRB-|-lrb-|-LRB-|_ Axon|axon|NN|_ instruments|instrument|NNS|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ analysis|analysis|NN|_ .|.|.|_ The|the|DT|_ normalized|normalize|VBN|_ data|datum|NNS|_ for|for|IN|_ all|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ converted|convert|VBN|_ into|into|IN|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ Fluor|Fluor|NNP|_ 647|647|CD|_
EDL|edl|NN|_ -LRB-|-lrb-|-LRB-|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ Sakai|Sakai|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Overnight|overnight|JJ|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ in|in|IN|_ BHI|BHI|NNP|_ broth|broth|NN|_ .|.|.|_
referece|referece|NN|_ :|:|:|_ The|the|DT|_ three|three|CD|_ genomes|genome|NNS|_ contributing|contribute|VBG|_ to|to|TO|_ the|the|DT|_ ORFs|orf|NNS|_ on|on|IN|_ the|the|DT|_ microarray|microarray|NN|_ .|.|.|_
Sakai|Sakai|NNP|_ -LRB-|-lrb-|-LRB-|_ O157|O157|NNP|_ :|:|:|_ H7|h7|NN|_ -RRB-|-rrb-|-RRB-|_
See|see|VB|_ the|the|DT|_ paper|paper|NN|_ Variation|variation|NN|_ in|in|IN|_ the|the|DT|_ Genomic|genomic|JJ|_ islands|island|NNS|_ of|of|IN|_ porcine|porcine|NN|_ enteropathogenic|enteropathogenic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strains|strain|NNS|_ of|of|IN|_ serogroup|serogroup|NN|_ O45|o45|NN|_ revealed|reveal|VBN|_ by|by|IN|_ comparative|comparative|JJ|_ genomic|genomic|JJ|_ hybridization|hybridization|NN|_ and|and|CC|_ PCR|pcr|NN|_ by|by|IN|_ Bruant|Bruant|NNP|_ and|and|CC|_ Zhang|Zhang|NNP|_ et|et|FW|_ al.|al.|FW|_ 2009|2009|CD|_
strain|strain|NN|_ :|:|:|_ EHEC|ehec|NN|_ strain|strain|NN|_
strain|strain|NN|_ :|:|:|_ Porcine|porcine|NN|_ EPEC|epec|NN|_ strain|strain|NN|_ O45|o45|NN|_
strain|strain|NN|_ :|:|:|_ Rabbit|rabbit|NN|_ EPEC|epec|NN|_ strain|strain|NN|_ O103|o103|NN|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 8000|8000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 100|100|CD|_ μg|μg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
FRIK2000|frik2000|NN|_ Cy3|cy3|NN|_ rep1|rep1|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy5|cy5|NN|_
FRIK2000|frik2000|CD|_ Cy3|cy3|NN|_ rep3|rep3|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy5|cy5|NN|_
FRIK2000|frik2000|CD|_ Cy5|cy5|NN|_ rep2|rep2|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy3|cy3|NN|_
FRIK2000|frik2000|CD|_ Cy5|cy5|NN|_ rep4|rep4|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy3|cy3|NN|_
FRIK966|frik966|NN|_ Cy3|cy3|NN|_ rep1|rep1|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy5|cy5|NN|_
FRIK966|frik966|NN|_ Cy3|cy3|NN|_ rep3|rep3|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy5|cy5|NN|_
FRIK966|frik966|NN|_ Cy5|cy5|NN|_ rep2|rep2|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy3|cy3|NN|_
FRIK966|frik966|NN|_ Cy5|cy5|NN|_ rep4|rep4|NN|_ vs|vs|CC|_ EDL933|edl933|NN|_ pool|pool|NN|_ Cy3|cy3|NN|_
isolate|isolate|NN|_ :|:|:|_ bovine|bovine|JJ|_ isolate|isolate|NN|_ of|of|IN|_ e|e|SYM|_ coli|coli|FW|_ o157|o157|FW|_ :|:|:|_ H7|h7|NN|_ FRIK2000|frik2000|NN|_ lineage|lineage|NN|_ II|ii|CD|_
isolate|isolate|NN|_ :|:|:|_ bovine|bovine|JJ|_ isolate|isolate|NN|_ of|of|IN|_ e|e|SYM|_ coli|coli|FW|_ o157|o157|FW|_ :|:|:|_ H7|h7|NN|_ FRIK966|frik966|NN|_ lineage|lineage|NN|_ II|ii|CD|_
isolate|isolate|NN|_ :|:|:|_ clinical|clinical|JJ|_ isolate|isolate|JJ|_ e|e|SYM|_ coli|coli|FW|_ o157|o157|FW|_ :|:|:|_ H7|h7|NN|_ lineage|lineage|NN|_ I|I|PRP|_
late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ grown|grow|VBN|_ e|e|SYM|_ coli|coli|NNS|_ 966|966|CD|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ solution|solution|NN|_ ,|,|,|_ RNA|rna|NN|_ extracted|extract|VBN|_ with|with|IN|_ qiagen|qiagen|NN|_ RNA|rna|NN|_ bacteria|bacterium|NNS|_ kits|kit|NNS|_
late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ grown|grow|VBN|_ e|e|SYM|_ coli|coli|FW|_ EDL933|edl933|FW|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ solution|solution|NN|_ ,|,|,|_ RNA|rna|NN|_ extracted|extract|VBN|_ with|with|IN|_ qiagen|qiagen|NN|_ RNA|rna|NN|_ bacteria|bacterium|NNS|_ kits|kit|NNS|_
Microarray|Microarray|NNP|_ data|data|NN|_ analyses|analysis|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Acuity|acuity|NN|_ 4.0|4.0|CD|_ software|software|NN|_ .|.|.|_ Slides|slide|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ standard|standard|JJ|_ ratio-based|ratio-based|JJ|_ methods|method|NNS|_ .|.|.|_ Data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ based|base|VBN|_ upon|upon|IN|_ Log|log|NN|_ ratio|ratio|NN|_ -LRB-|-lrb-|-LRB-|_ 635|635|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ EDL933|edl933|NN|_ pooled|pool|VBD|_ reference|reference|NN|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK2000|frik2000|NN|_ rep|rep|NN|GEN 1|1|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK2000|frik2000|NN|_ rep|rep|NN|GEN 2|2|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK2000|frik2000|NN|_ rep|rep|NN|GEN 3|3|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK2000|frik2000|NN|_ rep|rep|NN|GEN 4|4|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK966|frik966|NN|_ rep|rep|NN|GEN 1|1|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK966|frik966|NN|_ rep|rep|NN|GEN 2|2|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK966|frik966|NN|_ rep|rep|NN|GEN 3|3|CD|_
RNA|rna|NN|_ from|from|IN|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ E|e|NN|_ coli|coli|NN|_ FRIK966|frik966|NN|_ rep|rep|NN|GEN 4|4|CD|_
strain|strain|NN|_ :|:|:|_ EDL933|edl933|NN|_
strain|strain|NN|_ :|:|:|_ FRIK2000|frik2000|CD|_
strain|strain|NN|_ :|:|:|_ FRIK966|frik966|NN|_
e.coli|e.coli|NNS|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_
E.coli|e.coli|NN|_ ,37|,37|CD|_ °C|°c|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_
E.coli|e.coli|NN|_ ，|，|NN|_ 37|37|CD|_ °C|°c|NN|_ ，|，|CD|_ 60|60|CD|_ min|min|NN|_
e.coli|e.coli|NNS|_ ,|,|,|_ 43|43|CD|_ °C|°c|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ 43|43|CD|_ °C|°c|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_
E.coli|e.coli|NN|_ ,43|,43|CD|_ °C|°c|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_
E.coli|e.coli|NN|_ ，|，|CD|_ 43|43|CD|_ °C|°c|NN|_ ，|，|CD|_ 60|60|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ heat|heat|NN|_ shock|shock|NN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ using|use|VBG|_ direct|direct|JJ|_ labeling|labeling|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ replicate-1|replicate-1|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ heat|heat|NN|_ shock|shock|NN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ using|use|VBG|_ direct|direct|JJ|_ labeling|labeling|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ replicate-2|replicate-2|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ heat|heat|NN|_ shock|shock|NN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ using|use|VBG|_ PAOD|paod|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ replicate-1|replicate-1|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ heat|heat|NN|_ shock|shock|NN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ using|use|VBG|_ PAOD|paod|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ replicate-2|replicate-2|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ heat|heat|NN|_ shock|shock|NN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ using|use|VBG|_ random|random|JJ|_ priming|priming|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ replicate-1|replicate-1|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ heat|heat|NN|_ shock|shock|NN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ using|use|VBG|_ random|random|JJ|_ priming|priming|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ replicate-2|replicate-2|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
strain|strain|NN|_ :|:|:|_ DH5α|dh5α|NN|_
The|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ a|a|DT|_ space|space|NN|_ and|and|CC|_ intensity-dependant|intensity-dependant|JJ|_ LOWESS|lowess|NN|_ program|program|NN|_ .|.|.|_ Data|datum|NNS|_ from|from|IN|_ faint|faint|JJ|_ spots|spot|NNS|_ were|be|VBD|_ removed|remove|VBN|_ ,|,|,|_ in|in|IN|_ which|which|WDT|_ the|the|DT|_ intensity|intensity|NN|_ was|be|VBD|_ lower|lower|JJR|_ than|than|IN|_ the|the|DT|_ average|average|JJ|_ intensity|intensity|NN|_ plus|plus|CC|_ 2|2|CD|_ standard|standard|JJ|_ deviations|deviation|NNS|_ of|of|IN|_ the|the|DT|_ negative|negative|JJ|_ controls|control|NNS|_ on|on|IN|_ the|the|DT|_ array|array|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ experimental|experimental|JJ|_ and|and|CC|_ control|control|JJ|_ sample|sample|NN|_ ,|,|,|_ amplification|amplification|NN|_ and|and|CC|_ hybridization|hybridization|NN|_ were|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ a|a|DT|_ dye-swap|dye-swap|JJ|_ strategy|strategy|NN|_ in|in|IN|_ two|two|CD|_ independent|independent|JJ|_ experiments|experiment|NNS|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ with|with|IN|_ at|at|IN|_ least|least|JJS|_ 2|2|CD|_ fold|fold|JJ|_ changes|change|NNS|_ and|and|CC|_ q|q|VB|_ <|<|JJR|_ 0.001|0.001|CD|_ criteria|criterion|NNS|_ using|use|VBG|_ SAM|SAM|NNP|_ software|software|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ E.coli|e.coli|JJ|_ cells|cell|NNS|_ using|use|VBG|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|SYM|_ RNA|rna|NN|_ II|ii|CD|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ '|'|POS|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ Macherey|Macherey|NNP|_ Nagel|Nagel|NNP|_ ,|,|,|_ Duren|Duren|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ examined|examine|VBN|_ in|in|IN|_ a|a|DT|_ 1.5|1.5|CD|_ %|%|NN|_ denaturing|denature|VBG|_ agarose|agarose|NN|_ gel|gel|NN|_ ,|,|,|_ quantitated|quantitate|VBN|_ by|by|IN|_ absorbance|absorbance|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ and|and|CC|_ stored|store|VBN|_ until|until|IN|_ further|further|JJ|_ use|use|NN|_ for|for|IN|_ microarray|microarray|NN|_ and|and|CC|_ RT-PCR|rt-pcr|NN|_ verification|verification|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ E.coli|e.coli|JJ|_ cells|cell|NNS|_ using|use|VBG|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|SYM|_ RNA|rna|NN|_ II|ii|CD|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ '|'|POS|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ Macherey|Macherey|NNP|_ Nagel|Nagel|NNP|_ ,|,|,|_ Duren|Duren|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ examined|examine|VBN|_ in|in|IN|_ a|a|DT|_ 1.5|1.5|CD|_ %|%|NN|_ denaturing|denature|VBG|_ agarose|agarose|NN|_ gel|gel|NN|_ ,|,|,|_ quantitated|quantitate|VBN|_ by|by|IN|_ absorbance|absorbance|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ and|and|CC|_ stored|store|VBN|_ until|until|IN|_ further|further|JJ|_ use|use|NN|_ for|for|IN|_ microarray|microarray|NN|_ and|and|CC|_ RT-PCR|rt-pcr|NN|_ verification|verification|NN|_ .|.|.|_
DNA|dna|NN|_ detected|detect|VBN|_ with|with|IN|_ GyrA|gyra|NN|_ immunoglobulin|immunoglobulin|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|NN|_ 1|1|CD|_
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|NN|_ 2|2|CD|_
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|RB|_ 3|3|CD|_
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|RB|_ 4|4|CD|_
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|RB|_ 5|5|CD|_
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|RB|_ 6|6|CD|_
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|NN|_ 7|7|CD|_
gyrase|gyrase|NN|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ ChIP-chip|chip-chip|NN|_ -RRB-|-rrb-|-RRB-|_ no.|no.|VBP|_ 8|8|CD|_
Reference|Reference|NNP|_ Genomic|genomic|JJ|_ DNA|dna|NN|_
Acidic|acidic|JJ|_ Hot|Hot|NNP|_ Phenol|Phenol|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Bertani|Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ media|media|NNS|_ at|at|IN|_ 37C|37c|NN|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ with|with|IN|_ single|single|JJ|_ ,|,|,|_ independent|independent|JJ|_ colonies|colony|NNS|_ in|in|IN|_ triplicate|triplicate|NN|_ ,|,|,|_ incubated|incubate|VBN|_ aerobically|aerobically|RB|_ overnight|overnight|JJ|_ at|at|IN|_ 37oC|37oc|NN|_ ,|,|,|_ and|and|CC|_ sub-cultured|sub-cultured|JJ|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.0001|0.0001|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ in|in|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase and|and|CC|_ at|at|IN|_ OD600|od600|NN|_ =|=|JJ|_ 1.5|1.5|CD|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Exponential|exponential|JJ|_ phase|phase|NN|_ culture|culture|NN|_ of|of|IN|_ EDL933|edl933|NN|_ rpoS|rpos|NN|GEN mutants|mutant|NNS|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_
Exponential|exponential|JJ|_ phase|phase|NN|_ culture|culture|NN|_ of|of|IN|_ EDL933|edl933|NN|_ wild|wild|JJ|_ type|type|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_
Exp-rpoS-rep1|exp-rpos-rep1|NN|_
Exp-rpoS-rep2|exp-rpos-rep2|NN|_
Exp-rpoS-rep3|exp-rpos-rep3|NN|_
Exp-WT-rep1|exp-wt-rep1|NN|_
Exp-WT-rep2|exp-wt-rep2|NN|_
Exp-WT-rep3|exp-wt-rep3|NN|_
GCRMA|gcrma|NN|_ method|method|NN|_
genotype|genotype|NN|_ :|:|:|_ rpoS|rpos|NN|GEN
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stationary|stationary|JJ|_
Stationary|stationary|JJ|_ phase|phase|NN|_ culture|culture|NN|_ of|of|IN|_ EDL933|edl933|NN|_ rpoS|rpos|NN|GEN mutants|mutant|NNS|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ OD600|od600|NN|_ of|of|IN|_ 1.5|1.5|CD|_
Stationary|stationary|JJ|_ phase|phase|NN|_ culture|culture|NN|_ of|of|IN|_ EDL933|edl933|NN|_ wild|wild|JJ|_ type|type|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ OD600|od600|NN|_ of|of|IN|_ 1.5|1.5|CD|_
Stat-rpoS-rep1|stat-rpos-rep1|NN|_
Stat-rpoS-rep2|stat-rpos-rep2|NN|_
Stat-rpoS-rep3|stat-rpos-rep3|NN|_
Stat-WT-rep1|stat-wt-rep1|NN|_
Stat-WT-rep2|stat-wt-rep2|NN|_
Stat-WT-rep3|stat-wt-rep3|NN|_
agent|agent|NN|_ :|:|:|_ no|no|DT|_ triclosan|triclosan|NN|_
agent|agent|NN|_ :|:|:|_ triclosan|triclosan|NN|_
E.|E.|NNP|_ coli|coli|NN|_ imp|imp|NN|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ -LSB-|-lsb-|-LRB-|_ control|control|NN|_ -RSB-|-rsb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G94V|g94v|NN|_ -RRB-|-rrb-|-RRB-|_ -LSB-|-lsb-|-LRB-|_ control|control|NN|_ -RSB-|-rsb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
imp|imp|NN|_ mutation|mutation|NN|_ :|:|:|_ contains|contain|VBZ|_ a|a|DT|_ 23|23|CD|_ codon|codon|NN|_ deletion|deletion|NN|_ allele|allele|NN|_ in|in|IN|_ imp|imp|NN|_ -LRB-|-lrb-|-LRB-|_ increased|increase|VBN|_ membrane|membrane|NN|_ permeability|permeability|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ the|the|DT|_ 93th|93th|JJ|_ codon|codon|NN|_ of|of|IN|_ fabI|fabi|NN|GEN ,|,|,|_ NTG|NTG|NNP|_ treatment|treatment|NN|_ ;|;|:|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ Gly|gly|NN|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ 93th|93th|JJ|_ codon|codon|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ fabI|fabi|NN|GEN with|with|IN|_ Val|val|NN|_ ,|,|,|_ NTG|NTG|NNP|_ treatment|treatment|NN|_ to|to|TO|_ be|be|VB|_ high|high|JJ|_ resistance|resistance|NN|_ to|to|TO|_ triclosan|triclosan|NN|_
imp|imp|NN|_ mutation|mutation|NN|_ :|:|:|_ contains|contain|VBZ|_ a|a|DT|_ 23|23|CD|_ codon|codon|NN|_ deletion|deletion|NN|_ allele|allele|NN|_ in|in|IN|_ imp|imp|NN|_ -LRB-|-lrb-|-LRB-|_ increased|increase|VBN|_ membrane|membrane|NN|_ permeability|permeability|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ the|the|DT|_ 94th|94th|JJ|_ codon|codon|NN|_ of|of|IN|_ fabI|fabi|NN|GEN ,|,|,|_ NTG|NTG|NNP|_ treatment|treatment|NN|_ ;|;|:|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ Gly|gly|NN|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ 94th|94th|JJ|_ codon|codon|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ fabI|fabi|NN|GEN with|with|IN|_ Val|val|NN|_ ,|,|,|_ NTG|NTG|NNP|_ treatment|treatment|NN|_ to|to|TO|_ be|be|VB|_ high|high|JJ|_ resistance|resistance|NN|_ to|to|TO|_ triclosan|triclosan|NN|_
imp|imp|NN|_ mutation|mutation|NN|_ :|:|:|_ contains|contain|VBZ|_ a|a|DT|_ 23|23|CD|_ codon|codon|NN|_ detion|detion|NN|_ allele|allele|NN|_ in|in|IN|_ imp|imp|NN|_ -LRB-|-lrb-|-LRB-|_ increased|increase|VBN|_ membrane|membrane|NN|_ permeability|permeability|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ the|the|DT|_ 93th|93th|JJ|_ codon|codon|NN|_ of|of|IN|_ fabI|fabi|NN|GEN ;|;|:|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ Gly|gly|NN|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ 93th|93th|JJ|_ codon|codon|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ fabI|fabi|NN|GEN with|with|IN|_ Val|val|NN|_
imp|imp|NN|_ mutation|mutation|NN|_ :|:|:|_ contains|contain|VBZ|_ a|a|DT|_ 23|23|CD|_ codon|codon|NN|_ detion|detion|NN|_ allele|allele|NN|_ in|in|IN|_ imp|imp|NN|_ -LRB-|-lrb-|-LRB-|_ increased|increase|VBN|_ membrane|membrane|NN|_ permeability|permeability|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ the|the|DT|_ 94th|94th|JJ|_ codon|codon|NN|_ of|of|IN|_ fabI|fabi|NN|GEN ;|;|:|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ Gly|gly|NN|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ 94th|94th|JJ|_ codon|codon|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ fabI|fabi|NN|GEN with|with|IN|_ Val|val|NN|_
LOWESS|lowess|NN|_ normalized|normalize|VBD|_ ,|,|,|_ background|background|NN|_ subtracted|subtract|VBD|_ data|datum|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ log2|log2|NN|_ of|of|IN|_ processed|process|VBN|_ Red|red|JJ|_ signal|signal|NN|_
No|no|DT|_ triclosan|triclosan|NN|_ treatment|treatment|NN|_
NTG-treated|ntg-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ -LSB-|-lsb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ IFN4|ifn4|NN|_ -RSB-|-rsb-|-RRB-|_
NTG-treated|ntg-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ -LSB-|-lsb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ IFN5|ifn5|NN|_ -RSB-|-rsb-|-RRB-|_
ntg|ntg|NN|_ treatment|treatment|NN|_ :|:|:|_ yes|yes|UH|_
passage|passage|NN|_ :|:|:|_ 4|4|CD|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ 4231|4231|CD|_ -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ 4231|4231|CD|_ -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ the|the|DT|_ 93th|93th|JJ|_ codon|codon|NN|_ of|of|IN|_ fabI|fabI|NNP|GEN
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ 4231|4231|CD|_ -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ substitution|substitution|NN|_ of|of|IN|_ the|the|DT|_ 94th|94th|JJ|_ codon|codon|NN|_ of|of|IN|_ fabI|fabi|NN|GEN
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED containing|contain|VBG|_ 2|2|CD|_ mg|mg|NN|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ RNAprotect|rnaprotect|NN|_ Bacterial|bacterial|JJ|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ an|a|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Transcription|transcription|NN|_ profiles|profile|NNS|_ of|of|IN|_ NTG-treated|ntg-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ its|its|PRP$|_ control|control|NN|_ strain|strain|NN|_ in|in|IN|_ the|the|DT|_ absence|absence|NN|_ of|of|IN|_ triclosan|triclosan|NN|_
Transcription|transcription|NN|_ profiles|profile|NNS|_ of|of|IN|_ NTG-treated|ntg-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ imp|imp|FW|_ fabI|fabi|NN|GEN -LRB-|-lrb-|-LRB-|_ G93V|g93v|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ its|its|PRP$|_ control|control|NN|_ strain|strain|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ triclosan|triclosan|NN|_
Treatment|treatment|NN|_ of|of|IN|_ sub-lethal|sub-lethal|JJ|_ triclosan|triclosan|NN|_ ;|;|:|_ 50|50|CD|_ mg|mg|NN|_
5mL|5ml|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 5mL|5ml|NN|_ of|of|IN|_ hot|hot|JJ|_ acid|acid|NN|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ held|hold|VBN|_ at|at|IN|_ 65ºC|65ºc|NN|_ with|with|IN|_ periodic|periodic|JJ|_ shaking|shake|VBG|_ for|for|IN|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ minutes|minute|NNS|_ before|before|IN|_ centrifuging|centrifuge|VBG|_ at|at|IN|_ 4000|4000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ .|.|.|_ Supernatant|supernatant|NN|_ was|be|VBD|_ extracted|extract|VBN|_ again|again|RB|_ with|with|IN|_ acid-phenol|acid-phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ and|and|CC|_ then|then|RB|_ with|with|IN|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 24.1|24.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ precipitated|precipitated|JJ|_ overnight|overnight|JJ|_ at|at|IN|_ --|--|:|_ 80ºC|80ºc|NN|_ in|in|IN|_ 2.5|2.5|CD|_ V|v|NN|_ 100|100|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ and|and|CC|_ 1|1|CD|_
EcJR-8|ecjr-8|NN|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ in|in|IN|_ DMEM-MOPS|dmem-mops|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ a|a|DT|_ 10:1|10:1|CD|_ flask-to-media|flask-to-media|NN|_ volume|volume|NN|_ in|in|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
EcJR-8|ecjr-8|NN|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.8|1.8|CD|_ in|in|IN|_ DMEM-MOPS|dmem-mops|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ a|a|DT|_ 10:1|10:1|CD|_ flask-to-media|flask-to-media|NN|_ volume|volume|NN|_ in|in|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ Sakai|Sakai|NNP|_
genotype|genotype|NN|_ :|:|:|_ rpoN|rpon|NN|GEN mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ EcJR-8|ecjr-8|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ in|in|IN|_ DMEM-MOPS|dmem-mops|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ transition|transition|NN|_ phase|phase|NN|_ in|in|IN|_ DMEM-MOPS|dmem-mops|NN|_
Logarithmic|logarithmic|JJ|_ phase|phase|NN|_ sample|sample|NN|_ 1|1|CD|_
Logarithmic|logarithmic|JJ|_ phase|phase|NN|_ sample|sample|NN|_ 2|2|CD|_
Logarithmic|logarithmic|JJ|_ phase|phase|NN|_ sample|sample|NN|_ 3|3|CD|_
Logarithmic|logarithmic|JJ|_ phase|phase|NN|_ sample|sample|NN|_ 4|4|CD|_
rpoN|rpon|NN|GEN mutant|mutant|JJ|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_
rpoN|rpon|NN|GEN mutant|mutant|JJ|_ grown|grow|VBN|_ to|to|TO|_ transition|transition|NN|_ phase|phase|NN|_
Sakai|Sakai|NNP|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 1.8|1.8|CD|_ in|in|IN|_ DMEM-MOPS|dmem-mops|NN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ a|a|DT|_ 10:1|10:1|CD|_ flask-to-media|flask-to-media|NN|_ volume|volume|NN|_ in|in|IN|_ a|a|DT|_ rotary|rotary|JJ|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 2.2.1|2.2.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ MAANOVA|MAANOVA|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.98.8|0.98.8|CD|_ -RRB-|-rrb-|-RRB-|_ package|package|NN|_ .|.|.|_ Raw|raw|NN|_ intensity|intensity|NN|_ values|value|NNS|_ from|from|IN|_ replicate|replicate|VBP|_ probes|probe|NNS|_ were|be|VBD|_ averaged|average|VBN|_ and|and|CC|_ log2|log2|NN|_ transformed|transform|VBN|_ after|after|IN|_ normalization|normalization|NN|_ with|with|IN|_ the|the|DT|_ pin-tip|pin-tip|JJ|_ LOWESS|lowess|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ normalized|normalize|VBN|_ intensity|intensity|NN|_ values|value|NNS|_ were|be|VBD|_ fitted|fit|VBN|_ to|to|TO|_ a|a|DT|_ mixed|mixed|JJ|_ model|model|NN|_ ANOVA|ANOVA|NNP|_ considering|consider|VBG|_ array|array|NN|_ and|and|CC|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ as|as|IN|_ random|random|JJ|_ factors|factor|NNS|_ and|and|CC|_ dye|dye|VB|_ ,|,|,|_ strain|strain|NN|_ and|and|CC|_ growth|growth|NN|_ phase|phase|NN|_ as|as|IN|_ fixed|fixed|JJ|_ factors|factor|NNS|_ .|.|.|_ The|the|DT|_ linear|linear|JJ|_ model|model|NN|_ tested|test|VBN|_ was|be|VBD|_ Y|y|NN|_ -LRB-|-lrb-|-LRB-|_ intensity|intensity|NN|_ -RRB-|-rrb-|-RRB-|_ =|=|JJ|_ array|array|NN|_ +|+|CC|_ dye|dye|VB|_ +|+|CC|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ wild|wild|JJ|_ type|type|NN|_ or|or|CC|_ mutant|mutant|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ growth|growth|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ exponential|exponential|JJ|_ or|or|CC|_ stationary|stationary|JJ|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ strain|strain|NN|_ *|*|SYM|_ growth|growth|NN|_ phase|phase|NN|_ +|+|CC|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ biological|biological|JJ|_ replicate|replicate|VBP|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ error|error|NN|_ .|.|.|_ Significant|significant|JJ|_ differences|difference|NNS|_ in|in|IN|_ expression|expression|NN|_ due|due|JJ|_ to|to|TO|_ strain|strain|NN|_ ,|,|,|_ growth|growth|NN|_ phase|phase|NN|_ and|and|CC|_ strain|strain|NN|_ *|*|SYM|_ growth|growth|NN|_ phase|phase|NN|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ Fs|f|NNS|_ test|test|NN|_ in|in|IN|_ MAANOVA|MAANOVA|NNP|_ which|which|WDT|_ uses|use|VBZ|_ a|a|DT|_ shrinkage|shrinkage|NN|_ estimator|estimator|NN|_ for|for|IN|_ gene-specific|gene-specific|JJ|_ variance|variance|NN|_ components|component|NNS|_ that|that|WDT|_ makes|make|VBZ|_ no|no|DT|_ assumption|assumption|NN|_ about|about|IN|_ the|the|DT|_ variances|variance|NNS|_ across|across|IN|_ genes|gene|NNS|_ with|with|IN|_ 500|500|CD|_ random|random|JJ|_ permutations|permutation|NNS|_ to|to|TO|_ estimate|estimate|VB|_ the|the|DT|_ p-values|p-value|NNS|_ .|.|.|_ The|the|DT|_ q-value|q-value|JJ|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ determining|determine|VBG|_ the|the|DT|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Transition|transition|NN|_ phase|phase|NN|_ sample|sample|NN|_ 1|1|CD|_
Transition|transition|NN|_ phase|phase|NN|_ sample|sample|NN|_ 2|2|CD|_
Transition|transition|NN|_ phase|phase|NN|_ sample|sample|NN|_ 3|3|CD|_
Transition|transition|NN|_ phase|phase|NN|_ sample|sample|NN|_ 4|4|CD|_
wild|wild|JJ|_ type|type|NN|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_
wild|wild|JJ|_ type|type|NN|_ grown|grow|VBN|_ to|to|TO|_ transition|transition|NN|_ phase|phase|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ 1-h|1-h|NN|_ ,|,|,|_ serine|serine|NN|_ hydroxamate|hydroxamate|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Fifteen|fifteen|CD|_ mL|ml|NN|_ fermentation|fermentation|NN|_ broth|broth|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ each|each|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ Harvested|harvest|VBN|_ cells|cell|NNS|_ were|be|VBD|_ rapidly|rapidly|RB|_ cooled|cool|VBN|_ in|in|IN|_ a|a|DT|_ -80|-80|CD|_ °C|°c|NN|_ ethanol|ethanol|NN|_ bath|bath|NN|_ ,|,|,|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000|5000|CD|_ g|g|NN|_ for|for|IN|_ seven|seven|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Thawed|thaw|VBN|_ -LRB-|-lrb-|-LRB-|_ on|on|IN|_ ice|ice|NN|_ -RRB-|-rrb-|-RRB-|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ suspended|suspend|VBN|_ in|in|IN|_ 150|150|CD|_ mL|ml|NN|_ of|of|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.6|7.6|CD|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 0.75|0.75|CD|_ mg|mg|NN|_
Microarray|microarray|NN|_ suit|suit|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ Affymetrix|Affymetrix|NNP|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ average|average|VB|_ the|the|DT|_ scans|scan|NNS|_ and|and|CC|_ process|process|NN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ further|further|RB|_ data|data|NN|_ analysis|analysis|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ ®|®|NNP|_ Data|Data|NNP|_ Mining|Mining|NNP|_ Tool|Tool|NNP|_ -LRB-|-lrb-|-LRB-|_ DMT|DMT|NNP|_ 3.0|3.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
One|one|CD|_ set|set|NN|_ of|of|IN|_ fermentations|fermentation|NNS|_ were|be|VBD|_ exposed|expose|VBN|_ to|to|TO|_ 5|5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ and|and|CC|_ one|one|CD|_ set|set|NN|_ was|be|VBD|_ not|not|RB|_ exposed|expose|VBN|_ to|to|TO|_ IPTG|IPTG|NNP|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ ,|,|,|_ and|and|CC|_ 4|4|CD|_ hours|hour|NNS|_ post-synchronization|post-synchronization|JJ|_ -LRB-|-lrb-|-LRB-|_ Time|time|NN|_ S0|s0|NN|_ ,|,|,|_ S1|s1|NN|_ ,|,|,|_ and|and|CC|_ S4|s4|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
plasmid|plasmid|NN|_ :|:|:|_ pPROEx-CAT|pproex-cat|NN|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ 0|0|CD|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ 4|4|CD|_ h|h|NN|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S0|S0|NNP|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 1|1|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S0|S0|NNP|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 2|2|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S0|S0|NNP|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 3|3|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S1|s1|NN|_ ,|,|,|_ IPTG|iptg|NN|_ ,|,|,|_ 1|1|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S1|s1|NN|_ ,|,|,|_ IPTG|iptg|NN|_ ,|,|,|_ 2|2|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S1|s1|NN|_ ,|,|,|_ IPTG|iptg|NN|_ ,|,|,|_ 3|3|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S1|s1|NN|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 1|1|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S1|s1|NN|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 2|2|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S1|s1|NN|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 3|3|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S4|S4|NNP|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 1|1|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S4|S4|NNP|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 2|2|CD|_
Recombinant|recombinant|JJ|_ ,|,|,|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ ,|,|,|_ Time|Time|NNP|_ S4|S4|NNP|_ ,|,|,|_ no|no|DT|_ IPTG|iptg|NN|_ ,|,|,|_ 3|3|CD|_
Serine|serine|NN|_ Hydroxamate|hydroxamate|NN|_ stressed|stress|VBD|_ ,|,|,|_ replicate|replicate|VB|_ #|#|#|_ 1|1|CD|_
Serine|serine|NN|_ Hydroxamate|hydroxamate|NN|_ stressed|stress|VBD|_ ,|,|,|_ replicate|replicate|VB|_ #|#|#|_ 2|2|CD|_
Serine|serine|NN|_ Hydroxamate|hydroxamate|NN|_ stressed|stress|VBD|_ ,|,|,|_ replicate|replicate|VB|_ #|#|#|_ 3|3|CD|_
Serine|serine|NN|_ hydrxamate|hydrxamate|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mg|mg|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ strain|strain|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ pPROEx-CAT|pproex-cat|NN|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ a|a|DT|_ fed-batch|fed-batch|JJ|_ fermenter|fermenter|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED w|w|NN|_
The|the|DT|_ strain|strain|NN|_ MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ pPROEx-CAT|pproex-cat|NN|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ a|a|DT|_ fed-batch|fed-batch|JJ|_ fermenter|fermenter|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED w|w|NN|_
1A|1a|NN|_ 1y|1y|NN|_
1A|1a|NN|_ 4y|4y|NN|_
1A|1a|NN|_ T0|t0|NN|_
2A|2a|NN|_ 1y|1y|NN|_
2A|2a|NN|_ 4y|4y|NN|_
3A|3a|NN|_ 1m|1m|NN|_
3A|3a|NN|_ 1y|1y|NN|_
3A|3a|NN|_ 4y|4y|NN|_
4A|4a|NN|_ 1m|1m|NN|_
4A|4a|NN|_ 1y|1y|NN|_
4A|4a|NN|_ 4y|4y|NN|_
5A|5a|NN|_ 1m|1m|NN|_
6A|6a|NN|_ 1m|1m|NN|_
9A|9a|NN|_ 3y|3y|JJ|_
9A|9a|NN|_ 5y|5y|JJ|_
9A|9a|NN|_ T0|t0|NN|_
Alert|Alert|NNP|_
Archaea|Archaea|NNP|_
Bacteria|bacterium|NNS|_
Bio1|bio1|NN|_ 1m|1m|NN|_
Bio1|bio1|NN|_ 1y|1y|NN|_
Bio2|bio2|NN|_ 1m|1m|NN|_
Bio2|bio2|NN|_ 1y|1y|NN|_
Bio3|bio3|NN|_ 1m|1m|NN|_
Bio3|bio3|NN|_ 1y|1y|NN|_
Bio4|bio4|NN|_ 1m|1m|NN|_
Bio4|bio4|NN|_ 1y|1y|NN|_
Bio-6|bio-6|NN|_
Bio|bio|NN|_ Contro|contro|NN|_
bioremediation|bioremediation|NN|_ treatment|treatment|NN|_ :|:|:|_ Alert|Alert|NNP|_ -LRB-|-lrb-|-LRB-|_ ex|ex|FW|_ situ|situ|FW|_ -RRB-|-rrb-|-RRB-|_
bioremediation|bioremediation|NN|_ treatment|treatment|NN|_ :|:|:|_ Eureka|Eureka|NNP|_ -LRB-|-lrb-|-LRB-|_ in|in|FW|_ situ|situ|FW|_ -RRB-|-rrb-|-RRB-|_
BZNT|bznt|JJ|_
CompA|compa|NN|_
CompB|compb|NN|_
contamination|contamination|NN|_ status|status|NN|_ :|:|:|_ hydrocarbon|hydrocarbon|NN|_ contaminated|contaminate|VBN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Eureka|eureka|FW|_
Lambda|Lambda|NNP|_ phage|phage|NN|_
NFNT|nfnt|JJ|_
phage|phage|NN|_ :|:|:|_ Lambda|Lambda|NNP|_
Poly|Poly|NNP|_
sample|sample|NN|_ :|:|:|_ 1A|1a|NN|_
sample|sample|NN|_ :|:|:|_ 23S|23s|NN|_
sample|sample|NN|_ :|:|:|_ 2A|2a|NN|_
sample|sample|NN|_ :|:|:|_ 32D|32d|NN|_
sample|sample|NN|_ :|:|:|_ 33D|33d|NN|_
sample|sample|NN|_ :|:|:|_ 35B|35b|NN|_
sample|sample|NN|_ :|:|:|_ 3A|3a|NN|_
sample|sample|NN|_ :|:|:|_ 4A|4a|NN|_
sample|sample|NN|_ :|:|:|_ 5A|5a|NN|_
sample|sample|NN|_ :|:|:|_ #|#|#|_ 6|6|CD|_
sample|sample|NN|_ :|:|:|_ 6A|6a|NN|_
sample|sample|NN|_ :|:|:|_ 9A|9a|NN|_
sample|sample|NN|_ :|:|:|_ Bio-1|bio-1|NN|_
sample|sample|NN|_ :|:|:|_ Bio-2|bio-2|NN|_
sample|sample|NN|_ :|:|:|_ Bio-3|bio-3|NN|_
sample|sample|NN|_ :|:|:|_ Bio-4|bio-4|NN|_
sample|sample|NN|_ :|:|:|_ Biopile|Biopile|NNP|_ control|control|NN|_
sample|sample|NN|_ :|:|:|_ BZ-NT|bz-nt|JJ|_
sample|sample|NN|_ :|:|:|_ Composite|Composite|NNP|_ A|A|NNP|_
sample|sample|NN|_ :|:|:|_ Composite|Composite|NNP|_ B|B|NNP|_
sample|sample|NN|_ :|:|:|_ LC-1|lc-1|NN|_
sample|sample|NN|_ :|:|:|_ NC|nc|NN|_
sample|sample|NN|_ :|:|:|_ NF-NT|nf-nt|JJ|_
sample|sample|NN|_ :|:|:|_ Polygons|polygon|NNS|_
sample|sample|NN|_ :|:|:|_ Vegetated|vegetated|JJ|_
Soil|soil|NN|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ a|a|DT|_ 0.5|0.5|CD|_ g|g|NN|_ soil|soil|NN|_ sub-sample|sub-sample|NN|_ using|use|VBG|_ the|the|DT|_ MoBio|mobio|NN|_ DNA|dna|NN|_ Power|power|NN|_ Soil|soil|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ MoBio|mobio|NN|_ Laboratories|Laboratories|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ intensity|intensity|NN|_ of|of|IN|_ each|each|DT|_ spot|spot|NN|_ was|be|VBD|_ measured|measure|VBN|_ with|with|IN|_ ScanArray|ScanArray|NNP|_ Express|Express|NNP|_ using|use|VBG|_ the|the|DT|_ histogram|histogram|NN|_ quantitation|quantitation|NN|_ method|method|NN|_ ;|;|:|_ the|the|DT|_ percentile|percentile|NN|_ ranges|range|VBZ|_ for|for|IN|_ histograms|histogram|NNS|_ were|be|VBD|_ 80|80|CD|_ %|%|NN|_ for|for|IN|_ low|low|JJ|_ signal|signal|NN|_ range|range|NN|_ ,|,|,|_ 95|95|CD|_ %|%|NN|_ for|for|IN|_ high|high|JJ|_ signal|signal|NN|_ range|range|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ for|for|IN|_ low|low|JJ|_ background|background|NN|_ range|range|NN|_ and|and|CC|_ 20|20|CD|_ %|%|NN|_ for|for|IN|_ high|high|JJ|_ background|background|NN|_ range|range|NN|_ .|.|.|_ The|the|DT|_ median|median|JJ|_ intensity|intensity|NN|_ minus|minus|CC|_ the|the|DT|_ median|median|JJ|_ background|background|NN|_ intensity|intensity|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ further|further|JJ|_ calculations|calculation|NNS|_ performed|perform|VBN|_ in|in|IN|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ .|.|.|_ The|the|DT|_ background|background|NN|_ measurement|measurement|NN|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ local|local|JJ|_ spot|spot|NN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_ Prior|prior|RB|_ to|to|TO|_ normalization|normalization|NN|_ ,|,|,|_ all|all|DT|_ spots|spot|NNS|_ with|with|IN|_ a|a|DT|_ Signal-to-Noise|Signal-to-Noise|NNP|_ ratio|ratio|NN|_ -LRB-|-lrb-|-LRB-|_ SNR|snr|NN|_ -RRB-|-rrb-|-RRB-|_ lower|lower|JJR|_ than|than|IN|_ 3|3|CD|_ were|be|VBD|_ removed|remove|VBN|_ .|.|.|_ The|the|DT|_ SNR|snr|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ formula|formula|NN|_ :|:|:|_ -LRB-|-lrb-|-LRB-|_ Median|median|JJ|_ Signal|signal|NN|_ --|--|:|_ Median|median|JJ|_ Background|background|NN|_ -RRB-|-rrb-|-RRB-|_
year|year|NN|_ :|:|:|_ 2000|2000|CD|_
year|year|NN|_ :|:|:|_ 2001|2001|CD|_
year|year|NN|_ :|:|:|_ 2003|2003|CD|_
year|year|NN|_ :|:|:|_ 2004|2004|CD|_
year|year|NN|_ :|:|:|_ 2005|2005|CD|_
year|year|NN|_ :|:|:|_ 2006|2006|CD|_
year|year|NN|_ :|:|:|_ 2007|2007|CD|_
year|year|NN|_ :|:|:|_ 2008|2008|CD|_
0.5|0.5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w|w|NN|_
0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_
0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 5|5|CD|_ min|min|NN|_
0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 60|60|CD|_ min|min|NN|_
Affymetrix|Affymetrix|NNP|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37C|37c|NN|_ prior|prior|RB|_ to|to|TO|_ extraction|extraction|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0.5|0.5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w|w|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 5|5|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 5|5|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.coliO157|e.colio157|NN|_ _|_|CD|_ 0|0|CD|_ %|%|NN|_ sodiumbenzoate|sodiumbenzoate|NN|_ _|_|CD|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
One|one|CD|_ hundred|hundred|CD|_ µl|µl|NN|_ tris-EDTA|tris-edta|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-Cl|tris-cl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ ph|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ Promega|Promega|NNP|_ ;|;|:|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ mg|mg|NN|_
Stationary|stationary|JJ|_ phase|phase|NN|_ growth|growth|NN|_ -LRB-|-lrb-|-LRB-|_ 24|24|CD|_ hr|hr|NN|_ -RRB-|-rrb-|-RRB-|_ ~|~|NN|_ 8|8|CD|_ log|log|NN|_ CFU|CFU|NNP|_
The|The|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ ;|;|:|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ cultures|culture|NNS|_ .|.|.|_ RNAlater|rnalater|NN|_ Stabilization|stabilization|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ 1.2|1.2|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ;|;|:|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ combined|combine|VBN|_ with|with|IN|_ 0.6|0.6|CD|_ ml|ml|NN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ the|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 8000|8000|CD|_ x|x|CC|_ g|g|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ under|under|IN|_ refrigeration|refrigeration|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ the|the|DT|_ bacterial|bacterial|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ until|until|IN|_ further|further|JJ|_ processed|process|VBN|_ -LRB-|-lrb-|-LRB-|_ 2-10|2-10|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
0.5|0.5|CD|_ hour|hour|NN|_ expression|expression|NN|_ of|of|IN|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|dx|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_
1.5|1.5|CD|_ hour|hour|NN|_ expression|expression|NN|_ of|of|IN|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|dx|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_
1|1|CD|_ hour|hour|NN|_ expression|expression|NN|_ of|of|IN|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|dx|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_
2|2|CD|_ hour|hour|NN|_ expression|expression|NN|_ of|of|IN|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|dx|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_
3.5|3.5|CD|_ hour|hour|NN|_ expression|expression|NN|_ of|of|IN|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|dx|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_
3|3|CD|_ hour|hour|NN|_ expression|expression|NN|_ of|of|IN|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|dx|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_
4|4|CD|_ hour|hour|NN|_ expression|expression|NN|_ of|of|IN|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|dx|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_
According|accord|VBG|_ to|to|TO|_ Invitrogen|Invitrogen|NNP|_ PureLink|PureLink|NNP|_ Micro-to-Midi|Micro-to-Midi|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Purification|purification|NN|_ System|system|NN|_
Data|Data|NNP|_ was|be|VBD|_ processed|process|VBN|_ by|by|IN|_ MATLAB|MATLAB|NNP|_ to|to|TO|_ median|median|JJ|_ normalize|normalize|VB|_ each|each|DT|_ channel|channel|NN|_ and|and|CC|_ lowess|lowess|NN|_ normalize|normalize|VBP|_ the|the|DT|_ sample|sample|NN|_ set|set|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ containing|contain|VBG|_ a|a|DT|_ pBAD18|pbad18|NN|_ vector|vector|NN|_ encoding|encode|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ exposed|expose|VBN|_ to|to|TO|_ arabinose|arabinose|VB|_ inducer|inducer|NN|_ for|for|IN|_ 0.5|0.5|CD|_ h.|h.|NN|_ RNA|rna|NN|_ extracted|extract|VBN|_ with|with|IN|_ Invitrogen|Invitrogen|NNP|_ PureLink|PureLink|NNP|_ kit|kit|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Identical|identical|JJ|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ with|with|IN|_ no|no|DT|_ arabinose|arabinose|NN|_ added|add|VBD|_
reference|reference|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ TOP10|top10|NN|_ containing|contain|VBG|_ pBAD18|pbad18|NN|_ vector|vector|NN|_ with|with|IN|_ no|no|DT|_ arabinose|arabinose|NN|_ added|add|VBD|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ 0.5|0.5|CD|_ hours|hour|NNS|_ after|after|IN|_ inoculation|inoculation|NN|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ 1.5|1.5|CD|_ hours|hour|NNS|_ after|after|IN|_ inoculation|inoculation|NN|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ 2|2|CD|_ hours|hour|NNS|_ after|after|IN|_ inoculation|inoculation|NN|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ 3.5|3.5|CD|_ hours|hour|NNS|_ after|after|IN|_ inoculation|inoculation|NN|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ 3|3|CD|_ hours|hour|NNS|_ after|after|IN|_ inoculation|inoculation|NN|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ 4|4|CD|_ hours|hour|NNS|_ after|after|IN|_ inoculation|inoculation|NN|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ expressing|express|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ for|for|IN|_ 0.5|0.5|CD|_ hours|hour|NNS|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ expressing|express|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ for|for|IN|_ 1.5|1.5|CD|_ hours|hour|NNS|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ expressing|express|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ for|for|IN|_ 1|1|CD|_ hours|hour|NNS|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ expressing|express|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ expressing|express|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ for|for|IN|_ 3.5|3.5|CD|_ hours|hour|NNS|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ expressing|express|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ for|for|IN|_ 3|3|CD|_ hours|hour|NNS|_
RNA|rna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ expressing|express|VBG|_ synthetic|synthetic|JJ|_ protein|protein|NN|_ DX|DX|NNP|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_
test|test|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ TOP10|top10|NN|_ containing|contain|VBG|_ pBAD18|pbad18|NN|_ vector|vector|NN|_ exposed|expose|VBN|_ to|to|TO|_ arabinose|arabinose|VB|_ inducer|inducer|NN|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ biofilm|biofilm|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ biofilm|biofilm|NN|_ grown|grow|VBN|_ on|on|IN|_ glass|glass|NN|_ wool|wool|NN|_ ,|,|,|_ 37C|37c|NN|_
MAS|mas|NN|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|Setting|NNP|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
pCA24N-hns|pca24n-hn|NNS|_ biofilm|biofilm|NN|_
pCA24N-hnsK57N|pca24n-hnsk57n|NN|_ biofilm|biofilm|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_ hha|hha|NN|GEN hns|hn|VBZ|GEN
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
time|time|NN|_ :|:|:|_ 7|7|CD|_ hours|hour|NNS|_
Adapted|adapt|VBN|_ E.|e.|FW|_ coli|coli|FW|_ -LRB-|-lrb-|-LRB-|_ DST160|dst160|NN|_ ,|,|,|_ tolerant|tolerant|JJ|_ to|to|TO|_ high|high|JJ|_ succinic|succinic|JJ|_ acid|acid|NN|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_
High|High|NNP|_ succinic|succinic|JJ|_ acid|acid|NN|_ tolerance|tolerance|NN|_ E.coli|e.coli|NNS|_ _|_|VBP|_ rep|rep|NN|GEN Dn|dn|NN|_
High|High|NNP|_ succinic|succinic|JJ|_ acid|acid|NN|_ tolerance|tolerance|NN|_ E.coli|e.coli|NNS|_ _|_|VBP|_ rep|rep|NN|GEN Up|up|IN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ control|control|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ test|test|NN|_
Scanned|scan|VBD|_ images|image|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 3.0|3.0|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Axon|Axon|NNP|_ Instruments|Instruments|NNP|_ ,|,|,|_ Union|Union|NNP|_ City|City|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ gene|gene|NN|_ expression|expression|NN|_ ratios|ratio|NNS|_ .|.|.|_ Logged|log|VBN|_ gene|gene|NN|_ expression|expression|NN|_ ratios|ratio|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ LOWESS|lowess|NN|_ regression|regression|NN|_ -LRB-|-lrb-|-LRB-|_ Yang|Yang|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2002|2002|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ 7.3|7.3|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ medium|medium|NN|_ for|for|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ contained|contain|VBD|_ 3|3|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP medium|medium|NN|_ consisted|consist|VBD|_ with|with|IN|_ 0.8|0.8|CD|_ g|g|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.5|0.5|CD|_ g|g|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 7.5|7.5|CD|_ g|g|NN|_ Na2HPO4|na2hpo4|NN|_ •|•|SYM|_ 2H2O|2h2o|NN|_ ,|,|,|_ 3|3|CD|_ g|g|NN|_ KH2PO4|kh2po4|NN|_ with|with|IN|_ separately|separately|RB|_ added|add|VBN|_ trace|trace|NN|_ element|element|NN|_ of|of|IN|_ 0.2|0.2|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ •|•|SYM|_ 7H2O|7H2O|NNP|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mg|mg|NN|_ thiamine|thiamine|NN|SUPP per|per|IN|_ liter|liter|NN|_ and|and|CC|_ the|the|DT|_ concentraiton|concentraiton|NN|_ of|of|IN|_ added|add|VBN|_ succinate|succinate|JJ|SUPP gradually|gradually|RB|_ was|be|VBD|_ raised|raise|VBN|_ from|from|IN|_ 30|30|CD|_ g|g|NN|_
The|the|DT|_ medium|medium|NN|_ for|for|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ contained|contain|VBD|_ 3|3|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP medium|medium|NN|_ consisted|consist|VBD|_ with|with|IN|_ 0.8|0.8|CD|_ g|g|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.5|0.5|CD|_ g|g|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 7.5|7.5|CD|_ g|g|NN|_ Na2HPO4|na2hpo4|NN|_ •|•|SYM|_ 2H2O|2h2o|NN|_ ,|,|,|_ 3|3|CD|_ g|g|NN|_ KH2PO4|kh2po4|NN|_ with|with|IN|_ separately|separately|RB|_ added|add|VBN|_ trace|trace|NN|_ element|element|NN|_ of|of|IN|_ 0.2|0.2|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ •|•|SYM|_ 7H2O|7H2O|NNP|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mg|mg|NN|_ thiamine|thiamine|NN|SUPP per|per|IN|_ liter|liter|NN|_ .|.|.|_ The|the|DT|_ fermentor|fermentor|NN|_ was|be|VBD|_ maintained|maintain|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ ,|,|,|_ 350|350|CD|_ rpm|rpm|NN|_ with|with|IN|_ air|air|NN|_ gas|gas|NN|_ flushing|flushing|NN|_ and|and|CC|_ the|the|DT|_ feeding|feeding|NN|_ and|and|CC|_ outlet|outlet|NN|_ pumps|pump|NNS|_ were|be|VBD|_ maintained|maintain|VBN|_ at|at|IN|_ flow|flow|NN|_ rate|rate|NN|_ of|of|IN|_ 0.1|0.1|CD|_ h-1|h-1|NN|_ .|.|.|_
The|the|DT|_ medium|medium|NN|_ for|for|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ contained|contain|VBD|_ 3|3|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP medium|medium|NN|_ consisted|consist|VBD|_ with|with|IN|_ 0.8|0.8|CD|_ g|g|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.5|0.5|CD|_ g|g|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 7.5|7.5|CD|_ g|g|NN|_ Na2HPO4|na2hpo4|NN|_ •|•|SYM|_ 2H2O|2h2o|NN|_ ,|,|,|_ 3|3|CD|_ g|g|NN|_ KH2PO4|kh2po4|NN|_ with|with|IN|_ separately|separately|RB|_ added|add|VBN|_ trace|trace|NN|_ element|element|NN|_ of|of|IN|_ 0.2|0.2|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ •|•|SYM|_ 7H2O|7H2O|NNP|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mg|mg|NN|_ thiamine|thiamine|NN|SUPP per|per|IN|_ liter|liter|NN|_ .|.|.|_ The|the|DT|_ fermentor|fermentor|NN|_ was|be|VBD|_ maintained|maintain|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ ,|,|,|_ 350|350|CD|_ rpm|rpm|NN|_ with|with|IN|_ air|air|NN|_ gas|gas|NN|_ flushing|flushing|NN|_ and|and|CC|_ the|the|DT|_ feeding|feeding|NN|_ and|and|CC|_ outlet|outlet|NN|_ pumps|pump|NNS|_ were|be|VBD|_ maintained|maintain|VBN|_ at|at|IN|_ flow|flow|NN|_ rate|rate|NN|_ of|of|IN|_ 0.1|0.1|CD|_ h-1|h-1|NN|_ .|.|.|_
Transcriptome|transcriptome|NN|_ of|of|IN|_ cells|cell|NNS|_ was|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ a|a|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ;|;|:|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_
Biofilms|Biofilms|NNPS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ nylon|nylon|NN|_ membranes|membrane|NNS|_ using|use|VBG|_ agar|agar|NN|_ as|as|IN|_ the|the|DT|_ source|source|NN|_ of|of|IN|_ nutrients|nutrient|NNS|_ and|and|CC|_ water|water|NN|_ .|.|.|_ Aliquots|aliquot|NNS|_ of|of|IN|_ 10|10|CD|_ ml|ml|NN|_ Luria|Luria|NNP|_ agar|agar|NN|_ were|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ petri|petri|VB|_ dishes|dish|NNS|_ to|to|TO|_ produce|produce|VB|_ layers|layer|NNS|_ of|of|IN|_ agar|agar|NN|_ approximately|approximately|RB|_ 3|3|CD|_ mm|mm|NN|_ in|in|IN|_ depth|depth|NN|_ .|.|.|_ Nylon|nylon|NN|_ membrane|membrane|NN|_ filters|filter|NNS|_ -LRB-|-lrb-|-LRB-|_ 47|47|CD|_ mm|mm|NN|_ diameter|diameter|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ 0.2|0.2|CD|_ μm|μm|NN|_ pore|pore|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ Whatman|whatman|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ autoclaved|autoclave|VBN|_ in|in|IN|_ Milli-Q|milli-q|JJ|_ water|water|NN|_ ,|,|,|_ dried|dry|VBD|_ and|and|CC|_ placed|place|VBD|_ on|on|IN|_ the|the|DT|_ agar|agar|NN|_ surface|surface|NN|_ .|.|.|_ A|a|DT|_ 100|100|CD|_ μl|μl|NN|_ aliquot|aliquot|NN|_ of|of|IN|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 108|108|CD|_ cells|cell|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ the|the|DT|_ membrane|membrane|NN|_ as|as|IN|_ a|a|DT|_ single|single|JJ|_ spot|spot|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ dry|dry|JJ|_ .|.|.|_ All|all|DT|_ of|of|IN|_ these|these|DT|_ steps|step|NNS|_ were|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ a|a|DT|_ level|level|NN|_ table|table|NN|_ so|so|RB|_ as|as|IN|_ not|not|RB|_ to|to|TO|_ introduce|introduce|VB|_ unwanted|unwanted|JJ|_ gradients|gradient|NNS|_ .|.|.|_ Dishes|dish|NNS|_ were|be|VBD|_ then|then|RB|_ inverted|inverted|JJ|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ oC|oc|NN|_ for|for|IN|_ 24|24|CD|_ h.|h.|NN|_
Biofilms|biofilm|NNS|_ were|be|VBD|_ individually|individually|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ incubator|incubator|NN|_ and|and|CC|_ ,|,|,|_ using|use|VBG|_ a|a|DT|_ small|small|JJ|_ scalpel|scalpel|NN|_ blade|blade|NN|_ and|and|CC|_ sterile|sterile|JJ|_ forceps|forceps|NNS|_ ,|,|,|_ the|the|DT|_ distinctive|distinctive|JJ|_ outer|outer|JJ|_ perimeter|perimeter|NN|_ of|of|IN|_ biofilm|biofilm|NN|_ growth|growth|NN|_ was|be|VBD|_ cut|cut|VBN|_ away|away|RB|_ from|from|IN|_ the|the|DT|_ rest|rest|NN|_ of|of|IN|_ the|the|DT|_ biofilm|biofilm|NN|_ .|.|.|_ The|the|DT|_ two|two|CD|_ resulting|result|VBG|_ sections|section|NNS|_ of|of|IN|_ membrane|membrane|NN|_ were|be|VBD|_ submerged|submerge|VBN|_ in|in|IN|_ separate|separate|JJ|_ volumes|volume|NNS|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ and|and|CC|_ vortexed|vortex|VBN|_ to|to|TO|_ release|release|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ sections|section|NNS|_ of|of|IN|_ membrane|membrane|NN|_ were|be|VBD|_ then|then|RB|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ resulting|result|VBG|_ suspension|suspension|NN|_ before|before|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 5,000|5,000|CD|_ g|g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ supplier|supplier|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ composition|composition|NN|_ of|of|IN|_ the|the|DT|_ RNeasy|rneasy|NN|_ solutions|solution|NNS|_ are|be|VBP|_ unknown|unknown|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ decanted|decant|VBN|_ and|and|CC|_ 200|200|CD|_ μl|μl|NN|_ of|of|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ in|in|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ -RRB-|-rrb-|-RRB-|_ plus|plus|CC|_ lysosyme|lysosyme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ resuspend|resuspend|VB|_ the|the|DT|_ pellet|pellet|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ mixed|mixed|JJ|_ vigorously|vigorously|RB|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ intermittent|intermittent|JJ|_ shaking|shake|VBG|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ Buffer|buffer|NN|_ RLT|rlt|NN|_ -LRB-|-lrb-|-LRB-|_ 700|700|CD|_ μl|μl|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ μl|μl|NN|_ of|of|IN|_ 14.3|14.3|CD|_ M|m|NN|_ β-mercaptoethanol|β-mercaptoethanol|NN|_ per|per|IN|_ 1|1|CD|_ ml|ml|NN|_ RTL|rtl|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ then|then|RB|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ .|.|.|_ The|the|DT|_ lysate|lysate|NN|_ was|be|VBD|_ then|then|RB|_ mixed|mix|VBN|_ with|with|IN|_ 500|500|CD|_ μl|μl|NN|_ of|of|IN|_ absolute|absolute|JJ|_ ethanol|ethanol|NN|_ before|before|IN|_ applying|apply|VBG|_ the|the|DT|_ solution|solution|NN|_ to|to|TO|_ an|a|DT|_ RNeasy|rneasy|NN|_ Mini|Mini|NNP|_ column|column|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ then|then|RB|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 15|15|CD|_ s|s|NNS|_ at|at|IN|_ 8,000|8,000|CD|_ x|x|CC|_ g.|g.|NNP|_ Buffer|Buffer|NNP|_ RW1|rw1|NN|_ -LRB-|-lrb-|-LRB-|_ 700|700|CD|_ μl|μl|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ the|the|DT|_ column|column|NN|_ and|and|CC|_ centrifuged|centrifuge|VBN|_ to|to|TO|_ wash|wash|VB|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ At|at|IN|_ this|this|DT|_ point|point|NN|_ an|a|DT|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ on-column|on-column|JJ|_ digest|digest|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ ,|,|,|_ before|before|IN|_ the|the|DT|_ wash|wash|NN|_ process|process|NN|_ was|be|VBD|_ repeated|repeat|VBN|_ twice|twice|RB|_ with|with|IN|_ 500|500|CD|_ μl|μl|NN|_ of|of|IN|_ RPE|rpe|NN|_ buffer|buffer|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ twice|twice|RB|_ in|in|IN|_ one|one|CD|_ 30|30|CD|_ μl|μl|NN|_ volume|volume|NN|_ of|of|IN|_ RNase-free|rnase-free|JJ|_ water|water|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -70|-70|CD|_ oC|oc|NN|_ .|.|.|_
Colony|Colony|NNP|_ Biofilm|Biofilm|NNP|_ Replicate|replicate|VB|_ 1|1|CD|_
Colony|Colony|NNP|_ Biofilm|Biofilm|NNP|_ Replicate|replicate|VB|_ 2|2|CD|_
Colony|Colony|NNP|_ Biofilm|Biofilm|NNP|_ Replicate|replicate|VB|_ 3|3|CD|_
Colony|Colony|NNP|_ Biofilm|Biofilm|NNP|_ Replicate|replicate|VB|_ 4|4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Colony|Colony|NNP|_ Biofilm|Biofilm|NNP|_ Interior|Interior|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Colony|Colony|NNP|_ Biofilm|Biofilm|NNP|_ Perimeter|Perimeter|NNP|_
strain|strain|NN|_ :|:|:|_ TG-1|tg-1|NN|_
strain|strain|NN|_ :|:|:|_ TG-2|tg-2|NN|_
The|the|DT|_ average|average|JJ|_ fluorescent|fluorescent|JJ|_ signal|signal|NN|_ intensity|intensity|NN|_ and|and|CC|_ local|local|JJ|_ background|background|NN|_ correction|correction|NN|_ for|for|IN|_ each|each|DT|_ spot|spot|NN|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ commercially|commercially|RB|_ available|available|JJ|_ software|software|NN|_ from|from|IN|_ Biodiscovery|Biodiscovery|NNP|_ Inc|Inc|NNP|_ -LRB-|-lrb-|-LRB-|_ Imagene|Imagene|NNP|_ ,|,|,|_ version|version|NN|_ 4.0|4.0|CD|_ and|and|CC|_ Genesight|Genesight|NNP|_ ,|,|,|_ version|version|NN|_ 3.5|3.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Spots|spot|NNS|_ with|with|IN|_ a|a|DT|_ signal|signal|NN|_ intensity|intensity|NN|_ lower|lower|JJR|_ than|than|IN|_ the|the|DT|_ background|background|NN|_ signal|signal|NN|_ or|or|CC|_ those|those|DT|_ with|with|IN|_ blemishes|blemish|NNS|_ were|be|VBD|_ omitted|omit|VBN|_ from|from|IN|_ subsequent|subsequent|JJ|_ analysis|analysis|NN|_ .|.|.|_ The|the|DT|_ mean|mean|NN|_ values|value|NNS|_ from|from|IN|_ each|each|DT|_ channel|channel|NN|_ were|be|VBD|_ then|then|RB|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ normalised|normalise|VBN|_ using|use|VBG|_ the|the|DT|_ LOWESS|lowess|NN|_ method|method|NN|_ to|to|TO|_ remove|remove|VB|_ intensity-dependent|intensity-dependent|JJ|_ effects|effect|NNS|_ in|in|IN|_ the|the|DT|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ ratios|ratio|NNS|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ .|.|.|_ The|the|DT|_ Cy3|cy3|NN|_
A-stat|a-stat|NN|_ gene|gene|NN|_ expression|expression|NN|_ changes|change|NNS|_ 0.3|0.3|CD|_
A-stat|a-stat|NN|_ gene|gene|NN|_ expression|expression|NN|_ changes|change|NNS|_ 0.47|0.47|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ :|:|:|_ 0.3|0.3|CD|_ h-1|h-1|NN|_
Specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.3|0.3|CD|_ h-1|h-1|NN|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ :|:|:|_ 0.47|0.47|CD|_ h-1|h-1|NN|_
Specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.47|0.47|CD|_ h-1|h-1|NN|_
Spot|spot|NN|_ intensities|intensity|NNS|_ and|and|CC|_ corresponding|corresponding|JJ|_ background|background|NN|_ signals|signal|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ with|with|IN|_ Genepix|Genepix|NNP|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 6|6|CD|_ ;|;|:|_ Axon|Axon|NNP|_ Instruments|Instruments|NNPS|_ -LSB-|-lsb-|-LRB-|_ http|http|NN|_ :|:|:|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RNase-Free|rnase-free|JJ|_ DNase|dnase|NN|_ Set|set|VB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
After|after|IN|_ collecting|collect|VBG|_ 50|50|CD|_ ml|ml|NN|_ culture|culture|NN|_ as|as|IN|_ `|`|``|_ non|non|JJ|_ crosslinked|crosslink|VBN|_ '|'|''|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ rest|rest|NN|_ of|of|IN|_ the|the|DT|_ cells|cell|NNS|_ was|be|VBD|_ crosslinked.Crosslinked|crosslinked.crosslinked|VBN|_ and|and|CC|_ non|non|JJ|_ crosslinked|crosslink|VBN|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ sonicated|sonicate|VBN|_ .|.|.|_ 400|400|CD|_ µl|µl|NN|_ of|of|IN|_ the|the|DT|_ sonicated|sonicated|JJ|_ extracts|extract|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 400|400|CD|_ µl|µl|NN|_ TE|te|NN|_ buffer|buffer|NN|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ 2|2|CD|_ µl|µl|NN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mg|mg|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.15|0.15|CD|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.15|0.15|CD|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 65|65|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.3|0.3|CD|_ .|.|.|_ Subsequently|subsequently|RB|_ 30|30|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ transformed|transform|VBN|_ to|to|TO|_ a|a|DT|_ pre|pre|JJ|_ warmed|warm|VBN|_ flask|flask|NN|_ at|at|IN|_ 43|43|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ remainder|remainder|NN|_ kept|keep|VBD|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ control|control|JJ|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 65|65|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.3|0.3|CD|_ .|.|.|_ Subsequently|subsequently|RB|_ 30|30|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ were|be|VBD|_ transformed|transform|VBN|_ to|to|TO|_ a|a|DT|_ pre|pre|JJ|_ warmed|warm|VBN|_ flask|flask|NN|_ at|at|IN|_ 43|43|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ heat|heat|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ remainder|remainder|NN|_ kept|keep|VBD|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ none|none|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ subunit|subunit|NN|_ β|β|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ SeqA|seqa|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ σ32|σ32|NN|_
Crosslink|Crosslink|NNP|_
Crosslinked|Crosslinked|NNP|_
Cultures|culture|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ and|and|CC|_ its|its|PRP$|_ derivates|derivate|NNS|_ were|be|VBD|_ cross|cross|JJ|_ linked|link|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ µl|µl|NN|_ of|of|IN|_ formaldehyde|formaldehyde|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ ml|ml|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 1|1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Crosslinking|crosslinking|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ slow|slow|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ followed|follow|VBN|_ by|by|IN|_ quenching|quench|VBG|_ with|with|IN|_ 0.2|0.2|CD|_ ml|ml|NN|_ of|of|IN|_ 2.5|2.5|CD|_ M|m|NN|_ glycine|glycine|NN|_ per|per|IN|_ ml|ml|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 0.5|0.5|CD|_ M|m|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ cold|cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ pH7|ph7|NN|_ .5|.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ resuspension|resuspension|NN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10mM|10mm|NN|_ Tris|tris|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 20|20|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ ,|,|,|_ 50mM|50mm|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 10mM|10mm|NN|_ EDTA|edta|NN|_ ,|,|,|_ 10|10|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
fraction|fraction|NN|_ :|:|:|_ input|input|NN|_ DNA|dna|NN|_
fraction|fraction|NN|_ :|:|:|_ input|input|NN|_ DNA|dna|NN|_ ,|,|,|_ SeqA|seqa|NN|_ ChIP|chip|NN|_ supernatant|supernatant|JJ|_
fraction|fraction|NN|_ :|:|:|_ input|input|NN|_ DNA|dna|NN|_ ,|,|,|_ σ32|σ32|NN|_ ChIP|chip|NN|_ supernatant|supernatant|JJ|_
genotype|genotype|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
genotype|genotype|NN|_ :|:|:|_ ΔseqA|δseqa|NN|_
Input|input|NN|_ DNA|dna|NN|_ from|from|IN|_ E.|E.|NNP|_ Coli|Coli|NNP|_ MG1655|MG1655|NNP|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ E.|E.|NNP|_ Coli|Coli|NNP|_ MG1655|MG1655|NNP|_ ΔseqA|ΔseqA|NNP|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ SeqA|seqa|NN|_ ChIP|chip|NN|_ supernatant|supernatant|JJ|_
Input|input|NN|_ DNA|dna|NN|_ from|from|IN|_ ΔseqA-SeqA|δseqa-seqa|NN|_ ChIP|chip|NN|_ supernatant|supernatant|JJ|_
Input|input|NN|_ DNA|dna|NN|_ from|from|IN|_ σ32|σ32|NN|_ ChIP|chip|NN|_ supernatant|supernatant|JJ|_
Non-crosslinked|non-crosslinked|JJ|_ DNA|dna|NN|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ ,|,|,|_ old|old|JJ|_ protocol|protocol|NN|_
RNAP|rnap|NN|_ old|old|JJ|_ rep1|rep1|NN|_
RNAP|rnap|NN|_ old|old|JJ|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ ,|,|,|_ new|new|JJ|_ protocol|protocol|NN|_
SeqA|seqa|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ ,|,|,|_ old|old|JJ|_ protocol|protocol|NN|_
SeqA|seqa|NN|_ new|new|JJ|_ deltaSeqA|deltaseqa|NN|_
SeqA|seqa|NN|_ new|new|JJ|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ new|new|JJ|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ old|old|JJ|_ deltaSeqA|deltaseqa|NN|_
SeqA|seqa|NN|_ old|old|JJ|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ old|old|JJ|_ rep2|rep2|NN|_
Spot|spot|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Feature|Feature|NNP|_ Extraction|extraction|NN|_ software|software|NN|_ 10.5.1.1|10.5.1.1|CD|_ from|from|IN|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ with|with|IN|_ a|a|DT|_ linear|linear|JJ|_ dye|dye|VB|_ normalization|normalization|NN|_ correction|correction|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ gProcessedSignal|gprocessedsignal|NN|_ and|and|CC|_ rProcessedSignal|rprocessedsignal|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ with|with|IN|_ the|the|DT|_ statistics|statistics|NNS|_ software|software|NN|_ R.|R.|NNP|_ Ratios|Ratios|NNP|_ of|of|IN|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ r|r|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ after|after|IN|_ background|background|NN|_ substraction|substraction|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ the|the|DT|_ array|array|NN|_ wide|wide|JJ|_ average|average|NN|_ .|.|.|_ Data|datum|NNS|_ points|point|NNS|_ with|with|IN|_ a|a|DT|_ value|value|NN|_ below|below|IN|_ 0|0|CD|_ after|after|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ were|be|VBD|_ set|set|VBN|_ `|`|``|_ null|null|NN|_ '|'|''|_ .|.|.|_ Data|datum|NNS|_ points|point|NNS|_ form|form|VBP|_ non-unique|non-unique|JJ|_ regions|region|NNS|_ on|on|IN|_ the|the|DT|_ chromosome|chromosome|NN|_ were|be|VBD|_ excluded|exclude|VBN|_ from|from|IN|_ analysis|analysis|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ ΔseqA|δseqa|NN|_
σ32|σ32|NN|_ 30|30|CD|_ °C|°c|NN|_ rep1|rep1|NN|_
σ32|σ32|NN|_ 30|30|CD|_ °C|°c|NN|_ rep2|rep2|NN|_
σ32|σ32|NN|_ 30|30|CD|_ °C|°c|NN|_ short|short|JJ|_ RNase|rnase|NN|_
σ32|σ32|NN|_ 43|43|CD|_ °C|°c|NN|_ rep1|rep1|NN|_
σ32|σ32|NN|_ 43|43|CD|_ °C|°c|NN|_ rep2|rep2|NN|_
σ32|σ32|NN|_ 43|43|CD|_ °C|°c|NN|_ short|short|JJ|_ RNase|rnase|NN|_
σ32|σ32|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ ,|,|,|_ control|control|NN|_
σ32|σ32|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ ,|,|,|_ heat|heat|NN|_
σ32|σ32|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ ,|,|,|_ short|short|JJ|_ RNase|rnase|NN|_ digestion|digestion|NN|_
At|at|IN|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ serine|serine|NN|_ hydroxamate|hydroxamate|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mg|mg|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ casamino|casamino|NN|_ acid|acid|NN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_
Delta|Delta|NNP|_ dksA|dksA|NNP|GEN Cells|cell|NNS|_
Delta|Delta|NNP|_ dksA|dksA|NNP|GEN Cells|cell|NNS|_ Replicate|replicate|VB|_ 1|1|CD|_
Delta|Delta|NNP|_ dksA|dksA|NNP|GEN Cells|cell|NNS|_ Replicate|replicate|VB|_ 2|2|CD|_
Delta|Delta|NNP|_ dksA|dksA|NNP|GEN Cells|cell|NNS|_ Replicate|replicate|VB|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
GenePix|GenePix|NNP|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_ 6.1|6.1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ normalization|normalization|NN|_ .|.|.|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
pooled|pool|VBD|_ reference|reference|NN|_ RNA|rna|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
SHX-treated|shx-treated|JJ|_ Delta|delta|NN|_ dksA|dksa|NN|GEN Cells|cell|NNS|_
SHX-treated|shx-treated|JJ|_ Delta|delta|NN|_ dksA|dksa|NN|GEN Cells|cell|NNS|_ Replicate|replicate|VB|_ 1|1|CD|_
SHX-treated|shx-treated|JJ|_ Delta|delta|NN|_ dksA|dksa|NN|GEN Cells|cell|NNS|_ Replicate|replicate|VB|_ 2|2|CD|_
SHX-treated|shx-treated|JJ|_ Delta|delta|NN|_ dksA|dksa|NN|GEN Cells|cell|NNS|_ Replicate|replicate|VB|_ 3|3|CD|_
SHX-treated|shx-treated|JJ|_ Wild-type|wild-type|JJ|_ Cells|cell|NNS|_
SHX-treated|shx-treated|JJ|_ Wild-type|wild-type|JJ|_ Cells|cell|NNS|_ Replicate|replicate|VB|_ 1|1|CD|_
SHX-treated|shx-treated|JJ|_ Wild-type|wild-type|JJ|_ Cells|cell|NNS|_ Replicate|replicate|VB|_ 2|2|CD|_
SHX-treated|shx-treated|JJ|_ Wild-type|wild-type|JJ|_ Cells|cell|NNS|_ Replicate|replicate|VB|_ 3|3|CD|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ lac|lac|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ lac|lac|NN|_ delta|delta|NN|_ dksA|dksa|NN|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ delta|delta|NN|_ lac|lac|NN|_ +|+|CC|_ MG1655|mg1655|NN|_ delta|delta|NN|_ lac|lac|NN|_ delta|delta|NN|_ dksA|dksa|NN|GEN
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ mg|mg|NN|_
treatment|treatment|NN|_ :|:|:|_ No|no|DT|_ treatment|treatment|NN|_
treatment|treatment|NN|_ :|:|:|_ Pooled|pool|VBN|_ RNA|rna|NN|_ from|from|IN|_ mixture|mixture|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ amount|amount|NN|_ of|of|IN|_ wt|wt|JJ|_ ,|,|,|_ wt|wt|JJ|_ +|+|CC|_ SHX|shx|NN|_ ,|,|,|_ dksA|dksa|NN|GEN ,|,|,|_ dksA|dksa|NN|GEN +|+|CC|_ SHX|shx|NN|_ RNA|rna|NN|_ samples|sample|NNS|_
Wild-type|wild-type|JJ|_ Cells|cell|NNS|_
Wild-type|wild-type|JJ|_ Cells|cell|NNS|_ Replicate|replicate|VBP|_ 1|1|CD|_
Wild-type|wild-type|JJ|_ Cells|cell|NNS|_ Replicate|replicate|VB|_ 2|2|CD|_
Wild-type|wild-type|JJ|_ Cells|cell|NNS|_ Replicate|replicate|VB|_ 3|3|CD|_
Biotinylated|biotinylate|VBN|_ GST|gst|NN|_ protein|protein|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
GSH-sepharose|gsh-sepharose|NN|_ 4b|4b|NN|_ purification|purification|NN|_
GST|gst|NN|_ control|control|NN|_ Protoarray|Protoarray|NNP|_ replicate|replicate|VB|_ 1|1|CD|_
protein|protein|NN|_ :|:|:|_ GST|gst|NN|_ expressed|express|VBN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ pGEX-4T-3|pgex-4t-3|NN|_
purification|purification|NN|_ :|:|:|_ Protein|protein|NN|_ purified|purify|VBN|_ using|use|VBG|_ GSH-sepharose|gsh-sepharose|JJ|_ 4b|4b|NN|_ -LRB-|-lrb-|-LRB-|_ GE|GE|NNP|_ Life|Life|NNP|_ Sciences|Sciences|NNPS|_ -RRB-|-rrb-|-RRB-|_
Scanned|scan|VBN|_ spot|spot|NN|_ signals|signal|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ internal|internal|JJ|_ Protoarray|Protoarray|NNP|_ control|control|NN|_ proteins|protein|NNS|_ and|and|CC|_ Z|z|NN|_ scores|score|NNS|_ subsequently|subsequently|RB|_ determined|determine|VBD|_ based|base|VBN|_ on|on|IN|_ comparisons|comparison|NNS|_ of|of|IN|_ mean|mean|NN|_ signals|signal|NNS|_ for|for|IN|_ each|each|DT|_ spot|spot|NN|_ pair|pair|NN|_ to|to|TO|_ the|the|DT|_ mean|mean|NN|_ spot|spot|NN|_ intensity|intensity|NN|_ for|for|IN|_ the|the|DT|_ array|array|NN|_ .|.|.|_ Z|z|NN|_ scores|score|NNS|_ greater|greater|JJR|_ than|than|IN|_ 3.0|3.0|CD|_ were|be|VBD|_ considered|consider|VBN|_ significant|significant|JJ|_
After|after|IN|_ the|the|DT|_ final|final|JJ|_ wash|wash|NN|_ &|&|CC|_ staining|staining|NN|_ step|step|NN|_ ,|,|,|_ Affymetrix|Affymetrix|NNP|_ GeneChip|GeneChip|NNP|_ ®|®|NNP|_ E.coli|E.coli|NNP|_ Genome|Genome|NNP|_ array|array|NN|_ was|be|VBD|_ scanned|scan|VBN|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ Model|Model|NNP|_ 3000|3000|CD|_ G7|G7|NNP|_ scanner|scanner|NN|_ and|and|CC|_ the|the|DT|_ image|image|NN|_ data|datum|NNS|_ was|be|VBD|_ extracted|extract|VBN|_ through|through|IN|_ Affymetrix|Affymetrix|NNP|_ Commnad|Commnad|NNP|_ Console|Console|NNP|_ software|software|NN|_ .|.|.|_ The|the|DT|_ raw|raw|JJ|_ .|.|.|_ cel|cel|NN|_ file|file|NN|_ generated|generate|VBN|_ through|through|IN|_ above|above|IN|_ procedure|procedure|NN|_ meant|mean|VBD|_ expression|expression|NN|_ intensity|intensity|NN|_ data|datum|NNS|_ and|and|CC|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ next|next|JJ|_ step|step|NN|_ .|.|.|_
EDL|edl|NN|_ 933|933|CD|_ at|at|IN|_ 37oC|37oc|NN|_ at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
EDL|edl|NN|_ 933|933|CD|_ with|with|IN|_ 0.1|0.1|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Expression|expression|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ microarray|microarray|NN|_ suite|suite|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ MAS5|mas5|NN|_ -RRB-|-rrb-|-RRB-|_ algorithm|algorithm|NN|_ implemented|implement|VBD|_ in|in|IN|_ Affymetrix|Affymetrix|NNP|_ expression|expression|NN|_ console|console|NN|_ software|software|NN|_ .|.|.|_ To|to|TO|_ reduce|reduce|VB|_ noise|noise|NN|_ for|for|IN|_ the|the|DT|_ significance|significance|NN|_ analysis|analysis|NN|_ ,|,|,|_ probe|probe|NN|_ sets|set|NNS|_ that|that|WDT|_ did|do|VBD|_ not|not|RB|_ show|show|VB|_ detection|detection|NN|_ call|call|NN|_ rate|rate|NN|_ at|at|IN|_ least|least|JJS|_ 50|50|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ in|in|IN|_ the|the|DT|_ comparison|comparison|NN|_ were|be|VBD|_ filtered|filter|VBN|_ out|out|RP|_ .|.|.|_ Highly|highly|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ that|that|WDT|_ showed|show|VBD|_ a|a|DT|_ 2-fold|2-fold|JJ|_ change|change|NN|_ in|in|IN|_ expression|expression|NN|_ were|be|VBD|_ selected|select|VBN|_ .|.|.|_
-LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
strain|strain|NN|_ :|:|:|_ EDL|edl|NN|_ 933|933|CD|_
The|the|DT|_ web-based|web-based|JJ|_ tool|tool|NN|_ ,|,|,|_ DAVID|DAVID|NNP|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ Database|database|NN|_ for|for|IN|_ Annotation|Annotation|NNP|_ ,|,|,|_ Visualization|visualization|NN|_ ,|,|,|_ and|and|CC|_ Integrated|Integrated|NNP|_ Discovery|Discovery|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ perform|perform|VB|_ the|the|DT|_ biological|biological|JJ|_ interpretation|interpretation|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ these|these|DT|_ genes|gene|NNS|_ were|be|VBD|_ classified|classify|VBN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ information|information|NN|_ of|of|IN|_ gene|gene|NN|_ function|function|NN|_ in|in|IN|_ Gene|Gene|NNP|_ ontology|ontology|NN|_ database|database|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Ribopure|Ribopure|NNP|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Huntingdon|Huntingdon|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ bioanalyser|bioanalyser|NN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Amstelveen|Amstelveen|NNP|_ ,|,|,|_ The|the|DT|_ Netherlands|Netherlands|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ quantity|quantity|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ ND-1000|nd-1000|NN|_ Spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ NanoDrop|NanoDrop|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ harvested|harvest|VBN|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ ,|,|,|_ spun|spin|VBD|_ ,|,|,|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ M9|m9|NN|_ medium|medium|NN|_ and|and|CC|_ shifted|shift|VBD|_ to|to|TO|_ limiting|limit|VBG|_ or|or|CC|_ no|no|DT|_ thymine|thymine|NN|_ medium|medium|NN|_ .|.|.|_ Samples|sample|NNS|_ taken|take|VBN|_ at|at|IN|_ listed|list|VBN|_ intervals|interval|NNS|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ nutrient|nutrient|NN|_ shift|shift|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ limiting|limit|VBG|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ thymineless|thymineless|JJ|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ limiting|limit|VBG|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ thymineless|thymineless|JJ|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ limiting|limit|VBG|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ thymineless|thymineless|JJ|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ limiting|limit|VBG|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ thymineless|thymineless|JJ|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 90|90|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ limiting|limit|VBG|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -|-|:|_ 90|90|CD|_ min|min|NN|_ after|after|IN|_ shift|shift|NN|_ to|to|TO|_ thymineless|thymineless|JJ|_ medium|medium|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ thyA|thya|NN|GEN -|-|:|_ cells|cell|NNS|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 20|20|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Lowess|lowess|NN|_ normalized|normalize|VBD|_ data|datum|NNS|_ .|.|.|_ Resultant|resultant|JJ|_ data|datum|NNS|_ is|be|VBZ|_ log2|log2|NN|_ normalized|normalize|VBD|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ thyA|thya|NN|GEN -|-|:|_
TLD-15-rep1|tld-15-rep1|NN|_
TLD-15-rep2|tld-15-rep2|NN|_
TLD-30-rep1|tld-30-rep1|NN|_
TLD-30-rep2|tld-30-rep2|NN|_
TLD-45-rep1|tld-45-rep1|NN|_
TLD-45-rep2|tld-45-rep2|NN|_
TLD-60-rep1|tld-60-rep1|NN|_
TLD-60-rep2|tld-60-rep2|NN|_
TLD-90-rep1|tld-90-rep1|NN|_
TLD-90-rep2|tld-90-rep2|NN|_
TLM-15|tlm-15|NN|_
TLM-30|tlm-30|NN|_
TLM-45|tlm-45|NN|_
TLM-60|tlm-60|NN|_
TLM-90|tlm-90|NN|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_
Channel|Channel|NNP|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ 86-24|86-24|CD|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ at|at|IN|_ OD|od|NN|_ 4.0|4.0|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ 86-24|86-24|CD|_ was|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ shake|shake|NN|_ flasks|flask|NNS|_ with|with|IN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ that|that|WDT|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ an|a|DT|_ absorbance|absorbance|NN|_ of|of|IN|_ 4.0|4.0|CD|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ chilled|chill|VBN|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ prevent|prevent|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ sec|sec|NN|_ before|before|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 13,000|13,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ;|;|:|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|frozen|JJ|_ immediately|immediately|RB|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ stored|store|VBD|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ at|at|IN|_ OD|od|NN|_ 4.0|4.0|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ shake|shake|NN|_ flasks|flask|NNS|_ with|with|IN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ that|that|WDT|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ an|a|DT|_ absorbance|absorbance|NN|_ of|of|IN|_ 4.0|4.0|CD|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ chilled|chill|VBN|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ prevent|prevent|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ sec|sec|NN|_ before|before|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 13,000|13,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ;|;|:|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|frozen|JJ|_ immediately|immediately|RB|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ stored|store|VBD|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
strain|strain|NN|_ :|:|:|_ 86-24|86-24|CD|_
strain|strain|NN|_ :|:|:|_ EDL933|edl933|NN|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ in|in|IN|_ a|a|DT|_ thermostatically|thermostatically|RB|_ controlled|control|VBN|_ 37oC|37oc|NN|_ culture|culture|NN|_ room|room|NN|_ .|.|.|_ Cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 150|150|CD|_ ml|ml|NN|_ culture|culture|NN|_ volume|volume|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ stirred|stir|VBN|_ by|by|IN|_ magnetic|magnetic|JJ|_ stirrers|stirrer|NNS|_ at|at|IN|_ 330|330|CD|_ rpm|rpm|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Variomag|Variomag|NNP|_ Multipoint|Multipoint|NNP|_ 6in|6in|JJ|_ -RRB-|-rrb-|-RRB-|_ 1000|1000|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ .|.|.|_ Starting|start|VBG|_ cultures|culture|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ and|and|CC|_ grown|grown|JJ|_ overnight|overnight|JJ|_ .|.|.|_ Each|each|DT|_ experimental|experimental|JJ|_ culture|culture|NN|_ was|be|VBD|_ then|then|RB|_ inoculated|inoculate|VBN|_ from|from|IN|_ such|such|JJ|_ an|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ at|at|IN|_ a|a|DT|_ dilution|dilution|NN|_ of|of|IN|_ 1:20|1:20|CD|_ into|into|IN|_ 150|150|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ in|in|IN|_ a|a|DT|_ 1000|1000|CD|_ ml|ml|NN|_ flask|flask|NN|_ .|.|.|_ The|the|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ used|use|VBN|_ for|for|IN|_ all|all|DT|_ experiments|experiment|NNS|_ was|be|VBD|_ a|a|DT|_ modification|modification|NN|_ of|of|IN|_ MOPS|mop|NNS|MED -LRB-|-lrb-|-LRB-|_ morpholinopropane|morpholinopropane|NN|_ sulfonate|sulfonate|NN|_ -RRB-|-rrb-|-RRB-|_ minimal|minimal|JJ|_ medium|medium|NN|_ obtained|obtain|VBN|_ from|from|IN|_ Teknova|Teknova|NNP|_ ,|,|,|_ CA|CA|NNP|_ -LRB-|-lrb-|-LRB-|_ product|product|NN|_ number|number|NN|_ M2006|m2006|NN|_ -RRB-|-rrb-|-RRB-|_ which|which|WDT|_ contains|contain|VBZ|_ 86|86|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 9.5|9.5|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP K2HPO4|k2hpo4|NN|_ and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint1|timepoint1|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint1|timepoint1|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint1|timepoint1|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint2|timepoint2|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint2|timepoint2|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint2|timepoint2|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint3|timepoint3|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint3|timepoint3|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint3|timepoint3|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint4|timepoint4|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint4|timepoint4|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint4|timepoint4|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint5|timepoint5|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint5|timepoint5|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint5|timepoint5|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint6|timepoint6|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint6|timepoint6|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint6|timepoint6|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint7|timepoint7|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint7|timepoint7|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint7|timepoint7|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ coldstress|coldstress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint1|timepoint1|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint1|timepoint1|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint1|timepoint1|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint1|timepoint1|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint1|timepoint1|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint1|timepoint1|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint2|timepoint2|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint2|timepoint2|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint2|timepoint2|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint3|timepoint3|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint3|timepoint3|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint3|timepoint3|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint4|timepoint4|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint4|timepoint4|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint4|timepoint4|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint5|timepoint5|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint5|timepoint5|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint5|timepoint5|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint6|timepoint6|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint6|timepoint6|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint6|timepoint6|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint7|timepoint7|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint7|timepoint7|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint7|timepoint7|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ heatstress|heatstress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep3|rep3|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ lactose|lactose|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint10|timepoint10|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint10|timepoint10|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint10|timepoint10|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint11|timepoint11|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint11|timepoint11|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint11|timepoint11|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint12|timepoint12|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint1|timepoint1|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint1|timepoint1|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint1|timepoint1|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint2|timepoint2|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint3|timepoint3|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint4|timepoint4|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint5|timepoint5|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint6|timepoint6|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint7|timepoint7|NN|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|VBP|_ _|_|SYM|_ timepoint8|timepoint8|CD|_ _|_|CD|_ rep4|rep4|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint9|timepoint9|NN|_ _|_|CD|_ rep1|rep1|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint9|timepoint9|NN|_ _|_|CD|_ rep2|rep2|NN|_
coli|coli|NN|_ _|_|NN|_ oxidativestress|oxidativestress|NN|_ _|_|CD|_ timepoint9|timepoint9|NN|_ _|_|CD|_ rep4|rep4|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ stress|stress|NN|_ experiment|experiment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ further|further|JJ|_ analyses|analysis|NNS|_ the|the|DT|_ processed|process|VBN|_ signal|signal|NN|_ intensities|intensity|NNS|_ of|of|IN|_ all|all|DT|_ coding|code|VBG|_ regions|region|NNS|_ and|and|CC|_ RNA|rna|NN|_ genes|gene|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ used|use|VBN|_ .|.|.|_ Variance|variance|NN|_ stabilization|stabilization|NN|_ and|and|CC|_ normalization|normalization|NN|_ of|of|IN|_ the|the|DT|_ extracted|extract|VBN|_ intensities|intensity|NNS|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ vsn|vsn|NN|_ packages|package|NNS|_ of|of|IN|_ the|the|DT|_ R|r|NN|_ software|software|NN|_ environment|environment|NN|_ -LRB-|-lrb-|-LRB-|_ R|r|NN|_ Development|development|NN|_ Core|core|NN|_ Team|Team|NNP|_ ,|,|,|_ 2007|2007|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ back-transformed|back-transformed|JJ|_ to|to|TO|_ normal|normal|JJ|_ intensity|intensity|NN|_ scale|scale|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ probeset|probeset|NN|_ ,|,|,|_ e.g.|e.g.|FW|_ all|all|DT|_ probes|probe|NNS|_ representing|represent|VBG|_ for|for|IN|_ example|example|NN|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ coding|coding|NN|_ gene|gene|NN|_ ,|,|,|_ outliers|outlier|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ boxplot|boxplot|NN|_ statistics|statistics|NNS|_ and|and|CC|_ the|the|DT|_ outlier-removed|outlier-removed|JJ|_ probe|probe|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ averaged|average|VBN|_ in|in|IN|_ a|a|DT|_ robust|robust|JJ|_ way|way|NN|_ by|by|IN|_ computing|compute|VBG|_ the|the|DT|_ Tukey|tukey|NN|_ biweight|biweight|NN|_ .|.|.|_
Oxidative|oxidative|JJ|_ stress|stress|NN|_ 200|200|CD|_ ug|ug|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ mechanical|mechanical|JJ|_ cell|cell|NN|_ disruption|disruption|NN|_ with|with|IN|_ glass|glass|NN|_ beads|bead|NNS|_ but|but|CC|_ without|without|IN|_ enzymatic|enzymatic|JJ|_ lysis|lysis|NN|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ lysis|lysis|NN|_ RLT|rlt|NN|_ buffer|buffer|NN|_ with|with|IN|_ beta-mercaptethanol|beta-mercaptethanol|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Mechanical|mechanical|JJ|_ cell|cell|NN|_ disruption|disruption|NN|_ was|be|VBD|_ completed|complete|VBN|_ through|through|IN|_ shaking|shake|VBG|_ for|for|IN|_ five|five|CD|_ min|min|NN|_ using|use|VBG|_ a|a|DT|_ Retsch|Retsch|NNP|_ mill|mill|NN|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|JJ|_ MM200|mm200|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ maximum|maximum|NN|_ speed|speed|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ subsequently|subsequently|RB|_ cleaned|clean|VBN|_ on-column|on-column|JJ|_ with|with|IN|_ an|a|DT|_ additional|additional|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ 79254|79254|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ of|of|IN|_ extracted|extract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ bioanalyzer|bioanalyzer|NN|_ having|have|VBG|_ used|use|VBN|_ an|a|DT|_ Agilent|agilent|JJ|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ cold|cold|JJ|_ stress|stress|NN|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ control|control|NN|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ heat|heat|NN|_ stress|stress|NN|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ lactose|lactose|NN|_ shift|shift|NN|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ oxidative|oxidative|JJ|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T10|t10|NN|_ :|:|:|_ 210|210|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T11|t11|NN|_ :|:|:|_ 235|235|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T12|t12|NN|_ :|:|:|_ 260|260|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T1|t1|NN|_ :|:|:|_ OD|od|NN|_ 0.3|0.3|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T1|t1|NN|_ :|:|:|_ OD|od|NN|_ 0.5|0.5|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T2|t2|NN|_ :|:|:|_ OD|od|NN|_ 0.5|0.5|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T2|t2|NN|_ :|:|:|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T3|t3|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ reaching|reach|VBG|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T3|t3|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T3|t3|NN|_ :|:|:|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T3|t3|NN|_ :|:|:|_ OD|od|NN|_ 0.7|0.7|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T4|t4|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ lag|lag|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T4|t4|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T4|t4|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ reaching|reach|VBG|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T4|t4|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T5|t5|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ lag|lag|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T5|t5|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T5|t5|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ reaching|reach|VBG|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T5|t5|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T6|t6|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ lag|lag|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T6|t6|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T6|t6|NN|_ :|:|:|_ 40|40|CD|_ min|min|NN|_ after|after|IN|_ reaching|reach|VBG|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T6|t6|NN|_ :|:|:|_ 40|40|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T7|t7|NN|_ :|:|:|_ 40|40|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ lag|lag|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T7|t7|NN|_ :|:|:|_ 40|40|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T7|t7|NN|_ :|:|:|_ 50|50|CD|_ min|min|NN|_ after|after|IN|_ reaching|reach|VBG|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T7|t7|NN|_ :|:|:|_ 50|50|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T8|t8|NN|_ :|:|:|_ 90|90|CD|_ min|min|NN|_ after|after|IN|_ reaching|reach|VBG|_ OD|od|NN|_ 0.6|0.6|CD|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T8|t8|NN|_ :|:|:|_ 90|90|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
treatment|treatment|NN|_ time|time|NN|_ :|:|:|_ T9|t9|NN|_ :|:|:|_ 150|150|CD|_ min|min|NN|_ after|after|IN|_ stress|stress|NN|_
bile|bile|NN|_ +1|+1|CD|_
bile|bile|NN|_ +2|+2|CD|_
bile|bile|NN|_ +3|+3|CD|_
ctrl1|ctrl1|NN|_
ctrl2|ctrl2|NN|_
ctrl3|ctrl3|NN|_
E.coli|e.coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
growth|growth|NN|_ media|media|NNS|_ :|:|:|_ LB|lb|NN|_
growth|growth|NN|_ media|media|NNS|_ :|:|:|_ LB|lb|NN|_ ;|;|:|_ 0.8|0.8|CD|_ %|%|NN|_ bile|bile|NN|_ salts|salt|NNS|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ extraction|extraction|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ Luria|Luria|NNP|MED broth|broth|NN|MED with|with|IN|_ or|or|CC|_ without|without|IN|_ 0.8|0.8|CD|_ %|%|NN|_ bile|bile|NN|_ salts|salt|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ strain|strain|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ FlexArray|FlexArray|NNP|_ using|use|VBG|_ gc-RMA|gc-rma|NN|_ preprocessing|preprocessing|NN|_ for|for|IN|_ analysis|analysis|NN|_ .|.|.|_
8|8|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
serotype|serotype|NN|_ :|:|:|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ clade|clade|NN|_ 2|2|CD|_ ,|,|,|_ stx|stx|NN|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_
serotype|serotype|NN|_ :|:|:|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ clade|clade|NN|_ 2|2|CD|_ ,|,|,|_ stx|stx|NN|_ 2|2|CD|_
serotype|serotype|NN|_ :|:|:|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ clade|clade|NN|_ 8|8|CD|_ ,|,|,|_ stx|stx|NN|_ 2|2|CD|_
serotype|serotype|NN|_ :|:|:|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ clade|clade|NN|_ 8|8|CD|_ ,|,|,|_ stx|stx|NN|_ 2|2|CD|_ and|and|CC|_ 2c|2c|JJ|_
strains|strain|NNS|_ TW014359|tw014359|NN|_ vs|vs|CC|_ TW04863|tw04863|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW014359|tw014359|NN|_ vs|vs|CC|_ TW11037|tw11037|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW02883|tw02883|NN|_ vs|vs|CC|_ TW11028|tw11028|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW04863|tw04863|NN|_ vs|vs|CC|_ TW14279|tw14279|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW07591|tw07591|NN|_ vs|vs|CC|_ TW09098|tw09098|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW07937|tw07937|NN|_ vs|vs|CC|_ TW11185|tw11185|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW07961|tw07961|NN|_ vs|vs|CC|_ TW08610|tw08610|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW07961|tw07961|NN|_ vs|vs|CC|_ TW11029|tw11029|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08030|tw08030|NN|_ vs|vs|CC|_ TW10045|tw10045|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08609|tw08609|NN|_ vs|vs|CC|_ TW08030|tw08030|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08609|tw08609|NN|_ vs|vs|CC|_ TW08623|tw08623|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08609|tw08609|NN|_ vs|vs|CC|_ TW11110|tw11110|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08610|tw08610|NN|_ vs|vs|CC|_ TW11110|tw11110|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08623|tw08623|NN|_ vs|vs|CC|_ TW02883|tw02883|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08623|tw08623|NN|_ vs|vs|CC|_ TW08030|tw08030|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW08635|tw08635|NN|_ vs|vs|CC|_ TW09098|tw09098|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW09098|tw09098|NN|_ vs|vs|CC|_ TW11308|tw11308|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW09189|tw09189|NN|_ vs|vs|CC|_ TW11032|tw11032|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW09189|tw09189|NN|_ vs|vs|CC|_ TW14279|tw14279|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW10012|tw10012|NN|_ vs|vs|CC|_ TW11037|tw11037|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW10012|tw10012|NN|_ vs|vs|CC|_ TW14313|tw14313|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW10045|tw10045|NN|_ vs|vs|CC|_ TW07937|tw07937|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11028|tw11028|NN|_ vs|vs|CC|_ TW07937|tw07937|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11028|tw11028|NN|_ vs|vs|CC|_ TW11308|tw11308|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11029|tw11029|NN|_ vs|vs|CC|_ TW02883|tw02883|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11029|tw11029|NN|_ vs|vs|CC|_ TW08610|tw08610|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11032|tw11032|NN|_ vs|vs|CC|_ TW04863|tw04863|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11032|tw11032|NN|_ vs|vs|CC|_ TW09189|tw09189|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11037|tw11037|NN|_ vs|vs|CC|_ TW08635|tw08635|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11110|tw11110|NN|_ vs|vs|CC|_ TW10012|tw10012|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11185|tw11185|NN|_ vs|vs|CC|_ TW014313|tw014313|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11185|tw11185|NN|_ vs|vs|CC|_ TW08635|tw08635|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW11308|tw11308|NN|_ vs|vs|CC|_ TW07591|tw07591|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW14279|tw14279|NN|_ vs|vs|CC|_ TW10045|tw10045|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW14313|tw14313|NN|_ vs|vs|CC|_ TW07591|tw07591|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strains|strain|NNS|_ TW14359|tw14359|NN|_ vs|vs|CC|_ TW07961|tw07961|NN|_ epithelial|epithelial|JJ|_ exposure|exposure|NN|_
strain|strain|NN|_ TW02883|tw02883|NN|_
strain|strain|NN|_ TW02883|tw02883|NN|_
strain|strain|NN|_ TW04863|tw04863|NN|_
strain|strain|NN|_ TW07591|tw07591|NN|_
strain|strain|NN|_ TW07937|tw07937|NN|_
strain|strain|NN|_ TW07961|tw07961|NN|_
strain|strain|NN|_ TW07961|tw07961|NN|_
strain|strain|NN|_ TW08030|tw08030|NN|_
strain|strain|NN|_ TW08609|tw08609|NN|_
strain|strain|NN|_ TW08609|tw08609|NN|_
strain|strain|NN|_ TW08610|tw08610|NN|_
strain|strain|NN|_ TW08623|tw08623|NN|_
strain|strain|NN|_ TW08635|tw08635|NN|_
strain|strain|NN|_ TW08635|tw08635|NN|_
strain|strain|NN|_ TW09098|tw09098|NN|_
strain|strain|NN|_ TW09098|tw09098|NN|_
strain|strain|NN|_ TW09189|tw09189|NN|_
strain|strain|NN|_ TW10012|tw10012|NN|_
strain|strain|NN|_ TW10045|tw10045|NN|_
strain|strain|NN|_ TW10045|tw10045|NN|_
strain|strain|NN|_ TW11028|tw11028|NN|_
strain|strain|NN|_ TW11029|tw11029|NN|_
strain|strain|NN|_ TW11029|tw11029|NN|_
strain|strain|NN|_ TW11032|tw11032|NN|_
strain|strain|NN|_ TW11032|tw11032|NN|_
strain|strain|NN|_ TW11037|tw11037|NN|_
strain|strain|NN|_ TW11110|tw11110|NN|_
strain|strain|NN|_ TW11110|tw11110|NN|_
strain|strain|NN|_ TW11185|tw11185|NN|_
strain|strain|NN|_ TW11185|tw11185|NN|_
strain|strain|NN|_ TW11308|tw11308|NN|_
strain|strain|NN|_ TW11308|tw11308|NN|_
strain|strain|NN|_ TW14279|tw14279|NN|_
strain|strain|NN|_ TW14279|tw14279|NN|_
strain|strain|NN|_ TW14313|tw14313|NN|_
strain|strain|NN|_ TW14359|tw14359|NN|_
Thirty-six|thirty-six|CD|_ dye-swap|dye-swap|JJ|_ hybridizations|hybridization|NNS|_ were|be|VBD|_ performed|perform|VBN|_ between|between|IN|_ four|four|CD|_ groups|group|NNS|_ with|with|IN|_ six|six|CD|_ strains|strain|NNS|_ per|per|IN|_ group|group|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ a|a|DT|_ balanced|balanced|JJ|_ double|double|JJ|_ loop|loop|NN|_ design|design|NN|_ .|.|.|_ Strains|strain|NNS|_ were|be|VBD|_ grouped|group|VBN|_ based|base|VBN|_ on|on|IN|_ cladestx|cladestx|NN|_ profiles|profile|NNS|_ and|and|CC|_ each|each|DT|_ strain|strain|NN|_ was|be|VBD|_ considered|consider|VBN|_ an|a|DT|_ independent|independent|JJ|_ biological|biological|JJ|_ replicate|replicate|VB|_ of|of|IN|_ its|its|PRP$|_ group|group|NN|_ -LRB-|-lrb-|-LRB-|_ n|n|NN|_ =|=|JJ|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ six|six|CD|_ strains|strain|NNS|_ from|from|IN|_ each|each|DT|_ group|group|NN|_ were|be|VBD|_ randomly|randomly|RB|_ hybridized|hybridize|VBN|_ with|with|IN|_ six|six|CD|_ strains|strain|NNS|_ from|from|IN|_ every|every|DT|_ other|other|JJ|_ group|group|NN|_ ;|;|:|_ each|each|DT|_ hybridization|hybridization|NN|_ compared|compare|VBN|_ a|a|DT|_ pair|pair|NN|_ of|of|IN|_ strains|strain|NNS|_ that|that|WDT|_ differed|differ|VBD|_ in|in|IN|_ either|either|CC|_ clade|clade|NN|_ or|or|CC|_ stx|stx|NN|_ profile|profile|NN|_ ,|,|,|_ or|or|CC|_ both|both|DT|_ .|.|.|_ Subsequent|subsequent|JJ|_ to|to|TO|_ local|local|JJ|_ Lowess|Lowess|NNP|_ normalization|normalization|NN|_ ,|,|,|_ averaging|averaging|NN|_ of|of|IN|_ replicate|replicate|VB|_ probes|probe|NNS|_ and|and|CC|_ log2|log2|NN|_ transformation|transformation|NN|_ ,|,|,|_ the|the|DT|_ microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ fitted|fit|VBN|_ to|to|TO|_ a|a|DT|_ 2-factor|2-factor|NN|_ mixed|mixed|JJ|_ ANOVA|ANOVA|NNP|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ intensity|intensity|NN|_ =|=|JJ|_ Array|array|NN|_ +|+|CC|_ Dye|dye|NN|_ +|+|CC|_ Clade|clade|NN|_ +|+|CC|_ Stx|stx|NN|_ +|+|CC|_ Clade|clade|NN|_ :|:|:|_ Stx|stx|NN|_ +|+|CC|_ Sample|sample|NN|_ ;|;|:|_ where|where|WRB|_ the|the|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ Sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ array|array|NN|_ effects|effect|NNS|_ were|be|VBD|_ considered|consider|VBN|_ random|random|JJ|_ effects|effect|NNS|_ ,|,|,|_ while|while|IN|_ all|all|DT|_ other|other|JJ|_ effects|effect|NNS|_ were|be|VBD|_ considered|consider|VBN|_ fixed|fixed|JJ|_ effects|effect|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ using|use|VBG|_ the|the|DT|_ MAANOVA|MAANOVA|NNP|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.98-8|0.98-8|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ R|r|NN|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.1|2.2.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ This|this|DT|_ model|model|NN|_ allows|allow|VBZ|_ independent|independent|JJ|_ consideration|consideration|NN|_ of|of|IN|_ the|the|DT|_ effect|effect|NN|_ of|of|IN|_ `|`|``|_ Clade|Clade|NNP|_ '|'|''|_ -LRB-|-lrb-|-LRB-|_ clade|clade|NN|_ divergence|divergence|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ `|`|``|_ Stx|stx|FW|_ '|'|''|_ -LRB-|-lrb-|-LRB-|_ stx|stx|NN|_ type|type|NN|_ variation|variation|NN|_ -RRB-|-rrb-|-RRB-|_ parameters|parameter|NNS|_ on|on|IN|_ differences|difference|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ among|among|IN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strains|strain|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ their|they|PRP$|_ interaction|interaction|NN|_ -LRB-|-lrb-|-LRB-|_ combined|combine|VBN|_ -RRB-|-rrb-|-RRB-|_ effect|effect|NN|_ -LRB-|-lrb-|-LRB-|_ Clade|clade|NN|_ :|:|:|_ Stx|stx|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Overall|overall|JJ|_ differences|difference|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ groups|group|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ Fs|f|NNS|_ test|test|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ pair-wise|pair-wise|JJ|_ contrasts|contrast|VBZ|_ to|to|TO|_ determine|determine|VB|_ significant|significant|JJ|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ pair|pair|NN|_ of|of|IN|_ groups|group|NNS|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ the|the|DT|_ Fs|f|NNS|_ statistic|statistic|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ for|for|IN|_ the|the|DT|_ `|`|``|_ Clade|clade|NN|_ '|'|''|_ effect|effect|NN|_ to|to|TO|_ determine|determine|VB|_ significant|significant|JJ|_ differences|difference|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ clades|clade|NNS|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ n|n|NN|_ =|=|JJ|_ 12|12|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ n|n|NN|_ =|=|JJ|_ 12|12|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ regardless|regardless|RB|_ of|of|IN|_ stx|stx|NN|_ profile|profile|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ Fs|f|NNS|_ statistic|statistic|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ for|for|IN|_ the|the|DT|_ `|`|``|_ Stx|stx|NN|_ '|'|''|_ effect|effect|NN|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ `|`|``|_ Clade|Clade|NNP|_ :|:|:|_ Stx|stx|NN|_ '|'|''|_ interaction|interaction|NN|_ effect|effect|NN|_ to|to|TO|_ examine|examine|VB|_ the|the|DT|_ combined|combined|JJ|_ effect|effect|NN|_ of|of|IN|_ clade|clade|NN|_ and|and|CC|_ stx|stx|NN|_ type|type|NN|_ on|on|IN|_ differences|difference|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ among|among|IN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strains|strain|NNS|_ .|.|.|_ In|in|IN|_ other|other|JJ|_ words|word|NNS|_ ,|,|,|_ this|this|DT|_ analysis|analysis|NN|_ will|will|MD|_ determine|determine|VB|_ whether|whether|IN|_ the|the|DT|_ expression|expression|NN|_ of|of|IN|_ any|any|DT|_ given|give|VBN|_ gene|gene|NN|_ among|among|IN|_ groups|group|NNS|_ with|with|IN|_ different|different|JJ|_ stx|stx|NN|_ types|type|NNS|_ is|be|VBZ|_ also|also|RB|_ dependent|dependent|JJ|_ on|on|IN|_ clade|clade|NN|_ .|.|.|_ An|a|DT|_ interaction|interaction|NN|_ effect|effect|NN|_ would|would|MD|_ be|be|VB|_ observed|observe|VBN|_ if|if|IN|_ expression|expression|NN|_ estimates|estimate|NNS|_ between|between|IN|_ strain|strain|NN|_ groups|group|NNS|_ clade8stx2|clade8stx2|NN|_ and|and|CC|_ clade2stx2|clade2stx2|NN|_ are|be|VBP|_ different|different|JJ|_ from|from|IN|_ expression|expression|NN|_ estimates|estimate|NNS|_ between|between|IN|_ strain|strain|NN|_ groups|group|NNS|_ clade8stx2|clade8stx2|VBP|_ ,2|,2|CD|_ c|c|NN|_ and|and|CC|_ clade2stx1|clade2stx1|NN|_ ,2|,2|CD|_ .|.|.|_ For|for|IN|_ every|every|DT|_ analysis|analysis|NN|_ ,|,|,|_ 1000|1000|CD|_ permutations|permutation|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ were|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ generate|generate|VB|_ P|p|NN|_ values|value|NNS|_ ;|;|:|_ estimates|estimate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ significant|significant|JJ|_ if|if|IN|_ the|the|DT|_ P|p|NN|_ value|value|NN|_ was|be|VBD|_ <|<|JJR|_ 0.05|0.05|CD|_ after|after|IN|_ adjusting|adjust|VBG|_ for|for|IN|_ multiple|multiple|JJ|_ comparisons|comparison|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ charged|charge|VBN|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ total|total|JJ|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 17|17|CD|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 17|17|CD|_ charged|charge|VBN|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 17|17|CD|_ total|total|JJ|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_ charged|charge|VBN|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_ total|total|JJ|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 32|32|CD|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 32|32|CD|_ charged|charge|VBN|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 32|32|CD|_ total|total|JJ|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 7|7|CD|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 7|7|CD|_ charged|charge|VBN|_
-|-|:|_ Leu|leu|NN|_ t|t|NN|_ =|=|JJ|_ 7|7|CD|_ total|total|JJ|_
Bear|Bear|NNP|_ feces|fece|VBZ|_ isolate|isolate|JJ|_ B1|b1|NN|_
Bear|Bear|NNP|_ feces|fece|VBZ|_ isolate|isolate|JJ|_ B3|b3|NN|_
Bear|Bear|NNP|_ feces|fece|VBZ|_ isolate|isolate|JJ|_ B5|b5|NN|_
Bear|Bear|NNP|_ III|III|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Bear|Bear|NNP|_ III|III|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VBP|_ 2|2|CD|_
Bear|Bear|NNP|_ II|II|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Bear|Bear|NNP|_ II|II|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Bear|Bear|NNP|_ I|I|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Bear|Bear|NNP|_ I|I|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VBP|_ 2|2|CD|_
Cattle|cattle|JJ|_ feces|fece|NNS|_ isolate|isolate|VBP|_ C1A|c1a|NN|_
Cattle|cattle|JJ|_ feces|fece|NNS|_ isolate|isolate|VBP|_ C4A|c4a|NN|_
Cattle|cattle|JJ|_ feces|fece|NNS|_ isolate|isolate|VBP|_ C6D|c6d|NN|_
Cattle|Cattle|NNP|_ III|III|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Cattle|Cattle|NNP|_ III|III|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Cattle|Cattle|NNP|_ II|II|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Cattle|Cattle|NNP|_ II|II|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Cattle|Cattle|NNP|_ I|I|PRP|_ versus|versus|CC|_ MG1655|mg1655|NN|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Cattle|Cattle|NNP|_ I|I|PRP|_ versus|versus|CC|_ MG1655|mg1655|NN|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Deer|deer|NNS|_ feces|fece|NNS|_ isolate|isolate|VBP|_ D1|d1|NN|_
Deer|deer|NNS|_ feces|fece|NNS|_ isolate|isolate|NN|_ D3|d3|NN|_
Deer|deer|NNS|_ feces|fece|NNS|_ isolate|isolate|VBP|_ W6A|w6a|NN|_
Deer|deer|NNS|_ III|iii|CD|_ versus|versus|CC|_ MG1655|mg1655|CD|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Deer|deer|NNS|_ III|iii|CD|_ versus|versus|CC|_ MG1655|mg1655|CD|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Deer|deer|NNS|_ II|ii|CD|_ versus|versus|CC|_ MG1655|mg1655|CD|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Deer|deer|NNS|_ II|ii|CD|_ versus|versus|CC|_ MG1655|mg1655|CD|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Deer|deer|NNS|_ I|I|PRP|_ versus|versus|CC|_ MG1655|mg1655|NN|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Deer|deer|NNS|_ I|I|PRP|_ versus|versus|CC|_ MG1655|mg1655|NN|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ SDS|sds|NN|_ lysis|lysis|NN|_
Human|human|JJ|_ III|iii|CD|_ versus|versus|CC|_ MG1655|mg1655|CD|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Human|Human|NNP|_ III|III|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Human|Human|NNP|_ II|II|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Human|Human|NNP|_ II|II|NNP|_ versus|versus|CC|_ MG1655|MG1655|NNP|_ technical|technical|JJ|_ replicate|replicate|VBP|_ 2|2|CD|_
Human|human|JJ|_ I|I|PRP|_ versus|versus|CC|_ MG1655|mg1655|NN|_ technical|technical|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
Human|Human|NNP|_ I|I|PRP|_ versus|versus|CC|_ MG1655|mg1655|NN|_ technical|technical|JJ|_ replicate|replicate|VBP|_ 2|2|CD|_
Human|human|JJ|_ sewage|sewage|NN|_ isolate|isolate|NN|_ H1|h1|NN|_
Human|human|JJ|_ sewage|sewage|NN|_ isolate|isolate|NN|_ H2|h2|NN|_
Human|human|JJ|_ sewage|sewage|NN|_ isolate|isolate|NN|_ H3|h3|NN|_
Images|image|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 6.0|6.0|CD|_ ,|,|,|_ the|the|DT|_ freely|freely|RB|_ available|available|JJ|_ TIGR|tigr|NN|_ TM4|tm4|NN|_ software|software|NN|_ suite|suite|NN|_ -LRB-|-lrb-|-LRB-|_ www.tm4.org|www.tm4.org|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ .|.|.|_ Spots|spot|NNS|_ with|with|IN|_ an|a|DT|_ intensity|intensity|NN|_ :|:|:|_ background|background|NN|_ ratio|ratio|NN|_ >|>|JJR|_ 1.5|1.5|CD|_ and|and|CC|_ overall|overall|JJ|_ intensity|intensity|NN|_ >|>|JJR|_ 350|350|CD|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ channel|channel|NN|_ and|and|CC|_ an|a|DT|_ intensity|intensity|NN|_ :|:|:|_ background|background|NN|_ ratio|ratio|NN|_ of|of|IN|_ >|>|JJR|_ 1.0|1.0|CD|_ in|in|IN|_ the|the|DT|_ experimental|experimental|JJ|_ channel|channel|NN|_ were|be|VBD|_ considered|consider|VBN|_ acceptable|acceptable|JJ|_ for|for|IN|_ downstream|downstream|JJ|_ processing|processing|NN|_ .|.|.|_ Local|local|JJ|_ background|background|NN|_ was|be|VBD|_ subtracted|subtract|VBN|_ for|for|IN|_ each|each|DT|_ spot|spot|NN|_ ,|,|,|_ the|the|DT|_ corresponding|corresponding|JJ|_ log2|log2|NN|_ ratios|ratio|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ total|total|JJ|_ intensity|intensity|NN|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ replicate|replicate|VB|_ spots|spot|NNS|_ were|be|VBD|_ averaged|average|VBN|_ using|use|VBG|_ TIGR|TIGR|NNP|_ MIDAS|MIDAS|NNP|_ .|.|.|_ Genes|gene|NNS|_ that|that|WDT|_ had|have|VBD|_ missing|missing|JJ|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ unacceptable|unacceptable|JJ|_ spots|spot|NNS|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ more|more|JJR|_ than|than|IN|_ one-third|one-third|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ from|from|IN|_ the|the|DT|_ downstream|downstream|JJ|_ analysis|analysis|NN|_ leaving|leave|VBG|_ 3993|3993|CD|_ ORFs|orf|NNS|_ in|in|IN|_ the|the|DT|_ final|final|JJ|_ data|data|NN|_ set|set|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ hybridized|hybridize|VBN|_ twice|twice|RB|_ and|and|CC|_ the|the|DT|_ results|result|NNS|_ averaged|average|VBD|_ in|in|IN|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ after|after|IN|_ processing|process|VBG|_ with|with|IN|_ MIDAS|MIDAS|NNP|_ .|.|.|_ A|a|DT|_ strict|strict|JJ|_ cutoff|cutoff|NN|_ of|of|IN|_ log2|log2|NN|_ ratio|ratio|NN|_ >|>|JJR|_ 0.9|0.9|CD|_ or|or|CC|_ <|<|JJR|_ 0.9|0.9|CD|_ was|be|VBD|_ applied|apply|VBN|_ for|for|IN|_ the|the|DT|_ determination|determination|NN|_ of|of|IN|_ gene|gene|NN|_ amplifications|amplification|NNS|_ and|and|CC|_ gene|gene|NN|_ absences|absence|NNS|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ Bear|Bear|NNP|_ feces|fece|VBZ|_ isolate|isolate|JJ|_ B1|b1|NN|_
strain|strain|NN|_ :|:|:|_ Bear|Bear|NNP|_ feces|fece|VBZ|_ isolate|isolate|JJ|_ B3|b3|NN|_
strain|strain|NN|_ :|:|:|_ Bear|Bear|NNP|_ feces|fece|VBZ|_ isolate|isolate|JJ|_ B5|b5|NN|_
strain|strain|NN|_ :|:|:|_ Cattle|Cattle|NNP|_ feces|fece|NNS|_ isolate|isolate|VBP|_ C1A|c1a|NN|_
strain|strain|NN|_ :|:|:|_ Cattle|Cattle|NNP|_ feces|fece|NNS|_ isolate|isolate|VBP|_ C4A|c4a|NN|_
strain|strain|NN|_ :|:|:|_ Cattle|Cattle|NNP|_ feces|fece|NNS|_ isolate|isolate|VBP|_ C6D|c6d|NN|_
strain|strain|NN|_ :|:|:|_ Deer|deer|NNS|_ feces|fece|NNS|_ isolate|isolate|VBP|_ D1|d1|NN|_
strain|strain|NN|_ :|:|:|_ Deer|deer|NNS|_ feces|fece|NNS|_ isolate|isolate|NN|_ D3|d3|NN|_
strain|strain|NN|_ :|:|:|_ Deer|deer|NNS|_ feces|fece|NNS|_ isolate|isolate|VBP|_ W6A|w6a|NN|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ Human|human|JJ|_ sewage|sewage|NN|_ isolate|isolate|NN|_ H1|h1|NN|_
strain|strain|NN|_ :|:|:|_ Human|human|JJ|_ sewage|sewage|NN|_ isolate|isolate|NN|_ H2|h2|NN|_
strain|strain|NN|_ :|:|:|_ Human|human|JJ|_ sewage|sewage|NN|_ isolate|isolate|NN|_ H3|h3|NN|_
At|at|IN|_ time|time|NN|_ point|point|NN|_ 0|0|CD|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 500ug|500ug|JJ|_
E.coli|e.coli|NN|_ strain|strain|NN|_ ,|,|,|_ DY330|dy330|NN|_ ,|,|,|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30C|NNP|_ in|in|IN|_ M9|M9|NNP|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ vitamins|vitamin|NNS|_ and|and|CC|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ lysates|lysate|NNS|_ by|by|IN|_ phenol|phenol|NN|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ obtained|obtain|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ .|.|.|_ All|all|DT|_ reads|read|VBZ|_ mapping|mapping|NN|_ with|with|IN|_ two|two|CD|_ or|or|CC|_ fewer|fewer|JJR|_ mismatches|mismatch|NNS|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Repeated|repeated|JJ|_ sequences|sequence|NNS|_ were|be|VBD|_ ignored|ignore|VBN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ counts|count|NNS|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ ssrA|ssra|NN|GEN RNA|rna|NN|_ and|and|CC|_ then|then|RB|_ converted|convert|VBD|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_ A|a|DT|_ value|value|NN|_ of|of|IN|_ 1|1|CD|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ every|every|DT|_ count|count|NN|_ before|before|IN|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ conversion|conversion|NN|_ to|to|TO|_ avoid|avoid|VB|_ an|a|DT|_ undefined|undefined|JJ|_ logarithm|logarithm|NN|_ of|of|IN|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ lifetime|lifetime|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ the|the|DT|_ inverse|inverse|NN|_ of|of|IN|_ the|the|DT|_ slope|slope|NN|_ of|of|IN|_ a|a|DT|_ linear|linear|JJ|_ fit|fit|NN|_ to|to|TO|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ values|value|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ DY330|dy330|NN|_ -LRB-|-lrb-|-LRB-|_ W3110|w3110|NN|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ measured|measure|VBN|_ lifetime|lifetime|NN|_ of|of|IN|_ mRNA|mrna|NN|_ is|be|VBZ|_ available|available|JJ|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ real_rna_life.txt|real_rna_life.txt|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ Fragmentation|fragmentation|NN|_ Reagent|reagent|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ collected|collect|VBN|_ by|by|IN|_ Zymo|Zymo|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ columns|column|NNS|_ .|.|.|_ RNA|rna|NN|_ seq|seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ according|accord|VBG|_ to|to|TO|_ Illumna|Illumna|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ ,|,|,|_ using|use|VBG|_ NEB|neb|NN|_ enzymes|enzyme|NNS|_ and|and|CC|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ with|with|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ II|II|NNP|_ machine|machine|NN|_ -LRB-|-lrb-|-LRB-|_ Center|center|NN|_ for|for|IN|_ Systems|Systems|NNP|_ Biology|Biology|NNP|_ ,|,|,|_ Harvard|Harvard|NNP|_ University|University|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
time|time|NN|_ point|point|NN|_ 0|0|CD|_
time|time|NN|_ point|point|NN|_ 2|2|CD|_
time|time|NN|_ point|point|NN|_ 4|4|CD|_
time|time|NN|_ point|point|NN|_ 6|6|CD|_
time|time|NN|_ point|point|NN|_ 8|8|CD|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 0|0|CD|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 2|2|CD|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 4|4|CD|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 6|6|CD|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP time|time|NN|_ point|point|NN|_ 8|8|CD|_
10|10|CD|_ min|min|NN|_
10|10|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ additional|additional|JJ|_ -RRB-|-rrb-|-RRB-|_
15|15|CD|_ min|min|NN|_
15|15|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ additional|additional|JJ|_ -RRB-|-rrb-|-RRB-|_
5|5|CD|_ min|min|NN|_
5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ additional|additional|JJ|_ -RRB-|-rrb-|-RRB-|_
control|control|NN|_
control|control|NN|_ -LRB-|-lrb-|-LRB-|_ additional|additional|JJ|_ -RRB-|-rrb-|-RRB-|_
E.|E.|NNP|_ coli|coli|NN|_ cell|cell|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Cells|cell|NNS|_ grew|grow|VBD|_ in|in|IN|_ MOPS|MOPS|NNP|MED minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP K2HPO4|k2hpo4|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ the|the|DT|_ OD600|od600|NN|_ value|value|NN|_ of|of|IN|_ 1.0|1.0|CD|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ PhoB|phob|NN|TF knock-out|knock-out|JJ|_ strain|strain|NN|_ grows|grow|VBZ|_ under|under|IN|_ phosphate|phosphate|NN|_ starvation|starvation|NN|_ condition|condition|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ wildtype|wildtype|JJ|_ strain|strain|NN|_ grows|grow|VBZ|_ under|under|IN|_ phosphate|phosphate|NN|_ starvation|starvation|NN|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
PhoB|phob|NN|TF knock-out|knock-out|JJ|_ strain|strain|NN|_ ,|,|,|_ rep1|rep1|NN|_
PhoB|phob|NN|TF knock-out|knock-out|JJ|_ strain|strain|NN|_ ,|,|,|_ rep2|rep2|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ RMA|rma|NN|_ method|method|NN|_ and|and|CC|_ then|then|RB|_ analyzed|analyze|VBN|_ by|by|IN|_ limma|limma|NN|_ package|package|NN|_ to|to|TO|_ identify|identify|VB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Trizol|trizol|NN|_ extraction|extraction|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Wildtype|wildtype|NN|_ strain|strain|NN|_ ,|,|,|_ rep1|rep1|NN|_
wildtype|wildtype|JJ|_ strain|strain|NN|_ ,|,|,|_ rep2|rep2|NN|_
E4|e4|NN|_ -|-|:|_ O2|o2|CD|_ 1|1|CD|_
E4|e4|NN|_ +|+|CC|_ O2|o2|CD|_ 1|1|CD|_
E4|e4|NN|_ -|-|:|_ O2|o2|CD|_ 2|2|CD|_
E4|e4|NN|_ +|+|CC|_ O2|o2|CD|_ 2|2|CD|_
E4|e4|NN|_ -|-|:|_ O2|o2|CD|_ 3|3|CD|_
E4|e4|NN|_ +|+|CC|_ O2|o2|CD|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ M9|m9|NN|_ media|media|NNS|_ with|with|IN|_ 4|4|CD|_ g|g|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
No|no|DT|_ specific|specific|JJ|_ treatment|treatment|NN|_ was|be|VBD|_ done|do|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ in|in|IN|_ the|the|DT|_ mid-log|mid-log|JJ|_ growth|growth|NN|_ phase|phase|NN|_ for|for|IN|_ expression|expression|NN|_ analysis|analysis|NN|_
Respiratory|respiratory|JJ|_ defecient|defecient|JJ|_ E.|e.|FW|_ coli|coli|FW|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ ECOM4|ecom4|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ M9|m9|NN|_ media|media|NNS|_ with|with|IN|_ 4|4|CD|_ g|g|NN|_
strain|strain|NN|_ :|:|:|_ ECOM4|ecom4|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ ArrayStar|arraystar|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ DNASTAR|dnastar|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ RMA|RMA|NNP|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ Genes|gene|NNS|_ with|with|IN|_ at|at|IN|_ least|least|JJS|_ two-fold|two-fold|JJ|_ expression|expression|NN|_ level|level|NN|_ change|change|NN|_ and|and|CC|_ FDR-adjusted|fdr-adjusted|JJ|_ P-value|p-value|NN|_ -LRB-|-lrb-|-LRB-|_ T-test|t-test|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ less|less|JJR|_ than|than|IN|_ 0.05|0.05|CD|_ were|be|VBD|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extreacted|extreact|VBN|_ using|use|VBG|_ Quagen|quagen|JJ|_ RNA|rna|NN|_ mini|minus|NNS|_ kit|kit|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ an|a|DT|_ Thermo|Thermo|NNP|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ .|.|.|_
Wild|Wild|NNP|_ type|type|NN|_ and|and|CC|_ the|the|DT|_ mutant|mutant|NN|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ minimal|minimal|JJ|_ M9|m9|NN|_ media|media|NNS|_ with|with|IN|_ 4|4|CD|_ g|g|NN|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_ 1|1|CD|_
WT|wt|NN|_ +|+|CC|_ O2|o2|CD|_ 1|1|CD|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_ 2|2|CD|_
WT|wt|NN|_ +|+|CC|_ O2|o2|CD|_ 2|2|CD|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_ 3|3|CD|_
WT|wt|NN|_ +|+|CC|_ O2|o2|CD|_ 3|3|CD|_
Cells|cell|NNS|_ grew|grow|VBD|_ in|in|IN|_ MOPS|MOPS|NNP|MED minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP K2HPO4|k2hpo4|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ the|the|DT|_ OD600|od600|NN|_ value|value|NN|_ of|of|IN|_ 1.0|1.0|CD|_ .|.|.|_
ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ _|_|CD|_ PhoB|phob|NN|TF _|_|CD|_ FLAG|flag|NN|_
ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ wild|wild|JJ|_ type|type|NN|_ strain|strain|NN|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ the|the|DT|_ OD600|od600|NN|_ value|value|NN|_ of|of|IN|_ 1.0|1.0|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ To|to|TO|_ quench|quench|VB|_ the|the|DT|_ reaction|reaction|NN|_ ,|,|,|_ glycine|glycine|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ the|the|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.125|0.125|CD|_ M|m|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.4|7.4|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 0.1|0.1|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ and|and|CC|_ 0.5|0.5|CD|_ %|%|NN|_ Tween-20|tween-20|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ washed|wash|VBN|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ lysed|lyse|VBN|_ with|with|IN|_ the|the|DT|_ lysis|lysis|NN|_ buffer|buffer|NN|_ containing|contain|VBG|_ 8|8|CD|_ KU|KU|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
PhoB|phob|NN|TF _|_|CD|_ ChIP|chip|NN|_ ,|,|,|_ rep1|rep1|NN|_
PhoB|phob|NN|TF _|_|CD|_ ChIP|chip|NN|_ ,|,|,|_ rep2|rep2|NN|_
PhoB|phob|NN|TF _|_|CD|_ ChIP|chip|NN|_ ,|,|,|_ rep3|rep3|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ R|r|NN|_ package|package|NN|_ ,|,|,|_ Ringo|Ringo|NNP|_ ,|,|,|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ read|read|VB|_ the|the|DT|_ pair|pair|NN|_ files|file|NNS|_ and|and|CC|_ the|the|DT|_ limma|limma|NN|_ package|package|NN|_ for|for|IN|_ within|within|IN|_ -|-|:|_ and|and|CC|_ between-array|between-array|JJ|_ normalization|normalization|NN|_ .|.|.|_ ChIP-chip|ChIP-chip|NNP|_ data|datum|NNS|_ were|be|VBD|_ bi-weighted|bi-weighted|JJ|_ scaled|scale|VBN|_ within|within|IN|_ each|each|DT|_ array|array|NN|_ and|and|CC|_ aquantile|aquantile|NN|_ normalized|normalize|VBD|_ between|between|IN|_ arrays|array|NNS|_ .|.|.|_
0.15|0.15|CD|_ %|%|NN|_ Bile|Bile|NNP|_ Salt|Salt|NNP|_ Mix|Mix|NNP|_ Stress|stress|NN|_ ,|,|,|_ 90|90|CD|_ minutes|minute|NNS|_ ,|,|,|_ static|static|JJ|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -LRB-|-lrb-|-LRB-|_ EHEC|ehec|NN|_ strain|strain|NN|_ :|:|:|_ 86-24|86-24|CD|_ -RRB-|-rrb-|-RRB-|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED overnight|overnight|JJ|_ and|and|CC|_ subcultured|subculture|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ .|.|.|_ Bacteria|bacterium|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ ,|,|,|_ media|media|NNS|_ removed|remove|VBD|_ and|and|CC|_ repalced|repalce|VBD|_ with|with|IN|_ DMEM|dmem|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED overnight|overnight|JJ|_ and|and|CC|_ subcultured|subculture|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ .|.|.|_ Bacteria|bacterium|NNS|_ were|be|VBD|_ then|then|RB|_ spun|spin|VBN|_ down|down|RP|_ ,|,|,|_ media|media|NNS|_ removed|remove|VBD|_ and|and|CC|_ repalced|repalce|VBD|_ with|with|IN|_ DMEM|dmem|NN|_ plus|plus|CC|_ 0.15|0.15|CD|_ %|%|NN|_ bile|bile|NN|_ salt|salt|NN|_ mix|mix|NN|_ .|.|.|_
Bile|Bile|NNP|_ salt|salt|NN|_ stress|stress|NN|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ DMEM|dmem|NN|_ at|at|IN|_ pH|ph|NN|_ 7.4|7.4|CD|_ -LRB-|-lrb-|-LRB-|_ unbuffered|unbuffered|JJ|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ ,|,|,|_ static|static|JJ|_ incubation|incubation|NN|_ for|for|IN|_ 90|90|CD|_ minutes|minute|NNS|_
Control|Control|NNP|_ treatment|treatment|NN|_ .|.|.|_ Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 7.4|7.4|CD|_ ,|,|,|_ 90|90|CD|_ minutes|minute|NNS|_ ,|,|,|_ 37C|37c|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ ,|,|,|_ static|static|JJ|_ -LRB-|-lrb-|-LRB-|_ unstressed|unstressed|JJ|_ -RRB-|-rrb-|-RRB-|_
Cy3|cy3|NN|_ labeled|label|VBN|_ EHEC|EHEC|NNP|_ grown|grow|VBN|_ in|in|IN|_ DMEM|DMEM|NNP|_ pH|ph|NN|_ 7.4|7.4|CD|_ ,|,|,|_ 90|90|CD|_ minutes|minute|NNS|_
Cy5|cy5|NN|_ labeled|label|VBN|_ EHEC|EHEC|NNP|_ bile|bile|NN|_ salt-stressed|salt-stressed|JJ|_ in|in|IN|_ DMEM|DMEM|NNP|_ ,|,|,|_ 90|90|CD|_ minutes|minute|NNS|_
ehec|ehec|NN|_ strain|strain|NN|_ :|:|:|_ 86-24|86-24|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_
Signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ averaged|average|VBN|_ among|among|IN|_ the|the|DT|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_ Two|two|CD|_ types|type|NNS|_ of|of|IN|_ data|data|NN|_ analysis|analysis|NN|_ were|be|VBD|_ performed|perform|VBN|_ :|:|:|_ to|to|TO|_ indentify|indentify|VB|_ density-dependent|density-dependent|JJ|_ changes|change|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ ,|,|,|_ single|single|JJ|_ averaged|average|VBD|_ normalized|normalize|VBN|_ signal|signal|NN|_ intensities|intensity|NNS|_ for|for|IN|_ each|each|DT|_ treatment|treatment|NN|_ point|point|NN|_ were|be|VBD|_ compared|compare|VBN|_ to|to|TO|_ the|the|DT|_ average|average|NN|_ of|of|IN|_ corresponding|corresponding|JJ|_ unstressed|unstressed|JJ|_ control|control|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ .|.|.|_ Genes|gene|NNS|_ which|which|WDT|_ showed|show|VBD|_ a|a|DT|_ relative|relative|JJ|_ signal|signal|NN|_ log2ratio|log2ratio|NN|_ -LRB-|-lrb-|-LRB-|_ SLR|slr|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ above|above|IN|_ 1.0|1.0|CD|_ or|or|CC|_ below|below|IN|_ -1.0|-1.0|CD|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
After|after|IN|_ quality|quality|NN|_ controls|control|NNS|_ of|of|IN|_ data|datum|NNS|_ distribution|distribution|NN|_ the|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ CEL|cel|NN|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ perform|perform|VB|_ ,|,|,|_ normalization|normalization|NN|_ and|and|CC|_ probe|probe|NN|_ set|set|VBD|_ summarization|summarization|NN|_ through|through|IN|_ RMA|RMA|NNP|_ algorithm|algorithm|NN|_ -LRB-|-lrb-|-LRB-|_ Robust|robust|JJ|_ Multiarray|Multiarray|NNP|_ Analysis|analysis|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ Gene|Gene|NNP|_ Expression|expression|NN|_ Console|Console|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ www.affymetrix.com|www.affymetrix.com|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Normalized|normalize|VBN|_ data|datum|NNS|_ were|be|VBD|_ then|then|RB|_ uploaded|upload|VBN|_ into|into|IN|_ OneChannelGUI|OneChannelGUI|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ http|http|JJ|_ :|:|:|_
E.coli|e.coli|NNS|_ _|_|VBP|_ IVT-RNA|ivt-rna|NN|_ _|_|CD|_ sigma70-1|sigma70-1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ IVT-RNA|ivt-rna|NN|_ _|_|CD|_ sigma70-2|sigma70-2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ IVT-RNA|ivt-rna|NN|_ _|_|CD|_ sigmaS|sigmas|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ IVT-RNA|ivt-rna|NN|_ _|_|CD|_ sigmaS-2|sigmas-2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ core|core|NN|_ enzyme|enzyme|NN|_ was|be|VBD|_ purchased|purchase|VBN|_ from|from|IN|_ Epicentre|Epicentre|NNP|_ -LRB-|-lrb-|-LRB-|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Histidine-tagged|histidine-tagged|JJ|_ σ|σ|NN|_ factors|factor|NNS|_ were|be|VBD|_ produced|produce|VBN|_ and|and|CC|_ purified|purify|VBN|_ as|as|IN|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Lacour|Lacour|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2003|2003|CD|_ ;|;|:|_ Checroun|Checroun|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2004|2004|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ proteins|protein|NNS|_ appeared|appear|VBD|_ pure|pure|JJ|_ from|from|IN|_ contaminants|contaminant|NNS|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ denaturing|denature|VBG|_ protein|protein|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ -LRB-|-lrb-|-LRB-|_ data|datum|NNS|_ not|not|RB|_ shown|show|VBN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ reconstitution|reconstitution|NN|_ of|of|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ holoenzymes|holoenzyme|NNS|_ ,|,|,|_ the|the|DT|_ core|core|NN|_ enzyme|enzyme|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ σS|σs|NN|_ or|or|CC|_ σ70|σ70|NN|_ at|at|IN|_ a|a|DT|_ 1:10|1:10|CD|_ ratio|ratio|NN|_ .|.|.|_ For|for|IN|_ calculation|calculation|NN|_ of|of|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ concentrations|concentration|NNS|_ in|in|IN|_ transcription|transcription|NN|_ assays|assay|NNS|_ ,|,|,|_ it|it|PRP|_ was|be|VBD|_ assumed|assume|VBN|_ that|that|IN|_ ,|,|,|_ after|after|IN|_ reconstitution|reconstitution|NN|_ ,|,|,|_ core|core|NN|_ enzyme|enzyme|NN|_ would|would|MD|_ be|be|VB|_ 100|100|CD|_ %|%|NN|_ active|active|JJ|_ and|and|CC|_ fully|fully|RB|_ saturated|saturate|VBN|_ by|by|IN|_ either|either|CC|_ σ|σ|NN|_ factor|factor|NN|_ .|.|.|_ 2|2|CD|_ ug|ug|NN|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ digested|digest|VBN|_ with|with|IN|_ EcoRI|ecori|NN|_ were|be|VBD|_ used|use|VBN|_ in|in|IN|_ transcription|transcription|NN|_ assays|assay|NNS|_ for|for|IN|_ ROMA|roma|NN|_ experiments|experiment|NNS|_ .|.|.|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ holoenzyme|holoenzyme|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ 100|100|CD|_ nM|nm|NN|_ in|in|IN|_ 50|50|CD|_ ul|ul|NN|_ reaction|reaction|NN|_ mixture|mixture|NN|_ .|.|.|_ Ten|ten|CD|_ independent|independent|JJ|_ run-off|run-off|JJ|_ transcription|transcription|NN|_ assays|assay|NNS|_ were|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ and|and|CC|_ transcripts|transcript|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ -LRB-|-lrb-|-LRB-|_ ca.|ca.|FW|_ 1|1|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
RNA|rna|NN|_ produced|produce|VBN|_ by|by|IN|_ in|in|FW|_ vitro|vitro|FW|_ transcription|transcription|NN|_ ,|,|,|_ with|with|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ E|e|NN|_ σ70|σ70|NN|_ ,|,|,|_ of|of|IN|_ 2|2|CD|_ ug|ug|NN|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ digested|digest|VBN|_ with|with|IN|_ EcoRI|ecori|NN|_
RNA|rna|NN|_ produced|produce|VBN|_ by|by|IN|_ in|in|FW|_ vitro|vitro|FW|_ transcription|transcription|NN|_ ,|,|,|_ with|with|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ E|e|NN|_ σS|σs|NN|_ ,|,|,|_ of|of|IN|_ 2|2|CD|_ ug|ug|NN|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ digested|digest|VBN|_ with|with|IN|_ EcoRI|ecori|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ cDNA|cdna|NN|_ produced|produce|VBN|_ by|by|IN|_ RT|rt|NN|_ of|of|IN|_ RNA|rna|NN|_ deriving|derive|VBG|_ from|from|IN|_ vitro|vitro|FW|_ transcription|transcription|NN|_ ,|,|,|_ with|with|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ E|e|NN|_ σ70|σ70|NN|_ ,|,|,|_ of|of|IN|_ 2|2|CD|_ ug|ug|NN|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ digested|digest|VBN|_ with|with|IN|_ EcoRI|ecori|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ cDNA|cdna|NN|_ produced|produce|VBN|_ by|by|IN|_ RT|rt|NN|_ of|of|IN|_ RNA|rna|NN|_ deriving|derive|VBG|_ from|from|IN|_ vitro|vitro|FW|_ transcription|transcription|NN|_ ,|,|,|_ with|with|IN|_ RNA|rna|NN|_ polymerase|polymerase|NN|_ E|e|NN|_ σS|σs|NN|_ ,|,|,|_ of|of|IN|_ 2|2|CD|_ ug|ug|NN|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ digested|digest|VBN|_ with|with|IN|_ EcoRI|ecori|NN|_
Cells|cell|NNS|_ in|in|IN|_ RNAlater|rnalater|NN|_ were|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ two|two|CD|_ .|.|.|_ One|one|CD|_ served|serve|VBD|_ as|as|IN|_ non-sorted|non-sorted|JJ|_ cells|cell|NNS|_ and|and|CC|_ kept|keep|VBD|_ at|at|IN|_ 4|4|CD|_ degree|degree|NN|_ C|c|NN|_ .|.|.|_ The|the|DT|_ other|other|JJ|_ aliquot|aliquot|NN|_ was|be|VBD|_ homogenized|homogenize|VBN|_ with|with|IN|_ OMNI|OMNI|NNP|_ TH|th|NN|_ homogenizer|homogenizer|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ further|further|JJ|_ aliquoted|aliquote|VBN|_ into|into|IN|_ small|small|JJ|_ vials|vial|NNS|_ .|.|.|_ Cells|cell|NNS|_ in|in|IN|_ each|each|DT|_ vial|vial|NN|_ were|be|VBD|_ then|then|RB|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ nuclease-free|nuclease-free|JJ|_ phosphate|phosphate|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ ,|,|,|_ incubated|incubate|VBN|_ with|with|IN|_ anti-E|anti-e|JJ|_ .|.|.|_ coli|coli|NN|_ antibody|antibody|NN|_ and|and|CC|_ microbeads|microbead|NNS|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ separation|separation|NN|_ on|on|IN|_ a|a|DT|_ MACS|macs|NN|_ separator|separator|NN|_ -LRB-|-lrb-|-LRB-|_ Miltenyi|Miltenyi|NNP|_ ,|,|,|_ Auburn|Auburn|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ degree|degree|NN|_ C.|c.|NN|_ Sorted|sort|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ into|into|IN|_ RNAlater|rnalater|NN|_ .|.|.|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ software|software|NN|_ Acuity|acuity|NN|_ 4.0|4.0|CD|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ ,|,|,|_ Sunnyvale|Sunnyvale|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ three|three|CD|_ iterations|iteration|NNS|_ using|use|VBG|_ a|a|DT|_ smoothing|smoothing|NN|_ factor|factor|NN|_ of|of|IN|_ 0.4|0.4|CD|_ .|.|.|_ Hybridized|hybridize|VBN|_ spots|spot|NNS|_ having|have|VBG|_ a|a|DT|_ high|high|JJ|_ QC|qc|NN|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ >|>|JJR|_ 0.1|0.1|CD|_ ,|,|,|_ good|good|JJ|_ flag|flag|NN|_ tags|tag|NNS|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ ,|,|,|_ B|b|NN|_ and|and|CC|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ both|both|CC|_ Cy3|cy3|NN|_
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ annular|annular|JJ|_ reactor|reactor|NN|_ -LRB-|-lrb-|-LRB-|_ BioSurface|BioSurface|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Bozeman|Bozeman|NNP|_ ,|,|,|_ MT|MT|NNP|_ -RRB-|-rrb-|-RRB-|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ and|and|CC|_ supplied|supply|VBN|_ with|with|IN|_ fresh|fresh|JJ|_ 10-fold|10-fold|JJ|_ diluted|diluted|JJ|_ Luria|Luria|NNP|MED broth|broth|NN|MED at|at|IN|_ 100|100|CD|_ ml|ml|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
growth|growth|NN|_ mode|mode|NN|_ :|:|:|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ in|in|IN|_ annular|annular|JJ|_ reactor|reactor|NN|_
growth|growth|NN|_ time|time|NN|_ :|:|:|_ 7-day|7-day|JJ|_
non-sorted|non-sorted|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ culture|culture|NN|_ 1|1|CD|_
non-sorted|non-sorted|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ culture|culture|NN|_ 2|2|CD|_
RNAlater|rnalater|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ cells|cell|NNS|_ by|by|IN|_ filtration|filtration|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ SDS|sds|NN|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ culture|culture|NN|_ 1|1|CD|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ culture|culture|NN|_ 2|2|CD|_
sorted|sort|VBD|_ vs.|vs.|CC|_ non-sorted|non-sorted|JJ|_ cells|cell|NNS|_ bioreplicate|bioreplicate|VBP|_ 1|1|CD|_ technical|technical|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
sorted|sort|VBD|_ vs.|vs.|CC|_ non-sorted|non-sorted|JJ|_ cells|cell|NNS|_ bioreplicate|bioreplicate|VBP|_ 1|1|CD|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
sorted|sort|VBD|_ vs.|vs.|CC|_ non-sorted|non-sorted|JJ|_ cells|cell|NNS|_ bioreplicate|bioreplicate|VBP|_ 2|2|CD|_ technical|technical|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
sorted|sort|VBD|_ vs.|vs.|CC|_ non-sorted|non-sorted|JJ|_ cells|cell|NNS|_ bioreplicate|bioreplicate|VBP|_ 2|2|CD|_ technical|technical|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ PHL644|phl644|NN|_
treatment|treatment|NN|_ :|:|:|_ non-sorted|non-sorted|JJ|_
treatment|treatment|NN|_ :|:|:|_ sorted|sort|VBN|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ direct|direct|JJ|_ injection|injection|NN|_ of|of|IN|_ the|the|DT|_ mouse|mouse|NN|_ bladder|bladder|NN|_ ,|,|,|_ and|and|CC|_ kidney|kidney|NN|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ at|at|IN|_ day|day|NN|_ 2|2|CD|_ post-infection|post-infection|JJ|_
cDNA|cdna|NN|_ made|make|VBN|_ from|from|IN|_ strain|strain|NN|_ KMD|kmd|NN|_ extracted|extract|VBN|_ from|from|IN|_ mouse|mouse|NN|_ kidney|kidney|NN|_ on|on|IN|_ day|day|NN|_ 2|2|CD|_ post|post|NN|_ infection|infection|NN|_
cDNA|cdna|NN|_ made|make|VBN|_ from|from|IN|_ strain|strain|NN|_ PC1012|pc1012|NN|_ -LRB-|-lrb-|-LRB-|_ marArobsoxS|mararobsoxs|NN|_ -RRB-|-rrb-|-RRB-|_ extracted|extract|VBN|_ from|from|IN|_ mouse|mouse|NN|_ kidney|kidney|NN|_ on|on|IN|_ day|day|NN|_ 2|2|CD|_ post|post|NN|_ infection|infection|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Infected|infected|JJ|_ kidney|kidney|NN|_ solutions|solution|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 5000xg|5000xg|CD|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ to|to|TO|_ separate|separate|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ pellet|pellet|NN|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ kidney|kidney|NN|_ -LRB-|-lrb-|-LRB-|_ surface|surface|NN|_ of|of|IN|_ RNA-later|rna-later|NN|_ solution|solution|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ kidney|kidney|NN|_ cells|cell|NNS|_ were|be|VBD|_ evacuated|evacuate|VBN|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ of|of|IN|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ remaining|remain|VBG|_ solution|solution|NN|_ was|be|VBD|_ spun|spin|VBN|_ once|once|RB|_ more|more|RBR|_ at|at|IN|_ 12000xg|12000xg|CD|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ disposal|disposal|NN|_ of|of|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ .|.|.|_ Pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 1|1|CD|_ mg|mg|NN|_
KMD|kmd|NN|_ 1|1|CD|_
KMD|kmd|NN|_ 2|2|CD|_
KMD|kmd|NN|_ 3|3|CD|_
Mouse|mouse|NN|_ kidneys|kidney|NNS|_ were|be|VBD|_ homogonized|homogonize|VBN|_ in|in|IN|_ RNALater|rnalater|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bacterial|bacterial|JJ|_ titers|titer|NNS|_ were|be|VBD|_ taken|take|VBN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBD|_ as|as|IN|_ described|describe|VBN|_ below|below|IN|_
PC|pc|NN|_ 1|1|CD|_
PC|pc|NN|_ 2|2|CD|_
PC|pc|NN|_ 3|3|CD|_
strain|strain|NN|_ :|:|:|_ KMD|KMD|NNP|_
strain|strain|NN|_ :|:|:|_ PC1012|pc1012|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ MAS|mas|NN|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ trimmed|trim|VBN|_ mean|mean|NN|_ target|target|NN|_ intensity|intensity|NN|_ of|of|IN|_ each|each|DT|_ array|array|NN|_ was|be|VBD|_ arbitrarily|arbitrarily|RB|_ set|set|VBN|_ to|to|TO|_ 100|100|CD|_ .|.|.|_
tissue|tissue|NN|_ source|source|NN|_ :|:|:|_ kidney|kidney|NN|_ from|from|IN|_ CD-1|cd-1|JJ|_ mice|mouse|NNS|_
Cells|cell|NNS|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ MOPS|MOPS|NNP|MED
Control|Control|NNP|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ WT|WT|NNP|_ _|_|NNP|_ 100uM|100uM|NNP|_ _|_|SYM|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample1|sample1|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ WT|wt|JJ|_ _|_|NN|_ 100uM|100um|NN|_ _|_|CD|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample1|sample1|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ WT|wt|JJ|_ _|_|NN|_ 100uM|100um|NN|_ _|_|CD|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ WT|wt|JJ|_ _|_|NN|_ 100uM|100um|NN|_ _|_|CD|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample2|sample2|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ WT|wt|JJ|_ _|_|NN|_ 100uM|100um|NN|_ _|_|CD|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ WT|wt|JJ|_ _|_|NN|_ 100uM|100um|NN|_ _|_|CD|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample3|sample3|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ WT|wt|JJ|_ _|_|NN|_ 100uM|100um|NN|_ _|_|CD|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample4|sample4|FW|_ _|_|FW|_ TechRep1|techrep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ WT|wt|JJ|_ _|_|NN|_ 100uM|100um|NN|_ _|_|CD|_ KCN|KCN|NNP|_ _|_|SYM|_ Sample4|sample4|FW|_ _|_|FW|_ TechRep2|techrep2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ scans|scan|NNS|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ ImaGene|imagene|NN|_ -LRB-|-lrb-|-LRB-|_ Version|version|NN|_ 6.0.1|6.0.1|CD|_ ;|;|:|_ BioDiscovery|BioDiscovery|NNP|_ ;|;|:|_ El|El|NNP|_ Segundo|Segundo|NNP|_ ,|,|,|_ CA|CA|NNP|_ ;|;|:|_ www.biodiscovery.com|www.biodiscovery.com|NNP|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ with|with|IN|_ the|the|DT|_ results|result|NNS|_ presented|present|VBN|_ in|in|IN|_ the|the|DT|_ associated|associate|VBN|_ text|text|NN|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ normalized|normalize|VBN|_ data|datum|NNS|_ VALUE|value|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ LOWESS|LOWESS|NNP|_ normalization|normalization|NN|_ with|with|IN|_ rank|rank|NN|_ invariant|invariant|JJ|_ selection|selection|NN|_ ,|,|,|_ as|as|IN|_ implemented|implement|VBN|_ in|in|IN|_ lcDNA|lcdna|NN|_ -LRB-|-lrb-|-LRB-|_ receptor.seas.ucla.edu|receptor.seas.ucla.edu|JJ|_
RNA|rna|NN|_ extracted|extract|VBN|_ by|by|IN|_ hot|hot|JJ|_ phenol|phenol|NN|_ choloroform|choloroform|NN|_ folled|foll|VBN|_ by|by|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Midi|midi|NN|_ column|column|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ uM|um|NN|_ KCN|kcn|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ before|before|IN|_ harvesting|harvest|VBG|_
Untreated|untreated|JJ|_
Astat|astat|NN|_ _|_|NN|_ chemostat|chemostat|NN|_
A-stat|a-stat|NN|_ ,|,|,|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.48|0.48|CD|_ 1|1|CD|_
chemostat|chemostat|NN|_ ,|,|,|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.51|0.51|CD|_ 1|1|CD|_
cultivation|cultivation|NN|_ :|:|:|_ continuous|continuous|JJ|_ cultivation|cultivation|NN|_ ,|,|,|_ A-stat|a-stat|JJ|_
cultivation|cultivation|NN|_ :|:|:|_ continuous|continuous|JJ|_ cultivation|cultivation|NN|_ ,|,|,|_ chemostat|chemostat|NN|_
eco|eco|NN|GEN _|_|CD|_ 0.21|0.21|CD|_ _|_|SYM|_ 0.11|0.11|CD|_
eco|eco|NN|GEN _|_|CD|_ 0.26|0.26|CD|_ _|_|SYM|_ 0.11|0.11|CD|_
eco|eco|NN|GEN _|_|CD|_ 0.31|0.31|CD|_ _|_|SYM|_ 0.11|0.11|CD|_
eco|eco|NN|GEN _|_|CD|_ 0.36|0.36|CD|_ _|_|SYM|_ 0.11|0.11|CD|_
eco|eco|NN|GEN _|_|CD|_ 0.40|0.40|CD|_ _|_|SYM|_ 0.11|0.11|CD|_
eco|eco|NN|GEN _|_|CD|_ 0.48|0.48|CD|_ _|_|SYM|_ 0.11|0.11|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ cultivated|cultivate|VBN|_ using|use|VBG|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED containing|contain|VBG|_ 4.5|4.5|CD|_ g|g|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Image|image|NN|_ was|be|VBD|_ analized|analize|VBN|_ with|with|IN|_ Genepix|Genepix|NNP|_ 6|6|CD|_ pro|pro|JJ|_ followed|follow|VBN|_ by|by|IN|_ background|background|NN|_ substration|substration|NN|_ and|and|CC|_ global|global|JJ|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ in|in|IN|_ R|r|NN|_ environment|environment|NN|_ -LRB-|-lrb-|-LRB-|_ KTH|kth|NN|_ package|package|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Spots|spot|NNS|_ with|with|IN|_ signal|signal|NN|_ to|to|TO|_ noise|noise|NN|_ ratio|ratio|NN|_ lower|lower|JJR|_ that|that|IN|_ 3|3|CD|_ and|and|CC|_
RNA|rna|NN|_ degradation|degradation|NN|_ was|be|VBD|_ stopped|stop|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.11|0.11|CD|_ 1|1|CD|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.21|0.21|CD|_ 1|1|CD|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.26|0.26|CD|_ 1|1|CD|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.31|0.31|CD|_ 1|1|CD|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.36|0.36|CD|_ 1|1|CD|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.40|0.40|CD|_ 1|1|CD|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.48|0.48|CD|_ 1|1|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_
Bordetella|bordetella|NN|_ sp.|sp.|NN|_ .|.|.|_ IITR-02|iitr-02|NN|_
ECDH5|ecdh5|NN|_ _|_|CD|_ GD|gd|NN|_ _|_|CD|_ RP1|rp1|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5|dh5|NN|_ -LSB-|-lsb-|-LRB-|_ alpha|alpha|NN|_ -RSB-|-rsb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ of|of|IN|_ all|all|DT|_ strains|strain|NNS|_ -LRB-|-lrb-|-LRB-|_ degraders|degrader|NNS|_ and|and|CC|_ non-degraders|non-degrader|NNS|_ -RRB-|-rrb-|-RRB-|_ isolated|isolate|VBN|_ individually|individually|RB|_ and|and|CC|_ mixed|mix|VBN|_ in|in|IN|_ equal|equal|JJ|_ ratio|ratio|NN|_ -LRB-|-lrb-|-LRB-|_ 500ng|500ng|CD|_ each|each|DT|_ -RRB-|-rrb-|-RRB-|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5α|dh5α|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ of|of|IN|_ mixed|mixed|JJ|_ culture|culture|NN|_ containing|contain|VBG|_ only|only|RB|_ non-degraders|non-degraders|JJ|_ in|in|IN|_ equal|equal|JJ|_ ratio|ratio|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ of|of|IN|_ mixed|mixed|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ Degraders|degrader|NNS|_ and|and|CC|_ non-degraders|non-degrader|NNS|_ in|in|IN|_ 2:1|2:1|CD|_ ratio|ratio|NN|_ -RRB-|-rrb-|-RRB-|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ of|of|IN|_ mixed|mixed|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ Degraders|degrader|NNS|_ :|:|:|_ NM-05|nm-05|NN|_ ,|,|,|_ IITR-02|iitr-02|NN|_ ,|,|,|_ RHA1|rha1|NN|_ ;|;|:|_ Non-degraders|non-degrader|NNS|_ :|:|:|_ DH5α|dh5α|NN|_ ,|,|,|_ BL21|bl21|NN|_ and|and|CC|_ K12|k12|NN|_ in|in|IN|_ equal|equal|JJ|_ ratio|ratio|NN|_ -RRB-|-rrb-|-RRB-|_
Images|image|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ 10.5.1.1|10.5.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ obtained|obtain|VBN|_ background|background|NN|_ subtracted|subtract|VBN|_ and|and|CC|_ spatially|spatially|RB|_ detrended|detrend|VBD|_ Processed|processed|JJ|_ Signal|signal|NN|_ intensities|intensity|NNS|_ .|.|.|_
Images|image|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 9.5.1.1|9.5.1.1|CD|_ &|&|CC|_ 10.5.1.1|10.5.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ obtained|obtain|VBN|_ background|background|NN|_ subtracted|subtract|VBN|_ and|and|CC|_ spatially|spatially|RB|_ detrended|detrend|VBD|_ Processed|processed|JJ|_ Signal|signal|NN|_ intensities|intensity|NNS|_ .|.|.|_
isolation|isolation|NN|_ source|source|NN|_ :|:|:|_ Mixed|mixed|JJ|_ culture|culture|NN|_
isolation|isolation|NN|_ source|source|NN|_ :|:|:|_ Pure|pure|JJ|_ culture|culture|NN|_
MC|MC|NNP|_ _|_|NNP|_ Val|val|NN|_ _|_|SYM|_ G1|g1|NN|_
MC|MC|NNP|_ _|_|NNP|_ Val|val|NN|_ _|_|SYM|_ G2|g2|NN|_
MC|MC|NNP|_ _|_|NNP|_ Val|val|NN|_ _|_|SYM|_ G3|g3|NN|_
MC|MC|NNP|_ _|_|NNP|_ Val|val|NN|_ _|_|CD|_ G5|g5|NN|_
Rhodococcus|rhodococcus|NN|_ jostii|jostii|NN|_ RHA1|rha1|NN|_
Sphingomonas|sphingomonas|FW|_ sp.|sp.|FW|_ .|.|.|_ NM05|nm05|NN|_
The|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ pure|pure|JJ|_ and|and|CC|_ mixed|mixed|JJ|_ bacterial|bacterial|JJ|_ cultures|culture|NNS|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Wizard|Wizard|NNP|_ genomic|genomic|JJ|_ DNA|dna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|Promega|NNP|_ corporation|corporation|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ DNA|dna|NN|_ was|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Nanodrop|Nanodrop|NNP|_ Technologies|Technologies|NNPS|_ Inc|Inc|NNP|_ ,|,|,|_ Rockland|Rockland|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ on|on|IN|_ DNA|dna|NN|_ 12000|12000|CD|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ Sciences|Sciences|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Palo|Palo|NNP|_ Alto|Alto|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ Sphingomonas|sphingomonas|JJ|_ sp.|sp.|NN|_ strain|strain|NN|_ NM-05|nm-05|NN|_ used|use|VBN|_ in|in|IN|_ the|the|DT|_ study|study|NN|_ is|be|VBZ|_ a|a|DT|_ known|known|JJ|_ degrader|degrader|NN|_ of|of|IN|_ γ-hexachlorocyclohexane|γ-hexachlorocyclohexane|NN|_ -LRB-|-lrb-|-LRB-|_ γ-HCH|γ-hch|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ has|have|VBZ|_ been|be|VBN|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ vicinity|vicinity|NN|_ of|of|IN|_ an|a|DT|_ industry|industry|NN|_ India|India|NNP|_ Pesticide|Pesticide|NNP|_ Limited|Limited|NNP|_ ,|,|,|_ Chinhat|Chinhat|NNP|_ industrial|industrial|JJ|_ area|area|NN|_ ,|,|,|_ Lucknow|Lucknow|NNP|_ which|which|WDT|_ is|be|VBZ|_ involved|involve|VBN|_ in|in|IN|_ manufacturing|manufacture|VBG|_ chlorinated|chlorinate|VBN|_ pesticides|pesticide|NNS|_ for|for|IN|_ last|last|JJ|_ 25|25|CD|_ years|year|NNS|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ mineral|mineral|NN|_ salt|salt|NN|_ medium|medium|NN|_ with|with|IN|_ 0.34|0.34|CD|_ mM|mm|NN|KWSUPP γ-HCH|γ-hch|NN|_ as|as|IN|_ sole|sole|JJ|_ source|source|NN|_ of|of|IN|_ carbon|carbon|NN|_ and|and|CC|_ energy|energy|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ Bordetella|bordetella|NN|_ sp.|sp.|NN|_ strain|strain|NN|_ IITR-02|iitr-02|NN|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ has|have|VBZ|_ been|be|VBN|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ vicinity|vicinity|NN|_ of|of|IN|_ the|the|DT|_ industry|industry|NN|_ India|India|NNP|_ Pesticide|Pesticide|NNP|_ Limited|Limited|NNP|_ ,|,|,|_ Chinhat|Chinhat|NNP|_ ,|,|,|_ Lucknow|Lucknow|NNP|_ and|and|CC|_ is|be|VBZ|_ found|find|VBN|_ to|to|TO|_ be|be|VB|_ a|a|DT|_ degrader|degrader|NN|_ of|of|IN|_ 1,2|1,2|CD|_ -|-|:|_ ,|,|,|_ 1,4-dichloro|1,4-dichloro|NN|_ and|and|CC|_ 1,2,3|1,2,3|SYM|_ -|-|:|_ and|and|CC|_ 1,2,4-trichlorobenzene|1,2,4-trichlorobenzene|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ mineral|mineral|NN|_ salt|salt|NN|_ medium|medium|NN|_ with|with|IN|_ 3.2|3.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ 1,2,4-trichlorobenzene|1,2,4-trichlorobenzene|NN|_ as|as|IN|_ sole|sole|JJ|_ source|source|NN|_ of|of|IN|_ carbon|carbon|NN|_ and|and|CC|_ energy|energy|NN|_ .|.|.|_ The|the|DT|_ bacterium|bacterium|NN|_ Rhodococcus|rhodococcus|NN|_ sp.|sp.|NN|_ strain|strain|NN|_ RHA1|rha1|NN|_ which|which|WDT|_ is|be|VBZ|_ a|a|DT|_ known|known|JJ|_ degrader|degrader|NN|_ of|of|IN|_ polychlorinated|polychlorinate|VBN|_ biphenyls|biphenyl|NNS|_ ,|,|,|_ substituted|substitute|VBN|_ phenols|phenol|NNS|_ ,|,|,|_ benzoates|benzoate|NNS|_ and|and|CC|_ phthalates|phthalate|NNS|_ was|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ 0.2|0.2|CD|_ %|%|NN|_ biphenyl|biphenyl|NN|_ and|and|CC|_ 20mM|20mm|NN|_ of|of|IN|_ benzoate|benzoate|NN|_ as|as|IN|_ carbon|carbon|NN|_ sources|source|NNS|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5α|dh5α|NN|_ and|and|CC|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ medium|medium|NN|_ and|and|CC|_ strain|strain|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ nutrient|nutrient|NN|_ broth|broth|NN|_ to|to|TO|_ an|a|DT|_ OD560nm|od560nm|NN|_ of|of|IN|_ 0.4|0.4|CD|_ at|at|IN|_ 37|37|CD|_ degree|degree|NN|_ centigrade|centigrade|NN|_ with|with|IN|_ continuous|continuous|JJ|_ shaking|shake|VBG|_ .|.|.|_
The|the|DT|_ Sphingomonas|sphingomonas|JJ|_ sp.|sp.|NN|_ strain|strain|NN|_ NM-05|nm-05|NN|_ used|use|VBN|_ in|in|IN|_ the|the|DT|_ study|study|NN|_ is|be|VBZ|_ a|a|DT|_ known|known|JJ|_ degrader|degrader|NN|_ of|of|IN|_ γ-hexachlorocyclohexane|γ-hexachlorocyclohexane|NN|_ -LRB-|-lrb-|-LRB-|_ γ-HCH|γ-hch|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ has|have|VBZ|_ been|be|VBN|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ vicinity|vicinity|NN|_ of|of|IN|_ an|a|DT|_ industry|industry|NN|_ India|India|NNP|_ Pesticide|Pesticide|NNP|_ Limited|Limited|NNP|_ ,|,|,|_ Chinhat|Chinhat|NNP|_ industrial|industrial|JJ|_ area|area|NN|_ ,|,|,|_ Lucknow|Lucknow|NNP|_ which|which|WDT|_ is|be|VBZ|_ involved|involve|VBN|_ in|in|IN|_ manufacturing|manufacture|VBG|_ chlorinated|chlorinate|VBN|_ pesticides|pesticide|NNS|_ for|for|IN|_ last|last|JJ|_ 25|25|CD|_ years|year|NNS|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ mineral|mineral|NN|_ salt|salt|NN|_ medium|medium|NN|_ with|with|IN|_ 0.34|0.34|CD|_ mM|mm|NN|KWSUPP γ-HCH|γ-hch|NN|_ as|as|IN|_ sole|sole|JJ|_ source|source|NN|_ of|of|IN|_ carbon|carbon|NN|_ and|and|CC|_ energy|energy|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH-5α|dh-5α|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ O.D.|o.d.|NN|_ of|of|IN|_ 0.4|0.4|CD|_ at|at|IN|_ 37|37|CD|_ degree|degree|NN|_ centigrade|centigrade|NN|_ with|with|IN|_ continuous|continuous|JJ|_ shaking|shake|VBG|_ .|.|.|_ The|the|DT|_ soil|soil|NN|_
The|the|DT|_ total|total|JJ|_ DNA|dna|NN|_ to|to|TO|_ be|be|VB|_ used|use|VBN|_ as|as|IN|_ target|target|NN|_ for|for|IN|_ microarray|microarray|NN|_ hybridization|hybridization|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ soil|soil|NN|_
Data|Data|NNP|_ from|from|IN|_ two|two|CD|_ independent|independent|JJ|_ experiments|experiment|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ and|and|CC|_ then|then|RB|_ analyzed|analyze|VBN|_ using|use|VBG|_ the|the|DT|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 3.0|3.0|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Axon|Axon|NNP|_ Instruments|Instruments|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ptsN|ptsn|NN|GEN mutant|mutant|JJ|_ strain|strain|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism wild|wild|JJ|_ type|type|NN|_ strain|strain|NN|_
genotype|genotype|NN|_
ptsN|ptsn|NN|GEN mutant|mutant|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
ptsN|ptsn|NN|GEN mutant|mutant|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ each|each|DT|_ sample|sample|NN|_ using|use|VBG|_ a|a|DT|_ QIAGEN|QIAGEN|NNP|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_
The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ and|and|CC|_ its|its|PRP$|_ isogenic|isogenic|JJ|_ ptsN|ptsn|NN|GEN mutant|mutant|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED containing|contain|VBG|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP as|as|IN|_ carbon|carbon|NN|_ source|source|NN|_ .|.|.|_ Cells|cell|NNS|_ from|from|IN|_ duplicate|duplicate|VBP|_ experiments|experiment|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ when|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ A600|a600|NN|_ of|of|IN|_ 0.4|0.4|CD|_ .|.|.|_
Cells|cell|NNS|_ for|for|IN|_ inoculation|inoculation|NN|_ were|be|VBD|_ from|from|IN|_ overnight|overnight|JJ|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ in|in|IN|_ 10|10|CD|_ %|%|NN|_ Luria-Bertani|luria-bertani|JJ|_ broth|broth|NN|_ at|at|IN|_ 30|30|CD|_ degree|degree|NN|_ Celsius|Celsius|NNP|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ fresh|fresh|JJ|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|MED broth|broth|NN|MED before|before|IN|_ inoculation|inoculation|NN|_ and|and|CC|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 5|5|CD|_ ml|ml|NN|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|_ in|in|IN|_ a|a|DT|_ disposable|disposable|JJ|_ petri|petri|JJ|_ dish|dish|NN|_ -LRB-|-lrb-|-LRB-|_ 60|60|CD|_ mm|mm|NN|_ x|x|CC|_ 15|15|CD|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 50|50|CD|_ ul|ul|NN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ for|for|IN|_ mono-species|mono-species|NNS|_ pure|pure|JJ|_ culture|culture|NN|_ .|.|.|_ 50|50|CD|_ ul|ul|NN|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ 10|10|CD|_ ul|ul|NN|_ S.|S.|NNP|_ maltophilia|maltophilia|NNP|_ were|be|VBD|_ mixed|mixed|JJ|_ and|and|CC|_ inoculated|inoculate|VBN|_ for|for|IN|_ mixed-species|mixed-species|JJ|_ culture|culture|NN|_ .|.|.|_ Petri|petri|JJ|_ dishes|dish|NNS|_ were|be|VBD|_ set|set|VBN|_ static|static|JJ|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 18|18|CD|_ h|h|NN|_ for|for|IN|_ biofilm|biofilm|NN|_ growth|growth|NN|_ .|.|.|_
culture|culture|NN|_ media|media|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ Luria|Luria|NNP|MED broth|broth|NN|MED
culture|culture|NN|_ system|system|NN|_ :|:|:|_ static|static|JJ|_ petri|petri|JJ|_ dish|dish|NN|_ -LRB-|-lrb-|-LRB-|_ disposable|disposable|JJ|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ time|time|NN|_ :|:|:|_ 18|18|CD|_ h|h|NN|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ software|software|NN|_ Acuity|acuity|NN|_ 4.0|4.0|CD|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ ,|,|,|_ Sunnyvale|Sunnyvale|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Hybridized|hybridize|VBN|_ spots|spot|NNS|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ having|have|VBG|_ a|a|DT|_ high|high|JJ|_ QC|qc|NN|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ >|>|JJR|_ 0.1|0.1|CD|_ ,|,|,|_ good|good|JJ|_ flag|flag|NN|_ tags|tag|NNS|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ ,|,|,|_ B|b|NN|_ and|and|CC|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ both|both|CC|_ Cy3|cy3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP|_ _|_|CD|_ bioreplicate1|bioreplicate1|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP|_ _|_|CD|_ bioreplicate1|bioreplicate1|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP|_ _|_|CD|_ bioreplicate1|bioreplicate1|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP|_ _|_|CD|_ bioreplicate2|bioreplicate2|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP|_ _|_|CD|_ bioreplicate2|bioreplicate2|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 2|2|CD|_
RNAlater|rnalater|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ cells|cell|NNS|_ by|by|IN|_ filtration|filtration|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ SDS|sds|NN|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ dual-species|dual-species|JJ|_ biofilms|biofilm|NNS|_ 1|1|CD|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ dual-species|dual-species|JJ|_ biofilms|biofilm|NNS|_ 2|2|CD|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ mono-species|mono-species|JJ|_ biofilms|biofilm|NNS|_ 1|1|CD|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ mono-species|mono-species|JJ|_ biofilms|biofilm|NNS|_ 2|2|CD|_
Suspended|suspend|VBN|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ removed|remove|VBN|_ and|and|CC|_ biofilms|biofilm|NNS|_ were|be|VBD|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|MED broth|broth|NN|MED .|.|.|_ Biofilms|biofilm|NNS|_ from|from|IN|_ each|each|DT|_ petri|petri|NN|_ dish|dish|NN|_ were|be|VBD|_ then|then|RB|_ scraped|scrape|VBN|_ into|into|IN|_ a|a|DT|_ vial|vial|NN|_ containing|contain|VBG|_ 1|1|CD|_ ml|ml|NN|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|_ .|.|.|_ Scraped|scraped|JJ|_ biofilms|biofilm|NNS|_ in|in|IN|_ each|each|DT|_ vial|vial|NN|_ were|be|VBD|_ concentrated|concentrate|VBN|_ from|from|IN|_ 1|1|CD|_ ml|ml|NN|_ into|into|IN|_ 50|50|CD|_ ul|ul|NN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ 500|500|CD|_ ul|ul|NN|_ RNAlater|rnalater|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ mixed|mix|VBN|_ well|well|RB|_ .|.|.|_ Samples|sample|NNS|_ in|in|IN|_ RNAlater|rnalater|NN|_ were|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ 4C|4c|NN|_ fridge|fridge|NN|_ overnight|overnight|JJ|_ .|.|.|_ Each|each|DT|_ vial|vial|NN|_ was|be|VBD|_ homogenized|homogenize|VBN|_ with|with|IN|_ OMNI|OMNI|NNP|_ TH|th|NN|_ homogenizer|homogenizer|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ further|further|JJ|_ aliquoted|aliquote|VBN|_ into|into|IN|_ small|small|JJ|_ vials|vial|NNS|_ .|.|.|_ Cells|cell|NNS|_ in|in|IN|_ each|each|DT|_ vial|vial|NN|_ were|be|VBD|_ then|then|RB|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ nuclease-free|nuclease-free|JJ|_ phosphate|phosphate|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ ,|,|,|_ incubated|incubate|VBN|_ with|with|IN|_ anti-E|anti-e|JJ|_ .|.|.|_ coli|coli|NN|_ antibody|antibody|NN|_ -LRB-|-lrb-|-LRB-|_ ViroStat|virostat|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ microbeads|microbead|NNS|_ -LRB-|-lrb-|-LRB-|_ Miltenyi|miltenyi|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ separation|separation|NN|_ on|on|IN|_ a|a|DT|_ MACS|macs|NN|_ separator|separator|NN|_ -LRB-|-lrb-|-LRB-|_ Miltenyi|Miltenyi|NNP|_ ,|,|,|_ Auburn|Auburn|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ degree|degree|NN|_ C.|c.|NN|_ Sorted|sort|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ into|into|IN|_ RNAlater|rnalater|NN|_ until|until|IN|_ RNA|rna|NN|_ extractions|extraction|NNS|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ with|with|IN|_ homogenization|homogenization|NN|_ and|and|CC|_ separation|separation|NN|_
Cells|cell|NNS|_ for|for|IN|_ inoculation|inoculation|NN|_ were|be|VBD|_ from|from|IN|_ overnight|overnight|JJ|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ in|in|IN|_ 10|10|CD|_ %|%|NN|_ Luria-Bertani|luria-bertani|JJ|_ broth|broth|NN|_ at|at|IN|_ 30|30|CD|_ degree|degree|NN|_ Celsius|Celsius|NNP|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ fresh|fresh|JJ|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|MED broth|broth|NN|MED before|before|IN|_ inoculated|inoculate|VBN|_ into|into|IN|_ 30|30|CD|_ ml|ml|NN|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|_ in|in|IN|_ a|a|DT|_ flask|flask|NN|_ .|.|.|_ 300|300|CD|_ ul|ul|NN|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ for|for|IN|_ mono-species|mono-species|NNS|_ pure|pure|JJ|_ culture|culture|NN|_ .|.|.|_ 150|150|CD|_ ul|ul|NN|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ 60|60|CD|_ ul|ul|NN|_ S.|S.|NNP|_ maltophilia|maltophilia|NNP|_ were|be|VBD|_ mixed|mixed|JJ|_ and|and|CC|_ inoculated|inoculate|VBN|_ for|for|IN|_ mixed-species|mixed-species|NNS|_ cultures|culture|NNS|_ .|.|.|_ Flasks|flask|NNS|_ were|be|VBD|_ set|set|VBN|_ on|on|IN|_ a|a|DT|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 18|18|CD|_ h.|h.|NN|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ and|and|CC|_ kept|keep|VBD|_ in|in|IN|_ 4C|4c|NN|_ fridge|fridge|NN|_ overnight|overnight|JJ|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ vials|vial|NNS|_ containing|contain|VBG|_ around|around|IN|_ 2x10|2x10|JJ|_ ^|^|NN|_ 8|8|CD|_ cells|cell|NNS|_ .|.|.|_ Cells|cell|NNS|_ in|in|IN|_ each|each|DT|_ vial|vial|NN|_ were|be|VBD|_ then|then|RB|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ nuclease-free|nuclease-free|JJ|_ phosphate|phosphate|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ ,|,|,|_ incubated|incubate|VBN|_ with|with|IN|_ anti-E|anti-e|JJ|_ .|.|.|_ coli|coli|NN|_ antibody|antibody|NN|_ -LRB-|-lrb-|-LRB-|_ ViroStat|virostat|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ microbeads|microbead|NNS|_ -LRB-|-lrb-|-LRB-|_ Miltenyi|miltenyi|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ separation|separation|NN|_ on|on|IN|_ a|a|DT|_ MACS|macs|NN|_ separator|separator|NN|_ -LRB-|-lrb-|-LRB-|_ Miltenyi|Miltenyi|NNP|_ ,|,|,|_ Auburn|Auburn|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ degree|degree|NN|_ C.|c.|NN|_ Sorted|sort|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ into|into|IN|_ RNAlater|rnalater|NN|_ until|until|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
culture|culture|NN|_ media|media|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ Luria|Luria|NNP|MED broth|broth|NN|MED
culture|culture|NN|_ system|system|NN|_ :|:|:|_ flask|flask|NN|_ with|with|IN|_ continous|continous|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ system|system|NN|_ :|:|:|_ flask|flask|NN|_ with|with|IN|_ continuous|continuous|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ time|time|NN|_ :|:|:|_ 18|18|CD|_ h|h|NN|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ software|software|NN|_ Acuity|acuity|NN|_ 4.0|4.0|CD|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ ,|,|,|_ Sunnyvale|Sunnyvale|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Hybridized|hybridize|VBN|_ spots|spot|NNS|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ having|have|VBG|_ a|a|DT|_ high|high|JJ|_ QC|qc|NN|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ >|>|JJR|_ 0.1|0.1|CD|_ ,|,|,|_ good|good|JJ|_ flag|flag|NN|_ tags|tag|NNS|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ ,|,|,|_ B|b|NN|_ and|and|CC|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ both|both|CC|_ Cy3|cy3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP|_ _|_|CD|_ bioreplicate1|bioreplicate1|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP|_ _|_|CD|_ bioreplicate1|bioreplicate1|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP|_ _|_|CD|_ bioreplicate2|bioreplicate2|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP|_ _|_|CD|_ bioreplicate2|bioreplicate2|NN|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 2|2|CD|_
RNAlater|rnalater|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ cells|cell|NNS|_ by|by|IN|_ filtration|filtration|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ SDS|sds|NN|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ dual-species|dual-species|JJ|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ 1|1|CD|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ dual-species|dual-species|JJ|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ 2|2|CD|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ mono-species|mono-species|NNS|_ pure|pure|JJ|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ 1|1|CD|_
sorted|sort|VBD|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ mono-species|mono-species|NNS|_ pure|pure|JJ|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ 2|2|CD|_
treatment|treatment|NN|_ :|:|:|_ with|with|IN|_ homogenization|homogenization|NN|_ and|and|CC|_ separation|separation|NN|_
Cells|cell|NNS|_ for|for|IN|_ inoculation|inoculation|NN|_ were|be|VBD|_ from|from|IN|_ overnight|overnight|JJ|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ in|in|IN|_ 10|10|CD|_ %|%|NN|_ Luria-Bertani|luria-bertani|JJ|_ broth|broth|NN|_ at|at|IN|_ 30|30|CD|_ degree|degree|NN|_ Celsius|Celsius|NNP|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ in|in|IN|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ fresh|fresh|JJ|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|MED broth|broth|NN|MED before|before|IN|_ inoculation|inoculation|NN|_ .|.|.|_ Planktonic|planktonic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ flasks|flask|NNS|_ with|with|IN|_ 30|30|CD|_ ml|ml|NN|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|_ ,|,|,|_ inoculated|inoculate|VBN|_ with|with|IN|_ 300|300|CD|_ ul|ul|NN|_ E.|e.|FW|_ coli|coli|FW|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ Flasks|flask|NNS|_ were|be|VBD|_ set|set|VBN|_ on|on|IN|_ a|a|DT|_ shaker|shaker|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 18|18|CD|_ h.|h.|NN|_ Biofilms|biofilm|NNS|_ were|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ static|static|JJ|_ disposable|disposable|JJ|_ petri|petri|NN|_ dishes|dish|NNS|_ -LRB-|-lrb-|-LRB-|_ 60|60|CD|_ mm|mm|NN|_ x|x|CC|_ 15|15|CD|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|_ ,|,|,|_ inoculated|inoculate|VBN|_ with|with|IN|_ 50|50|CD|_ ul|ul|NN|_ E.|e.|FW|_ coli|coli|FW|_ overnight|overnight|JJ|_ culture|culture|NN|_ .|.|.|_ The|the|DT|_ petri|petri|JJ|_ dishes|dish|NNS|_ were|be|VBD|_ set|set|VBN|_ static|static|JJ|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 18|18|CD|_ h.|h.|NN|_
culture|culture|NN|_ media|media|NNS|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ Luria|Luria|NNP|MED broth|broth|NN|MED
culture|culture|NN|_ system|system|NN|_ :|:|:|_ flask|flask|NN|_ with|with|IN|_ continuous|continuous|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ system|system|NN|_ :|:|:|_ static|static|JJ|_ petri|petri|JJ|_ dish|dish|NN|_ -LRB-|-lrb-|-LRB-|_ disposable|disposable|JJ|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_
culture|culture|NN|_ time|time|NN|_ :|:|:|_ 18|18|CD|_ h|h|NN|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ software|software|NN|_ Acuity|acuity|NN|_ 4.0|4.0|CD|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ ,|,|,|_ Sunnyvale|Sunnyvale|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Hybridized|hybridize|VBN|_ spots|spot|NNS|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ having|have|VBG|_ a|a|DT|_ high|high|JJ|_ QC|qc|NN|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ >|>|JJR|_ 0.1|0.1|CD|_ ,|,|,|_ good|good|JJ|_ flag|flag|NN|_ tags|tag|NNS|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ ,|,|,|_ B|b|NN|_ and|and|CC|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ both|both|CC|_ Cy3|cy3|NN|_
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ from|from|IN|_ biofilm|biofilm|NN|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ from|from|IN|_ biofilm|biofilm|NN|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ from|from|IN|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ from|from|IN|_ planktonic|planktonic|JJ|_ culture|culture|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ Biofilm|Biofilm|NNP|_ _|_|SYM|_ bioreplicate1|bioreplicate1|CD|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ Biofilm|Biofilm|NNP|_ _|_|SYM|_ bioreplicate1|bioreplicate1|CD|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ Biofilm|Biofilm|NNP|_ _|_|SYM|_ bioreplicate2|bioreplicate2|CD|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|SYM|_ Biofilm|Biofilm|NNP|_ _|_|SYM|_ bioreplicate2|bioreplicate2|CD|_ _|_|NN|_ techreplicate|techreplicate|NN|_ _|_|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Planktonic|planktonic|JJ|_ cultures|culture|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAlater|rnalater|NN|_ and|and|CC|_ kept|keep|VBD|_ in|in|IN|_ 4C|4c|NN|_ fridge|fridge|NN|_ overnight|overnight|JJ|_ .|.|.|_ Suspended|suspend|VBN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ petri|petri|JJ|_ dishes|dish|NNS|_ and|and|CC|_ biofilms|biofilm|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ fresh|fresh|JJ|_ 10|10|CD|_ %|%|NN|_ LB|lb|NN|_ before|before|IN|_ being|be|VBG|_ craped|crap|VBN|_ from|from|IN|_ the|the|DT|_ bottom|bottom|JJ|_ surface|surface|NN|_ of|of|IN|_ petri|petri|NN|_ dishes|dish|NNS|_ .|.|.|_ Biofilms|biofilm|NNS|_ were|be|VBD|_ also|also|RB|_ re-suspeded|re-suspeded|JJ|_ into|into|IN|_ RNAlater|rnalater|NN|_ and|and|CC|_ kept|keep|VBD|_ at|at|IN|_ 4C|4c|NN|_ overnight|overnight|JJ|_ .|.|.|_ Both|both|DT|_ planktonic|planktonic|JJ|_ and|and|CC|_ biofilm|biofilm|NN|_ samples|sample|NNS|_ were|be|VBD|_ homogenized|homogenize|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ on|on|IN|_ ice|ice|NN|_ with|with|IN|_ an|a|DT|_ Omni|Omni|NNP|_ TH|th|NN|_ homogenizer|homogenizer|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ aliquoted|aliquote|VBN|_ into|into|IN|_ vials|vial|NNS|_ containing|contain|VBG|_ around|around|IN|_ 2x10|2x10|JJ|_ ^|^|NN|_ 8|8|CD|_ cells|cell|NNS|_ .|.|.|_ Cells|cell|NNS|_ in|in|IN|_ each|each|DT|_ vial|vial|NN|_ were|be|VBD|_ then|then|RB|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ nuclease-free|nuclease-free|JJ|_ phosphate|phosphate|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ ,|,|,|_ incubated|incubate|VBN|_ with|with|IN|_ anti-E|anti-e|JJ|_ .|.|.|_ coli|coli|NN|_ antibody|antibody|NN|_ and|and|CC|_ microbeads|microbead|NNS|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ separation|separation|NN|_ on|on|IN|_ a|a|DT|_ MACS|macs|NN|_ separator|separator|NN|_ -LRB-|-lrb-|-LRB-|_ Miltenyi|Miltenyi|NNP|_ ,|,|,|_ Auburn|Auburn|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 4|4|CD|_ degree|degree|NN|_ C.|c.|NN|_ Sorted|sort|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ into|into|IN|_ RNAlater|rnalater|NN|_ .|.|.|_
RNAlater|rnalater|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ cells|cell|NNS|_ by|by|IN|_ filtration|filtration|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ SDS|sds|NN|_
treatment|treatment|NN|_ :|:|:|_ with|with|IN|_ homogenization|homogenization|NN|_ and|and|CC|_ separation|separation|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ FLAG|flag|NN|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ RNAP|rnap|NN|_ beta|beta|NN|_ subunit|subunit|NN|_ antibody|antibody|NN|_
ChIP-Seq|chip-seq|NN|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ fis|fi|VBZ|GEN early-exponential|early-exponential|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ fis|fi|VBZ|GEN mid-exponential|mid-exponential|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ H-NS|h-ns|NN|_ early-exponential|early-exponential|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ H-NS|h-ns|NN|_ mid-exponential|mid-exponential|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ H-NS|h-ns|NN|_ stationary|stationary|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ H-NS|h-ns|NN|_ transition-to-stationary|transition-to-stationary|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ rpo|rpo|NN|_ delfis|delfi|VBZ|_ mid-exponential|mid-exponential|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ rpo|rpo|NN|_ delhns|delhn|VBZ|_ mid-exponential|mid-exponential|JJ|_
-LSB-|-lsb-|-LRB-|_ E-MTAB-332|e-mtab-332|NN|_ -RSB-|-rsb-|-RRB-|_ rpo|rpo|NN|_ wt|wt|JJ|_ mid-exponential|mid-exponential|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Fis|fis|NN|TF ,|,|,|_ EE|ee|NN|_
Fis|Fis|NNP|TF ,|,|,|_ ME|ME|NNP|_
genotype|genotype|NN|_ :|:|:|_ del-fis|del-fis|JJ|_
genotype|genotype|NN|_ :|:|:|_ del-hns|del-hns|JJ|_
genotype|genotype|NN|_ :|:|:|_ fis|fi|NNS|GEN :|:|:|_ :|:|:|_ 3xFLAG|3xflag|NN|_
genotype|genotype|NN|_ :|:|:|_ hns|hn|NNS|GEN :|:|:|_ :|:|:|_ 3xFLAG|3xflag|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ _|_|NN|_ type|type|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ early-exponential|early-exponential|JJ|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ mid-exponential|mid-exponential|JJ|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ stationary|stationary|JJ|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ transition-to-stationary|transition-to-stationary|JJ|_
grow|grow|VBP|_ ||||SYM|_ The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ bacterial|bacterial|JJ|_ strains|strain|NNS|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ work|work|NN|_ are|be|VBP|_ the|the|DT|_ following|following|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ F|f|NN|_ -|-|:|_ lambda|lambda|NN|_ -|-|:|_ ilvG|ilvg|NN|_ -|-|:|_ rfb-50|rfb-50|NN|_ rph-1|rph-1|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ MG1655|mg1655|NN|_ hns|hn|NNS|GEN -LRB-|-lrb-|-LRB-|_ hns|hn|NNS|GEN :|:|:|_ :|:|:|_ Kanr|kanr|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ MG1655|mg1655|NN|_ fis|fis|NN|GEN -LRB-|-lrb-|-LRB-|_ fis|fis|NN|GEN :|:|:|_ :|:|:|_ Kanr|kanr|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ MG1655|mg1655|NN|_ hns-FLAG|hns-flag|NN|_ -LRB-|-lrb-|-LRB-|_ hns|hn|NNS|GEN :|:|:|_ :|:|:|_ 3xFLAG|3xflag|NN|_ :|:|:|_ :|:|:|_ Kanr|kanr|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ MG1655|mg1655|NN|_ fis-FLAG|fis-flag|NN|_ -LRB-|-lrb-|-LRB-|_ fis|fis|NN|GEN :|:|:|_ :|:|:|_ 3xFLAG|3xflag|NN|_ :|:|:|_ :|:|:|_ Kanr|kanr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Luria-Bertani|luria-bertani|JJ|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ %|%|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ g|g|NN|_
H-NS|h-ns|NN|_ ,|,|,|_ EE|ee|NN|_
H-NS|h-ns|NN|_ ,|,|,|_ ME|me|NN|_
H-NS|h-ns|NN|_ ,|,|,|_ S|s|NN|_
H-NS|h-ns|NN|_ ,|,|,|_ TS|ts|NN|_
material|material|NN|_ type|type|NN|_ :|:|:|_ whole|whole|JJ|_ _|_|JJ|_ organism|organism|NN|_
nucleic|nucleic|JJ|_ _|_|NN|_ acid|acid|NN|_ _|_|NN|_ extraction|extraction|NN|_ ||||SYM|_ ChIP|chip|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Grainger|Grainger|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2004|2004|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ to|to|TO|_ the|the|DT|_ protdegree|protdegree|NN|_ Col.|Col.|NNP|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37degree|37degree|CD|_ C|c|NN|_ to|to|TO|_ the|the|DT|_ desired|desire|VBN|_ OD600|od600|NN|_ and|and|CC|_ formaldehyde|formaldehyde|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ %|%|NN|_ .|.|.|_ After|after|IN|_ 20|20|CD|_ min|min|NN|_ of|of|IN|_ incubation|incubation|NN|_ ,|,|,|_ glycine|glycine|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ M|m|NN|_ to|to|TO|_ quench|quench|VB|_ the|the|DT|_ reaction|reaction|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ a|a|DT|_ further|further|JJ|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ Cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|tris|NN|_ -LSB-|-lsb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 20|20|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_
rpo|rpo|NN|_ ,|,|,|_ delfis|delfis|NN|_ ,|,|,|_ ME|me|NN|_
rpo|rpo|NN|_ ,|,|,|_ delhns|delhn|NNS|_ ,|,|,|_ ME|me|NN|_
rpo|rpo|NN|_ ,|,|,|_ wt|wt|JJ|_ ,|,|,|_ ME|me|JJ|_
Sequences|sequence|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ both|both|DT|_ strands|strand|NNS|_ of|of|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ BLAT|BLAT|NNP|_ allowing|allow|VBG|_ no|no|DT|_ gaps|gap|NNS|_ and|and|CC|_ up|up|RB|_ to|to|TO|_ two|two|CD|_ mismatches|mismatch|NNS|_ .|.|.|_ Each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ extended|extend|VBN|_ to|to|TO|_ 200bp|200bp|VB|_ the|the|DT|_ approximate|approximate|JJ|_ average|average|JJ|_ length|length|NN|_ of|of|IN|_ DNA|dna|NN|_ fragments|fragment|NNS|_ on|on|IN|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ which|which|WDT|_ mapped|map|VBD|_ to|to|TO|_ a|a|DT|_ single|single|JJ|_ region|region|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ base|base|NN|_ position|position|NN|_ on|on|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ that|that|IN|_ mapped|map|VBN|_ to|to|TO|_ that|that|DT|_ position|position|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ .|.|.|_
sequencing|sequencing|NN|_ ||||SYM|_ Immunoprecipitated|immunoprecipitate|VBN|_ samples|sample|NNS|_ and|and|CC|_ the|the|DT|_ sheared|sheared|JJ|_ DNA|dna|NN|_ following|follow|VBG|_ the|the|DT|_ Bioruptor|Bioruptor|NNP|_ were|be|VBD|_ de-crosslinked|de-crosslinked|JJ|_ in|in|IN|_ 0.5|0.5|CD|_ x|x|CC|_ elution|elution|NN|_ buffer|buffer|NN|_ containing|contain|VBG|_ 0.8|0.8|CD|_ mg|mg|NN|_
strainorline|strainorline|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ without|without|IN|_ shaking|shake|VBG|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ MOPS-based|mops-based|JJ|_ culture|culture|NN|_ medium|medium|NN|_ designed|design|VBN|_ by|by|IN|_ Neidhardt|Neidhardt|NNP|_ .|.|.|_ Mouse|mouse|NN|_ cecal|cecal|JJ|_ mucus|mucus|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ streptomycin-treated|streptomycin-treated|JJ|_ CD-1|cd-1|NN|_ mice|mouse|NNS|_ -LRB-|-lrb-|-LRB-|_ not|not|RB|_ colonized|colonize|VBN|_ with|with|IN|_ E.|e.|FW|_ coli|coli|FW|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ A600|a600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ containing|contain|VBG|_ glucose|glucose|NN|SUPP or|or|CC|_ mannose|mannose|NN|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ also|also|RB|_ in|in|IN|_ 10|10|CD|_ mg|mg|NN|_
Cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ DNA-RNA|DNA-RNA|NNP|_ Protect|Protect|NNP|_ -LRB-|-lrb-|-LRB-|_ Sierra|Sierra|NNP|_ Diagnostics|Diagnostics|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ inhibit|inhibit|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ and|and|CC|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNeasy|rneasy|NN|_ minkits|minkit|NNS|_ with|with|IN|_ the|the|DT|_ optional|optional|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ flhD|flhd|NN|GEN ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ on|on|IN|_ mucus|mucus|NN|_
E.|E.|NNP|_ coli|coli|NN|_ flhD|flhd|NN|GEN ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ on|on|IN|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ flhD|flhd|NN|GEN ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ on|on|IN|_ mannose|mannose|NN|_
E.|e.|FW|_ coli|coli|FW|_ flhD|flhd|NN|GEN ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ on|on|IN|_ mucus|mucus|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655star|mg1655star|NN|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ on|on|IN|_ mucus|mucus|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655star|mg1655star|NN|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ on|on|IN|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ MG1655star|mg1655star|NN|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ on|on|IN|_ mannose|mannose|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655star|mg1655star|NN|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ on|on|IN|_ mucus|mucus|NN|_
E.|E.|NNP|_ coli|coli|NN|_ wild-type|wild-type|JJ|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ on|on|IN|_ mucus|mucus|NN|_
E.|E.|NNP|_ coli|coli|NN|_ wild-type|wild-type|JJ|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ on|on|IN|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ wild-type|wild-type|JJ|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ on|on|IN|_ mannose|mannose|NN|_
E.|e.|FW|_ coli|coli|FW|_ wild-type|wild-type|JJ|_ ,|,|,|_ A600|a600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ on|on|IN|_ mucus|mucus|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
flhD-glucose|flhd-glucose|JJ|_
flhD-mannose|flhd-mannose|NN|_
flhD-mucus-P1|flhd-mucus-p1|NN|_
flhD-mucus-P2|flhd-mucus-p2|NN|_
genotype|genotype|NN|_
MG1655star-glucose|mg1655star-glucose|JJ|_
MG1655star-mannose|mg1655star-mannose|JJ|_
MG1655star-mucus-P1|mg1655star-mucus-p1|NN|_
MG1655star-mucus-P2|mg1655star-mucus-p2|NN|_
RMA|rma|NN|_ with|with|IN|_ quartile|quartile|JJ|_ normalization|normalization|NN|_ according|accord|VBG|_ to|to|TO|_ method|method|NN|_ of|of|IN|_ Irizarry|Irizarry|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2003|2003|CD|_ .|.|.|_ The|the|DT|_ raw|raw|JJ|_ .|.|.|_ cel|cel|NN|_ files|file|NNS|_ were|be|VBD|_ processed|process|VBN|_ in|in|IN|_ RMA|RMA|NNP|_ using|use|VBG|_ Bioconductor|Bioconductor|NNP|_ R|R|NNP|_ package|package|NN|_ :|:|:|_ affy|affy|VB|_ Version|Version|NNP|_ :|:|:|_ 1.8.1|1.8.1|CD|_ Date|date|NN|_ :|:|:|_ 2005-09-03|2005-09-03|CD|_ ,|,|,|_ with|with|IN|_ the|the|DT|_ option|option|NN|_ Filter.genes|filter.genes|NNS|_ containing|contain|VBG|_ a|a|DT|_ subset|subset|NN|_ of|of|IN|_ probesets|probeset|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ MG1655|mg1655|NN|_ genes|gene|NNS|_ and|and|CC|_ intergenic|intergenic|JJ|_ regions|region|NNS|_ listed|list|VBN|_ in|in|IN|_ the|the|DT|_ matrix|matrix|NN|_ data|datum|NNS|_ .|.|.|_ Replicates|replicate|VBZ|_ were|be|VBD|_ averaged|average|VBN|_ for|for|IN|_ ratio|ratio|NN|_ calculations|calculation|NNS|_ .|.|.|_
WT-glucose-Rep1|wt-glucose-rep1|NN|_
WT-glucose-Rep2|wt-glucose-rep2|NN|_
WT-mannose|wt-mannose|JJ|_
WT-mucus-P1|wt-mucus-p1|NN|_
WT-mucus-P2|wt-mucus-p2|NN|_
1|1|CD|_ .|.|.|_ Use|Use|NNP|_ Agilent|Agilent|NNP|_ software|software|NN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ to|to|TO|_ analyze|analyze|VB|_ spotted|spotted|JJ|_ arrays|array|NNS|_ .|.|.|_
252978410001|252978410001|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE001MS16|bce001ms16|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410001|252978410001|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE022DS6|bce022ds6|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410001|252978410001|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE063MS14|bce063ms14|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410001|252978410001|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ ETP98015|etp98015|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410002|252978410002|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE007|bce007|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410002|252978410002|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE041|bce041|NN|_ _|_|CD|_ MS11|ms11|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410002|252978410002|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE063|bce063|NN|_ _|_|CD|_ DS4|ds4|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410002|252978410002|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ ETP98028|etp98028|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410003|252978410003|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ C35662|c35662|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410003|252978410003|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 007|007|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410003|252978410003|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 017|017|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410003|252978410003|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98062|etp98062|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410004|252978410004|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE003|bce003|NN|_ _|_|CD|_ DS5|ds5|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410004|252978410004|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE058|bce058|NN|_ _|_|CD|_ MS13|ms13|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410004|252978410004|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE069|bce069|NN|_ _|_|CD|_ MS9|ms9|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410004|252978410004|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE129|bce129|NN|_ _|_|CD|_ DS2|ds2|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410005|252978410005|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE008|bce008|NN|_ _|_|CD|_ MS13|ms13|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410005|252978410005|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE013|bce013|NN|_ _|_|CD|_ DS1|ds1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410005|252978410005|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE035|bce035|NN|_ _|_|CD|_ MS8|ms8|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410005|252978410005|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE039|bce039|NN|_ _|_|CD|_ DS2|ds2|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410006|252978410006|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 012|012|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410006|252978410006|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 019|019|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410006|252978410006|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 026|026|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410006|252978410006|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 044|044|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410007|252978410007|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE002|bce002|NN|_ _|_|CD|_ MS12|ms12|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410007|252978410007|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE021|bce021|NN|_ _|_|CD|_ DS7|ds7|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410007|252978410007|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE049|bce049|NN|_ _|_|CD|_ MS9|ms9|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410007|252978410007|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98061|etp98061|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410008|252978410008|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 180050|180050|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410008|252978410008|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98103|etp98103|NN|_ _|_|CD|_ CY3.mev.refIsIB.ou|cy3.mev.refisib.ou|NN|_
252978410008|252978410008|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98111|etp98111|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410008|252978410008|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ TW03741|tw03741|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410009|252978410009|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1787|e1787|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410009|252978410009|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E747|e747|NN|_ _|_|NN|_ 0|0|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410009|252978410009|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ F595C|f595c|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410009|252978410009|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS3572A1.mev.refIsIB.out|ws3572a1.mev.refisib.out|NN|_
252978410010|252978410010|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ 229|229|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410010|252978410010|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p13|p13|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410010|252978410010|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p1|p1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410010|252978410010|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p4|p4|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410011|252978410011|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ DS26|ds26|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410011|252978410011|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1777|e1777|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410011|252978410011|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E9034A|e9034a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410011|252978410011|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ NN|NN|NNP|_ _|_|SYM|_ 34|34|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410012|252978410012|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ 42|42|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ C1|c1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410012|252978410012|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETEC|ETEC|NNP|_ _|_|SYM|_ 18|18|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410012|252978410012|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p12|p12|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410012|252978410012|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ LSN02|lsn02|NN|_ _|_|CD|_ 012560|012560|CD|_ _|_|NN|_ A|a|DT|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410013|252978410013|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 180600|180600|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410013|252978410013|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ ETEC|etec|NNS|_ _|_|VBP|_ 10|10|CD|_ _|_|SYM|_ 1|1|CD|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410013|252978410013|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ TW3574|tw3574|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410013|252978410013|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ TW3585|tw3585|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410014|252978410014|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E20738A|e20738a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410014|252978410014|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ PUTI|PUTI|NNP|_ _|_|SYM|_ O26|o26|CD|_ _|_|SYM|_ UMN|UMN|NNP|_ _|_|SYM|_ O26|o26|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410014|252978410014|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH450|sprh450|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410015|252978410015|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1392|e1392|NN|_ _|_|CD|_ 75|75|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410015|252978410015|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p5|p5|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410015|252978410015|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p8|p8|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410015|252978410015|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH613|sprh613|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410016|252978410016|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ D02|d02|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410016|252978410016|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ E1785|e1785|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410016|252978410016|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ ETP98068|etp98068|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410016|252978410016|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p11|p11|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410017|252978410017|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ C35776|c35776|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410017|252978410017|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1788|e1788|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410017|252978410017|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETEC|ETEC|NNP|_ _|_|NNP|_ JURUA|JURUA|NNP|_ _|_|VBD|_ 18|18|CD|_ _|_|SYM|_ 11|11|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410017|252978410017|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p9|p9|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410018|252978410018|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ARG3|arg3|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410018|252978410018|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1792|e1792|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410018|252978410018|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ MG1655|mg1655|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410018|252978410018|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH21|sprh21|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410019|252978410019|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1786|e1786|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410019|252978410019|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS0115A|ws0115a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410020|252978410020|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 179550|179550|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410020|252978410020|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE046|bce046|NN|_ _|_|CD|_ DS2|ds2|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410020|252978410020|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE046|bce046|NN|_ _|_|CD|_ DS7|ds7|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410020|252978410020|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98114|etp98114|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410021|252978410021|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 1080200|1080200|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410021|252978410021|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE008|bce008|NN|_ _|_|CD|_ MS1|ms1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410021|252978410021|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE054|bce054|NN|_ _|_|CD|_ MS24|ms24|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410021|252978410021|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 046|046|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410022|252978410022|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE062|bce062|NN|_ _|_|CD|_ DS2|ds2|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410022|252978410022|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE069|bce069|NN|_ _|_|CD|_ DS2|ds2|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410022|252978410022|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ ETP98038|etp98038|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410022|252978410022|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98042|etp98042|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410023|252978410023|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 173150|173150|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410023|252978410023|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 174750|174750|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410023|252978410023|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 178850|178850|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410023|252978410023|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ ETP98115|etp98115|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410024|252978410024|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE018|bce018|NN|_ _|_|CD|_ DS6|ds6|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410024|252978410024|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE019|bce019|NN|_ _|_|CD|_ MS16|ms16|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410024|252978410024|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE046|bce046|NN|_ _|_|CD|_ MS16|ms16|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410024|252978410024|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE069|bce069|NN|_ _|_|CD|_ MS15|ms15|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410025|252978410025|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE007|bce007|NN|_ _|_|CD|_ MS11|ms11|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410025|252978410025|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE039|bce039|NN|_ _|_|CD|_ MS13|ms13|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410025|252978410025|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ C35959|c35959|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410025|252978410025|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 050|050|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410026|252978410026|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E24377A|e24377a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410026|252978410026|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH|sprh|NN|_ _|_|NN|_ 418|418|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410026|252978410026|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS1896A|ws1896a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410026|252978410026|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS2068A|ws2068a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410027|252978410027|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ LSN03|lsn03|NN|_ _|_|SYM|_ 016011|016011|CD|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410027|252978410027|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH|sprh|NN|_ _|_|NN|_ 414|414|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410027|252978410027|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH|sprh|NN|_ _|_|NN|_ 420|420|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410027|252978410027|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ ETEC20|etec20|NN|_ _|_|SYM|_ 10|10|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410028|252978410028|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98073|etp98073|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410028|252978410028|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ TW3439|tw3439|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410028|252978410028|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ TW3576|tw3576|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410028|252978410028|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS3080A|ws3080a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410029|252978410029|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH|sprh|NN|_ _|_|NN|_ 403|403|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410029|252978410029|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH|sprh|NN|_ _|_|NN|_ 443|443|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410029|252978410029|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH|sprh|NN|_ _|_|NN|_ 604|604|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410029|252978410029|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH|sprh|NN|_ _|_|NN|_ 606|606|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410030|252978410030|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ C36255|c36255|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410030|252978410030|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 008|008|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410030|252978410030|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98105|etp98105|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410030|252978410030|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ ETP98066|etp98066|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410031|252978410031|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE054|bce054|NN|_ _|_|CD|_ DS4|ds4|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410031|252978410031|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE068|bce068|NN|_ _|_|CD|_ MS10|ms10|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410031|252978410031|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE068|bce068|NN|_ _|_|CD|_ MS23.mev.refIsIB.out|ms23.mev.refisib.out|NN|_
252978410031|252978410031|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 015|015|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410032|252978410032|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE011|bce011|NN|_ _|_|CD|_ DS3|ds3|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410032|252978410032|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE049|bce049|NN|_ _|_|CD|_ DS3|ds3|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410032|252978410032|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE062|bce062|NN|_ _|_|CD|_ MS24|ms24|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410032|252978410032|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE066|bce066|NN|_ _|_|CD|_ DS5|ds5|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410033|252978410033|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE035|bce035|NN|_ _|_|CD|_ DS6|ds6|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410033|252978410033|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ C35209|c35209|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410033|252978410033|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP|etp|NN|_ _|_|SYM|_ 98004|98004|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410033|252978410033|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98056|etp98056|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410034|252978410034|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE005|bce005|NN|_ _|_|CD|_ MS23|ms23|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410034|252978410034|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ BCE061|bce061|NN|_ _|_|CD|_ DS1|ds1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410034|252978410034|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 038|038|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410034|252978410034|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98053|etp98053|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410035|252978410035|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ BCE055|bce055|NN|_ _|_|CD|_ DS1|ds1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410035|252978410035|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 016|016|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410035|252978410035|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 020|020|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410035|252978410035|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 039|039|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410058|252978410058|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 178900|178900|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410058|252978410058|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 179100|179100|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410058|252978410058|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 009|009|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410058|252978410058|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 010|010|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410059|252978410059|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ 532|532|CD|_ _|_|NN|_ WS6866B1|ws6866b1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410059|252978410059|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 047|047|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410059|252978410059|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98097|etp98097|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410059|252978410059|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98112|etp98112|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410060|252978410060|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ARG2|arg2|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410060|252978410060|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ C35134|c35134|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410060|252978410060|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1791|e1791|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410060|252978410060|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ WS3596|ws3596|NN|_ _|_|CD|_ A4|a4|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410061|252978410061|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ COCAR07|cocar07|CD|_ _|_|SYM|_ 40|40|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410061|252978410061|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ COSIN07|cosin07|CD|_ _|_|SYM|_ 88|88|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410061|252978410061|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ COSIN07|cosin07|CD|_ _|_|SYM|_ 92|92|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410062|252978410062|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ DS168|ds168|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410062|252978410062|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ PE360|pe360|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410062|252978410062|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS4087|ws4087|NN|_ _|_|CD|_ A1|a1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410062|252978410062|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ WS7179|ws7179|NN|_ _|_|CD|_ A2|a2|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410063|252978410063|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ B7A|b7a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410063|252978410063|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ COSIN07|cosin07|CD|_ _|_|SYM|_ 14|14|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410063|252978410063|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH372|sprh372|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410063|252978410063|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ TW3452|tw3452|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410064|252978410064|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1789|e1789|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410064|252978410064|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E1790|e1790|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410064|252978410064|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ HS|hs|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410064|252978410064|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH609|sprh609|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410065|252978410065|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ 350C1A|350c1a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410065|252978410065|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E2528|e2528|NN|_ _|_|CD|_ C1|c1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410065|252978410065|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E8775|e8775|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410065|252978410065|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ M424|m424|NN|_ _|_|CD|_ C1|c1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410066|252978410066|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 2230|2230|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410066|252978410066|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|CD|_ P|p|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410066|252978410066|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS1933D|ws1933d|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410066|252978410066|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS6582|ws6582|NN|_ _|_|CD|_ A1|a1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410067|252978410067|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ B2C|b2c|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410067|252978410067|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ ETEC|etec|NNS|_ _|_|VBP|_ 8|8|CD|_ _|_|SYM|_ 11|11|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410067|252978410067|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ F5656|f5656|NN|_ _|_|CD|_ C1|c1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410067|252978410067|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS7162|ws7162|NN|_ _|_|CD|_ A1|a1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410068|252978410068|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ CFT073|cft073|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410068|252978410068|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p|p|NN|_ _|_|SYM|_ 10|10|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410068|252978410068|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ M408C1|m408c1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410068|252978410068|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS3294A|ws3294a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410069|252978410069|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ 278485|278485|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410069|252978410069|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH25|sprh25|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410069|252978410069|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH421|sprh421|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410069|252978410069|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH610|sprh610|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410070|252978410070|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p7|p7|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410070|252978410070|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ NR|nr|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410070|252978410070|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH20|sprh20|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410070|252978410070|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH612|sprh612|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410071|252978410071|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ 292|292|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410071|252978410071|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ COCAR07|cocar07|NN|_ _|_|NN|_ 043|043|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410071|252978410071|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ COSIN07|cosin07|CD|_ _|_|SYM|_ 61|61|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410071|252978410071|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ O157|o157|NN|_ _|_|CD|_ h7|h7|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410072|252978410072|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ COSIN07|cosin07|CD|_ _|_|SYM|_ 36|36|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410072|252978410072|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ICDDR|icddr|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ p6|p6|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410072|252978410072|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ O63|o63|NN|_ _|_|CD|_ nm|nm|NN|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410072|252978410072|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH605|sprh605|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410073|252978410073|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ 214|214|CD|_ _|_|NN|_ 4|4|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410073|252978410073|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ E7476A|e7476a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410073|252978410073|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ WS1896|ws1896|NN|_ _|_|CD|_ A1|a1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410073|252978410073|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS2173A|ws2173a|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410075|252978410075|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 011|011|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410075|252978410075|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 035|035|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410075|252978410075|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ O78|o78|CD|_ _|_|CD|_ h11|h11|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410075|252978410075|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ sPRH445|sprh445|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410076|252978410076|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 178200|178200|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410076|252978410076|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ C35213|c35213|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410076|252978410076|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ C35605|c35605|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410076|252978410076|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP98109|etp98109|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410077|252978410077|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|SYM|_ 174900|174900|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410077|252978410077|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ C34666|c34666|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410077|252978410077|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 002|002|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410077|252978410077|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ ETP05|etp05|NN|_ _|_|NN|_ 003|003|CD|_ _|_|SYM|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410078|252978410078|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410078|252978410078|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS2741|ws2741|NN|_ _|_|CD|_ A1|a1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410078|252978410078|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS4264|ws4264|NN|_ _|_|CD|_ A1|a1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
252978410078|252978410078|CD|_ _|_|NN|_ B7A|b7a|NN|_ _|_|CD|_ CY5|cy5|NN|_ _|_|CD|_ WS5874|ws5874|NN|_ _|_|CD|_ A1|a1|NN|_ _|_|CD|_ CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN|_
2|2|CD|_ .|.|.|_ Use|use|NN|_ TM4|tm4|NN|_ suite|suite|NN|_ software|software|NN|_ ExpressConverter|expressconverter|NN|_ to|to|TO|_ modify|modify|VB|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ file|file|NN|_ into|into|IN|_ *|*|NN|_ .|.|.|_ mev|mev|NN|_ .|.|.|_
3a|3a|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ If|if|IN|_ both|both|DT|_ channels|channel|NNS|_ -LRB-|-lrb-|-LRB-|_ QUERY|query|NN|_ _|_|CD|_ MEDIAN|MEDIAN|NNP|_ _|_|CD|_ INTENSITY|intensity|NN|_ and|and|CC|_ REF|ref|NN|_ _|_|CD|_ MEDIAN|MEDIAN|NNP|_ _|_|CD|_ INTENSITY|intensity|NN|_ -RRB-|-rrb-|-RRB-|_ are|be|VBP|_ zero|zero|CD|_ ,|,|,|_ assign|assign|VBP|_ the|the|DT|_ value|value|NN|_ null|null|NN|_ .|.|.|_
3b|3b|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ If|if|IN|_ one|one|CD|_ channel|channel|NN|_ is|be|VBZ|_ zero|zero|CD|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ is|be|VBZ|_ not|not|RB|_ zero|zero|CD|_ ,|,|,|_ substitute|substitute|VB|_ the|the|DT|_ zero|zero|CD|_ with|with|IN|_ one|one|CD|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ ,|,|,|_ assign|assign|VB|_ the|the|DT|_ log2|log2|NN|_ ratio|ratio|NN|_ of|of|IN|_ QUERY|QUERY|NNP|_ _|_|NNP|_ MEDIAN|MEDIAN|NNP|_ _|_|SYM|_ INTENSITY|intensity|NN|_
3|3|CD|_ .|.|.|_ Calculate|calculate|VB|_ the|the|DT|_ value|value|NN|_ of|of|IN|_ log2|log2|NN|_ ratio|ratio|NN|_ -LRB-|-lrb-|-LRB-|_ Reference|Reference|NNP|_
3c|3c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ If|if|IN|_ neither|neither|DT|_ channel|channel|NN|_ is|be|VBZ|_ zero|zero|CD|_ ,|,|,|_ assign|assign|VB|_ the|the|DT|_ log2|log2|NN|_ ratio|ratio|NN|_ of|of|IN|_ QUERY|QUERY|NNP|_ _|_|NNP|_ MEDIAN|MEDIAN|NNP|_ _|_|SYM|_ INTENSITY|intensity|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celcius|celcius|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ DNA|dna|NN|_ purified|purify|VBN|_ from|from|IN|_ wild|wild|JJ|_ type|type|NN|_ bacteri|bacteri|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ purified|purify|VBN|_ from|from|IN|_ wild|wild|JJ|_ type|type|NN|_ bacteria|bacterium|NNS|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ lysozyme|lysozyme|NN|_ and|and|CC|_ proteinase|proteinase|NN|_ K|k|NN|_ treatment|treatment|NN|_ .|.|.|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ lysozyme|lysozyme|NN|_ and|and|CC|_ proteinase|proteinase|NN|_ K|k|NN|_ treatment|treatment|NN|_ .|.|.|_
mev|mev|NN|_ data|datum|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ feature|feature|NN|_ extraction|extraction|NN|_ file|file|NN|_ used|use|VBN|_ ,|,|,|_ no|no|DT|_ further|further|JJ|_ normalization|normalization|NN|_ needed|need|VBD|_
None|None|NNP|_
Procedures|procedure|NNS|_ to|to|TO|_ calculate|calculate|VB|_ the|the|DT|_ value|value|NN|_ of|of|IN|_ log2|log2|NN|_ ratio|ratio|NN|_ :|:|:|_
strain|strain|NN|_ :|:|:|_ 173150|173150|CD|_
strain|strain|NN|_ :|:|:|_ 174750|174750|CD|_
strain|strain|NN|_ :|:|:|_ 174900|174900|CD|_
strain|strain|NN|_ :|:|:|_ 178200|178200|CD|_
strain|strain|NN|_ :|:|:|_ 178850|178850|CD|_
strain|strain|NN|_ :|:|:|_ 178900|178900|CD|_
strain|strain|NN|_ :|:|:|_ 179100|179100|CD|_
strain|strain|NN|_ :|:|:|_ 179550|179550|CD|_
strain|strain|NN|_ :|:|:|_ 180050|180050|CD|_
strain|strain|NN|_ :|:|:|_ 180200|180200|CD|_
strain|strain|NN|_ :|:|:|_ 180600|180600|CD|_
strain|strain|NN|_ :|:|:|_ 2-1|2-1|CD|_
strain|strain|NN|_ :|:|:|_ 214-4|214-4|CD|_
strain|strain|NN|_ :|:|:|_ 2230|2230|CD|_
strain|strain|NN|_ :|:|:|_ 229-1|229-1|CD|_
strain|strain|NN|_ :|:|:|_ 278485-1|278485-1|CD|_
strain|strain|NN|_ :|:|:|_ 292-1|292-1|CD|_
strain|strain|NN|_ :|:|:|_ 350C1A|350c1a|NN|_
strain|strain|NN|_ :|:|:|_ 42-1|42-1|CD|_ C1|c1|NN|_
strain|strain|NN|_ :|:|:|_ ARG-2|arg-2|NN|_
strain|strain|NN|_ :|:|:|_ ARG-3|arg-3|NN|_
strain|strain|NN|_ :|:|:|_ B2C|b2c|NN|_
strain|strain|NN|_ :|:|:|_ B7A|b7a|NN|_
strain|strain|NN|_ :|:|:|_ BCE001|bce001|NN|_ ,|,|,|_ MS16|ms16|NN|_
strain|strain|NN|_ :|:|:|_ BCE002|bce002|NN|_ ,|,|,|_ MS12|ms12|NN|_
strain|strain|NN|_ :|:|:|_ BCE003|bce003|NN|_ ,|,|,|_ DS5|ds5|NN|_
strain|strain|NN|_ :|:|:|_ BCE005|bce005|NN|_ ,|,|,|_ MS23|ms23|NN|_
strain|strain|NN|_ :|:|:|_ BCE007|bce007|NN|_
strain|strain|NN|_ :|:|:|_ BCE007|bce007|NN|_ ,|,|,|_ MS11|ms11|NN|_
strain|strain|NN|_ :|:|:|_ BCE008|bce008|NN|_ _|_|CD|_ MS1|ms1|NN|_
strain|strain|NN|_ :|:|:|_ BCE008|bce008|NN|_ ,|,|,|_ MS13|ms13|NN|_
strain|strain|NN|_ :|:|:|_ BCE011|bce011|NN|_ ,|,|,|_ DS3|ds3|NN|_
strain|strain|NN|_ :|:|:|_ BCE013|bce013|NN|_ ,|,|,|_ DS1|ds1|NN|_
strain|strain|NN|_ :|:|:|_ BCE018|bce018|NN|_ ,|,|,|_ DS6|ds6|NN|_
strain|strain|NN|_ :|:|:|_ BCE019|bce019|NN|_ ,|,|,|_ MS16|ms16|NN|_
strain|strain|NN|_ :|:|:|_ BCE021|bce021|NN|_ ,|,|,|_ DS7|ds7|NN|_
strain|strain|NN|_ :|:|:|_ BCE022DS6|bce022ds6|NN|_
strain|strain|NN|_ :|:|:|_ BCE035|bce035|NN|_ ,|,|,|_ DS6|ds6|NN|_
strain|strain|NN|_ :|:|:|_ BCE035|bce035|NN|_ ,|,|,|_ MS8|ms8|NN|_
strain|strain|NN|_ :|:|:|_ BCE039|bce039|NN|_ ,|,|,|_ DS2|ds2|NN|_
strain|strain|NN|_ :|:|:|_ BCE039|bce039|NN|_ ,|,|,|_ MS13|ms13|NN|_
strain|strain|NN|_ :|:|:|_ BCE041|bce041|NN|_ ,|,|,|_ MS11|ms11|NN|_
strain|strain|NN|_ :|:|:|_ BCE046|bce046|NN|_ ,|,|,|_ DS2|ds2|NN|_
strain|strain|NN|_ :|:|:|_ BCE046|bce046|NN|_ ,|,|,|_ DS7|ds7|NN|_
strain|strain|NN|_ :|:|:|_ BCE046|bce046|NN|_ ,|,|,|_ MS16|ms16|NN|_
strain|strain|NN|_ :|:|:|_ BCE049|bce049|NN|_ ,|,|,|_ DS3|ds3|NN|_
strain|strain|NN|_ :|:|:|_ BCE049|bce049|NN|_ ,|,|,|_ MS9|ms9|NN|_
strain|strain|NN|_ :|:|:|_ BCE054|bce054|NN|_ ,|,|,|_ DS4|ds4|NN|_
strain|strain|NN|_ :|:|:|_ BCE054|bce054|NN|_ ,|,|,|_ MS24|ms24|NN|_
strain|strain|NN|_ :|:|:|_ BCE055|bce055|NN|_ ,|,|,|_ DS1|ds1|NN|_
strain|strain|NN|_ :|:|:|_ BCE058|bce058|NN|_ ,|,|,|_ MS13|ms13|NN|_
strain|strain|NN|_ :|:|:|_ BCE061|bce061|NN|_ ,|,|,|_ DS1|ds1|NN|_
strain|strain|NN|_ :|:|:|_ BCE062|bce062|NN|_ ,|,|,|_ DS2|ds2|NN|_
strain|strain|NN|_ :|:|:|_ BCE062|bce062|NN|_ ,|,|,|_ MS24|ms24|NN|_
strain|strain|NN|_ :|:|:|_ BCE063|bce063|NN|_ ,|,|,|_ DS4|ds4|NN|_
strain|strain|NN|_ :|:|:|_ BCE063|bce063|NN|_ ,|,|,|_ MS14|ms14|NN|_
strain|strain|NN|_ :|:|:|_ BCE066|bce066|NN|_ ,|,|,|_ DS5|ds5|NN|_
strain|strain|NN|_ :|:|:|_ BCE068|bce068|NN|_ ,|,|,|_ MS10|ms10|NN|_
strain|strain|NN|_ :|:|:|_ BCE068|bce068|NN|_ ,|,|,|_ MS23|ms23|NN|_
strain|strain|NN|_ :|:|:|_ BCE069|bce069|NN|_ ,|,|,|_ DS2|ds2|NN|_
strain|strain|NN|_ :|:|:|_ BCE069|bce069|NN|_ ,|,|,|_ MS15|ms15|NN|_
strain|strain|NN|_ :|:|:|_ BCE069|bce069|NN|_ ,|,|,|_ MS9|ms9|NN|_
strain|strain|NN|_ :|:|:|_ BCE129|bce129|NN|_ ,|,|,|_ DS2|ds2|NN|_
strain|strain|NN|_ :|:|:|_ C-34666|c-34666|NN|_
strain|strain|NN|_ :|:|:|_ C-35134|c-35134|NN|_
strain|strain|NN|_ :|:|:|_ C-35209|c-35209|NN|_
strain|strain|NN|_ :|:|:|_ C-35213|c-35213|NN|_
strain|strain|NN|_ :|:|:|_ C-35605|c-35605|NN|_
strain|strain|NN|_ :|:|:|_ C-35662|c-35662|NN|_
strain|strain|NN|_ :|:|:|_ C-35776|c-35776|NN|_
strain|strain|NN|_ :|:|:|_ C-35959|c-35959|NN|_
strain|strain|NN|_ :|:|:|_ C-36255|c-36255|NN|_
strain|strain|NN|_ :|:|:|_ CFT073|cft073|NN|_
strain|strain|NN|_ :|:|:|_ cocar|cocar|NN|_ 07-043|07-043|CD|_
strain|strain|NN|_ :|:|:|_ cocar|cocar|NN|_ 07-40|07-40|CD|_
strain|strain|NN|_ :|:|:|_ cosin|cosin|NN|_ 07-14|07-14|CD|_
strain|strain|NN|_ :|:|:|_ cosin|cosin|NN|_ 07-36|07-36|CD|_
strain|strain|NN|_ :|:|:|_ cosin|cosin|NN|_ 07-61|07-61|CD|_
strain|strain|NN|_ :|:|:|_ cosin|cosin|NN|_ 07-88|07-88|CD|_
strain|strain|NN|_ :|:|:|_ cosin|cosin|NN|_ 07-92|07-92|CD|_
strain|strain|NN|_ :|:|:|_ D02-2|d02-2|NN|_
strain|strain|NN|_ :|:|:|_ DS168-1|ds168-1|NN|_
strain|strain|NN|_ :|:|:|_ DS26-1|ds26-1|NN|_
strain|strain|NN|_ :|:|:|_ E1392|e1392|NN|_
strain|strain|NN|_ :|:|:|_ E1777|e1777|NN|_
strain|strain|NN|_ :|:|:|_ E1785|e1785|NN|_
strain|strain|NN|_ :|:|:|_ E1786|e1786|NN|_
strain|strain|NN|_ :|:|:|_ E1787|e1787|NN|_
strain|strain|NN|_ :|:|:|_ E1788|e1788|NN|_
strain|strain|NN|_ :|:|:|_ E1789|e1789|NN|_
strain|strain|NN|_ :|:|:|_ E1790|e1790|NN|_
strain|strain|NN|_ :|:|:|_ E1791|e1791|NN|_
strain|strain|NN|_ :|:|:|_ E1792|e1792|NN|_
strain|strain|NN|_ :|:|:|_ E20738A|e20738a|NN|_
strain|strain|NN|_ :|:|:|_ E24377A|e24377a|NN|_
strain|strain|NN|_ :|:|:|_ E2528C1|e2528c1|NN|_
strain|strain|NN|_ :|:|:|_ E7473|e7473|NN|_
strain|strain|NN|_ :|:|:|_ E7476A|e7476a|NN|_
strain|strain|NN|_ :|:|:|_ E8775|e8775|NN|_
strain|strain|NN|_ :|:|:|_ E9034A|e9034a|NN|_
strain|strain|NN|_ :|:|:|_ ETEC|ETEC|NNP|_ 10|10|CD|_
strain|strain|NN|_ :|:|:|_ ETEC|ETEC|NNP|_ 18|18|CD|_
strain|strain|NN|_ :|:|:|_ ETEC|ETEC|NNP|_ 20|20|CD|_
strain|strain|NN|_ :|:|:|_ ETEC|etec|NNS|_ 8|8|CD|_
strain|strain|NN|_ :|:|:|_ ETEC|ETEC|NNP|_ Jurua|Jurua|NNP|_
strain|strain|NN|_ :|:|:|_ ETP05-002|etp05-002|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-003|etp05-003|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-007|etp05-007|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-008|etp05-008|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-009|etp05-009|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-010|etp05-010|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-011|etp05-011|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-012|etp05-012|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-015|etp05-015|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-016|etp05-016|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-017|etp05-017|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-019|etp05-019|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-020|etp05-020|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-026|etp05-026|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-035|etp05-035|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-038|etp05-038|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-039|etp05-039|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-044|etp05-044|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-046|etp05-046|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-047|etp05-047|NN|_
strain|strain|NN|_ :|:|:|_ ETP05-050|etp05-050|NN|_
strain|strain|NN|_ :|:|:|_ ETP98004|etp98004|NN|_
strain|strain|NN|_ :|:|:|_ ETP98015|etp98015|NN|_
strain|strain|NN|_ :|:|:|_ ETP98028|etp98028|NN|_
strain|strain|NN|_ :|:|:|_ ETP98038|etp98038|NN|_
strain|strain|NN|_ :|:|:|_ ETP98042|etp98042|NN|_
strain|strain|NN|_ :|:|:|_ ETP98053|etp98053|NN|_
strain|strain|NN|_ :|:|:|_ ETP98056|etp98056|NN|_
strain|strain|NN|_ :|:|:|_ ETP98061|etp98061|NN|_
strain|strain|NN|_ :|:|:|_ ETP98062|etp98062|NN|_
strain|strain|NN|_ :|:|:|_ ETP98066|etp98066|NN|_
strain|strain|NN|_ :|:|:|_ ETP98068|etp98068|NN|_
strain|strain|NN|_ :|:|:|_ ETP98073|etp98073|NN|_
strain|strain|NN|_ :|:|:|_ ETP98097|etp98097|NN|_
strain|strain|NN|_ :|:|:|_ ETP98103|etp98103|NN|_
strain|strain|NN|_ :|:|:|_ ETP98105|etp98105|NN|_
strain|strain|NN|_ :|:|:|_ ETP98109|etp98109|NN|_
strain|strain|NN|_ :|:|:|_ ETP98111|etp98111|NN|_
strain|strain|NN|_ :|:|:|_ ETP98112|etp98112|NN|_
strain|strain|NN|_ :|:|:|_ ETP98114|etp98114|NN|_
strain|strain|NN|_ :|:|:|_ ETP98115|etp98115|NN|_
strain|strain|NN|_ :|:|:|_ F5656-C1|f5656-c1|NN|_
strain|strain|NN|_ :|:|:|_ F595C|f595c|NN|_
strain|strain|NN|_ :|:|:|_ HS|hs|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p1|p1|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p10|p10|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p11|p11|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p12|p12|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p13|p13|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p2|p2|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p4|p4|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p5|p5|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|CD|_ p6|p6|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|NN|_ p7|p7|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|CD|_ p8|p8|NN|_
strain|strain|NN|_ :|:|:|_ ICDDR|icddr|NN|_ ,|,|,|_ B|b|NN|_ _|_|CD|_ p9|p9|NN|_
strain|strain|NN|_ :|:|:|_ LSN02-012560|lsn02-012560|NN|_
strain|strain|NN|_ :|:|:|_ LSN03-016011|lsn03-016011|NN|_
strain|strain|NN|_ :|:|:|_ M408C1|m408c1|NN|_
strain|strain|NN|_ :|:|:|_ M424C1|m424c1|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ NN-34-1-3|nn-34-1-3|NN|_
strain|strain|NN|_ :|:|:|_ NR-12|nr-12|NN|_
strain|strain|NN|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ h7|h7|NN|_
strain|strain|NN|_ :|:|:|_ O63|o63|NN|_ :|:|:|_ nm|nm|NN|_
strain|strain|NN|_ :|:|:|_ O78|o78|NN|_ :|:|:|_ h11|h11|NN|_
strain|strain|NN|_ :|:|:|_ PE360|pe360|NN|_
strain|strain|NN|_ :|:|:|_ PUTI|puti|NN|_ O26|o26|NN|_ UMN|umn|NN|_ O26|o26|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-20|sprh-20|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-21|sprh-21|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-25|sprh-25|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-372|sprh-372|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-403|sprh-403|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-414|sprh-414|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-418|sprh-418|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-420|sprh-420|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-421|sprh-421|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-443|sprh-443|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-445|sprh-445|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-450|sprh-450|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-604|sprh-604|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-605|sprh-605|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-606|sprh-606|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-609|sprh-609|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-610|sprh-610|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-612|sprh-612|NN|_
strain|strain|NN|_ :|:|:|_ sPRH-613|sprh-613|NN|_
strain|strain|NN|_ :|:|:|_ TW03439|tw03439|NN|_
strain|strain|NN|_ :|:|:|_ TW03452|tw03452|NN|_
strain|strain|NN|_ :|:|:|_ TW03574|tw03574|NN|_
strain|strain|NN|_ :|:|:|_ TW03576|tw03576|NN|_
strain|strain|NN|_ :|:|:|_ TW03585|tw03585|NN|_
strain|strain|NN|_ :|:|:|_ TW03741|tw03741|NN|_
strain|strain|NN|_ :|:|:|_ WS|ws|NN|_ 0115A|0115a|NN|_
strain|strain|NN|_ :|:|:|_ WS1896A|ws1896a|NN|_
strain|strain|NN|_ :|:|:|_ WS1896|ws1896|NN|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS|ws|NN|_ 1933D|1933d|NN|_
strain|strain|NN|_ :|:|:|_ WS2068A|ws2068a|NN|_
strain|strain|NN|_ :|:|:|_ WS|ws|NN|_ 2173A|2173a|NN|_
strain|strain|NN|_ :|:|:|_ WS2741|ws2741|NN|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS3080A|ws3080a|NN|_
strain|strain|NN|_ :|:|:|_ WS|ws|NN|_ 3294A|3294a|NN|_
strain|strain|NN|_ :|:|:|_ WS|w|NNS|_ 3572|3572|CD|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS|w|NNS|_ 3596|3596|CD|_ A-4|a-4|NN|_
strain|strain|NN|_ :|:|:|_ WS4087|ws4087|NN|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS4264|ws4264|NN|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS5874|ws5874|NN|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS6582|ws6582|NN|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS|ws|NN|_ 6866B-1|6866b-1|NN|_
strain|strain|NN|_ :|:|:|_ WS|w|NNS|_ 7162|7162|CD|_ A-1|a-1|NN|_
strain|strain|NN|_ :|:|:|_ WS7179|ws7179|NN|_ A-2|a-2|NN|_
CFT073|cft073|NN|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ after|after|IN|_ 5|5|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ .|.|.|_
CFT073|cft073|NN|_ in|in|IN|_ LB+PAC|lb+pac|NN|_ s|s|NNS|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ µg|µg|NN|_
CFT073|cft073|NN|_ _|_|CD|_ LB+PAC|lb+pac|NN|_ s|s|NNS|_ _|_|VBP|_ rep1|rep1|NN|_
CFT073|cft073|NN|_ _|_|CD|_ LB+PAC|lb+pac|NN|_ s|s|NNS|_ _|_|VBP|_ rep2|rep2|NN|_
CFT073|cft073|NN|_ _|_|CD|_ LB+PAC|lb+pac|NN|_ s|s|NNS|_ _|_|VBP|_ rep3|rep3|NN|_
CFT073|cft073|NN|_ _|_|CD|_ LB|lb|NN|_ _|_|CD|_ rep1|rep1|NN|_
CFT073|cft073|NN|_ _|_|CD|_ LB|lb|NN|_ _|_|CD|_ rep2|rep2|NN|_
CFT073|cft073|NN|_ _|_|CD|_ LB|lb|NN|_ _|_|CD|_ rep3|rep3|NN|_
Cultures|culture|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ CFT073|cft073|NN|_ were|be|VBD|_ maintained|maintain|VBN|_ at|at|IN|_ --|--|:|_ 80ºC|80ºc|NN|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ broth|broth|NN|_ with|with|IN|_ 15|15|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ streaked|streak|VBN|_ onto|onto|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ and|and|CC|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 150|150|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ in|in|IN|_ a|a|DT|_ 500|500|CD|_ mL|ml|NN|_ baffled|baffle|VBN|_ flask|flask|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ inoculated|inoculate|VBN|_ flasks|flask|NNS|_ contained|contain|VBD|_ LB|lb|NN|MED broth|broth|NN|MED alone|alone|RB|_ -LRB-|-lrb-|-LRB-|_ controls|control|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ three|three|CD|_ inoculated|inoculate|VBN|_ flasks|flask|NNS|_ were|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ cranberry|cranberry|NN|_ derived|derive|VBN|_ PAC|PAC|NNP|_ extract|extract|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ µg|µg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ LB|lb|NN|MED broth|broth|NN|MED alone|alone|RB|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ LB|lb|NN|MED broth|broth|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ cranberry|cranberry|NN|_ PACs|pac|NNS|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ µg|µg|NN|_
One|one|CD|_ volume|volume|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ two|two|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ on-column|on-column|JJ|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ I.|i.|NN|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ instructions|instruction|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ CFT073|cft073|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ FlexArray|FlexArray|NNP|_ 1.4.1|1.4.1|CD|_ software|software|NN|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Comparison|comparison|NN|_ cya|cya|NN|_ mutant|mutant|NN|_ with|with|IN|_ wt|wt|JJ|_ under|under|IN|_ glucose-limited|glucose-limited|JJ|_ conditions|condition|NNS|_ -LRB-|-lrb-|-LRB-|_ replicate|replicate|VB|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
Comparison|comparison|NN|_ cya|cya|NN|_ mutant|mutant|NN|_ with|with|IN|_ wt|wt|JJ|_ under|under|IN|_ glucose-limited|glucose-limited|JJ|_ conditions|condition|NNS|_ -LRB-|-lrb-|-LRB-|_ replicate|replicate|VB|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
Comparison|comparison|NN|_ cya|cya|NN|_ mutant|mutant|NN|_ with|with|IN|_ wt|wt|JJ|_ under|under|IN|_ glucose-limited|glucose-limited|JJ|_ conditions|condition|NNS|_ -LRB-|-lrb-|-LRB-|_ replicate|replicate|VB|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_
Comparison|comparison|NN|_ rpoS|rpos|NN|GEN mutant|mutant|NN|_ with|with|IN|_ wt|wt|JJ|_ under|under|IN|_ glucose-limited|glucose-limited|JJ|_ conditions|condition|NNS|_ -LRB-|-lrb-|-LRB-|_ replicate|replicate|VB|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
Comparison|comparison|NN|_ rpoS|rpos|NN|GEN mutant|mutant|NN|_ with|with|IN|_ wt|wt|JJ|_ under|under|IN|_ glucose-limited|glucose-limited|JJ|_ conditions|condition|NNS|_ -LRB-|-lrb-|-LRB-|_ replicate|replicate|VB|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
Comparison|comparison|NN|_ rpoS|rpos|NN|GEN mutant|mutant|NN|_ with|with|IN|_ wt|wt|JJ|_ under|under|IN|_ glucose-limited|glucose-limited|JJ|_ conditions|condition|NNS|_ -LRB-|-lrb-|-LRB-|_ replicate|replicate|VB|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_
condition|condition|NN|_ :|:|:|_ glucose|glucose|NN|SUPP limited|limited|JJ|_
control|control|NN|_
cya|cya|NN|_ mutant|mutant|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
genotype|genotype|NN|_ :|:|:|_ cya|cya|NN|_ mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ rpoS|rpos|NN|GEN mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ wild-type|wild-type|JJ|_
rpoS|rpos|NN|GEN mutant|mutant|JJ|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ data|datum|NNS|_ provided|provide|VBN|_ are|be|VBP|_ the|the|DT|_ original|original|JJ|_ data|datum|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Jaguar|Jaguar|NNP|_ software|software|NN|_ from|from|IN|_ the|the|DT|_ microarray|microarray|NN|_ images|image|NNS|_ .|.|.|_ The|the|DT|_ VALUEs|value|NNS|_ reported|report|VBD|_ represent|represent|VBP|_ normalized|normalize|VBN|_ log10|log10|NN|_ -LRB-|-lrb-|-LRB-|_ Cy5|cy5|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ as|as|IN|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Sambrook|Sambrook|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1989|1989|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ extracted|extract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ checked|check|VBN|_ for|for|IN|_ purity|purity|NN|_ by|by|IN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ was|be|VBD|_ quantified|quantify|VBN|_ by|by|IN|_ measuring|measure|VBG|_ extinction|extinction|NN|_ spectrophotometrically|spectrophotometrically|RB|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ .|.|.|_
200µl|200µl|NN|_ of|of|IN|_ prepared|prepared|JJ|_ E.coli|e.coli|NN|_ O157|o157|NN|_ cells|cell|NNS|_ within|within|IN|_ LB|lb|NN|MED broth|broth|NN|MED is|be|VBZ|_ spreaded|spread|VBN|_ to|to|TO|_ LB|LB|NNP|_ agar|agar|NN|_ plate|plate|NN|_ ,|,|,|_ and|and|CC|_ sterilized|sterilize|VBN|_ 6|6|CD|_ mm|mm|NN|_ filtered|filter|VBD|_ paper|paper|NN|_ disk|disk|NN|_ was|be|VBD|_ placed|place|VBN|_ on|on|IN|_ the|the|DT|_ plate|plate|NN|_ tightly|tightly|RB|_ ,|,|,|_ where|where|WRB|_ E.coli|e.coli|JJ|_ O157|o157|NN|_ is|be|VBZ|_ spreaded|spread|VBN|_ .|.|.|_ Each|each|DT|_ filtered|filter|VBN|_ fractions|fraction|NNS|_ are|be|VBP|_ injected|inject|VBN|_ to|to|TO|_ each|each|DT|_ paper|paper|NN|_ disk|disk|NN|_ and|and|CC|_ Distilled|Distilled|NNP|_ water|water|NN|_ and|and|CC|_ Ampicillin|ampicillin|NN|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ negative|negative|JJ|_ -|-|:|_ and|and|CC|_ positive|positive|JJ|_ control|control|NN|_ each|each|DT|_ and|and|CC|_ then|then|RB|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_ .|.|.|_ Finally|finally|RB|_ the|the|DT|_ diameter|diameter|NN|_ of|of|IN|_ the|the|DT|_ cleared|clear|VBN|_ zone|zone|NN|_ arisen|arise|VBN|_ around|around|IN|_ the|the|DT|_ paper|paper|NN|_ disk|disk|NN|_ was|be|VBD|_ measured|measure|VBN|_ .|.|.|_
50µl|50µl|CD|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ of|of|IN|_ the|the|DT|_ cells|cell|NNS|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ Chrysanthemum|Chrysanthemum|NNP|_ herba|herba|NN|_ methyl|methyl|NN|_ chloride|chloride|NN|_ fraction|fraction|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ procedure|procedure|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protect|protect|VBP|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 5000|5000|CD|_ g|g|NN|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ harvested|harvest|VBN|_ cells|cell|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_
Data|Data|NNP|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ .|.|.|_ Robust|robust|JJ|_ Multi-array|multi-array|JJ|_ Average|average|JJ|_ -LRB-|-lrb-|-LRB-|_ RMA|rma|NN|_ -RRB-|-rrb-|-RRB-|_ normalization|normalization|NN|_ performed|perform|VBN|_ using|use|VBG|_ of|of|IN|_ signal|signal|NN|_ intensity|intensity|NN|_ spot|spot|NN|_ data|datum|NNS|_ which|which|WDT|_ obtained|obtain|VBN|_ by|by|IN|_ scanning|scanning|NN|_ process|process|NN|_ and|and|CC|_ it|it|PRP|_ is|be|VBZ|_ indicated|indicate|VBN|_ as|as|IN|_ a|a|DT|_ scatter|scatter|NN|_ plot|plot|NN|_ data|datum|NNS|_ .|.|.|_ Distribution|distribution|NN|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ which|which|WDT|_ obtained|obtain|VBD|_ result|result|NN|_ of|of|IN|_ the|the|DT|_ experiment|experiment|NN|_ is|be|VBZ|_ indicated|indicate|VBN|_ as|as|IN|_ a|a|DT|_ histogram|histogram|NN|_ .|.|.|_ Accuracy|accuracy|NN|_ of|of|IN|_ the|the|DT|_ results|result|NNS|_ of|of|IN|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ determined|determine|VBN|_ through|through|IN|_ comparison|comparison|NN|_ of|of|IN|_ the|the|DT|_ histogram|histogram|NN|_ with|with|IN|_ the|the|DT|_ scatter|scatter|NN|_ plot|plot|NN|_ data|datum|NNS|_ .|.|.|_
EDL932|edl932|NN|_ exposure|exposure|NN|_ to|to|TO|_ CL|cl|NN|_ MC|MC|NNP|_ fraction|fraction|NN|_
EDL932|edl932|NN|_ unexposed|unexposed|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
O157|o157|NN|_ _|_|CD|_ CL|cl|NN|_ MC|MC|NNP|_ fraction|fraction|NN|_ vs|vs|CC|_ control|control|NN|_
strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL|edl|NN|_ 932|932|CD|_
The|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 17|17|CD|_ hours|hour|NNS|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ plate|plate|NN|_ .|.|.|_ An|a|DT|_ isolated|isolate|VBN|_ colony|colony|NN|_ was|be|VBD|_ picked|pick|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ into|into|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterilized|sterilize|VBN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 10g|10g|CD|_ of|of|IN|_ tryptone|tryptone|NN|SUPP ,|,|,|_ 5g|5g|NN|_ of|of|IN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP and|and|CC|_ 10g|10g|NN|_ of|of|IN|_ sodium|sodium|NN|SUPP chloride|chloride|NN|SUPP per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ overnight|overnight|JJ|_ for|for|IN|_ 17|17|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_ A|a|DT|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ pre-warmed|pre-warmed|JJ|_ LB|lb|NN|MED broth|broth|NN|MED .|.|.|_ The|the|DT|_ diluted|diluted|JJ|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250rpm|250rpm|NN|_ until|until|IN|_ a|a|DT|_ final|final|JJ|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.8|0.8|CD|_ -LRB-|-lrb-|-LRB-|_ early|early|JJ|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ attained|attain|VBN|_ .|.|.|_ A|a|DT|_ further|further|JJ|_ 1:10|1:10|CD|_ dilution|dilution|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
antibody|antibody|NN|_ :|:|:|_ 9E10|9e10|NN|_ Myc|myc|NN|_ tag|tag|NN|GEN antibody|antibody|NN|_
antibody|antibody|NN|_ manufacturer|manufacturer|NN|_ :|:|:|_ Upstate|upstate|JJ|_
antibody|antibody|NN|_ :|:|:|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_
ArgR|argr|NN|TF _|_|CD|_ Arginine|arginine|NN|_ _|_|NN|_ 1|1|CD|_
ArgR|argr|NN|TF _|_|CD|_ Arginine|arginine|NN|_ _|_|NN|_ 2|2|CD|_
ArgR|argr|NN|TF _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ 1|1|CD|_
ArgR|argr|NN|TF _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ 2|2|CD|_
Cells|cell|NNS|_ at|at|IN|_ appropriate|appropriate|JJ|_ cell|cell|NN|_ density|density|NN|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ by|by|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 25|25|CD|_ min|min|NN|_ .|.|.|_ Following|follow|VBG|_ quenching|quench|VBG|_ the|the|DT|_ unused|unused|JJ|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 125|125|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ Buffered|buffer|VBN|_ Saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ washed|wash|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ composed|compose|VBN|_ of|of|IN|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ ug|ug|NN|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ ArgR-8myc|argr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ 9E10|9e10|NN|_ myc|myc|NN|_ antibody|antibody|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ ArgR-8myc|argr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ using|use|VBG|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ Lrp-8myc|lrp-8myc|JJ|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ 9E10|9e10|NN|_ myc|myc|NN|_ antibody|antibody|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ Lrp-8myc|lrp-8myc|JJ|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ using|use|VBG|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ TrpR-8myc|trpr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ 9E10|9e10|NN|_ myc|myc|NN|_ antibody|antibody|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ TrpR-8myc|trpr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ using|use|VBG|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ .|.|.|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArgR|argr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ Arginine|arginine|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArgR|argr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ Arginine|arginine|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArgR|argr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ NH4Cl|nh4cl|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArgR|argr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ NH4Cl|nh4cl|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Lrp|Lrp|NNP|TF ChIP|chip|NN|_ DNA|dna|NN|_ Leucine|leucine|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Lrp|Lrp|NNP|TF ChIP|ChIP|NNP|_ DNA|DNA|NNP|_ Leucine|leucine|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Lrp|Lrp|NNP|TF ChIP|chip|NN|_ DNA|dna|NN|_ Leucine|leucine|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Lrp|Lrp|NNP|TF ChIP|ChIP|NNP|_ DNA|DNA|NNP|_ NH4Cl|nh4cl|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Lrp|Lrp|NNP|TF ChIP|ChIP|NNP|_ DNA|DNA|NNP|_ NH4Cl|nh4cl|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Lrp|Lrp|NNP|TF ChIP|ChIP|NNP|_ DNA|DNA|NNP|_ NH4Cl|nh4cl|NN|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ harboring|harbor|VBG|_ ArgR-8myc|argr-8myc|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strains|strain|NNS|_ harboring|harbor|VBG|_ Lrp-8myc|lrp-8myc|JJ|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strains|strain|NNS|_ harboring|harbor|VBG|_ TrpR-8myc|trpr-8myc|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_
E.|E.|NNP|_ Coli|Coli|NNP|_ TrpR|trpr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ glucose|glucose|NN|SUPP
E.|E.|NNP|_ Coli|Coli|NNP|_ TrpR|trpr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ Tryptophan|tryptophan|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ ArgR-8myc|argr-8myc|NN|_
genotype|genotype|NN|_ :|:|:|_ Lrp-8myc|lrp-8myc|JJ|_
genotype|genotype|NN|_ :|:|:|_ TrpR-8myc|trpr-8myc|NN|_
Lrp|lrp|VBP|TF _|_|SYM|_ Leu|Leu|NNP|_ _|_|SYM|_ 1|1|CD|_
Lrp|Lrp|NNP|TF _|_|NNP|_ Leu|Leu|NNP|_ _|_|NNP|_ 2|2|CD|_
Lrp|Lrp|NNP|TF _|_|NNP|_ Leu|Leu|NNP|_ _|_|NNP|_ 3|3|CD|_
Lrp|Lrp|NNP|TF _|_|SYM|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ 1|1|CD|_
Lrp|Lrp|NNP|TF _|_|SYM|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ 2|2|CD|_
Lrp|Lrp|NNP|TF _|_|SYM|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ 3|3|CD|_
The|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ per|per|IN|_ channel|channel|NN|_ quantile|quantile|NN|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 19|19|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 185|185|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ IP|IP|NNP|_
treatment|treatment|NN|_ :|:|:|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_
TrpR|trpr|NN|TF _|_|NN|_ glucose|glucose|NN|SUPP
TrpR|trpr|NN|TF _|_|CD|_ Trp|trp|NN|_
agent|agent|NN|_ :|:|:|_ H2O|h2o|NN|_
agent|agent|NN|_ :|:|:|_ ZnSO4|znso4|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 0|0|CD|_ mins|min|NNS|_
E.|e.|FW|_ coli|coli|FW|_ 10|10|CD|_ mins|min|NNS|_
E.|E.|NNP|_ coli|coli|NN|_ 2.5|2.5|CD|_ mins|min|NNS|_
E.|e.|FW|_ coli|coli|FW|_ 30|30|CD|_ mins|min|NNS|_
E.|E.|NNP|_ coli|coli|NN|_ 7|7|CD|_ mins|min|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Spots|spot|NNS|_ automatically|automatically|RB|_ flagged|flag|VBD|_ as|as|IN|_ bad|bad|JJ|_ ,|,|,|_ negative|negative|JJ|_ or|or|CC|_ poor|poor|JJ|_ in|in|IN|_ the|the|DT|_ Imagene|imagene|NN|_ software|software|NN|_ were|be|VBD|_ removed|remove|VBN|_ before|before|IN|_ the|the|DT|_ statistical|statistical|JJ|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ GeneSight|GeneSight|NNP|_ .|.|.|_ The|the|DT|_ mean|mean|NN|_ values|value|NNS|_ from|from|IN|_ each|each|DT|_ channel|channel|NN|_ were|be|VBD|_ log2|log2|NN|_ transformed|transform|VBN|_ and|and|CC|_ normalised|normalise|VBN|_ using|use|VBG|_ the|the|DT|_ Lowess|lowess|NN|_ method|method|NN|_ to|to|TO|_ remove|remove|VB|_ intensity-dependent|intensity-dependent|JJ|_ effects|effect|NNS|_ in|in|IN|_ the|the|DT|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ ratios|ratio|NNS|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ .|.|.|_ The|the|DT|_ Cy3|cy3|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ average|average|JJ|_ signal|signal|NN|_ intensity|intensity|NN|_ and|and|CC|_ local|local|JJ|_ background|background|NN|_ correction|correction|NN|_ were|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ software|software|NN|_ package|package|NN|_ from|from|IN|_ Biodiscovery|Biodiscovery|NNP|_ ,|,|,|_ Inc|Inc|NNP|_ -LRB-|-lrb-|-LRB-|_ Imagene|Imagene|NNP|_ ,|,|,|_ version|version|NN|_ 4.0|4.0|CD|_ and|and|CC|_ GeneSight|GeneSight|NNP|_ ,|,|,|_ version|version|NN|_ 3.5|3.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ mins|min|NNS|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ mins|min|NNS|_
time|time|NN|_ :|:|:|_ 2.5|2.5|CD|_ mins|min|NNS|_
time|time|NN|_ :|:|:|_ 30|30|CD|_ mins|min|NNS|_
time|time|NN|_ :|:|:|_ 7|7|CD|_ mins|min|NNS|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ 0A1|0a1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 0A2|0a2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 0B1|0b1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 0B2|0b2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 10A1|10a1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 10A2|10a2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 10A3|10a3|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 10B1|10b1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 10B2|10b2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 2.5|2.5|CD|_ A1|a1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 2.5|2.5|CD|_ A2|a2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 2.5|2.5|CD|_ B1|b1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 2.5|2.5|CD|_ B2|b2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 30A1|30a1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 30A2|30a2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 30B1|30b1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 30B2|30b2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 7A1|7a1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 7A2|7a2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 7B1|7b1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ profiling|profiling|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism during|during|IN|_ a|a|DT|_ transition|transition|NN|_ from|from|IN|_ zinc|zinc|NN|_ starvation|starvation|NN|_ to|to|TO|_ surfeit|surfeit|NN|_ -LRB-|-lrb-|-LRB-|_ slide|slide|NN|_ 7B2|7b2|NN|_ -RRB-|-rrb-|-RRB-|_
Zn-depleted|zn-depleted|JJ|_ custom-built|custom-built|JJ|_ chemostats|chemostat|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 50|50|CD|_ h|h|NN|_ .|.|.|_ At|at|IN|_ this|this|DT|_ point|point|NN|_ ,|,|,|_ ZnSO4|znso4|NN|_ .7|.7|CD|_ H2O|h2o|NN|_ in|in|IN|_ water|water|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.2|0.2|CD|_ M|m|NN|_ in|in|IN|_ the|the|DT|_ chemostat|chemostat|NN|_ .|.|.|_ A|a|DT|_ 10|10|CD|_ ml|ml|NN|_ sample|sample|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ using|use|VBG|_ a|a|DT|_ polypropylene|polypropylene|NN|_ pipette|pipette|NN|_ tip|tip|NN|_ immediately|immediately|RB|_ prior|prior|RB|_ to|to|TO|_ Zn|zn|NN|_ addition|addition|NN|_ and|and|CC|_ 2.5|2.5|CD|_ ,|,|,|_ 7|7|CD|_ ,|,|,|_ 10|10|CD|_ and|and|CC|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ pipetted|pipet|VBN|_ directly|directly|RB|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ as|as|IN|_ recommended|recommend|VBN|_ by|by|IN|_ the|the|DT|_ suppliers|supplier|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ BioPhotometer|biophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ control|control|NN|_ experiment|experiment|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ which|which|WDT|_ water|water|NN|_ was|be|VBD|_ added|add|VBN|_ .|.|.|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|SYM|_ 1-1|1-1|CD|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|NN|_ 1-2|1-2|CD|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|SYM|_ 2-1|2-1|CD|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|SYM|_ 2-2|2-2|CD|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|SYM|_ 3-1|3-1|CD|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|SYM|_ 3-2|3-2|CD|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|SYM|_ 4-1|4-1|CD|_
Butanol|Butanol|NNP|_ _|_|NNP|_ Challenge|Challenge|NNP|_ _|_|VBD|_ Step|step|NN|_ _|_|SYM|_ 4-2|4-2|CD|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 1-1|1-1|CD|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 1-2|1-2|CD|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 2-1|2-1|CD|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 2-2|2-2|CD|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 3-1|3-1|CD|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 3-2|3-2|CD|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 4-1|4-1|CD|_
Control|Control|NNP|_ _|_|NNP|_ Step|step|VB|_ _|_|SYM|_ 4-2|4-2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
extracted|extract|VBN|_ molecule|molecule|NN|_ :|:|:|_ plasmid|plasmid|NN|_ DNA|dna|NN|_
Genomic|genomic|JJ|_ Library|Library|NNP|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ enriched|enriched|JJ|_ via|via|IN|_ serial|serial|NN|_ transfers|transfer|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ g|g|NN|_
Non-challenged|non-challenged|JJ|_ Library|Library|NNP|_
other|other|JJ|_ extracted|extract|VBN|_ using|use|VBG|_ alkalyne|alkalyne|JJ|_ lysis|lysis|NN|_ preparation|preparation|NN|_ .|.|.|_ Plasmid|plasmid|NN|_ DNA|dna|NN|_ was|be|VBD|_ clean|clean|JJ|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ Zymo|Zymo|NNP|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrated|Concentrated|NNP|_ -5|-5|CD|_ kit|kit|NN|_
The|the|DT|_ image|image|NN|_ analysis|analysis|NN|_ performed|perform|VBN|_ using|use|VBG|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 6.0|6.0|CD|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ normalized|normalize|VBN|_ with|with|IN|_ MIDAS|midas|NN|_ -LRB-|-lrb-|-LRB-|_ LOWESS|lowess|NN|_ method|method|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ clustering|clustering|NN|_ analysis|analysis|NN|_ in|in|IN|_ MeV|mev|NN|_ -LRB-|-lrb-|-LRB-|_ CAST|cast|NN|_ -RRB-|-rrb-|-RRB-|_
Bacterial|bacterial|JJ|_ RNA|rna|NN|_ was|be|VBD|_ stabilized|stabilize|VBN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ by|by|IN|_ using|use|VBG|_ RNA|rna|NN|_ protect|protect|VBP|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Kits|kit|NNS|_ for|for|IN|_ RNA|rna|NN|_ purification|purification|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ of|of|IN|_ 0.4|0.4|CD|_ and|and|CC|_ then|then|RB|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ induce|induce|VB|_ the|the|DT|_ protein|protein|NN|_ expression|expression|NN|_
Data|Data|NNP|_ extraction|extraction|NN|_ from|from|IN|_ Images|image|NNS|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ software|software|NN|_ v|v|LS|_ 9.5.1|9.5.1|CD|_ of|of|IN|_ Agilent|Agilent|NNP|_ .|.|.|_ Feature|feature|NN|_ extracted|extract|VBN|_ raw|raw|JJ|_ data|datum|NNS|_ was|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ V|V|NNP|_ 7.3.1|7.3.1|CD|_ software|software|NN|_ from|from|IN|_ Agilent|Agilent|NNP|_ .|.|.|_ Normalization|normalization|NN|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ using|use|VBG|_ the|the|DT|_ recommended|recommend|VBN|_ one|one|CD|_ color|color|NN|_ Per|per|IN|_ Chip|chip|NN|_ and|and|CC|_ Per|per|IN|_ Gene|Gene|NNP|_ Data|Data|NNP|_ Transformation|transformation|NN|_ :|:|:|_ Set|set|VB|_ measurements|measurement|NNS|_ less|less|JJR|_ than|than|IN|_ 0.01|0.01|CD|_ to|to|TO|_ 0.01|0.01|CD|_ ,|,|,|_ Per|per|IN|_ Chip|chip|NN|_ :|:|:|_ Normalize|normalize|VB|_ to|to|TO|_ 50th|50th|JJ|_ percentile|percentile|NN|_ ,|,|,|_ Per|per|IN|_ Gene|gene|NN|_ :|:|:|_ Normalize|normalize|VB|_ to|to|TO|_ Specific|specific|JJ|_ Samples|sample|NNS|_ .|.|.|_ Significant|significant|JJ|_ genes|gene|NNS|_ up|up|RB|_ and|and|CC|_ down|down|RB|_ regulated|regulate|VBN|_ showing|show|VBG|_ one|one|CD|_ fold|fold|NN|_ and|and|CC|_ above|above|IN|_ among|among|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ identified|identify|VBN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ expressing|express|VBG|_ catalytically|catalytically|RB|_ inactive|inactive|JJ|_ mutant|mutant|NN|_ of|of|IN|_ M.HpyAVIB|m.hpyavib|NN|_
E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ expressing|express|VBG|_ wild-type|wild-type|JJ|_ M.HpyAVIB|m.hpyavib|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_
mutant|mutant|JJ|_
wild|wild|JJ|_ type|type|NN|_
antibody|antibody|NN|_ :|:|:|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ -LRB-|-lrb-|-LRB-|_ Upstate|upstate|JJ|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ at|at|IN|_ appropriate|appropriate|JJ|_ cell|cell|NN|_ density|density|NN|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ by|by|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 25|25|CD|_ min|min|NN|_ .|.|.|_ Following|follow|VBG|_ quenching|quench|VBG|_ the|the|DT|_ unused|unused|JJ|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 125|125|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ Buffered|buffer|VBN|_ Saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ washed|wash|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ composed|compose|VBN|_ of|of|IN|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ ug|ug|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ 9E10|9e10|NN|_ Myc|myc|NN|_ tag|tag|NN|GEN antibody|antibody|NN|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ PurR-8myc|purr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ 9E10|9e10|NN|_ myc|myc|NN|_ antibody|antibody|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ PurR-8myc|purr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ using|use|VBG|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ .|.|.|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|purr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ Adenine|adenine|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|purr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ Adenine|adenine|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|purr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ glucose|glucose|NN|SUPP 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|purr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ glucose|glucose|NN|SUPP 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|purr|NN|TF Input|input|NN|_ DNA|dna|NN|_ Adenine|adenine|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|purr|NN|TF Input|input|NN|_ DNA|dna|NN|_ Adenine|adenine|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|PurR|NNP|TF Input|Input|NNP|_ DNA|DNA|NNP|_ glucose|glucose|NN|SUPP 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ PurR|PurR|NNP|TF Input|Input|NNP|_ DNA|DNA|NNP|_ glucose|glucose|NN|SUPP 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ strains|strain|NNS|_ harboring|harbor|VBG|_ PurR-8myc|purr-8myc|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ minimal|minimal|JJ|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ PurR-8myc|purr-8myc|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Adenine|Adenine|NNP|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ glucose|glucose|NN|SUPP
PurR|purr|NN|TF _|_|CD|_ Adenine|Adenine|NNP|_ _|_|SYM|_ 1|1|CD|_
PurR|purr|NN|TF _|_|CD|_ Adenine|Adenine|NNP|_ _|_|NN|_ 2|2|CD|_
PurR|purr|NN|TF _|_|CD|_ glucose|glucose|NN|SUPP _|_|NN|_ 1|1|CD|_
PurR|purr|NN|TF _|_|CD|_ glucose|glucose|NN|SUPP _|_|NN|_ 2|2|CD|_
The|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ per|per|IN|_ channel|channel|NN|_ quantile|quantile|NN|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 19|19|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 185|185|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ IP|IP|NNP|_
10|10|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
12|12|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
13|13|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
14|14|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
15|15|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
17|17|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
18|18|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
19|19|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
1|1|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|CD|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
20|20|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
2|2|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|CD|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
3|3|CD|_ _|_|NN|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|CD|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
5|5|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ LP|lp|NN|_ _|_|CD|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
6|6|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
7|7|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
9|9|CD|_ _|_|SYM|_ HF|hf|NNS|_ _|_|VBP|_ HP|HP|NNP|_ _|_|SYM|_ noDP|nodp|NN|_ _|_|CD|_ noRh|norh|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
After|after|IN|_ dividing|divide|VBG|_ sequence|sequence|NN|_ runs|run|NNS|_ by|by|IN|_ barcode|barcode|NN|_ ,|,|,|_ we|we|PRP|_ mapped|map|VBD|_ the|the|DT|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ relevant|relevant|JJ|_ genomes|genome|NNS|_ using|use|VBG|_ the|the|DT|_ ssaha2|ssaha2|NN|_ algorithm|algorithm|NN|_ .|.|.|_ Minimum|Minimum|NNP|_ score|score|NN|_ thresholds|threshold|NNS|_ for|for|IN|_ ssaha|ssaha|NN|_ were|be|VBD|_ selected|select|VBN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ distribution|distribution|NN|_ of|of|IN|_ scores|score|NNS|_ for|for|IN|_ all|all|DT|_ mapped|map|VBN|_ reads|read|VBZ|_ of|of|IN|_ a|a|DT|_ 32nt|32nt|JJ|_ barcoded|barcoded|JJ|_ sample|sample|NN|_ and|and|CC|_ a|a|DT|_ 36-nt|36-nt|JJ|_ non-barcoded|non-barcoded|JJ|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ 29|29|CD|_ was|be|VBD|_ selected|select|VBN|_ as|as|IN|_ the|the|DT|_ minimum|minimum|JJ|_ score|score|NN|_ for|for|IN|_ 32nt|32nt|JJ|_ barcoded|barcoded|JJ|_ samples|sample|NNS|_ ;|;|:|_ 33|33|CD|_ was|be|VBD|_ the|the|DT|_ minimum|minimum|JJ|_ score|score|NN|_ used|use|VBN|_ for|for|IN|_ 36-nt|36-nt|JJ|_ non-barcoded|non-barcoded|JJ|_ samples|sample|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Although|although|IN|_ an|a|DT|_ 18-nt|18-nt|JJ|_ read|read|NN|_ is|be|VBZ|_ sufficient|sufficient|JJ|_ to|to|TO|_ map|map|VB|GEN more|more|JJR|_ than|than|IN|_ 90|90|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ ,|,|,|_ even|even|RB|_ at|at|IN|_ 32-36nt|32-36nt|JJ|_ there|there|EX|_ is|be|VBZ|_ a|a|DT|_ large|large|JJ|_ fraction|fraction|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ that|that|IN|_ map|map|NN|GEN to|to|TO|_ multiple|multiple|JJ|_ locations|location|NNS|_ within|within|IN|_ a|a|DT|_ genome|genome|NN|_ or|or|CC|_ across|across|IN|_ genomes|genome|NNS|_ .|.|.|_ Reads|read|NNS|_ that|that|WDT|_ map|map|VBP|GEN non-uniquely|non-uniquely|JJ|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
Bacteroides|Bacteroides|NNPS|_ caccae|caccae|FW|_ ATCC|atcc|NN|_ 43185|43185|CD|_
Bacteroides|Bacteroides|NNPS|_ ovatus|ovatus|NN|_ ATCC|atcc|NN|_ 8483|8483|CD|_
Bacteroides|Bacteroides|NNPS|_ thetaiotaomicron|thetaiotaomicron|RB|_ VPI-5482|vpi-5482|JJ|_
Blautia|blautia|NN|_ hydrogenotrophica|hydrogenotrophica|NN|_ DSM|DSM|NNP|_ 10507|10507|CD|_
-LSB-|-lsb-|-LRB-|_ Clostridium|clostridium|NN|_ -RSB-|-rsb-|-RRB-|_ symbiosum|symbiosum|NN|_
Collinsella|collinsella|NN|_ aerofaciens|aerofacien|NNS|_ ATCC|atcc|NN|_ 25986|25986|CD|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 4|4|CD|_ _|_|CD|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D2|d2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|SYM|_ m1|m1|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m10|m10|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m11|m11|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m12|m12|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m13|m13|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m2|m2|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m3|m3|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m4|m4|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m5|m5|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m6|m6|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m7|m7|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m8|m8|NN|_
D3|d3|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m9|m9|NN|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 4|4|CD|_ _|_|CD|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D3|d3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|SYM|_ m1|m1|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m10|m10|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m11|m11|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m12|m12|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m13|m13|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m2|m2|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m3|m3|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m4|m4|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m5|m5|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m6|m6|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m7|m7|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m8|m8|NN|_
D4|d4|NN|_ _|_|CD|_ 10|10|CD|_ _|_|NN|_ m9|m9|NN|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m11|m11|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m10|m10|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m12|m12|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m13|m13|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 4|4|CD|_ _|_|CD|_ m9|m9|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
D4|d4|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
Desulfovibrio|desulfovibrio|NN|_ piger|piger|NN|_ GOR1|gor1|NN|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ a|a|DT|_ meal|meal|NN|_ of|of|IN|_ human|human|JJ|_ pureed|pureed|NN|_ food|food|NN|_ in|in|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ -LRB-|-lrb-|-LRB-|_ g|g|NN|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09049|.09049|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09050|.09050|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09051|.09051|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09052|.09052|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09053|.09053|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09054|.09054|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09055|.09055|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09055|.09055|CD|_ .|.|.|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09056|.09056|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09057|.09057|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09057|.09057|CD|_ .|.|.|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09058|.09058|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09059|.09059|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09620|.09620|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09621|.09621|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09622|.09622|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09623|.09623|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09624|.09624|CD|_
diet|diet|NN|_ :|:|:|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09625|.09625|CD|_
Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ II|II|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ followed|follow|VBN|_ by|by|IN|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ RNaseH|rnaseh|NN|_ ,|,|,|_ and|and|CC|_ E.coli|e.coli|NN|_ DNA|dna|NN|_ ligase|ligase|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ .|.|.|_
Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ II|II|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ followed|follow|VBN|_ by|by|IN|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ RNaseH|rnaseh|NN|_ ,|,|,|_ and|and|CC|_ E.coli|e.coli|NN|_ DNA|dna|NN|_ ligase|ligase|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ second|second|JJ|_ strand.isoamyl|strand.isoamyl|JJ|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ lysed|lyse|VBN|_ by|by|IN|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ -LRB-|-lrb-|-LRB-|_ BioSpec|BioSpec|NNP|_ Products|Products|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cellular|cellular|JJ|_ debris|debris|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 8,000|8,000|CD|_ g|g|NN|_ ;|;|:|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ nucleic|nucleic|JJ|_ acids|acid|NNS|_ were|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ and|and|CC|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ ul|ul|NN|_ TE|TE|NNP|_ .|.|.|_ The|the|DT|_ resuspension|resuspension|NN|_ was|be|VBD|_ further|further|JJ|_ purified|purify|VBN|_ with|with|IN|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ PCR|pcr|NN|_ column|column|NN|_ and|and|CC|_ eluted|elute|VBN|_ into|into|IN|_ 30|30|CD|_ ul|ul|NN|_ of|of|IN|_ EB|EB|NNP|_ buffer|buffer|NN|_ .|.|.|_
E11|e11|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|SYM|_ m1|m1|NN|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m2|m2|NN|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m3|m3|NN|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m4|m4|NN|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m8|m8|NN|_
E1|e1|NN|_ _|_|VBD|_ 14|14|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E11|e11|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E13|e13|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|VBD|_ 4|4|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|SYM|_ 6|6|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 6|6|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 6|6|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 6|6|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 6|6|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 6|6|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E15|e15|CD|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E17|e17|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E1|e1|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E19|e19|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m1|m1|NN|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m3|m3|NN|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m4|m4|NN|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m6|m6|NN|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m8|m8|NN|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E2|e2|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 14|14|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E3|e3|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|SYM|_ m1|m1|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 4|4|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|CD|_ 6|6|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m2|m2|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m3|m3|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m4|m4|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m5|m5|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m6|m6|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m7|m7|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
E9|e9|NN|_ _|_|NN|_ 7|7|CD|_ _|_|NN|_ m8|m8|NN|_ -LSB-|-lsb-|-LRB-|_ COPRO-Seq|copro-seq|NN|_ -RSB-|-rsb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
-LSB-|-lsb-|-LRB-|_ Eubacterium|eubacterium|NN|_ -RSB-|-rsb-|-RRB-|_ rectale|rectale|JJ|_ ATCC|atcc|NN|_ 33656|33656|CD|_
Fecal|fecal|JJ|_ samples|sample|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ mice|mouse|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processing|processing|NN|_ .|.|.|_ All|all|DT|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ suspended|suspend|VBN|_ in|in|IN|_ a|a|DT|_ solution|solution|NN|_ containing|contain|VBG|_ 500|500|CD|_ ul|ul|NN|_ of|of|IN|_ acid-washed|acid-washed|JJ|_ glass|glass|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Sigma-Aldrich|Sigma-Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 500|500|CD|_ ul|ul|NN|_ of|of|IN|_ extraction|extraction|NN|_ buffer|buffer|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mM|mm|NN|KWSUPP Tris|tris|NN|_ -LSB-|-lsb-|-LRB-|_ pH|ph|NN|_ 8|8|CD|_ -RSB-|-rsb-|-RRB-|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 200|200|CD|_ ul|ul|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ and|and|CC|_ 500|500|CD|_ ul|ul|NN|_ of|of|IN|_ a|a|DT|_ mixture|mixture|NN|_ of|of|IN|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ lysed|lyse|VBN|_ by|by|IN|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ -LRB-|-lrb-|-LRB-|_ BioSpec|BioSpec|NNP|_ Products|Products|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cellular|cellular|JJ|_ debris|debris|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 8,000|8,000|CD|_ g|g|NN|_ ;|;|:|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ nucleic|nucleic|JJ|_ acids|acid|NNS|_ were|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ and|and|CC|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 100|100|CD|_ ul|ul|NN|_ TE|TE|NNP|_ .|.|.|_ The|the|DT|_ resuspension|resuspension|NN|_ was|be|VBD|_ further|further|JJ|_ purified|purify|VBN|_ with|with|IN|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ PCR|pcr|NN|_ column|column|NN|_ and|and|CC|_ eluted|elute|VBN|_ into|into|IN|_ 30|30|CD|_ ul|ul|NN|_ of|of|IN|_ EB|EB|NNP|_ buffer|buffer|NN|_ .|.|.|_
Fecal|fecal|JJ|_ samples|sample|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ mice|mouse|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ processing|processing|NN|_ .|.|.|_ All|all|DT|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAProtect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ suspended|suspend|VBN|_ in|in|IN|_ a|a|DT|_ solution|solution|NN|_ containing|contain|VBG|_ 500|500|CD|_ μl|μl|NN|_ of|of|IN|_ acid-washed|acid-washed|JJ|_ glass|glass|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Sigma-Aldrich|Sigma-Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 500|500|CD|_ μl|μl|NN|_ of|of|IN|_ extraction|extraction|NN|_ buffer|buffer|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 210|210|CD|_ μl|μl|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ and|and|CC|_ 500|500|CD|_ μl|μl|NN|_ of|of|IN|_ a|a|DT|_ mixture|mixture|NN|_ of|of|IN|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ :|:|:|_ isoamyl|isoamyl|NN|_ alcohol|alcohol|NN|_ -LRB-|-lrb-|-LRB-|_ 125:24:1|125:24:1|CD|_ ,|,|,|_ pH|ph|NN|_ 4.5|4.5|CD|_ ;|;|:|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ lysed|lyse|VBN|_ by|by|IN|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ -LRB-|-lrb-|-LRB-|_ BioSpec|BioSpec|NNP|_ Products|Products|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cellular|cellular|JJ|_ debris|debris|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 8,000|8,000|CD|_ ×|×|CD|_ g|g|NN|_ ;|;|:|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ nucleic|nucleic|JJ|_ acids|acid|NNS|_ were|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ and|and|CC|_ sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Fecal|fecal|JJ|_ samples|sample|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ mice|mouse|NNS|_ were|be|VBD|_ span|span|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ¬|¬|CD|_ ∞|∞|NN|_ C|c|NN|_ and|and|CC|_ maintained|maintain|VBD|_ at|at|IN|_ this|this|DT|_ temperature|temperature|NN|_ prior|prior|RB|_ to|to|TO|_ processing|processing|NN|_ .|.|.|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepared|JJ|_ according|accord|VBG|_ to|to|TO|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instructions|instruction|NNS|_ accompanying|accompany|VBG|_ the|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ Sample|sample|NN|_ Kit|kit|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ sonicated|sonicate|VBN|_ in|in|IN|_ a|a|DT|_ biorupter|biorupter|NN|_ sonicator|sonicator|NN|_ ,|,|,|_ cleaned|clean|VBD|_ up|up|RP|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepared|JJ|_ according|accord|VBG|_ to|to|TO|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instructions|instruction|NNS|_ accompanying|accompany|VBG|_ the|the|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ Sample|sample|NN|_ Kit|kit|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ gDNA|gdna|NN|_ was|be|VBD|_ sonicated|sonicate|VBN|_ in|in|IN|_ a|a|DT|_ biorupter|biorupter|NN|_ sonicator|sonicator|NN|_ ,|,|,|_ cleaned|clean|VBD|_ up|up|RP|_
Marvinbryantia|Marvinbryantia|NNP|_ formatexigens|formatexigen|NNS|_ DSM|DSM|NNP|_ 14469|14469|CD|_
mouse|mouse|NN|_ feces|fece|VBZ|_
OTHER|OTHER|NNP|_
RNA-Seq|rna-seq|NN|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ :|:|:|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ run|run|VBN|_ over|over|IN|_ two|two|CD|_ MEGAClear|megaclear|NN|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ deplete|deplete|VB|_ tRNAs|trna|NNS|_ and|and|CC|_ 5S|5s|NN|_ rRNA|rrna|NN|_ .|.|.|_ In|in|IN|_ between|between|IN|_ the|the|DT|_ two|two|CD|_ column|column|NN|_ purifications|purification|NNS|_ ,|,|,|_ a|a|DT|_ second|second|JJ|_ DNAse|dnase|NN|_ digestion|digestion|NN|_ was|be|VBD|_ performed|perform|VBN|_ -LRB-|-lrb-|-LRB-|_ Baseline-ZERO|baseline-zero|JJ|_ Epicenter|epicenter|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 16S|16s|NN|_ and|and|CC|_ 23S|23s|NN|_ rRNA|rrna|NN|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ MICROBExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ custom|custom|NN|_ depletion|depletion|NN|_ oligos|oligo|NNS|_ -LRB-|-lrb-|-LRB-|_ Rey|Rey|NNP|_ et.al|et.al|NNP|_ .|.|.|_ 2010|2010|CD|_ ;|;|:|_ JBC|JBC|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09049|.09049|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09050|.09050|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09051|.09051|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09052|.09052|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09053|.09053|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09054|.09054|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09055|.09055|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09056|.09056|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09057|.09057|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09058|.09058|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09059|.09059|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09620|.09620|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09621|.09621|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09622|.09622|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09623|.09623|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09624|.09624|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 10-gut|10-gut|JJ|_ bacteria|bacterium|NNS|_ .|.|.|_ Mouse|mouse|NN|_ was|be|VBD|_ fed|feed|VBN|_ Harlan|Harlan|NNP|_ Teklad|Teklad|NNP|_ Diet|Diet|NNP|_ TD|TD|NNP|_ .09625|.09625|CD|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 8-gut|8-gut|JJ|_ bacteria|bacterium|NNS|_
sample|sample|NN|_ source|source|NN|_ :|:|:|_ Fecal|fecal|JJ|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ mouse|mouse|NN|_ -LRB-|-lrb-|-LRB-|_ c57Bl6|c57bl6|NN|_ -RRB-|-rrb-|-RRB-|_ colonized|colonize|VBN|_ with|with|IN|_ 9-gut|9-gut|JJ|_ bacteria|bacterium|NNS|_
time|time|NN|_ :|:|:|_ Sample|sample|NN|_ was|be|VBD|_ taken|take|VBN|_ after|after|IN|_ mouse|mouse|NN|_ was|be|VBD|_ on|on|IN|_ the|the|DT|_ diet|diet|NN|_ for|for|IN|_ 14|14|CD|_ days|day|NNS|_ .|.|.|_
time|time|NN|_ :|:|:|_ Sample|sample|NN|_ was|be|VBD|_ taken|take|VBN|_ after|after|IN|_ mouse|mouse|NN|_ was|be|VBD|_ on|on|IN|_ the|the|DT|_ diet|diet|NN|_ for|for|IN|_ 1|1|CD|_ days|day|NNS|_ .|.|.|_
time|time|NN|_ :|:|:|_ Sample|sample|NN|_ was|be|VBD|_ taken|take|VBN|_ after|after|IN|_ mouse|mouse|NN|_ was|be|VBD|_ on|on|IN|_ the|the|DT|_ diet|diet|NN|_ for|for|IN|_ 2|2|CD|_ days|day|NNS|_ .|.|.|_
time|time|NN|_ :|:|:|_ Sample|sample|NN|_ was|be|VBD|_ taken|take|VBN|_ after|after|IN|_ mouse|mouse|NN|_ was|be|VBD|_ on|on|IN|_ the|the|DT|_ diet|diet|NN|_ for|for|IN|_ 4|4|CD|_ days|day|NNS|_ .|.|.|_
time|time|NN|_ :|:|:|_ Sample|sample|NN|_ was|be|VBD|_ taken|take|VBN|_ after|after|IN|_ mouse|mouse|NN|_ was|be|VBD|_ on|on|IN|_ the|the|DT|_ diet|diet|NN|_ for|for|IN|_ 6|6|CD|_ days|day|NNS|_ .|.|.|_
time|time|NN|_ :|:|:|_ Sample|sample|NN|_ was|be|VBD|_ taken|take|VBN|_ after|after|IN|_ mouse|mouse|NN|_ was|be|VBD|_ on|on|IN|_ the|the|DT|_ diet|diet|NN|_ for|for|IN|_ 7|7|CD|_ days|day|NNS|_ .|.|.|_
AW1|aw1|NN|_ .7|.7|CD|_ ,|,|,|_ steady-state|steady-state|JJ|_ continuous|continuous|JJ|_ cultured|culture|VBN|_ experimental|experimental|JJ|_ samples|sample|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_
AW1|aw1|NN|_ .7|.7|CD|_ ,|,|,|_ steady-state|steady-state|JJ|_ continuous|continuous|JJ|_ cultured|culture|VBN|_ experimental|experimental|JJ|_ samples|sample|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ then|then|RB|_ 15|15|CD|_ minutes|minute|NNS|_ heatshock|heatshock|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_
Cultures|culture|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ ,|,|,|_ incubated|incubate|VBN|_ overnight|overnight|RB|_ ,|,|,|_ sub-cultured|sub-cultured|JJ|_ with|with|IN|_ a|a|DT|_ 1|1|CD|_ %|%|NN|_ inoculum|inoculum|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ the|the|DT|_ late|late|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ ,|,|,|_ corresponding|correspond|VBG|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ nm|nm|NN|_ of|of|IN|_ 0.6|0.6|CD|_ --|--|:|_ 0.7|0.7|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
First|First|NNP|_ biological|biological|JJ|_ repeat|repeat|NN|_ 37|37|CD|_ °C|°c|NN|_
First|First|NNP|_ biological|biological|JJ|_ repeat|repeat|NN|_ 50|50|CD|_ °C|°c|NN|_
For|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_ 0.5|0.5|CD|_ mL|ml|NN|_ of|of|IN|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ RNA|rna|NN|_ protect|protect|VBP|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Ontario|Ontario|NNP|_ ,|,|,|_ Canada|Canada|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ with|with|IN|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ Spectrophotometer|Spectrophotometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ scientific|scientific|JJ|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 30|30|CD|_ µg|µg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 1U|1u|NN|_ RNase|rnase|NN|_ free|free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Ontario|Ontario|NNP|_ ,|,|,|_ Canada|Canada|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 1U|1u|NN|_ RNase|rnase|NN|_ inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ prior|prior|RB|_ to|to|TO|_ storage|storage|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ reverse-transcribed|reverse-transcribed|JJ|_ using|use|VBG|_ the|the|DT|_ Array|array|NN|_ 900MPX|900mpx|NN|_ Expression|expression|NN|_ Array|array|NN|_ Detection|detection|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Genisphere|Genisphere|NNP|_ ,|,|,|_ Hatfield|Hatfield|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ instructions|instruction|NNS|_ of|of|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ MinElute|MinElute|NNP|_ PCR|pcr|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Quiagen|quiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ purified|purify|VBN|_ DNA|dna|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ microarray|microarray|NN|_ and|and|CC|_ qPCR|qpcr|NN|_ experiments|experiment|NNS|_ .|.|.|_
GGG10|ggg10|NN|_ ,|,|,|_ steady-state|steady-state|JJ|_ continuous|continuous|JJ|_ cultured|culture|VBN|_ experimental|experimental|JJ|_ samples|sample|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_
GGG10|ggg10|NN|_ ,|,|,|_ steady-state|steady-state|JJ|_ continuous|continuous|JJ|_ cultured|culture|VBN|_ experimental|experimental|JJ|_ samples|sample|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ then|then|RB|_ 15|15|CD|_ minutes|minute|NNS|_ heatshock|heatshock|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_
heat|heat|NN|_ sensitivity|sensitivity|NN|_ :|:|:|_ resistant|resistant|JJ|_
heat|heat|NN|_ sensitivity|sensitivity|NN|_ :|:|:|_ sensitive|sensitive|JJ|_
Raw|raw|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ and|and|CC|_ log2|log2|NN|_ transformed|transform|VBN|_ with|with|IN|_ the|the|DT|_ Acuity|acuity|NN|_ 4.0|4.0|CD|_ software|software|NN|_ package|package|NN|_ ,|,|,|_ and|and|CC|_ data|datum|NNS|_ with|with|IN|_ low|low|JJ|_ fluorescence|fluorescence|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ eliminated|eliminate|VBN|_ .|.|.|_ Genes|gene|NNS|_ were|be|VBD|_ considered|consider|VBN|_ to|to|TO|_ be|be|VB|_ differentially|differentially|RB|_ expressed|express|VBN|_ if|if|IN|_ the|the|DT|_ absolute|absolute|JJ|_ values|value|NNS|_ of|of|IN|_ log2|log2|NN|_ mean|mean|NN|_ expression|expression|NN|_ ratios|ratio|NNS|_ were|be|VBD|_ ≥|≥|CD|_ 1|1|CD|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ late|late|JJ|_ exponential|exponential|JJ|_ cultures|culture|NNS|_ ,|,|,|_ or|or|CC|_ from|from|IN|_ late|late|JJ|_ exponential|exponential|JJ|_ cells|cell|NNS|_ heat-shocked|heat-shock|VBN|_ by|by|IN|_ exposure|exposure|NN|_ to|to|TO|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ .|.|.|_
Second|Second|NNP|_ biological|biological|JJ|_ repeat|repeat|NN|_ 37|37|CD|_ °C|°c|NN|_
Second|second|JJ|_ biological|biological|JJ|_ repeat|repeat|NN|_ 50|50|CD|_ °C|°c|NN|_
strain|strain|NN|_ :|:|:|_ AW1|aw1|NN|_ .7|.7|CD|_
strain|strain|NN|_ :|:|:|_ GGG10|ggg10|NN|_
The|the|DT|_ data|datum|NNS|_ did|do|VBD|_ not|not|RB|_ undergo|undergo|VB|_ normalization|normalization|NN|_ across|across|IN|_ samples|sample|NNS|_ .|.|.|_
Third|Third|NNP|_ biological|biological|JJ|_ repeat|repeat|NN|_ 37|37|CD|_ °C|°c|NN|_
Third|third|JJ|_ biological|biological|JJ|_ repeat|repeat|NN|_ 50|50|CD|_ °C|°c|NN|_
treatment|treatment|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_
treatment|treatment|NN|_ :|:|:|_ 50|50|CD|_ °C|°c|NN|_ heatshock|heatshock|NN|_
agent|agent|NN|_ :|:|:|_ 0.05|0.05|CD|_ mg|mg|NN|_
agent|agent|NN|_ :|:|:|_ control|control|NN|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ at|at|IN|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ at|at|IN|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ with|with|IN|_ phloretin|phloretin|NN|_
E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ shake|shake|NN|_ flasks|flask|NNS|_ with|with|IN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ that|that|WDT|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 100|100|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 7|7|CD|_ hrs|hr|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ chilled|chill|VBN|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ prevent|prevent|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ sec|sec|NN|_ before|before|IN|_ centrifugation|centrifugation|NN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tubes|tube|NNS|_ at|at|IN|_ 13,000|13,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ;|;|:|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|frozen|JJ|_ immediately|immediately|RB|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ stored|store|VBD|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNase-free|RNase-free|NNP|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 79254|79254|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|Setting|NNP|_
rna|rna|NN|GEN extracted|extract|VBN|_ from|from|IN|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_
rna|rna|NN|GEN extracted|extract|VBN|_ from|from|IN|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 0.05|0.05|CD|_ mg|mg|NN|_
agent|agent|NN|_ :|:|:|_ 0.5|0.5|CD|_ %|%|NN|_ honey|honey|NN|_
agent|agent|NN|_ :|:|:|_ control|control|NN|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ for|for|IN|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ for|for|IN|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ with|with|IN|_ honey|honey|NN|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|_ in|in|IN|_ 1000|1000|CD|_ ml|ml|NN|_ shake|shake|NN|_ flasks|flask|NNS|_ with|with|IN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ that|that|WDT|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ shaken|shake|VBN|_ with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ glass|glass|NN|_ wool|wool|NN|_ at|at|IN|_ 100|100|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 7|7|CD|_ hrs|hr|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ chilled|chill|VBN|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ prevent|prevent|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ sec|sec|NN|_ before|before|IN|_ centrifugation|centrifugation|NN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tubes|tube|NNS|_ at|at|IN|_ 13,000|13,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ;|;|:|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|frozen|JJ|_ immediately|immediately|RB|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ stored|store|VBD|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNase-free|RNase-free|NNP|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 79254|79254|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|Setting|NNP|_
rna|rna|NN|GEN extracted|extract|VBN|_ from|from|IN|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_
rna|rna|NN|GEN extracted|extract|VBN|_ from|from|IN|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 0.5|0.5|CD|_ %|%|NN|_ honey|honey|NN|_
Cells|cell|NNS|_ were|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ the|the|DT|_ fresh|fresh|JJ|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ mM63|mm63|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ histidine|histidine|NN|_ .|.|.|_ The|the|DT|_ initial|initial|JJ|_ cell|cell|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ controlled|control|VBN|_ as|as|IN|_ 104-105|104-105|CD|_ cells|cell|NNS|_
Control|Control|NNP|_ strain|strain|NN|_ exponentially|exponentially|RB|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ absence|absence|NN|_ of|of|IN|_ histidine|histidine|NN|_
Control|Control|NNP|_ strain|strain|NN|_ exponentially|exponentially|RB|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ histidine|histidine|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisC|δhisc|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-rfp-tetR-zeocinr|Ptrc-rfp-tetR-zeocinr|NNP|_ ΔgalK|ΔgalK|NNP|_ :|:|:|_ :|:|:|_ PtetA-gfp-hisC-kanr|PtetA-gfp-hisC-kanr|NNP|_
genotype|genotype|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisC|δhisc|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-rfp-tetR-zeocinr|Ptrc-rfp-tetR-zeocinr|NNP|_ ΔgalK|ΔgalK|NNP|_ :|:|:|_ :|:|:|_ PtetA-gfp-kanr|PtetA-gfp-kanr|NNP|_
HisC|hisc|NN|_ rewired|rewire|VBD|_ strain|strain|NN|_ exponentially|exponentially|RB|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ absence|absence|NN|_ of|of|IN|_ histidine|histidine|NN|_
HisC|hisc|NN|_ rewired|rewire|VBD|_ strain|strain|NN|_ exponentially|exponentially|RB|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ histidine|histidine|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
log10|log10|NN|_ mRNA|mrna|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ pM|pm|NN|_ -RRB-|-rrb-|-RRB-|_ data|datum|NNS|_ are|be|VBP|_ provided|provide|VBN|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ SERIES|series|NN|_ record|record|NN|_ .|.|.|_
Microarray|Microarray|NNP|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ written|write|VBN|_ in|in|IN|_ R|r|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ finite|finite|JJ|_ hybridisation|hybridisation|NN|_ -LRB-|-lrb-|-LRB-|_ FH|fh|NN|_ -RRB-|-rrb-|-RRB-|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Ono|Ono|NNP|_ et|et|FW|_ al|al|FW|_ -LRB-|-lrb-|-LRB-|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ An|a|DT|_ improved|improve|VBN|_ physico-chemical|physico-chemical|JJ|_ model|model|NN|_ of|of|IN|_ hybridization|hybridization|NN|_ on|on|IN|_ high-density|high-density|JJ|_ oligonucleotide|oligonucleotide|NN|_ microarrays|microarray|NNS|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 24|24|CD|_ :|:|:|_ 1278-1285|1278-1285|CD|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ thermodynamic|thermodynamic|JJ|_ model|model|NN|_ of|of|IN|_ non-specific|non-specific|JJ|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ NSB|nsb|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ short|short|JJ|_ nucleotide|nucleotide|NN|_ microarrays|microarray|NNS|_ -LRB-|-lrb-|-LRB-|_ Furusawa|Furusawa|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
OSU11|osu11|NN|_ ,|,|,|_ nurishment|nurishment|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
OSU11|osu11|NN|_ ,|,|,|_ nurishment|nurishment|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
OSU11|osu11|NN|_ ,|,|,|_ nurishment|nurishment|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
OSU11|osu11|NN|_ ,|,|,|_ starved|starve|VBN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
OSU11|osu11|NN|_ ,|,|,|_ starved|starve|VBN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
OSU11|osu11|NN|_ ,|,|,|_ starved|starve|VBN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ nurishment|nurishment|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ nurishment|nurishment|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ nurishment|nurishment|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ starved|starve|VBN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ starved|starve|VBN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ starved|starve|VBN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
platform|platform|NN|_ _|_|CD|_ id|id|NN|_ design|design|NN|_ :|:|:|_ EcFS|ecfs|NN|_ _|_|NN|_ 1|1|CD|_
platform|platform|NN|_ _|_|CD|_ id|id|NN|_ design|design|NN|_ :|:|:|_ EcFS|ecfs|NN|_ _|_|NN|_ 2|2|CD|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ cold|cold|JJ|_ phenol-ethanol|phenol-ethanol|JJ|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ of|of|IN|_ phenol|phenol|NN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ prepared|prepare|VBN|_ in|in|IN|_ advance|advance|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 16,000|16,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
10|10|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ ice|ice|NN|_ cold|cold|JJ|_ killing|killing|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 20mM|20mm|NN|_ Tris|tris|NN|_ and|and|CC|_ 5mM|5mm|NN|_ MgCl2|mgcl2|NN|_ and|and|CC|_ 20mM|20mm|NN|_ NaN3|nan3|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ cells|cell|NNS|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 8000g|8000g|CD|_ ,|,|,|_ 4C|4c|NN|_ ,|,|,|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ resuspended|resuspend|VBN|_ in|in|IN|_ 300μL|300μL|NNP|_ TE|TE|NNP|_ with|with|IN|_ 40|40|CD|_ μl|μl|NN|_ 10|10|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ 3|3|CD|_ μl|μl|NN|_ 0.5|0.5|CD|_ M|m|NN|_ EDTA|edta|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ 750μl|750μl|CD|_ isopropanole|isopropanole|NN|_ was|be|VBD|_ added|add|VBN|_ before|before|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 15600|15600|CD|_ rcf|rcf|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500μL|500μl|NN|_ TE|te|NN|_ and|and|CC|_ 2μL|2μl|NN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 25|25|CD|_ mg|mg|NN|_
500|500|CD|_ ng|ng|NN|_ chrom|chrom|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ 10U|10u|NN|_ of|of|IN|_ MseI|msei|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10μL|10μl|NN|_ volume|volume|NN|_ for|for|IN|_ 3h|3h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ heat|heat|NN|_ inactivated|inactivate|VBD|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ .|.|.|_ To|to|TO|_ prepare|prepare|VB|_ adapters|adapter|NNS|_ 100pmol|100pmol|CD|_ of|of|IN|_ MseIlong|MseIlong|NNP|_ -LRB-|-lrb-|-LRB-|_ AGTGGGATTCCGCATGCTAGT|AGTGGGATTCCGCATGCTAGT|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MseIshortnewNo|mseishortnewno|NN|_ -LRB-|-lrb-|-LRB-|_ TAACTAGCATGC|taactagcatgc|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ annealed|anneal|VBN|_ in|in|IN|_ 8µl|8µl|JJ|_ ddH2O|ddh2o|NN|_ by|by|IN|_ heating|heat|VBG|_ to|to|TO|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ and|and|CC|_ than|than|IN|_ cooling|cool|VBG|_ to|to|TO|_ 70|70|CD|_ °C|°c|NN|_ and|and|CC|_ subsequently|subsequently|RB|_ to|to|TO|_ 15|15|CD|_ °C|°c|NN|_ with|with|IN|_ 1|1|CD|_ °C|°c|NN|_ per|per|IN|_ min|min|NN|_ .|.|.|_ At|at|IN|_ 15|15|CD|_ °C|°c|NN|_ 10µl|10µl|JJ|_ MseI|msei|NN|_ digested|digest|VBD|_ DNA|dna|NN|_ ,|,|,|_ 2µl|2µl|JJ|_ ligase|ligase|NN|_ buffer|buffer|NN|_ and|and|CC|_ 400U|400u|NN|_ T4-ligase|t4-ligase|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ and|and|CC|_ ligated|ligate|VBN|_ over|over|IN|_ night|night|NN|_ .|.|.|_ Ligase|ligase|NN|_ was|be|VBD|_ inactivated|inactivate|VBN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ One|one|CD|_ halve|halve|VBP|_ of|of|IN|_ the|the|DT|_ ligation|ligation|NN|_ mix|mix|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ 20|20|CD|_ U|U|NNP|_ DpnI|DpnI|NNP|_ for|for|IN|_ 2h|2h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ a|a|DT|_ volume|volume|NN|_ of|of|IN|_ 50µl|50µl|JJ|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ halve|halve|VBP|_ treated|treated|JJ|_ similar|similar|JJ|_ with|with|IN|_ water|water|NN|_ instead|instead|RB|_ of|of|IN|_ DpnI|dpni|NN|_ as|as|IN|_ control|control|NN|_ .|.|.|_ 5µl|5µl|NN|_ of|of|IN|_ the|the|DT|_ DNA|dna|NN|_ was|be|VBD|_ amplified|amplify|VBN|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ µl|µl|NN|_ PCR|pcr|NN|_ reaction|reaction|NN|_ with|with|IN|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 0.5|0.5|CD|_ µM|µm|NN|_ primer|primer|NN|_ MseIlong|MseIlong|NNP|_ ,|,|,|_ 10µl|10µl|JJ|_ Phusion|Phusion|NNP|_ HF|hf|NN|_ buffer|buffer|NN|_ and|and|CC|_ 1U|1u|NN|_ Phusion|phusion|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Finnzymes|finnzyme|NNS|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ the|the|DT|_ program|program|NN|_ 30sec|30sec|CD|_ 98|98|CD|_ °C|°c|NN|_ ,|,|,|_ 20x|20x|NN|_ -LRB-|-lrb-|-LRB-|_ 30sec|30sec|CD|_ 98|98|CD|_ °C|°c|NN|_ ,|,|,|_ 30|30|CD|_ sec|sec|NN|_ 62|62|CD|_ °C|°c|NN|_ ,|,|,|_ 60sec|60sec|JJ|_ 72|72|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ 72|72|CD|_ °C|°c|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ PCR|pcr|NN|_ cleanup|cleanup|NN|_ kit|kit|NN|_ .|.|.|_
Cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ cross|cross|JJ|_ linked|link|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ µl|µl|NN|_ of|of|IN|_ formaldehyde|formaldehyde|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ ml|ml|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 1|1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Crosslinking|crosslinking|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ slow|slow|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ followed|follow|VBN|_ by|by|IN|_ quenching|quench|VBG|_ with|with|IN|_ 0.2|0.2|CD|_ ml|ml|NN|_ of|of|IN|_ 2.5|2.5|CD|_ M|m|NN|_ glycine|glycine|NN|_ per|per|IN|_ ml|ml|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 0.5|0.5|CD|_ M|m|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ from|from|IN|_ 15|15|CD|_ ml|ml|NN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ cold|cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ pH7|ph7|NN|_ .5|.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ wa|wa|NN|_ resuspended|resuspend|VBN|_ in|in|IN|_ 300μL|300μL|NNP|_ TE|TE|NNP|_ with|with|IN|_ 40|40|CD|_ μl|μl|NN|_ 10|10|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ 3|3|CD|_ μl|μl|NN|_ 0.5|0.5|CD|_ M|m|NN|_ EDTA|edta|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ 750μl|750μl|CD|_ isopropanole|isopropanole|NN|_ was|be|VBD|_ added|add|VBN|_ before|before|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 15600|15600|CD|_ rcf|rcf|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500μL|500μl|NN|_ TE|te|NN|_ and|and|CC|_ 3μL|3μl|NN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 25|25|CD|_ mg|mg|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.07|0.07|CD|_ in|in|IN|_ AB|AB|NNP|_ glucose|glucose|NN|SUPP CAA|CAA|NNP|_ medium|medium|NN|_ ,|,|,|_ shifted|shift|VBD|_ to|to|TO|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ 70|70|CD|_ min|min|NN|_ and|and|CC|_ back|back|RB|_ to|to|TO|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.07|0.07|CD|_ in|in|IN|_ AB|AB|NNP|_ glucose|glucose|NN|SUPP CAA|CAA|NNP|_ medium|medium|NN|_ ,|,|,|_ shifted|shift|VBD|_ to|to|TO|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ 70|70|CD|_ min|min|NN|_ and|and|CC|_ back|back|RB|_ to|to|TO|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.07|0.07|CD|_ in|in|IN|_ AB|AB|NNP|_ glucose|glucose|NN|SUPP CAA|CAA|NNP|_ medium|medium|NN|_ ,|,|,|_ shifted|shift|VBD|_ to|to|TO|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ 70|70|CD|_ min|min|NN|_ and|and|CC|_ back|back|RB|_ to|to|TO|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 16|16|CD|_ min|min|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.07|0.07|CD|_ in|in|IN|_ AB|AB|NNP|_ glucose|glucose|NN|SUPP CAA|CAA|NNP|_ medium|medium|NN|_ ,|,|,|_ shifted|shift|VBD|_ to|to|TO|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ 70|70|CD|_ min|min|NN|_ and|and|CC|_ back|back|RB|_ to|to|TO|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 17|17|CD|_ min|min|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.07|0.07|CD|_ in|in|IN|_ AB|AB|NNP|_ glucose|glucose|NN|SUPP CAA|CAA|NNP|_ medium|medium|NN|_ ,|,|,|_ shifted|shift|VBD|_ to|to|TO|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ 70|70|CD|_ min|min|NN|_ and|and|CC|_ back|back|RB|_ to|to|TO|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 35|35|CD|_ min|min|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.07|0.07|CD|_ in|in|IN|_ AB|AB|NNP|_ glucose|glucose|NN|SUPP CAA|CAA|NNP|_ medium|medium|NN|_ ,|,|,|_ shifted|shift|VBD|_ to|to|TO|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ 70|70|CD|_ min|min|NN|_ and|and|CC|_ back|back|RB|_ to|to|TO|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ min|min|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.07|0.07|CD|_ in|in|IN|_ AB|AB|NNP|_ glucose|glucose|NN|SUPP CAA|CAA|NNP|_ medium|medium|NN|_ ,|,|,|_ shifted|shift|VBD|_ to|to|TO|_ 39|39|CD|_ °C|°c|NN|_ for|for|IN|_ 70|70|CD|_ min|min|NN|_ and|and|CC|_ back|back|RB|_ to|to|TO|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD450|od450|NN|_ of|of|IN|_ about|about|IN|_ 0.15|0.15|CD|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ AB|AB|NNP|_ acetate|acetate|NN|SUPP medium|medium|NN|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.15|0.15|CD|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ before|before|IN|_ crosslinking|crosslink|VBG|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ SeqA|seqa|NN|_
Cultures|culture|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ and|and|CC|_ its|its|PRP$|_ derivates|derivate|NNS|_ were|be|VBD|_ cross|cross|JJ|_ linked|link|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ µl|µl|NN|_ of|of|IN|_ formaldehyde|formaldehyde|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ ml|ml|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 1|1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Crosslinking|crosslinking|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ slow|slow|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ followed|follow|VBN|_ by|by|IN|_ quenching|quench|VBG|_ with|with|IN|_ 0.2|0.2|CD|_ ml|ml|NN|_ of|of|IN|_ 2.5|2.5|CD|_ M|m|NN|_ glycine|glycine|NN|_ per|per|IN|_ ml|ml|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ concentration|concentration|NN|_ 0.5|0.5|CD|_ M|m|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ cold|cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ pH7|ph7|NN|_ .5|.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ resuspension|resuspension|NN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10mM|10mm|NN|_ Tris|tris|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 20|20|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ ,|,|,|_ 50mM|50mm|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 10mM|10mm|NN|_ EDTA|edta|NN|_ ,|,|,|_ 10|10|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ dnaC2|dnac2|NN|_
genotype|genotype|NN|_ :|:|:|_ dnaC2|dnac2|NN|_ ,|,|,|_ pMQ430|pmq430|NN|_
genotype|genotype|NN|_ :|:|:|_ GATC-cluster|gatc-cluster|NN|_ :|:|:|_ :|:|:|_ hisA|hisA|NNP|GEN
genotype|genotype|NN|_ :|:|:|_ GATC-cluster|gatc-cluster|NN|_ :|:|:|_ :|:|:|_ srlA|srla|NN|GEN
genotype|genotype|NN|_ :|:|:|_ GATC-cluster|gatc-cluster|NN|_ :|:|:|_ :|:|:|_ ter|ter|NN|_
genotype|genotype|NN|_ :|:|:|_ GATC-cluster|gatc-cluster|NN|_ :|:|:|_ :|:|:|_ tnaA|tnaa|NN|GEN
genotype|genotype|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
input|input|NN|_ DNA|dna|NN|_
Methylation|methylation|NN|_ in|in|IN|_ 0|0|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
Methylation|methylation|NN|_ in|in|IN|_ 0|0|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
Methylation|methylation|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
Methylation|methylation|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 0|0|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 0|0|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ LB|lb|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ LB|lb|NN|_ dam|dam|NN|GEN +|+|CC|_ +|+|CC|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ LB|lb|NN|_ dam|dam|NN|GEN +|+|CC|_ +|+|CC|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 15|15|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep3|rep3|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 16|16|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 16|16|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 17|17|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 17|17|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 35|35|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 35|35|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 50|50|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 50|50|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 5|5|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ 5|5|CD|_ min|min|NN|_ dnaC2|dnac2|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ AB|AB|NNP|_ acetate|acetate|NN|SUPP rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ AB|AB|NNP|_ acetate|acetate|NN|SUPP rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ hisA|hisA|NNP|GEN GATC|GATC|NNP|_ cluster|cluster|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ hisA|hisA|NNP|GEN GATC|GATC|NNP|_ cluster|cluster|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ srlA|srla|NN|GEN GATC|gatc|NN|_ cluster|cluster|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ srlA|srla|NN|GEN GATC|gatc|NN|_ cluster|cluster|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ ter|ter|NN|_ GATC|gatc|NN|_ cluster|cluster|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ ter|ter|NN|_ GATC|gatc|NN|_ cluster|cluster|NN|_ rep2|rep2|NN|_
SeqA|seqa|NN|_ in|in|IN|_ tnaA|tnaa|NN|GEN GATC|gatc|NN|_ cluster|cluster|NN|_ rep1|rep1|NN|_
SeqA|seqa|NN|_ in|in|IN|_ tnaA|tnaa|NN|GEN GATC|gatc|NN|_ cluster|cluster|NN|_ rep2|rep2|NN|_
Spot|spot|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Feature|Feature|NNP|_ Extraction|extraction|NN|_ software|software|NN|_ 10.5.1.1|10.5.1.1|CD|_ from|from|IN|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ with|with|IN|_ a|a|DT|_ linear|linear|JJ|_ dye|dye|VB|_ normalization|normalization|NN|_ correction|correction|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ gProcessedSignal|gprocessedsignal|NN|_ and|and|CC|_ rProcessedSignal|rprocessedsignal|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ with|with|IN|_ the|the|DT|_ statistics|statistics|NNS|_ software|software|NN|_ R.|R.|NNP|_ Ratios|Ratios|NNP|_ of|of|IN|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ r|r|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ after|after|IN|_ background|background|NN|_ substraction|substraction|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ the|the|DT|_ array|array|NN|_ wide|wide|JJ|_ average|average|NN|_ .|.|.|_ Data|datum|NNS|_ points|point|NNS|_ with|with|IN|_ a|a|DT|_ value|value|NN|_ below|below|IN|_ 0|0|CD|_ after|after|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ were|be|VBD|_ set|set|VBN|_ `|`|``|_ null|null|NN|_ '|'|''|_ .|.|.|_ Data|datum|NNS|_ points|point|NNS|_ form|form|VBP|_ non-unique|non-unique|JJ|_ regions|region|NNS|_ on|on|IN|_ the|the|DT|_ chromosome|chromosome|NN|_ were|be|VBD|_ excluded|exclude|VBN|_ from|from|IN|_ analysis|analysis|NN|_ .|.|.|_
Spot|Spot|NNP|_ intensities|intensity|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Feature|Feature|NNP|_ Extraction|extraction|NN|_ software|software|NN|_ 10.5.1.1|10.5.1.1|CD|_ from|from|IN|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ with|with|IN|_ a|a|DT|_ linear|linear|JJ|_ dye|dye|VB|_ normalization|normalization|NN|_ correction|correction|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ gProcessedSignal|gprocessedsignal|NN|_ and|and|CC|_ rProcessedSignal|rprocessedsignal|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ with|with|IN|_ the|the|DT|_ statistics|statistics|NNS|_ software|software|NN|_ R.|R.|NNP|_ Ratios|Ratios|NNP|_ of|of|IN|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ r|r|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ after|after|IN|_ background|background|NN|_ substraction|substraction|NN|_ .|.|.|_ Data|datum|NNS|_ points|point|NNS|_ with|with|IN|_ a|a|DT|_ value|value|NN|_ below|below|IN|_ 0|0|CD|_ after|after|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ were|be|VBD|_ set|set|VBN|_ `|`|``|_ null|null|NN|_ '|'|''|_ .|.|.|_ Data|datum|NNS|_ points|point|NNS|_ form|form|VBP|_ non-unique|non-unique|JJ|_ regions|region|NNS|_ on|on|IN|_ the|the|DT|_ chromosome|chromosome|NN|_ were|be|VBD|_ excluded|exclude|VBN|_ from|from|IN|_ analysis|analysis|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ MG1655dnaC2|mg1655dnac2|NN|_
strain|strain|NN|_ :|:|:|_ TB16|tb16|NN|_
strain|strain|NN|_ :|:|:|_ TWx30|twx30|NN|_
strain|strain|NN|_ :|:|:|_ TWx31|twx31|NN|_
strain|strain|NN|_ :|:|:|_ TWx34|twx34|NN|_
strain|strain|NN|_ :|:|:|_ TWx48|twx48|NN|_
treatment|treatment|NN|_ :|:|:|_ control|control|NN|_
treatment|treatment|NN|_ :|:|:|_ DpnI|dpni|NN|_ digested|digest|VBD|_ DNA|dna|NN|_
untreated|untreated|JJ|_ control|control|NN|_
285c|285c|JJ|_
All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 25|25|CD|_ ug|ug|NN|_
Control|Control|NNP|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ 285c|285c|JJ|_
Data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ LOWESS|lowess|NN|_ -LRB-|-lrb-|-LRB-|_ MIDAS|midas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ analyzed|analyze|VBN|_ for|for|IN|_ statistical|statistical|JJ|_ significance|significance|NN|_ using|use|VBG|_ the|the|DT|_ Rank|Rank|NNP|_ Product|Product|NNP|_ method|method|NN|_ in|in|IN|_ the|the|DT|_ MultiExperimentViewer|MultiExperimentViewer|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ 285c|285c|JJ|_ rpoD|rpod|NN|GEN mutation|mutation|NN|_
Sigma70|sigma70|NN|_ LB|lb|NN|_
Sigma70|sigma70|NN|_ LB-1|lb-1|NN|_
Sigma70|sigma70|NN|_ LB-2|lb-2|NN|_
Sigma70|sigma70|NN|_ LB-3|lb-3|NN|_
Sigma70|sigma70|NN|_ LP|lp|NN|_
Sigma70|sigma70|NN|_ LP-1|lp-1|NN|_
Sigma70|sigma70|NN|_ LP-2|lp-2|NN|_
Sigma70|sigma70|NN|_ LP-3|lp-3|NN|_
The|the|DT|_ Zymo|Zymo|NNP|_ Fungal|fungal|JJ|_
transformation|transformation|NN|_ :|:|:|_ empty|empty|JJ|_ vector|vector|NN|_
transformation|transformation|NN|_ :|:|:|_ pSigma70-LB|psigma70-lb|NN|_
transformation|transformation|NN|_ :|:|:|_ pSigma70-LP|psigma70-lp|NN|_
treatment|treatment|NN|_ :|:|:|_ 30|30|CD|_ C|c|NN|_
treatment|treatment|NN|_ :|:|:|_ 42|42|CD|_ C|c|NN|_
Cells|cell|NNS|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ liquid|liquid|JJ|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ saturation|saturation|NN|_ .|.|.|_ Then|then|RB|_ 50|50|CD|_ µl|µl|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ K-medium|k-medium|NN|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ saturation|saturation|NN|_ again|again|RB|_ .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ the|the|DT|_ separate|separate|JJ|_ media|media|NNS|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ 25|25|CD|_ μl|μl|NN|_ into|into|IN|_ K-medium|k-medium|NN|_ ,|,|,|_ 50|50|CD|_ µl|µl|NN|_ into|into|IN|_ K-medium|k-medium|NN|_ +|+|CC|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 75|75|CD|_ µl|µl|NN|_ into|into|IN|_ K-medium|k-medium|NN|_ +|+|CC|_ 0.6|0.6|CD|_ M|m|NN|_ urea|urea|NN|_ ;|;|:|_ the|the|DT|_ final|final|JJ|_ volume|volume|NN|_ was|be|VBD|_ 5|5|CD|_ ml|ml|NN|_ in|in|IN|_ all|all|DT|_ cases|case|NNS|_ .|.|.|_ These|these|DT|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ in|in|IN|_ the|the|DT|_ three|three|CD|_ media|media|NNS|_ in|in|IN|_ a|a|DT|_ water|water|NN|_ bath|bath|NN|_ at|at|IN|_ 30ºC|30ºC|NNP|_ .|.|.|_
CFT073|cft073|NN|_ in|in|IN|_ K-med|k-med|JJ|_
CFT073|cft073|NN|_ in|in|IN|_ NaCl|nacl|NN|_
CFT073|cft073|NN|_ in|in|IN|_ urea|urea|NN|_
CFT073|cft073|NN|_ K-med|k-med|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
CFT073|cft073|NN|_ K-med|k-med|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
CFT073|cft073|NN|_ K-med|k-med|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
CFT073|cft073|NN|_ NaCl|nacl|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
CFT073|cft073|NN|_ NaCl|nacl|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
CFT073|cft073|NN|_ NaCl|nacl|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
CFT073|cft073|NN|_ urea|urea|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
CFT073|cft073|NN|_ urea|urea|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
CFT073|cft073|NN|_ urea|urea|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CFT073|cft073|NN|_
GCOS|gcos|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ obtain|obtain|VB|_ detection|detection|NN|_ calls|call|NNS|_ for|for|IN|_ each|each|DT|_ microarray|microarray|NN|_ .|.|.|_ The|the|DT|_ statistical|statistical|JJ|_ difference|difference|NN|_ for|for|IN|_ mRNA|mrna|NN|_ expression|expression|NN|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ CarmaWeb|CarmaWeb|NNP|_ .|.|.|_ Affymetrix|Affymetrix|NNP|_ GeneChip|GeneChip|NNP|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ MAS|MAS|NNP|_ for|for|IN|_ background|background|NN|_ correction|correction|NN|_ ,|,|,|_ VSN|VSN|NNP|_ for|for|IN|_ normalization|normalization|NN|_ ,|,|,|_ MAS|MAS|NNP|_ for|for|IN|_ PM|PM|NNP|_ correction|correction|NN|_ and|and|CC|_ Medianpolish|medianpolish|NN|_ for|for|IN|_ Expression|expression|NN|_ .|.|.|_ VSN|VSN|NNP|_ normalized|normalize|VBD|_ data|datum|NNS|_ not|not|RB|_ provided|provide|VBN|_ by|by|IN|_ submitter|submitter|NN|_ .|.|.|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ 25|25|CD|_ μl|μl|NN|_ into|into|IN|_ K-medium|k-medium|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ 50|50|CD|_ µl|µl|NN|_ into|into|IN|_ K-medium|k-medium|NN|_ +|+|CC|_ 0.3|0.3|CD|_ M|m|NN|_ NaCl|nacl|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ 75|75|CD|_ µl|µl|NN|_ into|into|IN|_ K-medium|k-medium|NN|_ +|+|CC|_ 0.6|0.6|CD|_ M|m|NN|_ urea|urea|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ by|by|IN|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ --|--|:|_ chloroform|chloroform|NN|_ method|method|NN|_ .|.|.|_
When|when|WRB|_ the|the|DT|_ samples|sample|NNS|_ had|have|VBD|_ reached|reach|VBN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.4-0.5|0.4-0.5|CD|_ ,|,|,|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ 2.5|2.5|CD|_ ml|ml|NN|_ mixture|mixture|NN|_ of|of|IN|_ cold|cold|JJ|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ to|to|TO|_ preserve|preserve|VB|_ the|the|DT|_ mRNA|mrna|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ cooled|cool|VBN|_ rapidly|rapidly|RB|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ immediately|immediately|RB|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ frozen|freeze|VBN|_ on|on|IN|_ dry|dry|JJ|_ ice|ice|NN|_ .|.|.|_
1|1|CD|_ .|.|.|_ library|library|NN|_ -LRB-|-lrb-|-LRB-|_ maanova|maanova|NN|_ -RRB-|-rrb-|-RRB-|_
2|2|CD|_ .|.|.|_ Read|Read|NNP|_ data|datum|NNS|_ :|:|:|_
3|3|CD|_ .|.|.|_ Log|log|VB|_ transformation|transformation|NN|_ :|:|:|_
4|4|CD|_ .|.|.|_ Normalization|normalization|NN|_ by|by|IN|_ Glowess|glowess|NN|_ method|method|NN|_ :|:|:|_
5|5|CD|_ .|.|.|_ Save|save|VB|_ the|the|DT|_ plot|plot|NN|_ files|file|VBZ|_
6|6|CD|_ .|.|.|_ close|close|RB|_ the|the|DT|_ graph|graph|NN|_ :|:|:|_
7|7|CD|_ .|.|.|_ output|output|NN|_ :|:|:|_
Add|add|VBP|_ 100|100|CD|_ μl|μl|NN|_ 1|1|CD|_ mg|mg|NN|_
Bacterial|bacterial|JJ|_ lysis|lysis|NN|_
Column|column|NN|_ purification|purification|NN|_
Data|Data|NNP|_ =|=|JJ|_ read.madata|read.madata|NN|_ -LRB-|-lrb-|-LRB-|_ \|\|CD|_ NormInput.txt|norminput.txt|NN|_ \|\|NN|_ ,|,|,|_ designfile|designfile|NN|_ =|=|JJ|_ \|\|CD|_ Designfile1.txt|designfile1.txt|NN|_ \|\|NN|_ ,|,|,|_ header|header|NN|_ =|=|JJ|_ TRUE|true|JJ|_ ,|,|,|_ spotflag|spotflag|NN|_ =|=|JJ|_ TRUE|true|JJ|_ ,|,|,|_ metarow|metarow|NN|_ =|=|JJ|_ 1|1|CD|_ ,|,|,|_ metacol|metacol|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ row|row|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ col|col|NN|_ =|=|JJ|_ 4|4|CD|_ ,|,|,|_ geneID|geneid|NN|_ =|=|JJ|_ 5|5|CD|_ ,|,|,|_ pmt|pmt|NN|_ =|=|JJ|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_
Data|Data|NNP|_ selection|selection|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ cells|cell|NNS|_ ,|,|,|_ M9|m9|NN|_ ,|,|,|_ 8|8|CD|_ h|h|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ WT|WT|NNP|_ _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ rep1|rep1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ WT|WT|NNP|_ _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ rep2|rep2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ ybjN|ybjn|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ ,|,|,|_ M9|m9|NN|_ ,|,|,|_ 8|8|CD|_ h|h|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ ybjN|ybjn|NN|GEN _|_|CD|_ MUTANT|mutant|JJ|_ _|_|NN|_ M9|m9|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ ybjN|ybjn|NN|GEN _|_|CD|_ MUTANT|mutant|JJ|_ _|_|NN|_ M9|m9|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ ybjN|ybjn|NN|GEN _|_|CD|_ MUTANT|mutant|JJ|_ _|_|NN|_ M9|m9|NN|_ _|_|CD|_ rep3|rep3|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ ybjN|ybjn|NN|GEN over-expression|over-expression|NN|_ cells|cell|NNS|_ ,|,|,|_ M9|m9|NN|_ ,|,|,|_ 8|8|CD|_ h|h|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ ybjN|ybjn|NN|GEN _|_|NN|_ OVER-EXPRESSION|over-expression|NN|_ _|_|CD|_ M9|m9|NN|_ _|_|CD|_ rep1|rep1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ ybjN|ybjn|NN|GEN _|_|NN|_ OVER-EXPRESSION|over-expression|NN|_ _|_|CD|_ M9|m9|NN|_ _|_|CD|_ rep2|rep2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ _|_|CD|_ ybjN|ybjn|NN|GEN _|_|NN|_ OVER-EXPRESSION|over-expression|NN|_ _|_|CD|_ M9|m9|NN|_ _|_|CD|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
genotype|genotype|NN|_ :|:|:|_ ybjN|ybjn|NN|GEN mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ ybjN|ybjn|NN|GEN over-expression|over-expression|NN|_
go|go|VBP|_ to|to|TO|_ the|the|DT|_ directory|directory|NN|_ :|:|:|_
graphics.off|graphics.off|NN|_ -LRB-|-lrb-|-LRB-|_ -RRB-|-rrb-|-RRB-|_
Grow|grow|VBP|_ bacteria|bacterium|NNS|_ overnight|overnight|JJ|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ reinoculate|reinoculate|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED at|at|IN|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ of|of|IN|_ 0.005|0.005|CD|_ .|.|.|_ After|after|IN|_ eight|eight|CD|_ hours|hour|NNS|_ growth|growth|NN|_ at|at|IN|_ 34|34|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|_ medium|medium|NN|_ ,|,|,|_ 2|2|CD|_ mL|ml|NN|_ of|of|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 1|1|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ at|at|IN|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.5-0.8|0.5-0.8|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ .|.|.|_ Centrifuge|Centrifuge|NNP|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4000|4000|CD|_ g.|g.|NNP|_ Decant|Decant|NNP|_ the|the|DT|_ supernatant|supernatant|NN|_ .|.|.|_
growing|grow|VBG|_ condition|condition|NN|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED
LogData|logdata|NN|_ =|=|JJ|_ createData|createdata|NN|_ -LRB-|-lrb-|-LRB-|_ Data|data|NN|_ ,|,|,|_ n.rep|n.rep|NN|_ =|=|JJ|_ 1|1|CD|_ ,|,|,|_ log.trans|log.trans|VBZ|_ =|=|JJ|_ TRUE|true|JJ|_ -RRB-|-rrb-|-RRB-|_
Microarray|microarray|NN|_ data|datum|NNS|_ normalization|normalization|NN|_
Microarray|Microarray|NNP|_ normalization|normalization|NN|_ is|be|VBZ|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ maanova|maanova|NN|_ function|function|NN|_ in|in|IN|_ R|r|NN|_ program|program|NN|_ version|version|NN|_ 2.2.1|2.2.1|CD|_ .|.|.|_ Eight|eight|CD|_ arrays|array|NNS|_ in|in|IN|_ one|one|CD|_ slide|slide|NN|_ were|be|VBD|_ globally|globally|RB|_ normalized|normalize|VBN|_ using|use|VBG|_ glowess|glowess|NN|_ method|method|NN|_ .|.|.|_
NormalData|normaldata|NN|_ =|=|JJ|_ transform.madata|transform.madata|NN|_ -LRB-|-lrb-|-LRB-|_ LogData|LogData|NNP|_ ,|,|,|_ method|method|NN|_ =|=|JJ|_ c|c|NN|_ -LRB-|-lrb-|-LRB-|_ \|\|CD|_ glowess|glowess|NN|_ \|\|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
norm.temp|norm.temp|NN|_ <|<|JJR|_ -|-|:|_ cbind|cbind|NN|_ -LRB-|-lrb-|-LRB-|_ NormalData|NormalData|NNP|_ $|$|$|_ metarow|metarow|JJ|_ ,|,|,|_ NormalData|NormalData|NNP|_ $|$|$|_ metacol|metacol|JJ|_ ,|,|,|_ NormalData|NormalData|NNP|_ $|$|$|_ row|row|NN|_ ,|,|,|_ NormalData|NormalData|NNP|_ $|$|$|_ col|col|CD|_ ,|,|,|_ NormalData|NormalData|NNP|_ $|$|$|_ geneID|geneid|JJ|_ ,|,|,|_ NormalData|NormalData|NNP|_ $|$|$|_ data|datum|NNS|_ -RRB-|-rrb-|-RRB-|_
postscript|postscript|NN|_ -LRB-|-lrb-|-LRB-|_ file|file|NN|_ =|=|JJ|_ \|\|CD|_ PlotGLOWESS.ps|plotglowess.ps|NNS|_ \|\|NN|_ -RRB-|-rrb-|-RRB-|_
postscript|postscript|NN|_ -LRB-|-lrb-|-LRB-|_ file|file|NN|_ =|=|JJ|_ \|\|CD|_ PlotRawData.ps|plotrawdata.ps|NNS|_ \|\|CD|_ -RRB-|-rrb-|-RRB-|_
riplot|riplot|NN|_ -LRB-|-lrb-|-LRB-|_ LogData|LogData|NNP|_ ,|,|,|_ onScreen|onscreen|NN|_ =|=|JJ|_ FALSE|false|NN|_ -RRB-|-rrb-|-RRB-|_
riplot|riplot|NN|_ -LRB-|-lrb-|-LRB-|_ NormalData|NormalData|NNP|_ ,|,|,|_ onScreen|onscreen|NN|_ =|=|JJ|_ FALSE|false|NN|_ -RRB-|-rrb-|-RRB-|_
Sample|sample|NN|_ collection|collection|NN|_ from|from|IN|_ M9|m9|NN|_ medium|medium|NN|_
setwd|setwd|NN|_ -LRB-|-lrb-|-LRB-|_ \|\|CD|_ C|c|NN|_ :|:|:|_ \|\|SYM|_ Documents|document|NNS|_ and|and|CC|_ Settings|setting|NNS|_ \|\|VBP|_ Wang|Wang|NNP|_ \|\|NNP|_ Desktop|Desktop|NNP|_ \|\|NNP|_ Erwinia|Erwinia|NNP|_ in|in|FW|_ vivo|vivo|FW|_ \|\|SYM|_ rcsC|rcsC|NNP|GEN MBMA|MBMA|NNP|_ \|\|NN|_ -RRB-|-rrb-|-RRB-|_
Stage|stage|NN|_ :|:|:|_ logarithm|logarithm|NN|_ phase|phase|NN|_
Statistical|statistical|JJ|_ comparisons|comparison|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ multiple|multiple|JJ|_ testing|testing|NN|_ procedures|procedure|NNS|_ to|to|TO|_ evaluate|evaluate|VB|_ statistical|statistical|JJ|_ significance|significance|NN|_ for|for|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ .|.|.|_ A|a|DT|_ modified|modify|VBN|_ t-test|t-test|NN|_ -LRB-|-lrb-|-LRB-|_ p-value|p-value|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ computed|compute|VBN|_ to|to|TO|_ measure|measure|VB|_ the|the|DT|_ significance|significance|NN|_ associated|associate|VBN|_ with|with|IN|_ each|each|DT|_ differential|differential|JJ|_ expression|expression|NN|_ value|value|NN|_ .|.|.|_ A|a|DT|_ gene|gene|NN|_ expression|expression|NN|_ value|value|NN|_ was|be|VBD|_ decided|decide|VBN|_ to|to|TO|_ be|be|VB|_ significantly|significantly|RB|_ different|different|JJ|_ in|in|IN|_ the|the|DT|_ mutant|mutant|JJ|_ and|and|CC|_ over-expression|over-expression|NN|_ strains|strain|NNS|_ when|when|WRB|_ the|the|DT|_ p-value|p-value|NN|_ was|be|VBD|_ less|less|JJR|_ than|than|IN|_ 0.05|0.05|CD|_ -LRB-|-lrb-|-LRB-|_ except|except|IN|_ otherwise|otherwise|RB|_ mentioned|mention|VBN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ expression|expression|NN|_ ratio|ratio|NN|_ was|be|VBD|_ ≥|≥|CD|_ 2.0|2.0|CD|_ or|or|CC|_ ≤|≤|CD|_ 0.5|0.5|CD|_ .|.|.|_ Gene|Gene|NNP|_ functions|function|NNS|_ were|be|VBD|_ assigned|assign|VBN|_ using|use|VBG|_ data|datum|NNS|_ from|from|IN|_ EcoCyc|ecocyc|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
Total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Protect|Protect|NNP|_ Bacteria|bacterium|NNS|_ system|system|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ .|.|.|_
Transfer|transfer|NN|_ 700|700|CD|_ μl|μl|NN|_ lysate|lysate|NN|_ into|into|IN|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ column|column|NN|_ place|place|NN|_ in|in|IN|_ a|a|DT|_ 2|2|CD|_ ml|ml|NN|_ collection|collection|NN|_ tube|tube|NN|_ and|and|CC|_ centrifuge|centrifuge|NN|_ for|for|IN|_ 30|30|CD|_ s|s|NNS|_ at|at|IN|_ highest|highest|JJS|_ speed|speed|NN|_ .|.|.|_ Add|add|VB|_ 350|350|CD|_ μl|μl|NN|_ Buffer|buffer|NN|_ RW1|rw1|NN|_ to|to|TO|_ the|the|DT|_ column|column|NN|_ and|and|CC|_ centrifuge|centrifuge|NN|_ for|for|IN|_ 30|30|CD|_ s.|s.|NN|_ Discard|Discard|NNP|_ flow-through|flow-through|JJ|_ and|and|CC|_ reuse|reuse|VB|_ the|the|DT|_ collection|collection|NN|_ tube|tube|NN|_ .|.|.|_ Add|add|VB|_ 10|10|CD|_ μl|μl|NN|_ DNase|dnase|NN|_ stock|stock|NN|_ solution|solution|NN|_ to|to|TO|_ 70|70|CD|_ μ|μ|NN|_ l|l|NN|_ RDD|RDD|NNP|_ Buffer|Buffer|NNP|_ .|.|.|_ Add|add|VB|_ the|the|DT|_ DNase|dnase|NN|_ I|i|CD|_ solution|solution|NN|_ into|into|IN|_ the|the|DT|_ column|column|NN|_ and|and|CC|_ incubate|incubate|VB|_ at|at|IN|_ RT|rt|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ .|.|.|_ Add|add|VB|_ 350|350|CD|_ μl|μl|NN|_ Buffer|buffer|NN|_ RW1|rw1|NN|_ to|to|TO|_ the|the|DT|_ column|column|NN|_ and|and|CC|_ wait|wait|VB|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ centrifuge|centrifuge|NN|_ for|for|IN|_ 30|30|CD|_ s.|s.|NN|_ Discard|Discard|NNP|_ the|the|DT|_ flow-through|flow-through|JJ|_ and|and|CC|_ collection|collection|NN|_ tubes|tube|NNS|_ .|.|.|_ Place|place|VB|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ spin|spin|VB|_ column|column|NN|_ in|in|IN|_ a|a|DT|_ new|new|JJ|_ 2|2|CD|_ ml|ml|NN|_ collection|collection|NN|_ tube|tube|NN|_ .|.|.|_ Add|add|VB|_ 500|500|CD|_ μl|μl|NN|_ Buffer|buffer|NN|_ RPE|rpe|NN|_ to|to|TO|_ the|the|DT|_ column|column|NN|_ .|.|.|_ Centrifuge|Centrifuge|NNP|_ for|for|IN|_ 30|30|CD|_ s.|s.|NN|_ Place|place|NN|_ the|the|DT|_ column|column|NN|_ in|in|IN|_ a|a|DT|_ new|new|JJ|_ 1.5|1.5|CD|_ ml|ml|NN|_ tube|tube|NN|_ ,|,|,|_ and|and|CC|_ centrifuge|centrifuge|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ to|to|TO|_ eliminate|eliminate|VB|_ any|any|DT|_ residue|residue|NN|_ ethanol|ethanol|NN|_ .|.|.|_ Place|place|VB|_ the|the|DT|_ column|column|NN|_ in|in|IN|_ a|a|DT|_ new|new|JJ|_ collection|collection|NN|_ tube|tube|NN|_ .|.|.|_ Add|add|VB|_ 50|50|CD|_ μl|μl|NN|_ RNase|rnase|NN|_ free|free|JJ|_ water|water|NN|_ ,|,|,|_ centrifuge|centrifuge|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ .|.|.|_ Store|store|NN|_ RNA|rna|NN|_ samples|sample|NNS|_ at|at|IN|_ -20|-20|CD|_ °C|°c|NN|_ .|.|.|_
write.table|write.table|JJ|_ -LRB-|-lrb-|-LRB-|_ norm.temp|norm.temp|JJ|_ ,|,|,|_ file|file|NN|_ =|=|JJ|_ \|\|CD|_ Normal|normal|JJ|_ _|_|NN|_ Data.csv|data.csv|NN|_ \|\|NN|_ ,|,|,|_ sep|sep|NN|_ =\|=\|NN|_ ,|,|,|_ \|\|NN|_ ,|,|,|_ row.names|row.names|NN|_ =|=|JJ|_ FALSE|false|NN|_ ,|,|,|_ col.names|col.names|NNS|_ =|=|JJ|_ TRUE|true|JJ|_ ,|,|,|_ quote|quote|NN|_ =|=|JJ|_ FALSE|false|NN|_ -RRB-|-rrb-|-RRB-|_
Average|average|JJ|_ Normalization|normalization|NN|_ using|use|VBG|_ GeneChip|GeneChip|NNP|_ Operating|Operating|NNP|_ Software|Software|NNP|_ Version|Version|NNP|_ 1.4|1.4|CD|_
Control|Control|NNP|_ Strain|Strain|NNP|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 0h|0h|NN|_
Control|Control|NNP|_ Strain|Strain|NNP|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 10h|10h|CD|_
Control|Control|NNP|_ Strain|Strain|NNP|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 16h|16h|NN|_
Control|Control|NNP|_ Strain|Strain|NNP|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 20h|20h|JJ|_
Control|Control|NNP|_ Strain|Strain|NNP|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 6h|6h|JJ|_
Control|Control|NNP|_ Strain|Strain|NNP|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 8h|8h|NN|_
Culture|culture|NN|_ samples|sample|NNS|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ methanol|methanol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Fed|Fed|NNP|_ batch|batch|NN|_ high|high|JJ|_ cell|cell|NN|_ density|density|NN|_ cultivation|cultivation|NN|_
Indole|Indole|NNP|_ treated|treat|VBN|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 0h|0h|NN|_
Indole|indole|FW|_ treated|treat|VBN|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 10h|10h|JJ|_
Indole|indole|FW|_ treated|treat|VBN|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 16h|16h|JJ|_
Indole|indole|FW|_ treated|treat|VBN|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 5h|5h|JJ|_
Indole|indole|FW|_ treated|treat|VBN|_ at|at|IN|_ specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ 0.5h-1|0.5h-1|JJ|_ 8h|8h|NN|_
Qiagen|qiagen|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_
specific|specific|JJ|_ growth|growth|NN|_ rate|rate|NN|_ :|:|:|_ 0.5h-1|0.5h-1|JJ|_
strain|strain|NN|_ :|:|:|_ W3110hns|w3110hn|NNS|_ ∆|∆|VBP|_ 93-1|93-1|CD|_
time|time|NN|_ post-induction|post-induction|JJ|_ :|:|:|_ 0h|0h|NN|_
time|time|NN|_ post-induction|post-induction|JJ|_ :|:|:|_ 10h|10h|CD|_
time|time|NN|_ post-induction|post-induction|JJ|_ :|:|:|_ 16h|16h|JJ|_
time|time|NN|_ post-induction|post-induction|JJ|_ :|:|:|_ 20h|20h|JJ|_
time|time|NN|_ post-induction|post-induction|JJ|_ :|:|:|_ 5h|5h|JJ|_
time|time|NN|_ post-induction|post-induction|JJ|_ :|:|:|_ 6h|6h|JJ|_
time|time|NN|_ post-induction|post-induction|JJ|_ :|:|:|_ 8h|8h|NN|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ control|control|NN|_
treatment|treatment|NN|_ group|group|NN|_ :|:|:|_ indole|indole|NN|_ treated|treat|VBN|_
Briefly|briefly|RB|_ ,|,|,|_ total|total|JJ|_ RNA|rna|NN|_ were|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ culture|culture|NN|_ with|with|IN|_ Total|total|JJ|_ RNA|rna|NN|_ Extraction|extraction|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ RBC|rbc|NN|_ Bioscience|bioscience|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ specifications|specification|NNS|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|promega|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
control|control|NN|_
double|double|JJ|_ mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ PPK1|ppk1|NN|_ and|and|CC|_ PPX|ppx|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
exopolyphosphatase|exopolyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ PPX|ppx|NN|_ -RRB-|-rrb-|-RRB-|_ mutant|mutant|JJ|_
genotype|genotype|NN|_
Microarray|Microarray|NNP|_ data|data|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ free|free|JJ|_ software|software|NN|_ genArise|genarise|NN|_ ,|,|,|_ developed|develop|VBN|_ in|in|IN|_ the|the|DT|_ Computing|Computing|NNP|_ Unit|unit|NN|_ of|of|IN|_ Cellular|cellular|JJ|_ Physiology|Physiology|NNP|_ Institute|Institute|NNP|_ of|of|IN|_ UNAM|UNAM|NNP|_ -LRB-|-lrb-|-LRB-|_ http|http|JJ|_ :|:|:|_
polyphosphate|polyphosphate|NN|_ kinase|kinase|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ PPK1|ppk1|NN|_ -RRB-|-rrb-|-RRB-|_ mutant|mutant|JJ|_
PPK1-PPX|ppk1-ppx|NN|_ double|double|JJ|_ mutant|mutant|JJ|_
single|single|JJ|_ mutant|mutant|NN|_ in|in|IN|_ exopolyphosphatase|exopolyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ PPX|ppx|NN|_ -RRB-|-rrb-|-RRB-|_
single|single|JJ|_ mutant|mutant|NN|_ in|in|IN|_ polyphosphate|polyphosphate|NN|_ kinase|kinase|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ PPK1|ppk1|NN|_ -RRB-|-rrb-|-RRB-|_
zi|zi|NN|_ =|=|JJ|_ -LRB-|-lrb-|-LRB-|_ Ri|Ri|NNP|_ --|--|:|_ mean|mean|NN|_ -LRB-|-lrb-|-LRB-|_ R|r|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ was|be|VBD|_ evolved|evolve|VBN|_ in|in|IN|_ chemostats|chemostat|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ g|g|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
growth|growth|NN|_ medium|medium|NN|_ :|:|:|_ liquid|liquid|JJ|_ culture|culture|NN|_
P2-08|p2-08|NN|_
P2-08|p2-08|NN|_ _|_|CD|_ R1|r1|NN|_
P2-08|p2-08|NN|_ _|_|CD|_ R2|r2|NN|_
P2-08|p2-08|NN|_ _|_|CD|_ R3|r3|NN|_
P2-51|p2-51|NN|_
P2-51|p2-51|NN|_ _|_|CD|_ R1|r1|NN|_
P2-51|p2-51|NN|_ _|_|CD|_ R2|r2|NN|_
P2-51|p2-51|NN|_ _|_|CD|_ R3|r3|NN|_
P2-58|p2-58|NN|_
P2-58|p2-58|NN|_ _|_|CD|_ R1|r1|NN|_
P2-58|p2-58|NN|_ _|_|CD|_ R2|r2|NN|_
P2-58|p2-58|NN|_ _|_|CD|_ R3|r3|NN|_
P2-66|p2-66|NN|_
P2-66|p2-66|NN|_ _|_|CD|_ R1|r1|NN|_
P2-66|p2-66|NN|_ _|_|CD|_ R2|r2|NN|_
P2-66|p2-66|NN|_ _|_|CD|_ R3|r3|NN|_
P2-77|p2-77|NN|_
P2-77|p2-77|NN|_ _|_|CD|_ R1|r1|NN|_
P2-77|p2-77|NN|_ _|_|CD|_ R2|r2|NN|_
P2-77|p2-77|NN|_ _|_|CD|_ R3|r3|NN|_
PF2-04|pf2-04|NN|_
PF2-04|pf2-04|NN|_ _|_|CD|_ R1|r1|NN|_
PF2-04|pf2-04|NN|_ _|_|CD|_ R2|r2|NN|_
PF2-04|pf2-04|NN|_ _|_|CD|_ R3|r3|NN|_
PF2-08|pf2-08|NN|_
PF2-08|pf2-08|NN|_ _|_|CD|_ R1|r1|NN|_
PF2-08|pf2-08|NN|_ _|_|CD|_ R2|r2|NN|_
PF2-08|pf2-08|NN|_ _|_|CD|_ R3|r3|NN|_
PF2-12|pf2-12|NN|_
PF2-12|pf2-12|NN|_ _|_|CD|_ R1|r1|NN|_
PF2-12|pf2-12|NN|_ _|_|CD|_ R2|r2|NN|_
PF2-12|pf2-12|NN|_ _|_|CD|_ R3|r3|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ SuperScript|SuperScript|NNP|_ indirect|indirect|JJ|_ cDNA|cdna|NN|_ labeling|labeling|NN|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ cDNA|cdna|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
The|the|DT|_ image|image|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 6.0|6.0|CD|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ with|with|IN|_ MIDAS|midas|NN|_ -LRB-|-lrb-|-LRB-|_ LOWESS|lowess|NN|_ method|method|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ clustering|clustering|NN|_ analysis|analysis|NN|_ in|in|IN|_ MeV|mev|NN|_ -LRB-|-lrb-|-LRB-|_ CAST|cast|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
wild-type|wild-type|JJ|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ P2-08|p2-08|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ P2-51|p2-51|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ P2-58|p2-58|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ P2-66|p2-66|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ P2-77|p2-77|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ PF2-04|pf2-04|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ PF2-08|pf2-08|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ PF2-12|pf2-12|NN|_
wt|wt|JJ|_ or|or|CC|_ mutant|mutant|JJ|_ :|:|:|_ WT|WT|NNP|_ @|@|SYM|_ 0.8|0.8|CD|_ %|%|NN|_ But|but|CC|_
cpxA-ala-1|cpxa-ala-1|NN|_
cpxA-ala-2|cpxa-ala-2|NN|_
cpxA|cpxa|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Ala|Ala|NNP|_ media|media|NNS|_
cpxA|cpxa|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Gln|gln|NN|_ media|media|NNS|_
cysQ-gln-1|cysq-gln-1|NN|_
cysQ-gln-2|cysq-gln-2|NN|_
cysQ|cysq|NN|GEN mutantin|mutantin|NN|_ Ala|ala|NN|_ media|media|NNS|_
cysQ|cysq|NN|GEN mutantin|mutantin|NN|_ Gln|gln|NN|_ media|media|NNS|_
dnaJ-ala-1|dnaj-ala-1|NN|_
dnaJ-ala-2|dnaj-ala-2|NN|_
dnaJ-gln-1|dnaj-gln-1|NN|_
dnaJ-gln-2|dnaj-gln-2|NN|_
dnaJ|dnaj|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Ala|Ala|NNP|_ media|media|NNS|_
dnaJ|dnaj|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Gln|gln|NN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
gcvT-ala-1|gcvt-ala-1|NN|_
gcvT-ala-2|gcvt-ala-2|NN|_
gcvT|gcvt|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Ala|Ala|NNP|_ media|media|NNS|_
gcvT|gcvt|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Gln|gln|NN|_ media|media|NNS|_
genotype|genotype|NN|_
hfq-gln-1|hfq-gln-1|NN|_
hfq-gln-2|hfq-gln-2|NN|_
hfq|hfq|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Ala|Ala|NNP|_ media|media|NNS|_
hfq|hfq|NN|GEN mutant|mutant|NN|_ in|in|IN|_ Gln|gln|NN|_ media|media|NNS|_
Irp|irp|NN|_ mutant|mutant|NN|_ in|in|IN|_ Ala|Ala|NNP|_ media|media|NNS|_
Irp|irp|NN|_ mutant|mutant|NN|_ in|in|IN|_ Gln|gln|NN|_ media|media|NNS|_
LB-grown|lb-grown|JJ|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ washed|wash|VBN|_ ,|,|,|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ M9-glutamine|m9-glutamine|NN|_ of|of|IN|_ M9-alanine|m9-alanine|NN|_ media|media|NNS|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ in|in|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.15|0.15|CD|_ for|for|IN|_ glutamine|glutamine|NN|_ and|and|CC|_ OD600|od600|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ for|for|IN|_ alanine|alanine|NN|_ on|on|IN|_ an|a|DT|_ Ultraspec|ultraspec|JJ|_ 3100|3100|CD|_ pro|pro|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ ~|~|NN|_ 5|5|CD|_ generations|generation|NNS|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ the|the|DT|_ media|media|NNS|_ .|.|.|_
lrp-gln-1|lrp-gln-1|NN|_
lrp-gln-2|lrp-gln-2|NN|_
pgi-ala-1|pgi-ala-1|NN|_
pgi-ala-2|pgi-ala-2|NN|_
pgi|pgi|NN|GEN mutantin|mutantin|NN|_ Ala|ala|NN|_ media|media|NNS|_
pgi|pgi|NN|GEN mutantin|mutantin|NN|_ Gln|gln|NN|_ media|media|NNS|_
strain|strain|NN|_ :|:|:|_ AH28|ah28|NN|_
strain|strain|NN|_ :|:|:|_ ZD1|zd1|NN|_
strain|strain|NN|_ :|:|:|_ ZD26|zd26|NN|_
strain|strain|NN|_ :|:|:|_ ZD51|zd51|NN|_
strain|strain|NN|_ :|:|:|_ ZD56|zd56|NN|_
strain|strain|NN|_ :|:|:|_ ZD59|zd59|NN|_
strain|strain|NN|_ :|:|:|_ ZD60|zd60|NN|_
strain|strain|NN|_ :|:|:|_ ZD8|zd8|NN|_
The|the|DT|_ `|`|``|_ LogRatio|LogRatio|NNP|_ '|'|''|_ value|value|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ subsequent|subsequent|JJ|_ analyses|analysis|NNS|_ .|.|.|_ All|all|DT|_ values|value|NNS|_ for|for|IN|_ the|the|DT|_ same|same|JJ|_ ORF|orf|NN|_ were|be|VBD|_ averaged|average|VBN|_ as|as|IN|_ were|be|VBD|_ the|the|DT|_ values|value|NNS|_ from|from|IN|_ the|the|DT|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ performed|perform|VBN|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ .|.|.|_
When|when|WRB|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ the|the|DT|_ desired|desire|VBN|_ density|density|NN|_ ,|,|,|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 4|4|CD|_ ml|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ at|at|IN|_ 5000|5000|CD|_ g|g|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|c.|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Norgen|Norgen|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Product|product|NN|_ #|#|#|_ 17200|17200|CD|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ directions|direction|NNS|_ except|except|IN|_ in|in|IN|_ the|the|DT|_ last|last|JJ|_ step|step|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 35|35|CD|_ uL|ul|NN|_ .|.|.|_
wild-type|wild-type|JJ|_ in|in|IN|_ ala|ala|NN|_ media|media|NNS|_ _|_|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ in|in|IN|_ ala|ala|NN|_ media|media|NNS|_ _|_|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ in|in|IN|_ gln|gln|NN|_ media|media|NNS|_ _|_|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ in|in|IN|_ gln|gln|NN|_ media|media|NNS|_ _|_|NN|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ for|for|IN|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ with|with|IN|_ DMSO|dmso|NN|_
E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ for|for|IN|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ with|with|IN|_ indole-3-acetaldehyde|indole-3-acetaldehyde|JJ|_
E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ shake|shake|NN|_ flasks|flask|NNS|_ with|with|IN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ that|that|WDT|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ shaken|shake|VBN|_ with|with|IN|_ 4|4|CD|_ g|g|NN|_ of|of|IN|_ glass|glass|NN|_ wool|wool|NN|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 7|7|CD|_ hrs|hr|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ immediately|immediately|RB|_ chilled|chill|VBN|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ prevent|prevent|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ sec|sec|NN|_ before|before|IN|_ centrifugation|centrifugation|NN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ centrifuge|centrifuge|NN|_ tubes|tube|NNS|_ at|at|IN|_ 13,000|13,000|CD|_ g|g|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ ;|;|:|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|frozen|JJ|_ immediately|immediately|RB|_ with|with|IN|_ dry|dry|JJ|_ ice|ice|NN|_ and|and|CC|_ stored|store|VBD|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNase-free|RNase-free|NNP|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 79254|79254|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ 0.1|0.1|CD|_ mg|mg|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ e.|e.|FW|_ coli|coli|FW|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ -LRB-|-lrb-|-LRB-|_ 7|7|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ DMSO|dmso|NN|_
serotype|serotype|NN|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
strain|strain|NN|_ :|:|:|_ EDL933|edl933|NN|_
Cells|cell|NNS|_ in|in|IN|_ log|log|NN|_ phase|phase|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ containing|contain|VBG|_ 50|50|CD|_ μg|μg|NN|_
Data|Data|NNP|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ GeneChip|GeneChip|NNP|_ Operating|Operating|NNP|_ Software|Software|NNP|_ Version|Version|NNP|_ 1.4|1.4|CD|_ -LRB-|-lrb-|-LRB-|_ Affymetrix|Affymetrix|NNP|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ ethanol-tolerant|ethanol-tolerant|JJ|_ mutant|mutant|JJ|_ E1|e1|NN|_ of|of|IN|_ IrrE|irre|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ IrrE|irre|NN|_
mutant|mutant|JJ|_ E1|e1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
mutant|mutant|JJ|_ E1|e1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
mutant|mutant|JJ|_ E1|e1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
strain|strain|NN|_ :|:|:|_ DH5a|dh5a|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ when|when|WRB|_ they|they|PRP|_ reached|reach|VBD|_ the|the|DT|_ log|log|NN|_ phase|phase|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ rapidly|rapidly|RB|_ chilled|chill|VBD|_ and|and|CC|_ stored|store|VBD|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ until|until|IN|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ DNA|dna|NN|_ microarray|microarray|NN|_ assay|assay|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cells|cell|NNS|_ stored|store|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ TRIzol|trizol|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNeasy|rneasy|NN|_ MinElute|MinElute|NNP|_ Cleanup|Cleanup|NNP|_ Kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_
wild|wild|JJ|_ type|type|NN|_ E0|e0|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
wild|wild|JJ|_ type|type|NN|_ E0|e0|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
wild|wild|JJ|_ type|type|NN|_ E0|e0|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
E.|e.|FW|_ coli|coli|FW|_ cultutures|cultuture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_ using|use|VBG|_ standard|standard|JJ|_ protocol|protocol|NN|_ ,|,|,|_ to|to|TO|_ log|log|VB|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.7-0.8|0.7-0.8|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ gss|gss|NN|GEN mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
gss-1|gss-1|NN|_
gss-2|gss-2|NN|_
gss-3|gss-3|NN|_
MAS|mas|NN|_ 5.0|5.0|CD|_
No|no|DT|_ treatment|treatment|NN|_ ,|,|,|_ just|just|RB|_ comparison|comparison|NN|_ of|of|IN|_ RNAs|rna|NNS|_ from|from|IN|_ wild|wild|JJ|_ type|type|NN|_ and|and|CC|_ mutant|mutant|NN|_ .|.|.|_
Trizol|trizol|NN|_ extraction|extraction|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
WT-1|wt-1|NN|_
WT-2|wt-2|NN|_
WT-3|wt-3|NN|_
Affymetrix|Affymetrix|NNP|_ GeneChip|GeneChip|NNP|_ Operating|Operating|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ GCOS|GCOS|NNP|_ -RRB-|-rrb-|-RRB-|_ Version|Version|NNP|_ 1.4|1.4|CD|_ Details|detail|NNS|_ :|:|:|_ Intra-chip|intra-chip|JJ|_ normalizations|normalization|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ Gene|Gene|NNP|_ Chip|Chip|NNP|_ Operating|Operating|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ GCOS|GCOS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Default|Default|NNP|_ statistical|statistical|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ normalize|normalize|VB|_ each|each|DT|_ chip|chip|NN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ target|target|NN|_ intensity|intensity|NN|_ -LRB-|-lrb-|-LRB-|_ 1500|1500|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ GeneChip|GeneChip|NNP|_ Expression|expression|NN|_ Analysis|analysis|NN|_ manual|manual|NN|_ .|.|.|_ All|all|DT|_ nine|nine|CD|_ possible|possible|JJ|_ inter-chip|inter-chip|NN|_ comparisons|comparison|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ GCOS|gcos|NN|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ exported|export|VBN|_ to|to|TO|_ a|a|DT|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ spreadsheet|spreadsheet|NN|_ for|for|IN|_ manipulation|manipulation|NN|_ .|.|.|_ Consensus|consensus|NN|_ ``|``|``|_ detection|detection|NN|_ p-value|p-value|NN|_ ''|''|''|_ ,|,|,|_ ``|``|``|_ change|change|NN|_ p-value|p-value|NN|_ ''|''|''|_ ,|,|,|_ and|and|CC|_ ``|``|``|_ signal|signal|NN|_ log|log|NN|_ ratios|ratio|NNS|_ ''|''|''|_ were|be|VBD|_ calculated|calculate|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ default|default|NN|_ E.|e.|FW|_ coli|coli|FW|_ array|array|NN|_ p-value|p-value|NN|_ cutoff|cutoff|NN|_ parameters|parameter|NNS|_ were|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ these|these|DT|_ consensus|consensus|NN|_ values|value|NNS|_ to|to|TO|_ estimate|estimate|VB|_ the|the|DT|_ transcript|transcript|NN|_ change|change|NN|_ between|between|IN|_ two|two|CD|_ conditions|condition|NNS|_ and|and|CC|_ the|the|DT|_ transcript|transcript|NN|_ presence|presence|NN|_ under|under|IN|_ each|each|DT|_ condition|condition|NN|_ .|.|.|_ Background-subtracted|background-subtracted|JJ|_ data|datum|NNS|_ sets|set|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ up-regulated|up-regulate|VBN|_ and|and|CC|_ down-regulated|down-regulate|VBN|_ genes|gene|NNS|_ based|base|VBN|_ on|on|IN|_ fold|fold|JJ|_ changes|change|NNS|_ of|of|IN|_ greater|greater|JJR|_ than|than|IN|_ 2|2|CD|_ .|.|.|_
E.coli|e.coli|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ with|with|IN|_ aeration|aeration|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ until|until|IN|_ early|early|JJ|_ log|log|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ strain|strain|NN|_ JM109|jm109|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
JM109-1|jm109-1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
JM109-2|jm109-2|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
JM109-3|jm109-3|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
JM109|jm109|NN|_ GLY-1|gly-1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
JM109|jm109|NN|_ GLY-2|gly-2|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
JM109|jm109|NN|_ GLY-3|gly-3|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ commercial|commercial|JJ|_ product|product|NN|_ TRIzol|trizol|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Disrupt|disrupt|VB|_ about|about|IN|_ 107cells|107cell|NNS|_ with|with|IN|_ a|a|DT|_ homogenizer|homogenizer|NN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ TRIzol|trizol|NN|_ Reafent|reafent|NN|_ on|on|IN|_ ice|ice|NN|_ .|.|.|_ Store|Store|NNP|_ the|the|DT|_ homogenate|homogenate|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ to|to|TO|_ permit|permit|VB|_ the|the|DT|_ complete|complete|JJ|_ dissociation|dissociation|NN|_ of|of|IN|_ nucleoprotein|nucleoprotein|NN|_ complexes|complex|NNS|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ supplement|supplement|VBP|_ the|the|DT|_ homogenate|homogenate|NN|_ with|with|IN|_ 0.2|0.2|CD|_ ml|ml|NN|_ chloroform|chloroform|NN|_ per|per|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ ,|,|,|_ cover|cover|VBP|_ the|the|DT|_ samples|sample|NNS|_ tightly|tightly|RB|_ and|and|CC|_ shake|shake|VB|_ vigorously|vigorously|RB|_ for|for|IN|_ 15|15|CD|_ seconds|seconds|NNS|_ .|.|.|_ Store|Store|NNP|_ the|the|DT|_ resulting|result|VBG|_ mixture|mixture|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 2-15|2-15|CD|_ minutes|minute|NNS|_ and|and|CC|_ centrifuge|centrifuge|NN|_ at|at|IN|_ 12,000|12,000|CD|_ g|g|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ C.|C.|NNP|_ Following|follow|VBG|_ centrifugation|centrifugation|NN|_ ,|,|,|_ the|the|DT|_ mixture|mixture|NN|_ separates|separate|VBZ|_ into|into|IN|_ a|a|DT|_ lower|lower|JJR|_ red|red|JJ|_ phenol-chloroform|phenol-chloroform|NN|_ phase|phase|NN|_ ,|,|,|_ interphase|interphase|NN|_ and|and|CC|_ the|the|DT|_ colorless|colorless|JJ|_ upper|upper|JJ|_ aqueous|aqueous|JJ|_ phase|phase|NN|_ .|.|.|_ Transfer|transfer|NN|_ the|the|DT|_ aqueous|aqueous|JJ|_ phase|phase|NN|_ to|to|TO|_ a|a|DT|_ fresh|fresh|JJ|_ tube|tube|NN|_ .|.|.|_ Precipitate|precipitate|VB|_ RNA|rna|NN|_ from|from|IN|_ the|the|DT|_ aqueous|aqueous|JJ|_ phase|phase|NN|_ by|by|IN|_ mixing|mix|VBG|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Use|Use|NNP|_ 0.5|0.5|CD|_ ml|ml|NN|_ of|of|IN|_ isopropanol|isopropanol|NN|_ per|per|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ used|use|VBD|_ for|for|IN|_ the|the|DT|_ initial|initial|JJ|_ homogenization|homogenization|NN|_ .|.|.|_ Store|Store|NNP|_ samples|sample|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5-10|5-10|CD|_ minutes|minute|NNS|_ and|and|CC|_ centrifuge|centrifuge|NN|_ at|at|IN|_ 12,000|12,000|CD|_ g|g|NN|_ for|for|IN|_ 8|8|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ -|-|:|_ 25|25|CD|_ C.|C.|NNP|_ Remove|remove|VB|_ the|the|DT|_ supernatant|supernatant|NN|_ and|and|CC|_ wash|wash|VB|_ the|the|DT|_ RNA|rna|NN|_ pellet|pellet|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ vortexing|vortex|VBG|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 75|75|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ and|and|CC|_ subsequent|subsequent|JJ|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 7,500|7,500|CD|_ g|g|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ 4|4|CD|_ -|-|:|_ 25|25|CD|_ C.|C.|NNP|_ Add|add|VB|_ at|at|IN|_ least|least|JJS|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ 75|75|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ per|per|IN|_ 1|1|CD|_ ml|ml|NN|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ used|use|VBD|_ for|for|IN|_ the|the|DT|_ initial|initial|JJ|_ homogenization|homogenization|NN|_ .|.|.|_ Remove|remove|VB|_ the|the|DT|_ ethanol|ethanol|NN|_ wash|wash|NN|_ and|and|CC|_ briefly|briefly|NN|_ air-dry|air-dry|VB|_ the|the|DT|_ RNA|rna|NN|_ pellet|pellet|NN|_ for|for|IN|_ 3|3|LS|_ -|-|:|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ Dissolve|dissolve|VB|_ RNA|rna|NN|_ in|in|IN|_ DEPC-treated|depc-treated|JJ|_ water|water|NN|_ by|by|IN|_ passing|pass|VBG|_ solution|solution|NN|_ a|a|DT|_ few|few|JJ|_ times|time|NNS|_ through|through|IN|_ a|a|DT|_ pipette|pipette|NN|_ tip|tip|NN|_ .|.|.|_ Using|use|VBG|_ an|a|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ purify|purify|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ 200|200|CD|_ mM|mm|NN|KWSUPP glyphosate|glyphosate|NN|_ shock|shock|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_
Treatment|Treatment|NNP|_ protocol|protocol|NN|_ -|-|:|_ E.coli|e.coli|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ at|at|IN|_ 37C|37c|NN|_ until|until|IN|_ early|early|JJ|_ log|log|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 200|200|CD|_ mM|mm|NN|KWSUPP glyphosate|glyphosate|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ after|after|IN|_ that|that|IN|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ to|to|TO|_ extract|extract|NN|_ RNA|rna|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ without|without|IN|_ salt|salt|NN|_ shock|shock|NN|_
BW25113|bw25113|NN|_ mqsR|mqsr|NN|GEN
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Planktonic|planktonic|JJ|_ cells|cell|NNS|_ harvested|harvest|VBN|_ at|at|IN|_ a|a|DT|_ turbidity|turbidity|NN|_ of|of|IN|_ 0.5|0.5|CD|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ ,|,|,|_ adjusted|adjust|VBN|_ to|to|TO|_ the|the|DT|_ turbidity|turbidity|NN|_ at|at|IN|_ 1|1|CD|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ exposed|expose|VBN|_ to|to|TO|_ 20|20|CD|_ μg|μg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
genotype|genotype|NN|_
MAS|mas|NN|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|Setting|NNP|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
strains|strain|NNS|_ :|:|:|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_
temp|temp|NN|_ :|:|:|_ 37ºC|37ºc|NN|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 0.25|0.25|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ Planktonic|planktonic|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ a|a|DT|_ turbidity|turbidity|NN|_ of|of|IN|_ 0.5|0.5|CD|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ adjusted|adjust|VBN|_ the|the|DT|_ turbidity|turbidity|NN|_ to|to|TO|_ 1|1|CD|_ ,|,|,|_ and|and|CC|_ exposed|expose|VBN|_ to|to|TO|_ 20|20|CD|_ μg|μg|NN|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 0.25|0.25|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ mL|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ Planktonic|planktonic|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ a|a|DT|_ turbidity|turbidity|NN|_ of|of|IN|_ 0.5|0.5|CD|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ adjusted|adjust|VBN|_ the|the|DT|_ turbidity|turbidity|NN|_ to|to|TO|_ 1|1|CD|_ ,|,|,|_ and|and|CC|_ exposed|expose|VBN|_ to|to|TO|_ 20|20|CD|_ μg|μg|NN|_
time|time|NN|_ :|:|:|_ 1|1|CD|_ h|h|NN|_ with|with|IN|_ 20|20|CD|_ μg|μg|NN|_
EM1456|em1456|NN|_ wild-type|wild-type|JJ|_ pNM12|pnm12|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
experiment|experiment|NN|_ #|#|#|_ 115|115|CD|_
experiment|experiment|NN|_ #|#|#|_ 116|116|CD|_
experiment|experiment|NN|_ #|#|#|_ 203|203|CD|_
experiment|experiment|NN|_ #|#|#|_ 204|204|CD|_
experiment|experiment|NN|_ #|#|#|_ 205|205|CD|_
experiment|experiment|NN|_ #|#|#|_ 206|206|CD|_
experiment|experiment|NN|_ #|#|#|_ 303|303|CD|_
experiment|experiment|NN|_ #|#|#|_ 305|305|CD|_
experiment|experiment|NN|_ #|#|#|_ 306|306|CD|_
fur|fur|NN|GEN mutant|mutant|JJ|_ pBAD-ryhB|pbad-ryhb|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
fur|fur|NN|GEN mutant|mutant|JJ|_ pBAD-ryhB|pbad-ryhb|NN|_ #|#|#|_ 2|2|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
fur|fur|NN|GEN mutant|mutant|JJ|_ pNM12|pnm12|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
fur|fur|NN|GEN mutant|mutant|JJ|_ pNM12|pnm12|NN|_ #|#|#|_ 2|2|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
Microarray|microarray|NN|_ suite|suite|NN|_ 5.0|5.0|CD|_
Strain|strain|NN|_ EM1453|em1453|NN|_ wild-type|wild-type|JJ|_ pBAD-ryhB|pbad-ryhb|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pBAD-ryhB|pbad-ryhb|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pBAD-ryhB|pbad-ryhb|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ FeSO4|feso4|NN|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pBAD-ryhB|pbad-ryhb|NN|_ #|#|#|_ 2|2|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pBAD-ryhB|pbad-ryhb|NN|_ #|#|#|_ 2|2|CD|_ +|+|CC|_ FeSO4|feso4|NN|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pNM12|pnm12|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pNM12|pnm12|NN|_ #|#|#|_ 1|1|CD|_ +|+|CC|_ FeSO4|feso4|NN|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pNM12|pnm12|NN|_ #|#|#|_ 2|2|CD|_ +|+|CC|_ arabinose|arabinose|NN|_
wild-type|wild-type|JJ|_ pNM12|pnm12|NN|_ #|#|#|_ 2|2|CD|_ +|+|CC|_ FeSO4|feso4|NN|_ +|+|CC|_ arabinose|arabinose|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pBADRNE|pbadrne|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pBAD-RNE|pbad-rne|NN|_ w|w|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pNRNE5|pnrne5|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pRNG3|prng3|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rng|rng|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rng|rng|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ pPM30|ppm30|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ pRNG3|prng3|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pBADRNE|pbadrne|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ Trial|trial|NN|_ B|b|NN|_ *|*|SYM|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pBAD-RNE|pbad-rne|NN|_ w|w|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pNRNE5|pnrne5|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ Trial|trial|NN|_ A|a|NN|_ *|*|SYM|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pNRNE5|pnrne5|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ Trial|trial|NN|_ B|b|NN|_ *|*|SYM|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pRNG3|prng3|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ Trial|trial|NN|_ A|a|NN|_ *|*|SYM|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rne|rne|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ pRNG3|prng3|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ Trial|trial|NN|_ B|b|NN|_ *|*|SYM|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rng|rng|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ Trial|trial|NN|_ B|b|NN|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ rng|rng|NN|GEN deletion|deletion|NN|_ -RRB-|-rrb-|-RRB-|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Trial|trial|NN|_ A|a|NN|_ *|*|SYM|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ pRNG3|prng3|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ Trial|trial|NN|_ A|a|DT|_ *|*|SYM|_
N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N3433|n3433|NN|_ -LRB-|-lrb-|-LRB-|_ wt|wt|JJ|_ -RRB-|-rrb-|-RRB-|_ pRNG3|prng3|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ Trial|trial|NN|_ B|b|NN|_ *|*|SYM|_
VALUE|VALUE|NNP|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
A10|a10|NN|_ :|:|:|_ LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ MMAcetat|mmacetat|NN|_
A11|a11|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30|ptm30|NN|_ MMAcetat|mmacetat|NN|_
A12|a12|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ MMAcetat|mmacetat|NN|_
A1|a1|NN|_ :|:|:|_ LJ110|lj110|NN|_ LBo|lbo|NN|_
A2|a2|NN|_ :|:|:|_ LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ LBo|lbo|FW|_
A3|a3|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30|ptm30|NN|_ LBo|lbo|NN|_
A4|a4|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ LBo|lbo|NN|_
A5|a5|NN|_ :|:|:|_ LJ110|lj110|NN|_ MMPyruvat|mmpyruvat|NN|_
A6|a6|NN|_ :|:|:|_ LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ MMPyruvat|mmpyruvat|NN|_
A7|a7|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30|ptm30|NN|_ MMPyruvat|mmpyruvat|NN|_
A8|a8|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ MMPyruvat|mmpyruvat|NN|_
A9|a9|NN|_ :|:|:|_ LJ110|lj110|NN|_ MMAcetat|mmacetat|NN|_
B10|b10|NN|_ :|:|:|_ LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ MMAcetat|mmacetat|NN|_
B11|b11|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30|ptm30|NN|_ MMAcetat|mmacetat|NN|_
B12|b12|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ MMAcetat|mmacetat|NN|_
B1|b1|NN|_ :|:|:|_ LJ110|lj110|NN|_ LBo|lbo|NN|_
B2|b2|NN|_ :|:|:|_ LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ LBo|lbo|FW|_
B3|b3|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30|ptm30|NN|_ LBo|lbo|NN|_
B4|b4|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ LBo|lbo|NN|_
B5|b5|NN|_ :|:|:|_ LJ110|lj110|NN|_ MMPyruvat|mmpyruvat|NN|_
B6|b6|NN|_ :|:|:|_ LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ MMPyruvat|mmpyruvat|NN|_
B7|b7|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30|ptm30|NN|_ MMPyruvat|mmpyruvat|NN|_
B8|b8|NN|_ :|:|:|_ LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ MMPyruvat|mmpyruvat|NN|_
B9|b9|NN|_ :|:|:|_ LJ110|lj110|NN|_ MMAcetat|mmacetat|NN|_
background|background|NN|_ strain|strain|NN|_ :|:|:|_ LJ110|lj110|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ the|the|DT|_ software|software|NN|_ package|package|NN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ 10.5.1.1|10.5.1.1|CD|_ using|use|VBG|_ protocol|protocol|NN|_ GE1|ge1|NN|_ _|_|NN|_ 105|105|CD|_ _|_|SYM|_ Dec08|dec08|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ;|;|:|_ Waldbronn|Waldbronn|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_
genetic|genetic|JJ|_ modification|modification|NN|_ :|:|:|_ empty|empty|JJ|_ plasmid|plasmid|NN|_ -LRB-|-lrb-|-LRB-|_ LJ110|lj110|NN|_
genetic|genetic|JJ|_ modification|modification|NN|_ :|:|:|_ PdhR|pdhr|NN|TF knockout|knockout|NN|_ mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ LJ110deltapdhR|lj110deltapdhr|NN|_ -RRB-|-rrb-|-RRB-|_
genetic|genetic|JJ|_ modification|modification|NN|_ :|:|:|_ PdhR|pdhr|NN|TF overexpression|overexpression|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ LJ110|lj110|NN|_
genetic|genetic|JJ|_ modification|modification|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ LJ110|lj110|CD|_
LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ LBo|lbo|FW|_
LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ MMAcetat|mmacetat|NN|_
LJ110|lj110|NN|_ del|del|FW|_ pdhr|pdhr|FW|_ MMPyruvat|mmpyruvat|NN|_
LJ110|lj110|NN|_ LBo|lbo|NN|_
LJ110|lj110|NN|_ MMAcetat|mmacetat|NN|_
LJ110|lj110|NN|_ MMPyruvat|mmpyruvat|NN|_
LJ110|lj110|NN|_ pTM30|ptm30|NN|_ LBo|lbo|NN|_
LJ110|lj110|NN|_ pTM30|ptm30|NN|_ MMAcetat|mmacetat|NN|_
LJ110|lj110|NN|_ pTM30|ptm30|NN|_ MMPyruvat|mmpyruvat|NN|_
LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ LBo|lbo|NN|_
LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ MMAcetat|mmacetat|NN|_
LJ110|lj110|NN|_ pTM30pdhr|ptm30pdhr|NN|_ MMPyruvat|mmpyruvat|NN|_
MMAcetat|mmacetat|NN|_
MMPyruvat|mmpyruvat|NN|_
RNAeasy|rnaeasy|NN|_
CRE|cre|NN|_ Multi|multi|JJ|_ 0uM|0um|NN|_ Rep1|rep1|NN|_ Plasmid|plasmid|NN|_
CRE|cre|NN|_ Multi|multi|JJ|_ 0uM|0um|NN|_ Rep2|rep2|NN|_ Plasmid|plasmid|NN|_
CRE|cre|NN|_ Multi|multi|JJ|_ 100uM|100um|NN|_ Rep1|rep1|NN|_ Plasmid|plasmid|NN|_
CRE|cre|NN|_ Multi|multi|JJ|_ 100uM|100um|NN|_ Rep2|rep2|NN|_ Plasmid|plasmid|NN|_
CRE|cre|NN|_ Single|single|JJ|_ 100uM|100um|NN|_ Rep1|rep1|NN|_ Plasmid|plasmid|NN|_
CRE|cre|NN|_ Single|single|JJ|_ 100uM|100um|NN|_ Rep2|rep2|NN|_ Plasmid|plasmid|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
HEK293T|hek293t|NN|_
IFNB|ifnb|NN|_ Multi|multi|JJ|_ SeV0|sev0|NN|_ Rep1|rep1|NN|_ Plasmid|plasmid|NN|_
IFNB|ifnb|NN|_ Multi|multi|JJ|_ SeV10|sev10|NN|_ Rep1|rep1|NN|_ Plasmid|plasmid|NN|_
IFNB|ifnb|NN|_ Single|single|JJ|_ SeV10|sev10|NN|_ Rep1|rep1|NN|_ Plasmid|plasmid|NN|_
Plasmid|plasmid|NN|_ pool|pool|NN|_
reporter|reporter|NN|_ :|:|:|_ CRE|cre|NN|_ multi-hit|multi-hit|JJ|_
reporter|reporter|NN|_ :|:|:|_ CRE|cre|NN|_ single-hit|single-hit|JJ|_
reporter|reporter|NN|_ :|:|:|_ IFNB|ifnb|NN|_ multi-hit|multi-hit|JJ|_
reporter|reporter|NN|_ :|:|:|_ IFNB|ifnb|NN|_ single-hit|single-hit|JJ|_
RNA-Seq|rna-seq|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ plasmid|plasmid|NN|_ pool|pool|NN|_
To|to|TO|_ infer|infer|VB|_ the|the|DT|_ tag|tag|NN|GEN copy|copy|NN|_ numbers|number|NNS|_ in|in|IN|_ each|each|DT|_ Tag-Seq|Tag-Seq|NNP|_ library|library|NN|_ ,|,|,|_ all|all|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ examined|examine|VBN|_ ,|,|,|_ regardless|regardless|RB|_ of|of|IN|_ their|they|PRP$|_ quality|quality|NN|_ scores|score|NNS|_ .|.|.|_ If|if|IN|_ the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ nucleotides|nucleotide|NNS|_ of|of|IN|_ a|a|DT|_ read|read|NN|_ perfectly|perfectly|RB|_ matched|match|VBD|_ one|one|CD|_ of|of|IN|_ the|the|DT|_ 13,000|13,000|CD|_ or|or|CC|_ 27,000|27,000|CD|_ designed|design|VBN|_ tags|tag|NNS|_ and|and|CC|_ the|the|DT|_ remaining|remain|VBG|_ nucleotides|nucleotide|NNS|_ matched|match|VBD|_ the|the|DT|_ expected|expect|VBN|_ upstream|upstream|JJ|_ MPRA|MPRA|NNP|_ construct|construct|NN|_ sequence|sequence|NN|_ ,|,|,|_ this|this|DT|_ was|be|VBD|_ counted|count|VBN|_ as|as|IN|_ one|one|CD|_ occurrence|occurrence|NN|_ of|of|IN|_ that|that|DT|_ tag|tag|NN|GEN .|.|.|_ All|all|DT|_ reads|read|VBZ|_ that|that|IN|_ did|do|VBD|_ not|not|RB|_ meet|meet|VB|_ this|this|DT|_ criterion|criterion|NN|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ lysates|lysate|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ MicroPoly|MicroPoly|NNP|_ -LRB-|-lrb-|-LRB-|_ A|A|NNP|_ -RRB-|-rrb-|-RRB-|_ Puristâ|Puristâ|NNP|_ ``|``|``|_ ¢|¢|$|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ I|i|CD|_ using|use|VBG|_ the|the|DT|_ Turbo|Turbo|NNP|_ DNA-freeâ|DNA-freeâ|NNP|_ ``|``|``|_ ¢|¢|$|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ from|from|IN|_ 400-700|400-700|CD|_ ng|ng|NN|_ mRNA|mrna|NN|_ using|use|VBG|_ High|high|JJ|_ Capacity|capacity|NN|_ RNA-to-cDNA|rna-to-cdna|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Tag-Seq|tag-seq|JJ|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ directly|directly|RB|_ from|from|IN|_ 12|12|CD|_ %|%|NN|_ of|of|IN|_ a|a|DT|_ cDNA|cdna|NN|_ reaction|reaction|NN|_ or|or|CC|_ 50|50|CD|_ ng|ng|NN|_ plasmid|plasmid|NN|_ DNA|dna|NN|_ by|by|IN|_ 26|26|CD|_ cycle|cycle|NN|_ PCR|pcr|NN|_ using|use|VBG|_ Pfu|pfu|NN|_ Ultra|Ultra|NNP|_ HS|hs|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ 2x|2x|NN|_ master|master|NN|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ primers|primer|NNS|_ AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT|AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT|NNP|_ and|and|CC|_ CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG|CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG|NNP|_ -LRB-|-lrb-|-LRB-|_ where|where|WRB|_ XXXXXXXX|XXXXXXXX|NNP|_ is|be|VBZ|_ a|a|DT|_ library-specific|library-specific|JJ|_ index|index|NN|_ sequence|sequence|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ resultant|resultant|JJ|_ PCR|pcr|NN|_ products|product|NNS|_ were|be|VBD|_ size-selected|size-selected|JJ|_ using|use|VBG|_ 2|2|CD|_ %|%|NN|_ agarose|agarose|NN|_ E-Gel|e-gel|NN|_ EX|ex|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ N|n|NN|_
0|0|CD|_ min|min|NN|_
10|10|CD|_ min|min|NN|_
30|30|CD|_ min|min|NN|_
60|60|CD|_ min|min|NN|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 9.5.3.1|9.5.3.1|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 0|0|CD|_ min|min|NN|_ vs|vs|CC|_ 10|10|CD|_ min|min|NN|_ Rep1|rep1|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 10|10|CD|_ min|min|NN|_ vs|vs|CC|_ 0|0|CD|_ min|min|NN|_ Rep2|rep2|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 30|30|CD|_ min|min|NN|_ vs|vs|CC|_ 60|60|CD|_ min|min|NN|_ Rep1|rep1|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism 60|60|CD|_ min|min|NN|_ vs|vs|CC|_ 30|30|CD|_ min|min|NN|_ Rep2|rep2|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
One|one|CD|_ conditions|condition|NNS|_ :|:|:|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_
Overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ BW25113|bw25113|NN|_ in|in|IN|_ LB|lb|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED with|with|IN|_ supplements|supplement|NNS|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ and|and|CC|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ Ceilsus|ceilsus|NN|_ degree|degree|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250rpm|250rpm|NN|_ until|until|IN|_ its|its|PRP$|_ OD600|od600|NN|_ reached|reach|VBD|_ 0.1|0.1|CD|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 60|60|CD|_ min|min|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ 5|5|CD|_ ml|ml|NN|_ cell|cell|NN|_ culture|culture|NN|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ and|and|CC|_ 60|60|CD|_ min|min|NN|_ incubation|incubation|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ isooctane|isooctane|NN|_ using|use|VBG|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_
treatment|treatment|NN|_ :|:|:|_ 5|5|CD|_ percent|percent|NN|_ isooctane|isooctane|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
normalized|normalize|VBD|_ using|use|VBG|_ lcDNA|lcdna|NN|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 15|15|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 15|15|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|NN|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 30|30|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 30|30|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
ppsA|ppsa|NN|GEN mutant|mutant|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
reference|reference|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ immediately|immediately|RB|_ prior|prior|RB|_ to|to|TO|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
strain|strain|NN|_ BW25113|bw25113|NN|_
Strain|strain|NN|_ BW25113|bw25113|NN|_
Strain|strain|NN|_ BW25113|bw25113|NN|_
strain|strain|NN|_ BW25113|bw25113|NN|_ ppsA|ppsa|NN|GEN deletion|deletion|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 15|15|CD|_ min|min|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 1|1|CD|_ hour|hour|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 2|2|CD|_ hour|hour|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 30|30|CD|_ min|min|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 3|3|CD|_ hour|hour|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 4|4|CD|_ hour|hour|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 5|5|CD|_ hour|hour|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 5|5|CD|_ min|min|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
time|time|NN|_ course|course|NN|_ sample|sample|NN|_ harvested|harvest|VBN|_ after|after|IN|_ 6|6|CD|_ hour|hour|NN|_ of|of|IN|_ glucose|glucose|NN|SUPP to|to|TO|_ acetate|acetate|NN|SUPP shift|shift|NN|_
wild-type|wild-type|JJ|_ 15|15|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 15|15|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 15|15|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 15|15|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 1|1|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 2|2|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 30|30|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 30|30|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 30|30|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 30|30|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 3|3|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 4|4|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 5|5|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
wild-type|wild-type|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 1|1|CD|_
wild-type|wild-type|JJ|_ 6|6|CD|_ hour|hour|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ slide|slide|NN|_ 2|2|CD|_
After|after|IN|_ 6|6|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ both|both|CC|_ control|control|NN|_ and|and|CC|_ test|test|NN|_ strains|strain|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ and|and|CC|_ harvested|harvest|VBN|_ 2|2|CD|_ hours|hour|NNS|_ post-induction|post-induction|JJ|_ .|.|.|_
EGS084|egs084|NN|_
EGS084|egs084|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 1|1|CD|_
EGS084|egs084|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 2|2|CD|_
EGS084|egs084|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 3|3|CD|_
EGS084|egs084|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 4|4|CD|_
EGS084|egs084|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|SYM|_ 5|5|CD|_
EGS084|egs084|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 6|6|CD|_
EGS212|egs212|NN|_
EGS212|egs212|NN|_ _|_|CD|_ MlfabH|mlfabh|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 1|1|CD|_
EGS212|egs212|NN|_ _|_|CD|_ MlfabH|mlfabh|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 2|2|CD|_
EGS212|egs212|NN|_ _|_|CD|_ MlfabH|mlfabh|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 3|3|CD|_
EGS212|egs212|NN|_ _|_|CD|_ MlfabH|mlfabh|NN|_ _|_|CD|_ rep|rep|NN|GEN _|_|NN|_ 4|4|CD|_
EGS212|egs212|NN|_ _|_|CD|_ MlfabH|mlfabh|NN|_ _|_|NN|_ rep|rep|NN|GEN _|_|CD|_ 5|5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH1|dh1|NN|_ ∆|∆|CD|_ fadE|fade|NN|GEN control|control|NN|_ and|and|CC|_ test|test|NN|_ strains|strain|NNS|_ were|be|VBD|_ seeded|seed|VBN|_ with|with|IN|_ OD600nm|od600nm|NN|_ 0.03|0.03|CD|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 15|15|CD|_ ml|ml|NN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ broth|broth|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 200rpm|200rpm|JJ|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
genotype|genotype|NN|_ :|:|:|_ ∆|∆|CD|_ fadE|fade|NN|GEN with|with|IN|_ overexpression|overexpression|NN|_ of|of|IN|_ `|`|``|_ tesA|tesa|NN|GEN and|and|CC|_ MlfabH|mlfabh|NN|_ via|via|IN|_ an|a|DT|_ IPTG-inudcible|iptg-inudcible|JJ|_ promoter|promoter|NN|_
genotype|genotype|NN|_ :|:|:|_ ∆|∆|CD|_ fadE|fade|NN|GEN with|with|IN|_ overexpression|overexpression|NN|_ of|of|IN|_ `|`|``|_ tesA|tesa|NN|GEN via|via|IN|_ an|a|DT|_ IPTG-inudcible|iptg-inudcible|JJ|_ promoter|promoter|NN|_
phenotype|phenotype|NN|_ :|:|:|_ normal|normal|JJ|_
phenotype|phenotype|NN|_ :|:|:|_ small|small|JJ|_ improvement|improvement|NN|_ in|in|IN|_ methyl|methyl|NN|_ ketone|ketone|NN|_ production|production|NN|_
substrain|substrain|NN|_ :|:|:|_ DH1|dh1|NN|_
The|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ RMA|rma|NN|_ -LRB-|-lrb-|-LRB-|_ Robust|robust|JJ|_ Multi-Array|multi-array|JJ|_ Analysis|analysis|NN|_ ;|;|:|_ Irizarry|Irizarry|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Biostatistics|biostatistic|NNS|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 249|249|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 19|19|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 185|185|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ background|background|NN|_ correction|correction|NN|_ as|as|IN|_ implemented|implement|VBN|_ in|in|IN|_ the|the|DT|_ NimbleScan|NimbleScan|NNP|_ software|software|NN|_ package|package|NN|_ ,|,|,|_ version|version|NN|_ 2.4.27|2.4.27|CD|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ NimbleGen|NimbleGen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ with|with|IN|_ the|the|DT|_ RNase-Free|rnase-free|JJ|_ DNase|dnase|NN|_ set|set|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ on|on|IN|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ ND-1000|nd-1000|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ bioanalyzer|bioanalyzer|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ thymine|thymine|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 120|120|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 120|120|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 120|120|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 120|120|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ thymine|thymine|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 120|120|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 120|120|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ thymine|thymine|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ thymine|thymine|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 90|90|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ +|+|CC|_ adenine|adenine|NN|_ +|+|CC|_ glycine|glycine|NN|_ +|+|CC|_ methionine|methionine|NN|SUPP treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ 90|90|CD|_ min|min|NN|_ after|after|IN|_ TMP|tmp|NN|_ treatment|treatment|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ in|in|IN|_ M9|m9|NN|_ media|media|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
LBTMP50|lbtmp50|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
LBTMP50|lbtmp50|NN|_ _|_|NN|_ 120|120|CD|_ min|min|NN|_
LBTMP50|lbtmp50|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_
LBTMP50|lbtmp50|NN|_ _|_|CD|_ 60|60|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|NN|_ 120|120|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ 60|60|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ 90|90|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ AdAA|adaa|NN|_ _|_|NN|_ 10|10|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ AdAA|adaa|NN|_ _|_|NN|_ 120|120|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ AdAA|adaa|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ AdAA|adaa|NN|_ _|_|NN|_ 60|60|CD|_ min|min|NN|_
M9TMP5|m9tmp5|NN|_ _|_|CD|_ AdAA|adaa|NN|_ _|_|NN|_ 90|90|CD|_ min|min|NN|_
M9|m9|NN|_ _|_|CD|_ TMP5|tmp5|NN|_ _|_|NN|_ THY|thy|NN|_ _|_|CD|_ Ad|ad|NN|_ _|_|SYM|_ AA|aa|SYM|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_
M9|m9|NN|_ _|_|CD|_ TMP5|tmp5|NN|_ _|_|CD|_ THY|THY|NNP|_ _|_|SYM|_ Ad|ad|FW|_ _|_|FW|_ AA|aa|NN|_ _|_|NN|_ 120|120|CD|_ min|min|NN|_
M9|m9|NN|_ _|_|CD|_ TMP5|tmp5|NN|_ _|_|CD|_ THY|THY|NNP|_ _|_|SYM|_ Ad|ad|FW|_ _|_|FW|_ AA|aa|NN|_ _|_|SYM|_ 30|30|CD|_ min|min|NN|_
M9|m9|NN|_ _|_|CD|_ TMP5|tmp5|NN|_ _|_|CD|_ THY|THY|NNP|_ _|_|SYM|_ Ad|ad|FW|_ _|_|FW|_ AA|aa|NN|_ _|_|NN|_ 60|60|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ AA|aa|NN|_ _|_|NN|_ 10|10|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ AA|aa|NN|_ _|_|NN|_ 120|120|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ AA|aa|NN|_ _|_|SYM|_ 30|30|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ AA|aa|NN|_ _|_|NN|_ 60|60|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ Ad|ad|NN|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ Ad|ad|NN|_ _|_|NN|_ 120|120|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ Ad|ad|NN|_ _|_|SYM|_ 30|30|CD|_ min|min|NN|_
M9TMP|m9tmp|NN|_ _|_|CD|_ Ad|ad|NN|_ _|_|SYM|_ 60|60|CD|_ min|min|NN|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ and|and|CC|_ TMP|tmp|NN|_ was|be|VBD|_ added|add|VBN|_ when|when|WRB|_ the|the|DT|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ 0.3-0.4|0.3-0.4|CD|_ .|.|.|_
Raw|raw|NN|_ fluorescence|fluorescence|NN|_ intensity|intensity|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Time-point|time-point|NN|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ every|every|DT|_ 15-30|15-30|CD|_ minutes|minute|NNS|_ from|from|IN|_ 15|15|CD|_ minutes|minute|NNS|_ to|to|TO|_ 2|2|CD|_ hours|hour|NNS|_ post|post|NN|_ treatment|treatment|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Chatsworth|Chatsworth|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
20|20|CD|_ ug|ug|NN|_ of|of|IN|_ Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ OD|od|NN|_ 600|600|CD|_ =|=|JJ|_ 0.8|0.8|CD|_
20|20|CD|_ ug|ug|NN|_ of|of|IN|_ Total|total|JJ|_ RNA|rna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ OD|od|NN|_ 600|600|CD|_ =|=|JJ|_ 0.8|0.8|CD|_
2|2|CD|_ ug|ug|NN|_ of|of|IN|_ Genomic|genomic|JJ|_ MG|mg|NN|_ 1655|1655|CD|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ DNA|dna|NN|_
2|2|CD|_ ug|ug|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ Genomic|genomic|JJ|_ DNA|dna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Transcript|transcript|NN|_ Abundance|abundance|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ OD600|od600|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ Trial|trial|NN|_ A|a|DT|_
Transcript|Transcript|NNP|_ Abundance|Abundance|NNP|_ in|in|IN|_ LB|LB|NNP|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ OD600|od600|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ Trial|trial|NN|_ B|b|NN|_
Transcript|transcript|NN|_ Abundance|abundance|NN|_ in|in|IN|_ M9|m9|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ OD600|od600|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ Trial|trial|NN|_ A|a|NN|_
Transcript|transcript|NN|_ Abundance|abundance|NN|_ in|in|IN|_ M9|m9|NN|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ OD600|od600|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ Trial|trial|NN|_ B|b|NN|_
VALUE|value|NN|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
2|2|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_
2|2|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ A|a|NN|_
2|2|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ B|b|NN|_
4|4|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_
4|4|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ A|a|NN|_
4|4|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ B|b|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ A|a|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ B|b|NN|_
8|8|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ MCM|mcm|NN|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ A|a|NN|_
8|8|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_
8|8|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ Trial|trial|NN|_ B|b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MG1655|mg1655|NN|_ 2|2|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ 4|4|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ 8|8|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ at|at|IN|_ 30|30|CD|_ Degrees|degree|NNS|_
MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ MCM|mcm|NN|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_
MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ MCM|mcm|NN|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ 8|8|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_
MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ 2|2|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ 4|4|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ Repaired|repair|VBN|_ NCM|NCM|NNP|_ 3416|3416|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_ 8|8|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
VALUE|value|NN|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ mean|mean|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
lrp|lrp|NN|GEN -|-|:|_ +|+|CC|_ Leu|Leu|NNP|_ vs.|vs.|FW|_ lrp|lrp|SYM|GEN -|-|:|_ -|-|:|_ Leu|leu|NN|_
lrp|lrp|NN|GEN -|-|:|_ -|-|:|_ Leu|leu|NN|_ vs.|vs.|CC|_ wt|wt|JJ|_ -|-|:|_ Leu|leu|NN|_
lrp|lrp|NN|GEN -|-|:|_ +|+|CC|_ Leu|Leu|NNP|_ vs.|vs.|FW|_ wt|wt|JJ|_ -|-|:|_ Leu|leu|NN|_
VALUE|value|NN|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
\|\|CD|_ W3110|w3110|NN|_ lrp|lrp|NN|GEN -|-|:|_ at|at|IN|_ OD420|od420|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ in|in|IN|_ MOPS|mop|NNS|MED -LRB-|-lrb-|-LRB-|_ ile|ile|FW|_ ,|,|,|_ val|val|NN|_ ,|,|,|_ thi|thi|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 20|20|CD|_ ug|ug|NN|_ total|total|NN|_ ,|,|,|_ 10|10|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_ \|\|SYM|_
\|\|SYM|_ W3110|w3110|CD|_ lrp|lrp|SYM|GEN -|-|:|_ at|at|IN|_ OD420|od420|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ in|in|IN|_ MOPS|mop|NNS|MED -LRB-|-lrb-|-LRB-|_ ile|ile|FW|_ ,|,|,|_ val|val|NN|_ ,|,|,|_ thi|thi|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ Leu|leu|NN|_ ,|,|,|_ 20|20|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,10|,10|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_ \|\|SYM|_
\|\|SYM|_ W3110|w3110|CD|_ lrp|lrp|SYM|GEN -|-|:|_ at|at|IN|_ OD420|od420|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ in|in|IN|_ MOPS|mop|NNS|MED -LRB-|-lrb-|-LRB-|_ ile|ile|FW|_ ,|,|,|_ val|val|NN|_ ,|,|,|_ thi|thi|NN|_ -RRB-|-rrb-|-RRB-|_ plus|plus|CC|_ Leu|leu|NN|_ ,|,|,|_ 20|20|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 10|10|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_ \|\|SYM|_
\|\|SYM|_ W3110|w3110|CD|_ lrp|lrp|SYM|GEN -|-|:|_ in|in|IN|_ MOPS|mop|NNS|MED -LRB-|-lrb-|-LRB-|_ ile|ile|FW|_ ,|,|,|_ val|val|NN|_ ,|,|,|_ thi|thi|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD420|od420|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ 20|20|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 10|10|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_ \|\|SYM|_
\|\|SYM|_ W3110|w3110|CD|_ wt|wt|JJ|_ in|in|IN|_ MOPS|mop|NNS|MED -LRB-|-lrb-|-LRB-|_ ile|ile|FW|_ ,|,|,|_ val|val|NN|_ ,|,|,|_ thi|thi|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD420|od420|CD|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ 20|20|CD|_ ug|ug|NN|_ total|total|JJ|_ ,10|,10|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_ \|\|SYM|_
\|\|SYM|_ W3110|w3110|CD|_ wt|wt|JJ|_ OD420|od420|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ in|in|IN|_ MOPS|mop|NNS|MED -LRB-|-lrb-|-LRB-|_ ile|ile|FW|_ ,|,|,|_ val|val|NN|_ ,|,|,|_ thi|thi|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ Leu|leu|NN|_ ,|,|,|_ 20|20|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 10|10|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_ \|\|CD|_
wt|wt|JJ|_ +|+|CC|_ Leu|leu|NN|_ vs.|vs.|CC|_ wt|wt|JJ|_ -|-|:|_ Leu|leu|NN|_
accession|accession|NN|_ :|:|:|_ U00006|U00006|NNP|_
Eco|Eco|NNP|_ 50ng|50ng|SYM|_ -|-|:|_ 0|0|CD|_ %|%|NN|_
Eco|eco|NN|_ 50ng|50ng|SYM|_ -|-|:|_ 10|10|CD|_ %|%|NN|_
Eco|eco|NN|_ 50ng|50ng|SYM|_ -|-|:|_ 15|15|CD|_ %|%|NN|_
Eco|eco|NN|_ 50ng|50ng|SYM|_ -|-|:|_ 20|20|CD|_ %|%|NN|_
Eco|eco|NN|_ 50ng|50ng|SYM|_ -|-|:|_ 25|25|CD|_ %|%|NN|_
Eco|eco|NN|_ 50ng|50ng|SYM|_ -|-|:|_ 32.5|32.5|CD|_ %|%|NN|_
Eco|eco|NN|_ 50ng|50ng|SYM|_ -|-|:|_ 45|45|CD|_ %|%|NN|_
Eco|eco|NN|_ 50ng|50ng|SYM|_ -|-|:|_ 5|5|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 0|0|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 10|10|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 15|15|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 20|20|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 25|25|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 32.5|32.5|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 45|45|CD|_ %|%|NN|_
Eco|eco|NN|_ 5ng|5ng|SYM|_ -|-|:|_ 5|5|CD|_ %|%|NN|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.3-0.4|0.3-0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Lennox|Lennox|NNP|_ LB|LB|NNP|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Becton|Becton|NNP|_ Dickinson|Dickinson|NNP|_ ,|,|,|_ Franklin|Franklin|NNP|_ Lakes|Lakes|NNP|_ ,|,|,|_ NJ|NJ|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ wild-type|wild-type|JJ|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Ultra|Ultra|NNP|_ Clean|Clean|NNP|_ Soil|Soil|NNP|_ DNA|dna|NN|_ -LRB-|-lrb-|-LRB-|_ MoBio|mobio|NN|_ Laboratories|Laboratories|NNPS|_ ,|,|,|_ Solana|Solana|NNP|_ Beach|Beach|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
genotype|genotype|NN|_ :|:|:|_ Wild|Wild|NNP|_ Type|type|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0|0|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 15|15|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 20|20|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 25|25|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 32.5|32.5|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 45|45|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ formamide|formamide|NN|_ content|content|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_ %|%|NN|_ formamide|formamide|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ rna|rna|NN|GEN -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_ ng|ng|NN|_
hybridization|hybridization|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ total|total|JJ|_ rna|rna|NN|GEN -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_ ng|ng|NN|_
phenotype|phenotype|NN|_ :|:|:|_ normal|normal|JJ|_
Raw|raw|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ Matlab|Matlab|NNP|_ -LRB-|-lrb-|-LRB-|_ The|the|DT|_ MathWorks|MathWorks|NNPS|_ ,|,|,|_ Natick|Natick|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ each|each|DT|_ probe|probe|NN|_ ,|,|,|_ the|the|DT|_ average|average|JJ|_ intensity|intensity|NN|_ of|of|IN|_ three|three|CD|_ replicates|replicate|VBZ|_ were|be|VBD|_ calculated|calculate|VBN|_ after|after|IN|_ the|the|DT|_ elimination|elimination|NN|_ of|of|IN|_ outliers|outlier|NNS|_ based|base|VBN|_ on|on|IN|_ a|a|DT|_ standard|standard|JJ|_ deviation|deviation|NN|_ test|test|NN|_ .|.|.|_ The|the|DT|_ average|average|NN|_ of|of|IN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ Nonsense|nonsense|NN|_ -RRB-|-rrb-|-RRB-|_ probes|probe|NNS|_ was|be|VBD|_ subtracted|subtract|VBN|_ from|from|IN|_ all|all|DT|_ averages|average|NNS|_ to|to|TO|_ obtain|obtain|VB|_ background-corrected|background-corrected|JJ|_ results|result|NNS|_ .|.|.|_
R.|R.|NNP|_ sphaeroides|sphaeroide|NNS|_ was|be|VBD|_ phototrophically|phototrophically|RB|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ 100-150|100-150|CD|_ kletts|klett|NNS|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Sistrom|Sistrom|NNP|_ 's|'s|POS|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Sistrom|sistrom|NN|_ ,|,|,|_ W.|W.|NNP|_ 1960|1960|CD|_ .|.|.|_ Journal|Journal|NNP|_ of|of|IN|_ General|General|NNP|_ Microbiology|Microbiology|NNP|_ .|.|.|_ 22:778-785|22:778-785|NN|_ -RRB-|-rrb-|-RRB-|_ amended|amend|VBN|_ with|with|IN|_ 33.9|33.9|CD|_ mM|mm|NN|KWSUPP succinate|succinate|NN|SUPP .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ M63|m63|NN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ cell|cell|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ controlled|control|VBN|_ ~|~|NN|_ 108|108|CD|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ heat|heat|NN|_ shock|shock|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ steady|steady|JJ|_ growth|growth|NN|_
heat|heat|NN|_ shock|shock|NN|_ response|response|NN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_
MDS42|mds42|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
MDS42|mds42|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
MDS42|mds42|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
MDS42|mds42|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 4|4|CD|_
MDS42|mds42|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 5|5|CD|_
MDS42|mds42|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 6|6|CD|_
MDS42|mds42|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 7|7|CD|_
MDS42|mds42|NN|_ exponentially|exponentially|RB|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_
MDS42|mds42|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
MDS42|mds42|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
MDS42|mds42|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 4|4|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 5|5|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 6|6|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 7|7|CD|_
MG1655|mg1655|NN|_ exponentially|exponentially|RB|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_
MG1655|mg1655|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
MG1655|mg1655|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ written|write|VBN|_ in|in|IN|_ R|r|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ finite|finite|JJ|_ hybridisation|hybridisation|NN|_ -LRB-|-lrb-|-LRB-|_ FH|fh|NN|_ -RRB-|-rrb-|-RRB-|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Ono|Ono|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ thermodynamic|thermodynamic|JJ|_ model|model|NN|_ of|of|IN|_ non-specific|non-specific|JJ|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ NSB|nsb|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ short|short|JJ|_ nucleotide|nucleotide|NN|_ microarrays|microarray|NNS|_ -LRB-|-lrb-|-LRB-|_ Furusawa|Furusawa|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MDS42|mds42|NN|_ -LRB-|-lrb-|-LRB-|_ genome|genome|NN|_ reduced|reduce|VBN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ parent|parent|NN|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ cold|cold|JJ|_ phenol-ethanol|phenol-ethanol|JJ|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ of|of|IN|_ phenol|phenol|NN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ prepared|prepare|VBN|_ in|in|IN|_ advance|advance|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 16,000|16,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
The|the|DT|_ log10|log10|NN|_ mRNA|mrna|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ pM|pm|NN|_ -RRB-|-rrb-|-RRB-|_ data|datum|NNS|_ are|be|VBP|_ provided|provide|VBN|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ SERIES|series|NN|_ record|record|NN|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 100|100|CD|_ µg|µg|NN|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 20|20|CD|_ mM|mm|NN|KWSUPP EDC|edc|NN|_ ,|,|,|_ pH|ph|NN|_ 5.8|5.8|CD|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 250|250|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.0|8.0|CD|_ ,|,|,|_ and|and|CC|_ 4|4|CD|_ mM|mm|NN|KWSUPP NaHCO3|nahco3|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ after|after|IN|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ were|be|VBD|_ pulverized|pulverize|VBN|_ by|by|IN|_ mixer|mixer|NN|_ milling|milling|NN|_ and|and|CC|_ thawed|thaw|VBN|_ in|in|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP DSP|DSP|NNP|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ quenched|quench|VBN|_ with|with|IN|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ Cl|Cl|NNP|_ 8.3|8.3|CD|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ cushion|cushion|NN|_ ,|,|,|_ and|and|CC|_ affinity|affinity|NN|_ purified|purify|VBN|_ via|via|IN|_ TF|tf|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
Clarified|clarify|VBD|_ extracts|extract|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ microccocal|microccocal|JJ|_ nuclease|nuclease|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ purified|purify|VBN|_ through|through|IN|_ a|a|DT|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ .|.|.|_ Ribosome-protected|ribosome-protected|JJ|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
DSP1|dsp1|NN|_ _|_|CD|_ AP|ap|NN|_
DSP1|dsp1|NN|_ _|_|CD|_ Total|total|JJ|_
DSP2|dsp2|NN|_ _|_|CD|_ AP|ap|NN|_
DSP2|dsp2|NN|_ _|_|CD|_ Total|total|JJ|_
DSP3|dsp3|NN|_ _|_|CD|_ AP|ap|NN|_
DSP3|dsp3|NN|_ _|_|CD|_ Total|total|JJ|_
EDC1|edc1|NN|_ _|_|CD|_ AP|ap|NN|_
EDC1|edc1|NN|_ _|_|CD|_ Total|total|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
Harvested|harvest|VBN|_ by|by|IN|_ chloramphenicol|chloramphenicol|NN|_ pre-treatment|pre-treatment|NN|_ and|and|CC|_ centrifugation|centrifugation|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ DSP|DSP|NNP|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ EDC|edc|NN|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ TF|tf|NN|_ crosslinked|crosslink|VBD|_ RNC|rnc|NN|_ footprints|footprint|NNS|_
Harvested|harvest|VBN|_ by|by|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ ;|;|:|_ EDC|edc|NN|_ treated|treat|VBN|_ ex|ex|FW|_ vivo|vivo|FW|_ ;|;|:|_ Total|total|JJ|_ footprints|footprint|NNS|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Ribosome|Ribosome|NNP|_ profiling|profile|VBG|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ Selective|selective|JJ|_ ribosome|ribosome|NN|_ profiling|profile|VBG|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
The|the|DT|_ .|.|.|_ align|align|VB|_ files|file|NNS|_ have|have|VBP|_ been|be|VBN|_ processed|process|VBN|_ using|use|VBG|_ tagalign|tagalign|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ first|first|JJ|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ extended|extend|VBN|_ to|to|TO|_ account|account|VB|_ for|for|IN|_ the|the|DT|_ linker|linker|NN|_ .|.|.|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 100|100|CD|_ µg|µg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ rep3|rep3|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ rep4|rep4|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ rep5|rep5|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ rep6|rep6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ hydroponic|hydroponic|JJ|_ system|system|NN|_ without|without|IN|_ interacting|interact|VBG|_ with|with|IN|_ the|the|DT|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ for|for|IN|_ 3|3|CD|_ days|day|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_ interacted|interact|VBD|_ with|with|IN|_ the|the|DT|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ for|for|IN|_ 3|3|CD|_ days|day|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED medium|medium|NN|MED until|until|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8,000|8,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ sterilized|sterilize|VBN|_ ,|,|,|_ plant|plant|NN|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Caspersen|Caspersen|NNP|_ et|et|FW|_ al.|al.|FW|_ 1999|1999|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ resultant|resultant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ plant|plant|NN|_ growth|growth|NN|_ medium|medium|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ approximately|approximately|RB|_ 10E9|10e9|JJ|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ roots|root|NNS|_ had|have|VBD|_ been|be|VBN|_ gently|gently|RB|_ rinsed|rinse|VBN|_ to|to|TO|_ remove|remove|VB|_ loosely|loosely|RB|_ attached|attach|VBN|_ bacteria|bacterium|NNS|_ and|and|CC|_ roots|root|NNS|_ were|be|VBD|_ cut|cut|VBN|_ directly|directly|RB|_ into|into|IN|_ 100|100|CD|_ ml|ml|NN|_ ice|ice|NN|_ cold|cold|JJ|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ H2O-saturated|h2o-saturated|JJ|_ phenol|phenol|NN|_ ,|,|,|_ pH|ph|NN|_ 4.3|4.3|CD|_ ,|,|,|_ in|in|IN|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Root|root|NN|_ extracts|extract|NNS|_ were|be|VBD|_ filtered|filter|VBN|_ using|use|VBG|_ 0.5|0.5|CD|_ µm|µm|NN|_ filters|filter|NNS|_ to|to|TO|_ separate|separate|JJ|_ bacteria|bacterium|NNS|_ cells|cell|NNS|_ from|from|IN|_ plant|plant|NN|_ cells|cell|NNS|_ in|in|IN|_ order|order|NN|_ to|to|TO|_ prevent|prevent|VB|_ interference|interference|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ labeling|labeling|NN|_ .|.|.|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ protect|protect|VB|_ solution|solution|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ during|during|IN|_ extraction|extraction|NN|_ .|.|.|_ Bacteria|bacterium|NNS|_ had|have|VBD|_ been|be|VBN|_ collected|collect|VBN|_ by|by|IN|_ shaking|shake|VBG|_ and|and|CC|_ washing|wash|VBG|_ and|and|CC|_ stored|store|VBN|_ in|in|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ using|use|VBG|_ for|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_
Signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ for|for|IN|_ spot|spot|NN|_ and|and|CC|_ slide|slide|NN|_ abnormalities|abnormality|NNS|_ with|with|IN|_ the|the|DT|_ spatial|spatial|JJ|_ Lowess|lowess|NN|_ algorithm|algorithm|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ by|by|IN|_ mixed-effect|mixed-effect|JJ|_ ANOVA|ANOVA|NNP|_ -LRB-|-lrb-|-LRB-|_ MAANOVA|MAANOVA|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Kerr|Kerr|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|DT|_ Lowess|lowess|NN|_ and|and|CC|_ MAANOVA|maanova|NN|_ are|be|VBP|_ part|part|NN|_ of|of|IN|_ the|the|DT|_ R|r|NN|_
Standard|standard|JJ|_ hot-phenol|hot-phenol|NN|_ method|method|NN|_
treatment|treatment|NN|_ :|:|:|_ control|control|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ the|the|DT|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ for|for|IN|_ 3|3|CD|_ days|day|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ using|use|VBG|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ stabilization|stabilization|NN|_ of|of|IN|_ RNA|rna|NN|_ .|.|.|_ Stabilized|stabilize|VBN|_ cultures|culture|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ MiniKit|minikit|NN|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ In|in|IN|_ brief|brief|NN|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ used|use|VBN|_ and|and|CC|_ processed|process|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ including|include|VBG|_ an|a|DT|_ on-column|on-column|JJ|_ DNaseI|dnasei|NN|_ treatment|treatment|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ assayed|assay|VBN|_ by|by|IN|_ denaturing|denature|VBG|_ urea-PAGE|urea-page|NN|_ and|and|CC|_ by|by|IN|_ measuring|measure|VBG|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ absorption|absorption|NN|_ at|at|IN|_ 260|260|CD|_
Data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ apt-probeset-summarize|apt-probeset-summarize|JJ|_ software|software|NN|_ version|version|NN|_ 1.10|1.10|CD|_ and|and|CC|_ RMA|RMA|NNP|_ algorithm|algorithm|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ normalization|normalization|NN|_ probes|probe|NNS|_ present|present|JJ|_ on|on|IN|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ GeneChip|GeneChip|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Exponential|exponential|JJ|_ cultures|culture|NNS|_ of|of|IN|_ transformants|transformant|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ fresh|fresh|JJ|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 25|25|CD|_ µg|µg|NN|_
genotype|genotype|NN|_ :|:|:|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_
genotype|genotype|NN|_ :|:|:|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ ctrl|ctrl|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 4|4|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pBglJ|pbglj|NN|_
K12Δ|k12δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pBglJ|pbglj|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
K12Δ|k12δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 4|4|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pLeuO|pleuo|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pLeuO|pleuo|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pLeuO|pleuo|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pLeuO|pleuo|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ pLeuO|pleuo|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 4|4|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ ctrl|ctrl|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 4|4|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔleuO|δleuo|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 4|4|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ ctrl|ctrl|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ ctrl|ctrl|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 4|4|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 1|1|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 3|3|CD|_
K12|k12|NN|_ Δ|δ|NN|_ -LRB-|-lrb-|-LRB-|_ yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN|_ -RRB-|-rrb-|-RRB-|_ ΔrcsB|δrcsb|NN|_ +|+|CC|_ pBglJ|pbglj|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 4|4|CD|_
overexpression|overexpression|NN|_ :|:|:|_ -|-|:|_
overexpression|overexpression|NN|_ :|:|:|_ BglJ|bglj|NN|_
overexpression|overexpression|NN|_ :|:|:|_ LeuO|leuo|NN|TF
plasmid|plasmid|NN|_ :|:|:|_ pKEDR13|pkedr13|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pKESK22|pkesk22|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pKETS1|pkets1|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 1a|1a|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 1b|1b|CD|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 1c|1c|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 1d|1d|CD|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 2a|2a|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 2b|2b|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 2c|2c|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 2d|2d|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 3a|3a|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 3b|3b|CD|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 3c|3c|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 3d|3d|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 4a|4a|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 4b|4b|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 4c|4c|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 4d|4d|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 5a|5a|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 5b|5b|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 5c|5c|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 5d|5d|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 6a|6a|FW|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 6b|6b|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 6c|6c|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 6d|6d|JJ|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 7a|7a|NN|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 7b|7b|CD|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 7c|7c|CD|_
sample|sample|NN|_ id|id|NN|_ :|:|:|_ 7d|7d|CD|_
strain|strain|NN|_ :|:|:|_ T175|t175|NN|_
strain|strain|NN|_ :|:|:|_ T177|t177|NN|_
strain|strain|NN|_ :|:|:|_ T75|t75|NN|_
control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ C1|c1|NN|_
control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ C2|c2|NN|_
control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ C3|c3|NN|_
control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ C4|c4|NN|_
control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ C5|c5|NN|_
control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ C6|c6|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP to0|to0|NN|_ .8|.8|CD|_ OD|od|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ to0|to0|NN|_ .8|.8|CD|_ OD|od|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism was|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ incubator|incubator|NN|_ shaker|shaker|NN|_ at|at|IN|_ 150|150|CD|_ r.p.m.|r.p.m.|NN|_
Experimental|experimental|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ G1|g1|NN|_
Experimental|experimental|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ G2|g2|NN|_
Experimental|experimental|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_ G3|g3|NN|_
Experimental|experimental|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ G4|g4|NN|_
Experimental|experimental|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ G5|g5|NN|_
Experimental|experimental|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_ G6|g6|NN|_
growth|growth|NN|_ medium|medium|NN|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP medium|medium|NN|_
growth|growth|NN|_ medium|medium|NN|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ culture|culture|NN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini-prep|mini-prep|NN|_ kit.cDNA|kit.cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ 5-10|5-10|CD|_ µg|µg|NN|_
strain|strain|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
The|the|DT|_ intensity|intensity|NN|_ cell|cell|NN|_ files|file|NNS|_ were|be|VBD|_ then|then|RB|_ imported|import|VBN|_ ,|,|,|_ normalized|normalize|VBN|_ for|for|IN|_ background|background|NN|_ correction|correction|NN|_ using|use|VBG|_ PLIER|plier|NN|_ and|and|CC|_ data|datum|NNS|_ analysed|analyse|VBN|_ using|use|VBG|_ Gene|Gene|NNP|_ Spring|Spring|NNP|_ 11.5|11.5|CD|_ software|software|NN|_ .|.|.|_
To|to|TO|_ study|study|VB|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ glycerol|glycerol|NN|SUPP ,|,|,|_ LB|lb|NN|_ was|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBD|_ 0|0|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBD|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 2.5|2.5|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
Culture|culture|NN|_ samples|sample|NNS|_ for|for|IN|_ microarray|microarray|NN|_ analysis|analysis|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ solution|solution|NN|_ ,|,|,|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 6,600|6,600|CD|_ g|g|NN|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ N2|n2|NN|_ before|before|IN|_ storing|store|VBG|_ at|at|IN|_ -80|-80|CD|_ degrees|degree|NNS|_ C|c|NN|_ until|until|IN|_ required|require|VBN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ stored|store|VBN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ ,|,|,|_ and|and|CC|_ labeled|label|VBN|_ Cy3|cy3|NN|_ and|and|CC|_ Cy5|cy5|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ 16|16|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ with|with|IN|_ 10|10|CD|_ ug|ug|NN|_ random|random|JJ|_ hexamer|hexamer|NN|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Coralville|Coralville|NNP|_ ,|,|,|_ IA|IA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Data|Data|NNP|_ filtered|filter|VBD|_ for|for|IN|_ PCR|pcr|NN|_ success|success|NN|_ ,|,|,|_ >|>|JJR|_ 3x|3x|NN|_ local|local|JJ|_ background|background|NN|_ and|and|CC|_ spot|spot|NN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ GenePix|GenePix|NNP|_ Flag|Flag|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Normalized|normalize|VBN|_ using|use|VBG|_ Lowess|Lowess|NNP|_ smoothing|smooth|VBG|_ from|from|IN|_ MA|MA|NNP|_ plot|plot|NN|_
EC12n090|ec12n090|NN|_ RpoE|rpoe|NN|_ 2.5|2.5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC12n091|ec12n091|NN|_ RpoE|rpoe|NN|_ 5|5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC12n092a|ec12n092a|NN|_ RpoE|rpoe|NN|_ 10|10|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC12n093|ec12n093|NN|_ RpoE|rpoe|NN|_ 20|20|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC12n094|ec12n094|NN|_ RpoE|rpoe|NN|_ 30|30|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC12n095|ec12n095|NN|_ RpoE|rpoe|NN|_ 60|60|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC12n096|ec12n096|NN|_ RpoE|rpoe|NN|_ 0|0|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC12n101|ec12n101|NN|_ RpoE|rpoe|NN|_ 0|0|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC7n018|ec7n018|NN|_ RpoE|rpoe|NN|_ 5|5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC7n019|ec7n019|NN|_ RpoE|rpoe|NN|_ 15|15|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC7n065|ec7n065|NN|_ RpoE|rpoe|NN|_ 5|5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC7n066|ec7n066|NN|_ RpoE|rpoe|NN|_ 15|15|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC7n067|ec7n067|NN|_ RpoE|rpoe|NN|_ 30|30|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC7n068|ec7n068|NN|_ RpoE|rpoe|NN|_ 60|60|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC7n071|ec7n071|NN|_ RpoE|rpoe|NN|_ 60|60|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC8n021|ec8n021|NN|_ RpoE|rpoe|NN|_ 2.5|2.5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC8n022|ec8n022|NN|_ RpoE|rpoe|NN|_ 5|5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC8n050|ec8n050|NN|_ RpoE|rpoe|NN|_ 10|10|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC8n051|ec8n051|NN|_ RpoE|rpoe|NN|_ 20|20|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC8n052|ec8n052|NN|_ RpoE|rpoe|NN|_ 30|30|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC8n053|ec8n053|NN|_ RpoE|rpoe|NN|_ 60|60|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
M9|m9|NN|_ minimal|minimal|JJ|_ complete|complete|JJ|_ media|media|NNS|_ ,|,|,|_ cultures|culture|NNS|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ in|in|IN|_ a|a|DT|_ gyratory|gyratory|JJ|_ water|water|NN|_ bath|bath|NN|_ shaking|shake|VBG|_ at|at|IN|_ 240|240|CD|_ rpm|rpm|NN|_
MG1655|mg1655|NN|_ rpoHp3|rpohp3|NN|Pr :|:|:|_ :|:|:|_ lacZ|lacz|NN|GEN delta|delta|NN|_ lacX74|lacx74|NN|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 60|60|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 60|60|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ was|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ The|the|DT|_ resulting|result|VBG|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 500-fold|500-fold|JJ|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ for|for|IN|_ 3.5|3.5|CD|_ hours|hour|NNS|_ such|such|JJ|_ that|that|IN|_ O.D.|O.D.|NNP|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ became|become|VBD|_ 0.30-0.35|0.30-0.35|CD|_ .|.|.|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ transcriptome|transcriptome|NN|_ _|_|NN|_ 1|1|CD|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ transcriptome|transcriptome|NN|_ _|_|NN|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ -LSB-|-lsb-|-LRB-|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ F|f|NN|_ -|-|:|_ ,|,|,|_ lambda|lambda|NN|_ -|-|:|_ ,|,|,|_ rph-1|rph-1|NN|_
reference|reference|NN|_ genome|genome|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
RNA|rna|NN|_ from|from|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ a|a|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ using|use|VBG|_ Phenol|Phenol|NNP|_ Chloroform|Chloroform|NNP|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-Negative|gram-negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ conventional|conventional|JJ|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ for|for|IN|_ mRNA|mrna|NN|_ Sequencing|sequencing|NN|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ was|be|VBD|_ applied|apply|VBN|_ with|with|IN|_ a|a|DT|_ few|few|JJ|_ modifications|modification|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Standard|Standard|NNP|_ Paired-End|Paired-End|NNP|_ Illumina|Illumina|NNP|_ Library|Library|NNP|_ Construction|Construction|NNP|_ Protocol|Protocol|NNP|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ modified|modify|VBN|_ adapters|adapter|NNS|_ containing|contain|VBG|_ optimized|optimize|VBN|_ 20|20|CD|_ bp|bp|NN|_ barcode|barcode|NN|_ sequences|sequence|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ original|original|JJ|_ paper|paper|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ with|with|IN|_ barcoded|barcoded|JJ|_ adapters|adapter|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ with|with|IN|_ a|a|DT|_ 2x101|2x101|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ sequencing|sequencing|NN|_ run|run|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 2x51|2x51|NN|_ -LRB-|-lrb-|-LRB-|_ for|for|IN|_ the|the|DT|_ second|second|JJ|_ -RRB-|-rrb-|-RRB-|_ base|base|NN|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ in|in|IN|_ one|one|CD|_ lane|lane|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Using|use|VBG|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ python|python|NN|_ -LRB-|-lrb-|-LRB-|_ 3.2.1|3.2.1|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ 0.12.7|0.12.7|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ sequencing|sequencing|NN|_ data|datum|NNS|_ ,|,|,|_ we|we|PRP|_ isolated|isolate|VBD|_ reads|read|VBZ|_ which|which|WDT|_ contained|contain|VBD|_ barcode|barcode|NN|_ sequences|sequence|NNS|_ that|that|WDT|_ corresponded|correspond|VBD|_ to|to|TO|_ our|we|PRP$|_ original|original|JJ|_ list|list|NN|_ of|of|IN|_ single|single|JJ|_ molecule|molecule|NN|_ barcodes|barcode|NNS|_ in|in|IN|_ both|both|CC|_ forward|forward|RB|_ and|and|CC|_ reverse|reverse|VB|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ sequence|sequence|NN|_ pair|pair|NN|_ that|that|WDT|_ had|have|VBD|_ at|at|IN|_ most|most|JJS|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ We|we|PRP|_ then|then|RB|_ aligned|align|VBD|_ the|the|DT|_ first|first|JJ|_ 28|28|CD|_ bases|basis|NNS|_ -LRB-|-lrb-|-LRB-|_ 26|26|CD|_ bases|basis|NNS|_ for|for|IN|_ the|the|DT|_ second|second|JJ|_ sequencing|sequencing|NN|_ run|run|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ targeted|target|VBN|_ sequence|sequence|NN|_ of|of|IN|_ both|both|CC|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ reads|read|VBZ|_ of|of|IN|_ each|each|DT|_ cluster|cluster|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ and|and|CC|_ kept|keep|VBD|_ the|the|DT|_ sequences|sequence|NNS|_ that|that|WDT|_ uniquely|uniquely|RB|_ align|align|VB|_ fewer|fewer|JJR|_ than|than|IN|_ three|three|CD|_ mismatches|mismatch|NNS|_ and|and|CC|_ where|where|WRB|_ the|the|DT|_ two|two|CD|_ reads|read|VBZ|_ did|do|VBD|_ not|not|RB|_ map|map|VB|GEN to|to|TO|_ the|the|DT|_ same|same|JJ|_ sense|sense|NN|_ or|or|CC|_ antisense|antisense|JJ|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_ We|we|PRP|_ used|use|VBD|_ a|a|DT|_ detailed|detailed|JJ|_ filtering|filter|VBG|_ process|process|NN|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ identity|identity|NN|_ of|of|IN|_ closely-mapped|closely-mapped|JJ|_ reads|read|VBZ|_ .|.|.|_ Mapped|map|VBN|_ sequence|sequence|NN|_ fragments|fragment|NNS|_ with|with|IN|_ a|a|DT|_ length|length|NN|_ of|of|IN|_ at|at|IN|_ least|least|JJS|_ 1,000|1,000|CD|_ bases|basis|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_ All|all|DT|_ sequences|sequence|NNS|_ within|within|IN|_ the|the|DT|_ same|same|JJ|_ transcription|transcription|NN|_ unit|unit|NN|_ that|that|WDT|_ had|have|VBD|_ the|the|DT|_ same|same|JJ|_ unique|unique|JJ|_ tag|tag|NN|GEN were|be|VBD|_ analyzed|analyze|VBN|_ further|further|RB|_ .|.|.|_ We|we|PRP|_ determined|determine|VBD|_ that|that|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ sequence|sequence|NN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ unique|unique|JJ|_ tag|tag|NN|GEN were|be|VBD|_ identical|identical|JJ|_ if|if|IN|_ the|the|DT|_ distance|distance|NN|_ between|between|IN|_ their|they|PRP$|_ center|center|NN|_ positions|position|NNS|_ was|be|VBD|_ less|less|JJR|_ than|than|IN|_ four|four|CD|_ base-pairs|base-pair|NNS|_ and|and|CC|_ if|if|IN|_ the|the|DT|_ difference|difference|NN|_ in|in|IN|_ length|length|NN|_ was|be|VBD|_ less|less|JJR|_ than|than|IN|_ 9|9|CD|_ base-pairs|base-pair|NNS|_ .|.|.|_ Then|then|RB|_ for|for|IN|_ each|each|DT|_ unique|unique|JJ|_ sequence|sequence|NN|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ unique|unique|JJ|_ barcode|barcode|NN|_ tags|tag|NNS|_ that|that|WDT|_ appeared|appear|VBD|_ to|to|TO|_ determine|determine|VB|_ the|the|DT|_ copy|copy|NN|_ number|number|NN|_ of|of|IN|_ each|each|DT|_ sequence|sequence|NN|_ and|and|CC|_ mapped|map|VBD|_ each|each|DT|_ of|of|IN|_ them|they|PRP|_ to|to|TO|_ genes|gene|NNS|_ .|.|.|_ We|we|PRP|_ include|include|VBP|_ indexed|index|VBN|_ genome|genome|NN|_ viewer|viewer|NN|_ files|file|NNS|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ sam|sam|NN|_ and|and|CC|_ .|.|.|_ sai|sai|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ both|both|DT|_ experiments|experiment|NNS|_ using|use|VBG|_ both|both|CC|_ the|the|DT|_ conventional|conventional|JJ|_ method|method|NN|_ and|and|CC|_ the|the|DT|_ digital|digital|JJ|_ method|method|NN|_ .|.|.|_
Cells|cell|NNS|_ in|in|IN|_ log|log|NN|_ phase|phase|NN|_ under|under|IN|_ furfural|furfural|JJ|_ stress|stress|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 50|50|CD|_ μg|μg|NN|_
Data|Data|NNP|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ GeneChip|GeneChip|NNP|_ Operating|Operating|NNP|_ Software|Software|NNP|_ Version|Version|NNP|_ 1.4|1.4|CD|_ -LRB-|-lrb-|-LRB-|_ Affymetrix|Affymetrix|NNP|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Furfural-tolerant|furfural-tolerant|JJ|_ IrrE|irre|NN|_ mutant|mutant|JJ|_ F1-37|f1-37|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
Furfural-tolerant|furfural-tolerant|JJ|_ IrrE|irre|NN|_ mutant|mutant|JJ|_ F1-37|f1-37|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Furfural-tolerant|furfural-tolerant|JJ|_ IrrE|irre|NN|_ mutant|mutant|JJ|_ F1-37|f1-37|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
genotype|genotype|NN|_ :|:|:|_ furfural-tolerant|furfural-tolerant|JJ|_ mutant|mutant|JJ|_ F1-37|f1-37|NN|_ of|of|IN|_ IrrE|irre|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ IrrE|irre|NN|_
strain|strain|NN|_ :|:|:|_ DH5a|dh5a|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ when|when|WRB|_ they|they|PRP|_ reached|reach|VBD|_ the|the|DT|_ log|log|NN|_ phase|phase|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ rapidly|rapidly|RB|_ chilled|chill|VBD|_ and|and|CC|_ stored|store|VBD|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ until|until|IN|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ DNA|dna|NN|_ microarray|microarray|NN|_ assay|assay|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ cells|cell|NNS|_ stored|store|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ TRIzol|trizol|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNeasy|rneasy|NN|_ MinElute|MinElute|NNP|_ Cleanup|Cleanup|NNP|_ Kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_
Wild-type|wild-type|JJ|_ IrrE|irre|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
Wild-type|wild-type|JJ|_ IrrE|irre|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Wild-type|wild-type|JJ|_ IrrE|irre|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ negativ|negativ|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ left|leave|VBD|_ _|_|RB|_ chamber|chamber|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ negativ|negativ|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ left|leave|VBD|_ _|_|RB|_ chamber|chamber|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ negativ|negativ|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ left|leave|VBD|_ _|_|RB|_ chamber|chamber|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ negativ|negativ|NN|_ _|_|NN|_ control|control|NN|_ _|_|RB|_ right|right|JJ|_ _|_|NN|_ chamber|chamber|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ negativ|negativ|NN|_ _|_|NN|_ control|control|NN|_ _|_|RB|_ right|right|JJ|_ _|_|NN|_ chamber|chamber|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ negativ|negativ|NN|_ _|_|NN|_ control|control|NN|_ _|_|RB|_ right|right|JJ|_ _|_|NN|_ chamber|chamber|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ response|response|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 1mM|1mm|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|NN|_ added|add|VBD|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ response|response|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 1mM|1mm|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|NN|_ added|add|VBD|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ response|response|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 1mM|1mm|NN|_ _|_|CD|_ H2O2|h2o2|NN|_ _|_|NN|_ added|add|VBD|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ response|response|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ water|water|NN|_ _|_|NN|_ added|add|VBD|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ response|response|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ water|water|NN|_ _|_|NN|_ added|add|VBD|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ response|response|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ water|water|NN|_ _|_|NN|_ added|add|VBD|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|FW|_ _|_|FW|_ powerline|powerline|FW|_ _|_|SYM|_ interm|interm|FW|_ _|_|FW|_ 15h|15h|FW|_ _|_|SYM|_ rep1|rep1|CD|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|FW|_ _|_|FW|_ powerline|powerline|FW|_ _|_|SYM|_ interm|interm|FW|_ _|_|FW|_ 15h|15h|FW|_ _|_|SYM|_ rep2|rep2|CD|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|FW|_ _|_|FW|_ powerline|powerline|FW|_ _|_|SYM|_ interm|interm|FW|_ _|_|FW|_ 15h|15h|FW|_ _|_|SYM|_ rep3|rep3|CD|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|NN|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|NN|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|NN|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 15h|15h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 15h|15h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 15h|15h|JJ|_ _|_|NN|_ rep3|rep3|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ sham|sham|VBP|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ powerline|powerline|FW|_ _|_|FW|_ interm|interm|FW|_ _|_|SYM|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 15h|15h|CD|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|SYM|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|NN|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|NN|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ cont|cont|NN|_ _|_|NN|_ 8|8|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 15h|15h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 15h|15h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 15h|15h|JJ|_ _|_|NN|_ rep3|rep3|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
E|e|NN|_ _|_|CD|_ coli|coli|NN|_ _|_|NN|_ treated|treat|VBN|_ _|_|SYM|_ sinusoidal|sinusoidal|JJ|_ _|_|NN|_ interm|interm|NN|_ _|_|CD|_ 2.5|2.5|CD|_ h|h|NN|_ _|_|SYM|_ rep3|rep3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ cultivated|cultivate|VBN|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ ~|~|SYM|_ 0.5|0.5|CD|_ l|l|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ steady-state|steady-state|JJ|_ continuous|continuous|JJ|_ cultivation|cultivation|NN|_ -LRB-|-lrb-|-LRB-|_ dilution|dilution|NN|_ rate|rate|NN|_ of|of|IN|_ 0.4|0.4|CD|_ h-1|h-1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ aerobic|aerobic|JJ|_
medium|medium|NN|_ :|:|:|_ defined|define|VBN|_ mineral|mineral|JJ|_ medium|medium|NN|_ with|with|IN|_ 1|1|CD|_ g|g|NN|_
Quality|quality|JJ|_ control|control|NN|_ and|and|CC|_ microarray|microarray|NN|_ data|data|NN|_ analysis|analysis|NN|_ of|of|IN|_ all|all|DT|_ 60|60|CD|_ chips|chip|NNS|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ R|r|NN|_
Samples|sample|NNS|_ of|of|IN|_ ~|~|NN|_ 7.2|7.2|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 0.8|0.8|CD|_ ml|ml|NN|_ stop|stop|NN|_ solution|solution|NN|_ ,|,|,|_ pelleted|pelleted|JJ|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNase|dnase|NN|_ treatment|treatment|NN|_ was|be|VBD|_ done|do|VBN|_ twice|twice|RB|_ with|with|IN|_ RQ1|rq1|NN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|promega|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ done|do|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ GeneChip|GeneChip|NNP|_ ®|®|NNP|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Technical|Technical|NNP|_ Manual|Manual|NNP|_ of|of|IN|_ Affymetrix|Affymetrix|NNP|_ using|use|VBG|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|promega|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ without|without|IN|_ DTT|dtt|NN|_ addition|addition|NN|_ .|.|.|_ 13|13|CD|_ µl|µl|NN|_ of|of|IN|_ EB|EB|NNP|_ buffer|buffer|NN|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ elution|elution|NN|_ of|of|IN|_ cDNA|cdna|NN|_ after|after|IN|_ its|its|PRP$|_ clean-up|clean-up|JJ|_ with|with|IN|_ the|the|DT|_ MiniElute|MiniElute|NNP|_ CR|cr|NN|_ purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ cDNA|cdna|NN|_ fragmentation|fragmentation|NN|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ a|a|DT|_ 20-µl|20-µl|JJ|_ reaction|reaction|NN|_ containing|contain|VBG|_ 3.5|3.5|CD|_ µg|µg|NN|_ cDNA|cdna|NN|_ ,|,|,|_ 2|2|CD|_ µl|µl|NN|_ 10x|10x|CD|_ One|one|CD|_ Phor-All|phor-all|NN|_ buffer|buffer|NN|_ ,|,|,|_ 2|2|CD|_ µl|µl|NN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ diluted|dilute|VBN|_ to|to|TO|_ 0.2|0.2|CD|_ U|U|NNP|_
Samples|sample|NNS|_ of|of|IN|_ magnetic|magnetic|JJ|_ field-treated|field-treated|JJ|_ or|or|CC|_ sham-treated|sham-treated|JJ|_ cells|cell|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ as|as|IN|_ fast|fast|JJ|_ as|as|IN|_ possible|possible|JJ|_ from|from|IN|_ the|the|DT|_ bioreactor|bioreactor|NN|_ -LRB-|-lrb-|-LRB-|_ not|not|RB|_ later|later|RB|_ than|than|IN|_ 3|3|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ the|the|DT|_ specified|specify|VBN|_ treatement|treatement|NN|_ period|period|NN|_ .|.|.|_ Samples|sample|NNS|_ taken|take|VBN|_ during|during|IN|_ intermittent|intermittent|JJ|_ exposure|exposure|NN|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ in|in|IN|_ the|the|DT|_ 4|4|CD|_ min|min|NN|_ exposure|exposure|NN|_ break|break|NN|_ .|.|.|_ Unexposed|unexposed|JJ|_ samples|sample|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ as|as|IN|_ fast|fast|JJ|_ as|as|IN|_ possible|possible|JJ|_ during|during|IN|_ steady-state|steady-state|JJ|_ conditions|condition|NNS|_ in|in|IN|_ the|the|DT|_ chemostat|chemostat|NN|_ .|.|.|_ In|in|IN|_ the|the|DT|_ response|response|NN|_ control|control|NN|_ experiment|experiment|NN|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ withdrawn|withdraw|VBN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP H2O2|h2o2|NN|_ -LRB-|-lrb-|-LRB-|_ treated|treated|JJ|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ the|the|DT|_ equivalent|equivalent|JJ|_ water|water|NN|_ volume|volume|NN|_ -LRB-|-lrb-|-LRB-|_ reference|reference|NN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
treatment|treatment|NN|_ duration|duration|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ duration|duration|NN|_ :|:|:|_ 15|15|CD|_ h|h|NN|_
treatment|treatment|NN|_ duration|duration|NN|_ :|:|:|_ 2.5|2.5|CD|_ h|h|NN|_
treatment|treatment|NN|_ duration|duration|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ duration|duration|NN|_ :|:|:|_ none|none|NN|_
treatment|treatment|NN|_ :|:|:|_ sham-treated|sham-treated|JJ|_ power|power|NN|_ line|line|NN|_ intermittent|intermittent|JJ|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ min|min|NN|_ on|on|IN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_ off|off|IN|_ -RRB-|-rrb-|-RRB-|_ magnetic|magnetic|JJ|_ field|field|NN|_
treatment|treatment|NN|_ :|:|:|_ sham-treated|sham-treated|JJ|_ sinusoidal|sinusoidal|JJ|_ continous|continous|JJ|_ magnetic|magnetic|JJ|_ field|field|NN|_
treatment|treatment|NN|_ :|:|:|_ sham-treated|sham-treated|JJ|_ sinusoidal|sinusoidal|JJ|_ intermittent|intermittent|JJ|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ min|min|NN|_ on|on|IN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_ off|off|IN|_ -RRB-|-rrb-|-RRB-|_ magnetic|magnetic|JJ|_ field|field|NN|_
treatment|treatment|NN|_ :|:|:|_ treated|treat|VBN|_ power|power|NN|_ line|line|NN|_ intermittent|intermittent|JJ|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ min|min|NN|_ on|on|IN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_ off|off|IN|_ -RRB-|-rrb-|-RRB-|_ magnetic|magnetic|JJ|_ field|field|NN|_
treatment|treatment|NN|_ :|:|:|_ treated|treat|VBN|_ sinusoidal|sinusoidal|JJ|_ continous|continous|JJ|_ magnetic|magnetic|JJ|_ field|field|NN|_
treatment|treatment|NN|_ :|:|:|_ treated|treat|VBN|_ sinusoidal|sinusoidal|JJ|_ intermittent|intermittent|JJ|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ min|min|NN|_ on|on|IN|_ ,|,|,|_ 4|4|CD|_ min|min|NN|_ off|off|IN|_ -RRB-|-rrb-|-RRB-|_ magnetic|magnetic|JJ|_ field|field|NN|_
treatment|treatment|NN|_ :|:|:|_ unexposed|unexposed|JJ|_ ,|,|,|_ left|leave|VBD|_ chamber|chamber|NN|_
treatment|treatment|NN|_ :|:|:|_ unexposed|unexposed|JJ|_ ,|,|,|_ right|right|JJ|_ chamber|chamber|NN|_
treatment|treatment|NN|_ :|:|:|_ unexposed|unexposed|JJ|_ ,|,|,|_ treated|treat|VBN|_ with|with|IN|_ 1mM|1mm|NN|_ H2O2|h2o2|NN|_
treatment|treatment|NN|_ :|:|:|_ unexposed|unexposed|JJ|_ ,|,|,|_ treated|treat|VBN|_ with|with|IN|_ water|water|NN|_
After|after|IN|_ each|each|DT|_ sequenced|sequence|VBN|_ fragments|fragment|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ the|the|DT|_ footprint|footprint|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ footprint|footprint|NN|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 12|12|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ More|more|RBR|_ at|at|IN|_ G.W.|G.W.|NNP|_ Li|Li|NNP|_ ,|,|,|_ E.|E.|NNP|_ Oh|oh|UH|_ ,|,|,|_ and|and|CC|_ J.S.|J.S.|NNP|_ Weissman|Weissman|NNP|_ ,|,|,|_ Nature|Nature|NNP|_ -LRB-|-lrb-|-LRB-|_ in|in|IN|_ press|press|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ recoded|recode|VBN|_ ompF|ompf|NN|GEN
E.|e.|FW|_ coli|coli|FW|_ recoded|recode|VBN|_ ompF|ompf|NN|GEN -LRB-|-lrb-|-LRB-|_ recoded|recode|VBN|_ ompF|ompf|NN|GEN gene|gene|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
medium|medium|NN|_ :|:|:|_ MOPS|mop|NNS|MED
OmpFrecode|ompfrecode|NN|_ _|_|CD|_ f.wig|f.wig|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_
OmpFrecode|ompfrecode|NN|_ _|_|CD|_ r.wig|r.wig|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Ribosome|Ribosome|NNP|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ '|'|''|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ More|more|RBR|_ at|at|IN|_ G.W.|G.W.|NNP|_ Li|Li|NNP|_ ,|,|,|_ E.|E.|NNP|_ Oh|oh|UH|_ ,|,|,|_ and|and|CC|_ J.S.|J.S.|NNP|_ Weissman|Weissman|NNP|_ ,|,|,|_ Nature|Nature|NNP|_ -LRB-|-lrb-|-LRB-|_ in|in|IN|_ press|press|NN|_ -RRB-|-rrb-|-RRB-|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BJW9|bjw9|NN|_ w|w|NN|_
treatment|treatment|NN|_ :|:|:|_ Ribosome-protected|ribosome-protected|JJ|_ mRNA|mrna|NN|_ ,|,|,|_ Ribosome|ribosome|NN|_ footprint|footprint|NN|_ sample|sample|NN|_ digested|digest|VBN|_ with|with|IN|_ 60|60|CD|_ units|unit|NNS|_ of|of|IN|_ micrococcal|micrococcal|JJ|_ nuclease|nuclease|NN|_ per|per|IN|_ A260|a260|NN|_ absorbance|absorbance|NN|_
aerobic|aerobic|JJ|_ reference|reference|NN|_
anaerobic|anaerobic|JJ|_ reference|reference|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
fnr|fnr|SYM|GEN -|-|:|_ aerobic|aerobic|JJ|_
fnr|fnr|SYM|GEN -|-|:|_ aerobic|aerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ aerobic|aerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ aerobic|aerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
fnr|fnr|SYM|GEN -|-|:|_ aerobic|aerobic|JJ|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ aerobic|aerobic|JJ|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ aerobic|aerobic|JJ|_ rep|rep|NN|GEN 3|3|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|JJ|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ rep|rep|NN|GEN 3|3|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ rep|rep|NN|GEN 3|3|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|JJ|_ rep|rep|NN|GEN 1|1|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|JJ|_ rep|rep|NN|GEN 2|2|CD|_
fnr|fnr|SYM|GEN -|-|:|_ anaerobic|anaerobic|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Genetic|Genetic|NNP|_ background|background|NN|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_
Genetic|Genetic|NNP|_ background|background|NN|_ :|:|:|_ wt|wt|JJ|_
Genetic|Genetic|NNP|_ background|background|NN|_ :|:|:|_ wt|wt|JJ|_
Genetic|Genetic|NNP|_ background|background|NN|_ :|:|:|_ wtGrowth|wtgrowth|NN|_ conditions|condition|NNS|_ :|:|:|_ aerobic|aerobic|JJ|_
Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ aaerobic|aaerobic|JJ|_
Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ aerobic|aerobic|JJ|_
Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_
Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO2|no2|NN|_
Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO3|no3|NN|_
narXL|narxl|NN|TU anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_
narXLP|narxlp|NN|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_
narXLP|narxlp|NN|_ rep|rep|NN|GEN 1|1|CD|_
narXLP|narxlp|NN|_ rep|rep|NN|GEN 2|2|CD|_
narXLP|narxlp|NN|_ rep|rep|NN|GEN 3|3|CD|_
narXL|narxl|NN|TU rep|rep|NN|GEN 1|1|CD|_
narXL|narxl|NN|TU rep|rep|NN|GEN 2|2|CD|_
narXL|narxl|NN|TU rep|rep|NN|GEN 3|3|CD|_
narXL|narxl|NN|TU rep|rep|NN|GEN 4|4|CD|_
Raw|raw|NN|_ ,|,|,|_ not|not|RB|_ normalised|normalised|JJ|_
Strain|Strain|NNP|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ aerobic|aerobic|JJ|_
Strain|Strain|NNP|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO2|no2|NN|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO3|no3|NN|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ narXL|narxl|NN|TU ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO2|no2|NN|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ narXLP|narxlp|NN|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO2|no2|NN|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ wt|wt|JJ|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ aerobic|aerobic|JJ|_
Strain|Strain|NNP|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ wt|wt|JJ|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ wt|wt|JJ|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO2|no2|NN|_
Strain|strain|NN|_ :|:|:|_ E.coli|e.coli|NNS|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ wt|wt|JJ|_ ,|,|,|_ Growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_ plus|plus|CC|_ NO3|no3|NN|_
wt|wt|JJ|_ aerobic|aerobic|JJ|_
wt|wt|JJ|_ aerobic|aerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ aerobic|aerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ aerobic|aerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
wt|wt|JJ|_ aerobic|aerobic|JJ|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ aerobic|aerobic|JJ|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ aerobic|aerobic|JJ|_ rep|rep|NN|GEN 3|3|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO2|no2|NN|_ rep|rep|NN|GEN 3|3|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ AN|a|DT|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ AN|a|DT|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ AN|a|DT|_ rep|rep|NN|GEN 3|3|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|NN|_ plus|plus|CC|_ NO3|no3|NN|_ rep|rep|NN|GEN 3|3|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_ rep|rep|NN|GEN 1|1|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_ rep|rep|NN|GEN 2|2|CD|_
wt|wt|JJ|_ anaerobic|anaerobic|JJ|_ rep|rep|NN|GEN 3|3|CD|_
A|a|DT|_ 5|5|CD|_ ml|ml|NN|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ for|for|IN|_ 18|18|CD|_ h|h|NN|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ ,|,|,|_ prewarmed|prewarmed|JJ|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ in|in|IN|_ a|a|DT|_ 125|125|CD|_ ml|ml|NN|_ Ehrlenmeyer|ehrlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ 150|150|CD|_ rpm|rpm|NN|_ in|in|IN|_ a|a|DT|_ New|New|NNP|_ Brunswick|Brunswick|NNP|_ Shaking|shake|VBG|_ water|water|NN|_ bath|bath|NN|_ until|until|IN|_ the|the|DT|_ culture|culture|NN|_ density|density|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_ Half|half|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ second|second|JJ|_ identical|identical|JJ|_ flask|flask|NN|_ containing|contain|VBG|_ menadione|menadione|NN|_ bisulphite|bisulphite|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mg|mg|NN|_
A|a|DT|_ 5|5|CD|_ ml|ml|NN|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ for|for|IN|_ 18|18|CD|_ h|h|NN|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ ,|,|,|_ prewarmed|prewarmed|JJ|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ in|in|IN|_ a|a|DT|_ 125|125|CD|_ ml|ml|NN|_ Ehrlenmeyer|ehrlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ 150|150|CD|_ rpm|rpm|NN|_ in|in|IN|_ a|a|DT|_ New|New|NNP|_ Brunswick|Brunswick|NNP|_ Shaking|shake|VBG|_ water|water|NN|_ bath|bath|NN|_ until|until|IN|_ the|the|DT|_ culture|culture|NN|_ density|density|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_ Half|half|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ second|second|JJ|_ identical|identical|JJ|_ flask|flask|NN|_ containing|contain|VBG|_ menadione|menadione|NN|_ bisulphite|bisulphite|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mg|mg|NN|_
A|a|DT|_ 5|5|CD|_ ml|ml|NN|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ for|for|IN|_ 18|18|CD|_ h|h|NN|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ ,|,|,|_ prewarmed|prewarmed|JJ|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ in|in|IN|_ a|a|DT|_ 125|125|CD|_ ml|ml|NN|_ Ehrlenmeyer|ehrlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ 150|150|CD|_ rpm|rpm|NN|_ in|in|IN|_ a|a|DT|_ New|New|NNP|_ Brunswick|Brunswick|NNP|_ Shaking|shake|VBG|_ water|water|NN|_ bath|bath|NN|_ until|until|IN|_ the|the|DT|_ culture|culture|NN|_ density|density|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_ Half|half|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ second|second|JJ|_ identical|identical|JJ|_ flask|flask|NN|_ containing|contain|VBG|_ menadione|menadione|NN|_ bisulphite|bisulphite|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mg|mg|NN|_
A|a|DT|_ 5|5|CD|_ ml|ml|NN|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ for|for|IN|_ 18|18|CD|_ h|h|NN|_ at|at|IN|_ 37C|37c|NN|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ ,|,|,|_ prewarmed|prewarmed|JJ|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ in|in|IN|_ a|a|DT|_ 125|125|CD|_ ml|ml|NN|_ Ehrlenmeyer|ehrlenmeyer|NN|_ flask|flask|NN|_ and|and|CC|_ shaken|shake|VBN|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ 150|150|CD|_ rpm|rpm|NN|_ in|in|IN|_ a|a|DT|_ New|New|NNP|_ Bruswick|Bruswick|NNP|_ Shaking|shake|VBG|_ water|water|NN|_ bath|bath|NN|_ until|until|IN|_ the|the|DT|_ culture|culture|NN|_ density|density|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_ Half|half|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ second|second|JJ|_ identical|identical|JJ|_ flask|flask|NN|_ containing|contain|VBG|_ menadione|menadione|NN|_ bisulphite|bisulphite|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mg|mg|NN|_
An|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Ltd|Ltd|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ according|accord|VBG|_ to|to|TO|_ manufacturers|manufacturer|NNS|_ '|'|POS|_ instructions|instruction|NNS|_ .|.|.|_ Contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ using|use|VBG|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Ltd|Ltd|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ determined|determine|VBN|_ with|with|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ nano|nano|NN|_ assay|assay|NN|_ Labchip|labchip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Stockport|Stockport|NNP|_ ,|,|,|_ United|United|NNP|_ Kingdom|Kingdom|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ untreated|untreated|JJ|_ -LRB-|-lrb-|-LRB-|_ reference|reference|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ rep|rep|NN|GEN #|#|#|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ untreated|untreated|JJ|_ -LRB-|-lrb-|-LRB-|_ reference|reference|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ rep|rep|NN|GEN #|#|#|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ untreated|untreated|JJ|_ -LRB-|-lrb-|-LRB-|_ reference|reference|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ rep|rep|NN|GEN #|#|#|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ untreated|untreated|JJ|_ -LRB-|-lrb-|-LRB-|_ reference|reference|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ rep|rep|NN|GEN #|#|#|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ untreated|untreated|JJ|_ -LRB-|-lrb-|-LRB-|_ reference|reference|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ rep|rep|NN|GEN #|#|#|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ untreated|untreated|JJ|_ -LRB-|-lrb-|-LRB-|_ reference|reference|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ rep|rep|NN|GEN #|#|#|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ treated|treat|VBN|_ with|with|IN|_ menadione|menadione|NN|_ _|_|CD|_ rep|rep|NN|GEN #|#|#|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ treated|treat|VBN|_ with|with|IN|_ menadione|menadione|NN|_ _|_|CD|_ rep|rep|NN|GEN #|#|#|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ treated|treat|VBN|_ with|with|IN|_ menadione|menadione|NN|_ _|_|CD|_ rep|rep|NN|GEN #|#|#|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ treated|treat|VBN|_ with|with|IN|_ menadione|menadione|NN|_ _|_|CD|_ rep|rep|NN|GEN #|#|#|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ treated|treat|VBN|_ with|with|IN|_ menadione|menadione|NN|_ _|_|CD|_ rep|rep|NN|GEN #|#|#|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ treated|treat|VBN|_ with|with|IN|_ menadione|menadione|NN|_ _|_|CD|_ rep|rep|NN|GEN #|#|#|_ 3|3|CD|_
GenePix|GenePix|NNP|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Axon|Axon|NNP|_ Instruments|Instruments|NNP|_ ,|,|,|_ Union|Union|NNP|_ City|City|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 5.1|5.1|CD|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ scanned|scan|VBN|_ data|datum|NNS|_ and|and|CC|_ generate|generate|VB|_ the|the|DT|_ gpr|gpr|NN|GEN files|file|NNS|_ .|.|.|_
medium|medium|NN|_ :|:|:|_ Neidhardt|Neidhardt|NNP|_ 's|'s|POS|_ EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|Teknova|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_
od600|od600|CD|_ :|:|:|_ 0.4|0.4|CD|_
Oxidative|oxidative|JJ|_ stress|stress|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ #|#|#|_ 1|1|CD|_
Oxidative|oxidative|JJ|_ stress|stress|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ #|#|#|_ 2|2|CD|_
Oxidative|oxidative|JJ|_ stress|stress|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ #|#|#|_ 3|3|CD|_
Oxidative|oxidative|JJ|_ stress|stress|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ #|#|#|_ 1|1|CD|_
Oxidative|oxidative|JJ|_ stress|stress|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ #|#|#|_ 2|2|CD|_
Oxidative|oxidative|JJ|_ stress|stress|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ #|#|#|_ 3|3|CD|_
strain|strain|NN|_ :|:|:|_ k-12|k-12|NN|_ MG1655|mg1655|NN|_ wild-type|wild-type|JJ|_
strain|strain|NN|_ :|:|:|_ o157|o157|NN|_ :|:|:|_ H7|h7|NN|_ -LRB-|-lrb-|-LRB-|_ Sakai|Sakai|NNP|_ -RRB-|-rrb-|-RRB-|_ wild-type|wild-type|JJ|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ mg|mg|NN|_
ampicilin|ampicilin|NN|_ treatment|treatment|NN|_
Ampicilin|ampicilin|NN|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ plasmidmappedreads|plasmidmappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012692.1|012692.1|CD|_
Amp|Amp|NNP|_ _|_|NNP|_ Treatment|treatment|NN|_ _|_|NN|_ genomemappedreads|genomemappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ ampicilin|ampicilin|NN|_ treatment|treatment|NN|_
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ florfenicol|florfenicol|NN|_ treatment|treatment|NN|_
bacteria|bacterium|NNS|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °|°|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ log|log|NN|_ phase|phase|NN|_ with|with|IN|_ streptomycin|streptomycin|NN|_ treatment|treatment|NN|_
cDNA|cdna|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ so|so|RB|_ that|that|IN|_ the|the|DT|_ quality|quality|NN|_ at|at|IN|_ each|each|DT|_ base|base|NN|_ position|position|NN|_ was|be|VBD|_ above|above|IN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 15-20|15-20|CD|_ bp|bp|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ mapped|map|VBD|_ either|either|CC|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ published|publish|VBN|_ genome|genome|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ the|the|DT|_ pAR060302|par060302|NN|_ published|publish|VBN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Genbank|Genbank|NNP|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ NC|nc|NN|_ _|_|SYM|_ 092692|092692|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ BOWTIE|BOWTIE|NNP|_ .|.|.|_ The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ DH5α|dh5α|NN|_ has|have|VBZ|_ an|a|DT|_ incomplete|incomplete|JJ|_ annotation|annotation|NN|_ and|and|CC|_ for|for|IN|_ this|this|DT|_ reason|reason|NN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ annotation|annotation|NN|_ was|be|VBD|_ used|use|VBN|_ ,|,|,|_ representing|represent|VBG|_ an|a|DT|_ estimation|estimation|NN|_ of|of|IN|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ due|due|JJ|_ to|to|TO|_ exposure|exposure|NN|_ of|of|IN|_ antimicrobials|antimicrobial|NNS|_ .|.|.|_ Mapped|map|VBN|_ reads|read|VBZ|_ for|for|IN|_ 3|3|CD|_ seperate|seperate|JJ|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ combined|combine|VBN|_ because|because|IN|_ some|some|DT|_ sequencing|sequencing|NN|_ runs|run|NNS|_ were|be|VBD|_ not|not|RB|_ fully|fully|RB|_ completed|complete|VBN|_ due|due|JJ|_ to|to|TO|_ technical|technical|JJ|_ difficulties|difficulty|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ condition|condition|NN|_ ,|,|,|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ were|be|VBD|_ generated|generate|VBN|_ and|and|CC|_ visualized|visualize|VBN|_ using|use|VBG|_ the|the|DT|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ -LRB-|-lrb-|-LRB-|_ IGV|igv|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Images|image|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ XplasMap|xplasmap|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ preparations|preparation|NNS|_ were|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ a|a|DT|_ DNase|dnase|NN|_ treatment|treatment|NN|_ to|to|TO|_ eliminate|eliminate|VB|_ DNA|dna|NN|_ contamination|contamination|NN|_ from|from|IN|_ the|the|DT|_ sample|sample|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ treatment|treatment|NN|_ was|be|VBD|_ also|also|RB|_ included|include|VBN|_ to|to|TO|_ deplete|deplete|VB|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ commercially|commercially|RB|_ available|available|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ MicrobExpress|MicrobExpress|NNP|_ ,|,|,|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ were|be|VBD|_ pooled|pool|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ DH5α|dh5α|NN|_ harboring|harbor|VBG|_ pAR060302|par060302|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ DifcoTM|difcotm|NN|_ Luria-Bertani|luria-bertani|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ aliquots|aliquot|NNS|_ at|at|IN|_ 37º|37º|CD|_ C|c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
florfenicol|florfenicol|NN|_ treatment|treatment|NN|_
Florfenicol|florfenicol|NN|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ plasmidmappedreads|plasmidmappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012692.1|012692.1|CD|_
Flor|Flor|NNP|_ _|_|JJ|_ treatment|treatment|NN|_ _|_|NN|_ genomemappedreads|genomemappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
no|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ pAR060302|par060302|NN|_ -RRB-|-rrb-|-RRB-|_
streptomycin|streptomycin|NN|_ treatment|treatment|NN|_
Streptomycin|Streptomycin|NNP|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ plasmidmappedreads|plasmidmappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 012692.1|012692.1|CD|_
Strep|strep|JJ|_ _|_|NN|_ treatment|treatment|NN|_ _|_|NN|_ genomemappedreads|genomemappedread|NNS|_ _|_|VBP|_ statistical|statistical|JJ|_ _|_|NN|_ output.txt|output.txt|NN|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_
treatment|treatment|NN|_ :|:|:|_ ampicillin|ampicillin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg|µg|NN|_
treatment|treatment|NN|_ :|:|:|_ florfenicol|florfenicol|NN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ µg|µg|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
treatment|treatment|NN|_ :|:|:|_ streptomycin|streptomycin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ µg|µg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_ slide|slide|NN|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_ slide|slide|NN|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_ slide|slide|NN|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_ slide|slide|NN|_ 4|4|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_ slide|slide|NN|_ 5|5|CD|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ interacted|interact|VBD|_ with|with|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_ slide|slide|NN|_ 6|6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism EDL|edl|NN|_ 933|933|CD|_ cells|cell|NNS|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ hydroponic|hydroponic|JJ|_ system|system|NN|_ without|without|IN|_ interacting|interact|VBG|_ with|with|IN|_ the|the|DT|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ for|for|IN|_ 3|3|CD|_ days|day|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism EDL|edl|NN|_ 933|933|CD|_ cells|cell|NNS|_ interacted|interact|VBD|_ with|with|IN|_ the|the|DT|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_ for|for|IN|_ 3|3|CD|_ days|day|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism EDL|edl|NN|_ 933|933|CD|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED medium|medium|NN|MED until|until|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8,000|8,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ twice|twice|RB|_ with|with|IN|_ sterilized|sterilize|VBN|_ ,|,|,|_ plant|plant|NN|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Caspersen|Caspersen|NNP|_ et|et|FW|_ al.|al.|FW|_ 1999|1999|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ resultant|resultant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ plant|plant|NN|_ growth|growth|NN|_ medium|medium|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ approximately|approximately|RB|_ 10E9|10e9|JJ|_ cells|cell|NNS|_
Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ roots|root|NNS|_ had|have|VBD|_ been|be|VBN|_ gently|gently|RB|_ rinsed|rinse|VBN|_ to|to|TO|_ remove|remove|VB|_ loosely|loosely|RB|_ attached|attach|VBN|_ bacteria|bacterium|NNS|_ and|and|CC|_ roots|root|NNS|_ were|be|VBD|_ cut|cut|VBN|_ directly|directly|RB|_ into|into|IN|_ 100|100|CD|_ ml|ml|NN|_ ice|ice|NN|_ cold|cold|JJ|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ H2O-saturated|h2o-saturated|JJ|_ phenol|phenol|NN|_ ,|,|,|_ pH|ph|NN|_ 4.3|4.3|CD|_ ,|,|,|_ in|in|IN|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Root|root|NN|_ extracts|extract|NNS|_ were|be|VBD|_ filtered|filter|VBN|_ using|use|VBG|_ 0.5|0.5|CD|_ µm|µm|NN|_ filters|filter|NNS|_ to|to|TO|_ separate|separate|JJ|_ bacteria|bacterium|NNS|_ cells|cell|NNS|_ from|from|IN|_ plant|plant|NN|_ cells|cell|NNS|_ in|in|IN|_ order|order|NN|_ to|to|TO|_ prevent|prevent|VB|_ interference|interference|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ labeling|labeling|NN|_ .|.|.|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ protect|protect|VB|_ solution|solution|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ during|during|IN|_ extraction|extraction|NN|_ .|.|.|_ Bacteria|bacterium|NNS|_ had|have|VBD|_ been|be|VBN|_ collected|collect|VBN|_ by|by|IN|_ shaking|shake|VBG|_ and|and|CC|_ washing|wash|VBG|_ and|and|CC|_ stored|store|VBN|_ in|in|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ using|use|VBG|_ for|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ .|.|.|_
genotype|genotype|NN|_
Signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ for|for|IN|_ spot|spot|NN|_ and|and|CC|_ slide|slide|NN|_ abnormalities|abnormality|NNS|_ with|with|IN|_ the|the|DT|_ spatial|spatial|JJ|_ Lowess|lowess|NN|_ algorithm|algorithm|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ by|by|IN|_ mixed-effect|mixed-effect|JJ|_ ANOVA|ANOVA|NNP|_ -LRB-|-lrb-|-LRB-|_ MAANOVA|MAANOVA|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Kerr|Kerr|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Both|both|DT|_ Lowess|lowess|NN|_ and|and|CC|_ MAANOVA|maanova|NN|_ are|be|VBP|_ part|part|NN|_ of|of|IN|_ the|the|DT|_ R|r|NN|_
Standard|standard|JJ|_ hot-phenol|hot-phenol|NN|_ method|method|NN|_
strain|strain|NN|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
treatment|treatment|NN|_ :|:|:|_ grown|grow|VBN|_ in|in|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_
treatment|treatment|NN|_ :|:|:|_ grown|grow|VBN|_ without|without|IN|_ lettuce|lettuce|NN|_ rhizosphere|rhizosphere|NN|_
control|control|NN|_ sample|sample|NN|_ at|at|IN|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
control|control|NN|_ sample|sample|NN|_ at|at|IN|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
control|control|NN|_ sample|sample|NN|_ at|at|IN|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
control|control|NN|_ sample|sample|NN|_ at|at|IN|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Data|Data|NNP|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ RMA|RMA|NNP|_ algorithm|algorithm|NN|_ from|from|IN|_ R|r|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ after|after|IN|_ 30|30|CD|_ min|min|NN|_ incubation|incubation|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ after|after|IN|_ 30|30|CD|_ min|min|NN|_ incubation|incubation|NN|_ following|follow|VBG|_ colicin|colicin|NN|_ M|m|NN|_ treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ after|after|IN|_ 60|60|CD|_ min|min|NN|_ incubation|incubation|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ after|after|IN|_ 60|60|CD|_ min|min|NN|_ incubation|incubation|NN|_ following|follow|VBG|_ colicin|colicin|NN|_ M|m|NN|_ treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:625|1:625|CD|_ into|into|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Roth|Roth|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
treated|treat|VBN|_ sample|sample|NN|_ at|at|IN|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
treated|treat|VBN|_ sample|sample|NN|_ at|at|IN|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
treated|treat|VBN|_ sample|sample|NN|_ at|at|IN|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
treated|treat|VBN|_ sample|sample|NN|_ at|at|IN|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
treatment|treatment|NN|_ :|:|:|_ treated|treated|JJ|_ culture|culture|NN|_
treatment|treatment|NN|_ :|:|:|_ untreated|untreated|JJ|_ culture|culture|NN|_
When|when|WRB|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ 0.6|0.6|CD|_ they|they|PRP|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ flasks|flask|NNS|_ ,|,|,|_ each|each|DT|_ containing|contain|VBG|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ .|.|.|_ One|one|CD|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ a|a|DT|_ subinhibitory|subinhibitory|JJ|_ concentration|concentration|NN|_ of|of|IN|_ purified|purify|VBN|_ colicin|colicin|NN|_ M|m|NN|_ ,|,|,|_ while|while|IN|_ the|the|DT|_ untreated|untreated|JJ|_ served|serve|VBD|_ as|as|IN|_ a|a|DT|_ control|control|NN|_ .|.|.|_ 2-ml|2-ml|JJ|_ culture|culture|NN|_ aliquotes|aliquote|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ each|each|DT|_ flask|flask|NN|_ after|after|IN|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ 60|60|CD|_ min|min|NN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 4|4|CD|_ ml|ml|NN|_ RNAProtect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Bacterial|bacterial|JJ|_ pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 350µl|350µl|CD|_ RNAwiz|rnawiz|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ kept|keep|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Data|Data|NNP|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ the|the|DT|_ robust|robust|JJ|_ multiarray|multiarray|JJ|_ average|average|JJ|_ algorithm|algorithm|NN|_ -LRB-|-lrb-|-LRB-|_ RMA|rma|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ normalization|normalization|NN|_ ,|,|,|_ background|background|NN|_ correction|correction|NN|_ and|and|CC|_ expression|expression|NN|_ value|value|NN|_ calculation|calculation|NN|_ .|.|.|_ The|the|DT|_ EB|EB|NNP|_ -LRB-|-lrb-|-LRB-|_ Wright|Wright|NNP|_ and|and|CC|_ Simon|Simon|NNP|_ -RRB-|-rrb-|-RRB-|_ test|test|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ fold|fold|JJ|_ change|change|NN|_ and|and|CC|_ the|the|DT|_ pvalue|pvalue|NN|_ calculation|calculation|NN|_ ,|,|,|_
E.|E.|NNP|_ coli|coli|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 15mL|15ml|NN|_ falcon|falcon|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 8mL|8ml|NN|_ of|of|IN|_ filtered|filter|VBN|_ rat|rat|NN|_ 's|'s|POS|_ caecal|caecal|JJ|_ content|content|NN|_ .|.|.|_ Growth|growth|NN|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ static|static|JJ|_ condition|condition|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ cultivated|cultivate|VBN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ in|in|IN|_ the|the|DT|_ caecal|caecal|JJ|_ content|content|NN|_ of|of|IN|_ rats|rat|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Germfree|germfree|JJ|_ rat|rat|NN|_ 's|'s|POS|_ caecum|caecum|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
Germfree|germfree|JJ|_ rat|rat|NN|_ 's|'s|POS|_ caecum|caecum|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Germfree|germfree|JJ|_ rat|rat|NN|_ 's|'s|POS|_ caecum|caecum|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ control|control|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ in|in|IN|_ the|the|DT|_ caecal|caecal|JJ|_ content|content|NN|_ of|of|IN|_ rats|rat|NNS|_ associated|associate|VBN|_ with|with|IN|_ the|the|DT|_ human|human|JJ|_ microbiota|microbiota|NN|_
Human|human|JJ|_ intestinal|intestinal|JJ|_ microbiota|microbiota|NN|_ associated|associate|VBN|_ rat|rat|NN|_ 's|'s|POS|_ caecum|caecum|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
Human|human|JJ|_ intestinal|intestinal|JJ|_ microbiota|microbiota|NN|_ associated|associate|VBN|_ rat|rat|NN|_ 's|'s|POS|_ caecum|caecum|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Human|human|JJ|_ intestinal|intestinal|JJ|_ microbiota|microbiota|NN|_ associated|associate|VBN|_ rat|rat|NN|_ 's|'s|POS|_ caecum|caecum|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
RNA|rna|NN|_ extractions|extraction|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboPure|RiboPure|NNP|_ ™|™|CD|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 9.5.3.1|9.5.3.1|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
control|control|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism control|control|NN|_ vs|vs|CC|_ H2O2|h2o2|NN|_ Rep1|rep1|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism control|control|NN|_ vs|vs|CC|_ H2O2|h2o2|NN|_ Rep2|rep2|JJ|_
H2O2|h2o2|NN|_
One|one|CD|_ conditions|condition|NNS|_ :|:|:|_ 1|1|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_
Overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ in|in|IN|_ LB|lb|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED with|with|IN|_ supplements|supplement|NNS|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.01|0.01|CD|_ and|and|CC|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ Ceilsus|ceilsus|NN|_ degree|degree|NN|_ witouth|witouth|NN|_ shaking|shake|VBG|_ until|until|IN|_ its|its|PRP$|_ OD600|od600|NN|_ reached|reach|VBD|_ 0.1|0.1|CD|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ W3110|w3110|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ 5|5|CD|_ ml|ml|NN|_ cell|cell|NN|_ culture|culture|NN|_ at|at|IN|_ 10|10|CD|_ min|min|NN|_ incubation|incubation|NN|_ with|with|IN|_ or|or|CC|_ without|without|IN|_ 1|1|CD|_ %|%|NN|_ Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_
treatment|treatment|NN|_ :|:|:|_ 1|1|CD|_ %|%|NN|_ H202|h202|NN|_ ,|,|,|_ anaerobic|anaerobic|JJ|_
treatment|treatment|NN|_ :|:|:|_ 1|1|CD|_ %|%|NN|_ H2O2|h2o2|NN|_ ,|,|,|_ anaerobic|anaerobic|JJ|_
treatment|treatment|NN|_ :|:|:|_ control|control|NN|_ ,|,|,|_ anaerobic|anaerobic|JJ|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ v.|v.|CC|_ 9.5.3.1|9.5.3.1|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism wild|wild|JJ|_ type|type|NN|_ vs|vs|CC|_ luxS|luxs|NN|GEN mutants|mutant|NNS|_ with|with|IN|_ 10|10|CD|_ %|%|NN|_ H2O2|h2o2|NN|_ Rep1|rep1|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism wild|wild|JJ|_ type|type|NN|_ vs|vs|CC|_ luxS|luxs|NN|GEN mutants|mutant|NNS|_ with|with|IN|_ 10|10|CD|_ %|%|NN|_ H2O2|h2o2|NN|_ Rep2|rep2|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism wild|wild|JJ|_ type|type|NN|_ vs|vs|CC|_ luxS|luxs|NN|GEN mutants|mutant|NNS|_ with|with|IN|_ 30|30|CD|_ %|%|NN|_ H2O2|h2o2|NN|_ Rep1|rep1|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism wild|wild|JJ|_ type|type|NN|_ vs|vs|CC|_ luxS|luxs|NN|GEN mutants|mutant|NNS|_ with|with|IN|_ 30|30|CD|_ %|%|NN|_ H2O2|h2o2|NN|_ Rep2|rep2|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism wild|wild|JJ|_ type|type|NN|_ vs|vs|CC|_ luxS|luxs|NN|GEN mutants|mutant|NNS|_ without|without|IN|_ H2O2|h2o2|NN|_ Rep1|rep1|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism wild|wild|JJ|_ type|type|NN|_ vs|vs|CC|_ luxS|luxs|NN|GEN mutants|mutant|NNS|_ without|without|IN|_ H2O2|h2o2|NN|_ Rep2|rep2|JJ|_
genotype|genotype|NN|_ :|:|:|_ luxS|luxs|NN|GEN
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
luxS|luxs|NN|GEN mutants|mutant|NNS|_ ,|,|,|_ 10|10|CD|_ %|%|NN|_ H2O2|h2o2|NN|_
luxS|luxs|NN|GEN mutants|mutant|NNS|_ ,|,|,|_ 30|30|CD|_ %|%|NN|_ H2O2|h2o2|NN|_
luxS|luxs|NN|GEN mutants|mutant|NNS|_ ,|,|,|_ without|without|IN|_ H2O2|h2o2|NN|_
Overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ in|in|IN|_ LB|lb|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ LB|lb|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.8|0.8|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.02|0.02|CD|_ and|and|CC|_ was|be|VBD|_ continuously|continuously|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ degree|degree|NN|_ celcius|celcius|NNS|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ its|its|PRP$|_ OD600|od600|NN|_ reached|reach|VBD|_ 1.0|1.0|CD|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ W3110|w3110|NN|_
three|three|CD|_ different|different|JJ|_ concentrations|concentration|NNS|_ ,|,|,|_ without|without|IN|_ H2O2|h2o2|NN|_ ,|,|,|_ 10|10|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ 5|5|CD|_ ml|ml|NN|_ cell|cell|NN|_ culture|culture|NN|_ after|after|IN|_ 30|30|CD|_ min|min|NN|_ incubation|incubation|NN|_ with|with|IN|_ or|or|CC|_ without|without|IN|_ H2O2|h2o2|NN|_ treatment|treatment|NN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_
treatment|treatment|NN|_ :|:|:|_ 10|10|CD|_ %|%|NN|_ H202|h202|NN|_
treatment|treatment|NN|_ :|:|:|_ 30|30|CD|_ %|%|NN|_ H202|h202|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
wild|wild|JJ|_ type|type|NN|_ ,|,|,|_ 10|10|CD|_ %|%|NN|_ H2O2|h2o2|NN|_
wild|wild|JJ|_ type|type|NN|_ ,|,|,|_ 30|30|CD|_ %|%|NN|_ H2O2|h2o2|NN|_
wild|wild|JJ|_ type|type|NN|_ ,|,|,|_ without|without|IN|_ H2O2|h2o2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
JCB570|jcb570|NN|_
JQ004|jq004|NN|_ -LRB-|-lrb-|-LRB-|_ rraA|rraa|NN|GEN -RRB-|-rrb-|-RRB-|_
rraA|rraa|NN|GEN deletion|deletion|NN|_ ,|,|,|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_
rraA|rraa|NN|GEN deletion|deletion|NN|_ ,|,|,|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_
rraA|rraa|NN|GEN deletion|deletion|NN|_ ,|,|,|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_
VALUE|value|NN|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
KSL2000|ksl2000|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
KSL2000|ksl2000|NN|_ ,|,|,|_ no|no|DT|_ arabinose|arabinose|NN|_
KSL2000|ksl2000|NN|_ plus|plus|CC|_ pTrc99A|ptrc99a|NN|_
KSL2000|ksl2000|NN|_ plus|plus|CC|_ pTrc99A-RraA|ptrc99a-rraa|NN|_
KSL2000-Rne|ksl2000-rne|NN|_ depletion|depletion|NN|_
KSL2000-RraA|ksl2000-rraa|NN|_ overexpression|overexpression|NN|_
KSL2009|ksl2009|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
KSL2009|ksl2009|NN|_ ,|,|,|_ no|no|DT|_ arabinose|arabinose|NN|_
KSL2009-N-Rne|ksl2009-n-rne|NN|_ depletion|depletion|NN|_
KSL2009|ksl2009|NN|_ plus|plus|CC|_ pTrc99A|ptrc99a|NN|_
KSL2009|ksl2009|NN|_ plus|plus|CC|_ pTrc99A-RraA|ptrc99a-rraa|NN|_
KSL2009-RraA|ksl2009-rraa|NN|_ overexpression|overexpression|NN|_
VALUE|value|NN|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_
genetic|genetic|JJ|_ background|background|NN|_ :|:|:|_ O157|o157|NN|_ H19|h19|NN|_
genotype|genotype|NN|_ :|:|:|_ triclosan|triclosan|NN|_ tolerant|tolerant|JJ|_ mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Microarray|microarray|NN|_ analysis|analysis|NN|_ including|include|VBG|_ pre-processing|pre-processing|JJ|_ ,|,|,|_ normalisation|normalisation|NN|_ anmd|anmd|NN|_ statistical|statistical|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ R|r|NN|_ ,|,|,|_ 2007|2007|CD|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 2.6|2.6|CD|_ and|and|CC|_ Bioconductor|Bioconductor|NNP|_ -LRB-|-lrb-|-LRB-|_ Gentleman|Gentleman|NNP|_ et|et|FW|_ al.|al.|FW|_ 2004|2004|CD|_ ,|,|,|_ Genome|Genome|NNP|_ Biol|Biol|NNP|_ .|.|.|_ 5|5|CD|_ :|:|:|_ R80|r80|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 2.1|2.1|CD|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ by|by|IN|_ Morris|Morris|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2009|2009|CD|_ ,|,|,|_ Physiol|Physiol|NNP|_ .|.|.|_ Genomics|genomic|NNS|_ 39:28-37|39:28-37|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Propagating|propagate|VBG|_ uncertainty|uncertainty|NN|_ in|in|IN|_ microarray|microarray|NN|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ puma|puma|NN|_ -RRB-|-rrb-|-RRB-|_ method|method|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ estimate|estimate|VB|_ fold|fold|JJ|_ changes|change|NNS|_ and|and|CC|_ P-like|p-like|JJ|_ values|value|NNS|_ of|of|IN|_ differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ Pearson|Pearson|NNP|_ et|et|FW|_ al.|al.|FW|_ 2009|2009|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ 10:211|10:211|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Mutant|mutant|JJ|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ treated|treat|VBN|_ with|with|IN|_ 6|6|CD|_ ug|ug|NN|_
Mutant|mutant|JJ|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ untreated|untreated|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Mutant|mutant|JJ|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ untreated|untreated|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Mutant|mutant|JJ|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ untreated|untreated|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
strain|strain|NN|_ :|:|:|_ T3|t3|NN|_ 5H5|5h5|NN|_
strain|strain|NN|_ :|:|:|_ T3|t3|NN|_ 5H5|5h5|NN|_ M|m|NN|_
The|the|DT|_ subculture|subculture|NN|_ was|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ 10|10|CD|_ ml|ml|NN|_ portions|portion|NNS|_ ,|,|,|_ one|one|CD|_ of|of|IN|_ which|which|WDT|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 6ug|6ug|JJ|_
The|the|DT|_ wildtype|wildtype|JJ|_ and|and|CC|_ mutant|mutant|JJ|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H19|h19|NN|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37c|37c|CD|_ x|x|CC|_ 24h|24h|CD|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ isolated|isolate|VBN|_ colony|colony|NN|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ was|be|VBD|_ selected|select|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37c|37c|CD|_ until|until|IN|_ growth|growth|NN|_ reached|reach|VBD|_ an|a|DT|_ optical|optical|JJ|_ density|density|NN|_ of|of|IN|_ 0.6|0.6|CD|_ at|at|IN|_ 600nm|600nm|CD|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ stabilised|stabilise|VBN|_ and|and|CC|_ subsequently|subsequently|RB|_ purified|purify|VBN|_ from|from|IN|_ a|a|DT|_ 500|500|CD|_ ul|ul|NN|_ portion|portion|NN|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ using|use|VBG|_ a|a|DT|_ RNAprotect|rnaprotect|NN|_ Bacterial|bacterial|JJ|_ Reagent|reagent|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Crawley|Crawley|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ triclosan|triclosan|NN|_
treatment|treatment|NN|_ :|:|:|_ untreated|untreated|JJ|_
Triclosan|Triclosan|NNP|_ tolerant|tolerant|JJ|_ mutant|mutant|JJ|_ triclosan|triclosan|NN|_ treated|treat|VBN|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Triclosan|Triclosan|NNP|_ tolerant|tolerant|JJ|_ mutant|mutant|JJ|_ triclosan|triclosan|NN|_ treated|treat|VBN|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Triclosan|Triclosan|NNP|_ tolerant|tolerant|JJ|_ mutant|mutant|JJ|_ triclosan|triclosan|NN|_ treated|treat|VBN|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Triclosan|triclosan|NN|_ tolerant|tolerant|JJ|_ mutant|mutant|JJ|_ untreated|untreated|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Triclosan|Triclosan|NNP|_ tolerant|tolerant|JJ|_ mutant|mutant|JJ|_ untreated|untreated|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Triclosan|Triclosan|NNP|_ tolerant|tolerant|JJ|_ mutant|mutant|JJ|_ untreated|untreated|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Wildtype|wildtype|NN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ treated|treat|VBN|_ with|with|IN|_ 6|6|CD|_ ug|ug|NN|_
Wildtype|wildtype|NN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ untreated|untreated|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Wildtype|wildtype|NN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ untreated|untreated|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Wildtype|wildtype|JJ|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ untreated|untreated|JJ|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Wildtype|wildtype|JJ|_ triclosan|triclosan|NN|_ treated|treat|VBN|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Wildtype|wildtype|JJ|_ triclosan|triclosan|NN|_ treated|treat|VBN|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Wildtype|wildtype|JJ|_ triclosan|triclosan|NN|_ treated|treat|VBN|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Wildtype|wildtype|JJ|_ untreated|untreated|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Wildtype|wildtype|JJ|_ untreated|untreated|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Wildtype|wildtype|JJ|_ untreated|untreated|JJ|_ biological|biological|JJ|_ rep|rep|NN|GEN 3|3|CD|_
0.5|0.5|CD|_ MIC|mic|NN|_ of|of|IN|_ CYA|CYA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
0.5|0.5|CD|_ MIC|mic|NN|_ of|of|IN|_ CYA|CYA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
0.5|0.5|CD|_ MIC|mic|NN|_ of|of|IN|_ CYA|CYA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anaerobic|anaerobic|JJ|_ incubator|incubator|NN|_ for|for|IN|_ 1h|1h|NN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ and|and|CC|_ drugs|drug|NNS|_ were|be|VBD|_ added|add|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ different|different|JJ|_ concentrations|concentration|NNS|_ .|.|.|_ The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ MIC|mic|NN|_ of|of|IN|_ cyadox|cyadox|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ DMSO|dmso|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism treated|treat|VBN|_ with|with|IN|_ MBC|mbc|NN|_ of|of|IN|_ cyadox|cyadox|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism treated|treat|VBN|_ with|with|IN|_ MBC|mbc|NN|_ of|of|IN|_ olaquindox|olaquindox|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism treated|treat|VBN|_ with|with|IN|_ MIC|mic|NN|_ of|of|IN|_ olaquindox|olaquindox|NN|_
MBC|mbc|NN|_ of|of|IN|_ CYA|CYA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
MBC|mbc|NN|_ of|of|IN|_ CYA|CYA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
MBC|mbc|NN|_ of|of|IN|_ CYA|CYA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
MBC|mbc|NN|_ of|of|IN|_ OLA|OLA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
MBC|mbc|NN|_ of|of|IN|_ OLA|OLA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
MBC|mbc|NN|_ of|of|IN|_ OLA|OLA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
MIC|mic|NN|_ of|of|IN|_ OLA|OLA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
MIC|mic|NN|_ of|of|IN|_ OLA|OLA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
MIC|mic|NN|_ of|of|IN|_ OLA|OLA|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
Solvent|solvent|JJ|_ control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
Solvent|solvent|JJ|_ control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Solvent|solvent|JJ|_ control|control|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
strain|strain|NN|_ :|:|:|_ CVCC2943|cvcc2943|NN|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 8000|8000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap-frozen|snap-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ kept|keep|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Partek|Partek|NNP|_ Genomics|Genomics|NNP|_ Suite|Suite|NNP|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_
Trizol|trizol|NN|_ extraction|extraction|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40mM|40mm|NN|_ Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40mM|40mm|NN|_ Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Pnp|Pnp|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Pnp|Pnp|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Pnp|Pnp|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
VALUE|VALUE|NNP|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ CMid|cmid|NN|_ Log|log|NN|_
Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ Eno|eno|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ A|A|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ Eno|eno|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ B|B|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ Eno|eno|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ A1|a1|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ Eno|eno|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ B1|b1|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ A2|a2|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ B2|b2|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ C2|c2|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ A|A|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ A1|a1|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ B|B|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ B1|b1|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ C|C|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ C1|c1|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ A|A|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|trial|NN|_ B|b|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ vs|vs|CC|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Trial|Trial|NNP|_ C|C|NNP|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A|A|NNP|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A1|a1|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B|B|NNP|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B1|b1|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc.at|suc.at|NN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ A|A|NNP|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ B|B|NNP|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A2|a2|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B2|b2|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ A|a|DT|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ A1|a1|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ B|b|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ B1|b1|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ ,|,|,|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ A|A|NNP|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc.at|suc.at|NN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ B|B|NNP|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A2|a2|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B2|b2|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ A1|a1|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ B1|b1|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A1|a1|NN|_
1.5|1.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B1|b1|NN|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1|1|CD|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ A|A|NNP|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ B|B|NNP|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 2|2|CD|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log1|log1|NN|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log1|log1|NN|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 2|2|CD|_
3|3|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1|1|CD|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1|1|CD|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 2|2|CD|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log1|log1|NN|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log1|log1|NN|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 2|2|CD|_
4.5|4.5|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ .2|.2|NN|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1|1|CD|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A|A|NNP|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A1|a1|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B|B|NNP|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B1|b1|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ A|A|NNP|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ B|B|NNP|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ A2|a2|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep.|Rep.|NNP|_ B2|b2|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ A|a|DT|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ A1|a1|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ B|b|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ B1|b1|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ A|A|NNP|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ B|B|NNP|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ A2|a2|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ A1|a1|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Replicate|replicate|VB|_ B1|b1|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ .2|.2|NN|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ B2|b2|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ A1|a1|NN|_
6|6|CD|_ '|'|''|_ RNA|rna|NN|_ Decay|decay|NN|_ of|of|IN|_ WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Rep|Rep|NNP|_ B1|b1|NN|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40mM|40mm|NN|_ Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1.5|1.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40mM|40mm|NN|_ Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3.0|3.0|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40mM|40mm|NN|_ Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Eno|Eno|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ DF261|df261|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40mM|40mm|NN|_ Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6.0|6.0|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1.5|1.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3|3|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
N-RNaseE|n-rnasee|NN|_ -LRB-|-lrb-|-LRB-|_ BZ453|bz453|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Pnp|Pnp|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Pnp|Pnp|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
Pnp|Pnp|NNP|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1.5|1.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3|3|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
Pnp|pnp|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ YHC012|yhc012|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1.5|1.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3|3|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3|3|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
RhlB|rhlb|NN|_ -|-|:|_ -LRB-|-lrb-|-LRB-|_ SU02|su02|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
VALUE|value|NN|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ 0C|0c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6.0|6.0|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1.5|1.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3|3|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6.0|6.0|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Suc|suc|NN|_ .|.|.|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ K10|k10|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ 40|40|CD|_ mM|mm|NN|KWSUPP Succinate|succinate|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1.5|1.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3.0|3.0|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3|3|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ N3433|n3433|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
WT|WT|NNP|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 1.5|1.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 3|3|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 4.5|4.5|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_ 6|6|CD|_ '|'|''|_ post|post|JJ|_ rif|rif|NN|_
WT|wt|NN|_ -LRB-|-lrb-|-LRB-|_ SH3208|sh3208|NN|_ -RRB-|-rrb-|-RRB-|_ M9|m9|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Tryptone|tryptone|NN|_ at|at|IN|_ 30|30|CD|_ C|c|NN|_ Mid|Mid|NNP|_ Log|Log|NNP|_
1mL|1ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ mixed|mix|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ Phenol|phenol|NN|_
B500|b500|CD|_ _|_|NN|_ 1|1|CD|_
Bacterial|bacterial|JJ|_ cell|cell|NN|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Clones|clone|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ with|with|IN|_ 0.4|0.4|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w|w|NN|_
Differentially|differentially|RB|_ expressed|express|VBN|_ -LRB-|-lrb-|-LRB-|_ DE|de|NN|_ -RRB-|-rrb-|-RRB-|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ stress|stress|NN|_ evolved|evolve|VBD|_ strains|strain|NNS|_ were|be|VBD|_ found|find|VBN|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ G500|g500|NN|_ strain|strain|NN|_ using|use|VBG|_ the|the|DT|_ edgeR|edger|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Differentially|differentially|RB|_ expressed|express|VBD|_ genes|gene|NNS|_ were|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ processing|process|VBG|_ raw|raw|JJ|_ counts|count|NNS|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ with|with|IN|_ edgeR|edger|NN|_ R|r|NN|_ library|library|NN|_ version|version|NN|_ 2.6.9|2.6.9|CD|_ .|.|.|_ Normalized|normalize|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ were|be|VBD|_ averaged|average|VBN|_ between|between|IN|_ two|two|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
G500|g500|CD|_ _|_|NN|_ 1|1|CD|_
Genes|gene|NNS|_ from|from|IN|_ the|the|DT|_ amplified|amplify|VBN|_ regions|region|NNS|_ in|in|IN|_ O500|o500|NN|_ -LRB-|-lrb-|-LRB-|_ 12-fold|12-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P500|p500|NN|_ -LRB-|-lrb-|-LRB-|_ two-fold|two-fold|JJ|_ -RRB-|-rrb-|-RRB-|_ strains|strain|NNS|_ are|be|VBP|_ significantly|significantly|RB|_ over-expressed|over-expressed|JJ|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ :|:|:|_ average|average|JJ|_ log|log|NN|_ Fold|Fold|NNP|_ Change|Change|NNP|_ for|for|IN|_ concentrations|concentration|NNS|_ is|be|VBZ|_ +3.6|+3.6|CD|_ and|and|CC|_ +0.8|+0.8|CD|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ with|with|IN|_ p-values|p-values|NN|_ <|<|JJR|_ 10-20|10-20|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genes|gene|NNS|_ with|with|IN|_ BH|bh|NN|_ -LRB-|-lrb-|-LRB-|_ Benjamini|Benjamini|NNP|_ and|and|CC|_ Hochberg|Hochberg|NNP|_ -RRB-|-rrb-|-RRB-|_ adjusted|adjust|VBN|_ p-values|p-value|NNS|_ below|below|IN|_ 0.05|0.05|CD|_ threshold|threshold|NN|_ were|be|VBD|_ selected|select|VBN|_ as|as|IN|_ DE|de|NN|_ genes|gene|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_
H500|h500|CD|_ _|_|NN|_ 1|1|CD|_
Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ SGA|SGA|NNP|_ version|version|NN|_ 0.9.9|0.9.9|CD|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ sga|sga|NN|_ preprocess|preprocess|NN|_ -|-|:|_ q|q|NN|_ 10|10|CD|_ -|-|:|_ f|f|LS|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ 25|25|CD|_ -LRB-|-lrb-|-LRB-|_ quality|quality|NN|_ trim|trim|JJ|_ 10|10|CD|_ ,|,|,|_ quality|quality|NN|_ filter|filter|NN|_ 10|10|CD|_ ,|,|,|_ minimal|minimal|JJ|_ length|length|NN|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_
O500|o500|CD|_ _|_|NN|_ 1|1|CD|_
O500|o500|CD|_ _|_|NN|_ 2|2|CD|_
P500|p500|CD|_ _|_|NN|_ 1|1|CD|_
preprocessed|preprocessed|JJ|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strain|strain|NN|_ K12|k12|NN|_ sub-strain|sub-strain|JJ|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ accession|accession|NN|_ no|no|DT|_ .|.|.|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ BWA|BWA|NNP|_ toolkit|toolkit|NN|_ version|version|NN|_ 0.5.9-r16|0.5.9-r16|NN|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ options|option|NNS|_ :|:|:|_ bwa|bwa|NN|_ aln|aln|NN|_ -|-|:|_ q|q|NN|_ 20|20|CD|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ 1st|1st|JJ|_ and|and|CC|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ linker|linker|NN|_ ligation|ligation|NN|_ and|and|CC|_ size|size|NN|_ selection|selection|NN|_ subjected|subject|VBN|_ to|to|TO|_ shotgun|shotgun|NN|_ sequencing|sequencing|NN|_ using|use|VBG|_ single|single|JJ|_ read|read|NN|_ 40bp|40bp|JJ|_ read|read|NN|_ length|length|NN|_ runs|run|VBZ|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ GAII|GAII|NNP|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG|mg|NN|_ 1655|1655|CD|_
stress|stress|NN|_ :|:|:|_ acidic|acidic|JJ|_
stress|stress|NN|_ :|:|:|_ Minimal|minimal|JJ|_ medium|medium|NN|_
stress|stress|NN|_ :|:|:|_ n-butanol|n-butanol|NN|_
stress|stress|NN|_ :|:|:|_ osmotic|osmotic|JJ|_
stress|stress|NN|_ :|:|:|_ oxidative|oxidative|JJ|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ includes|include|VBZ|_ :|:|:|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ levels|level|NNS|_ relative|relative|JJ|_ to|to|TO|_ the|the|DT|_ G500|g500|NN|_ strain|strain|NN|_ with|with|IN|_ corresponding|corresponding|JJ|_ p-values|p-value|NNS|_ and|and|CC|_ processed|process|VBN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ -LRB-|-lrb-|-LRB-|_ each|each|DT|_ normolized|normolized|NN|_ and|and|CC|_ averaged|average|VBD|_ between|between|IN|_ 2|2|CD|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Linked|link|VBN|_ as|as|IN|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ Series|Series|NNP|_ record|record|NN|_ .|.|.|_
technical|technical|JJ|_ replicates|replicate|VBZ|_ :|:|:|_ 2|2|CD|_
After|after|IN|_ reaching|reach|VBG|_ an|a|DT|_ OD600nm|od600nm|NN|_ of|of|IN|_ 0.9|0.9|CD|_ ,|,|,|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ placed|place|VBN|_ immediately|immediately|RB|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ water|water|NN|_ bath|bath|NN|_ along|along|IN|_ with|with|IN|_ another|another|DT|_ BHI|BHI|NNP|_ flask|flask|NN|_ carrying|carry|VBG|_ a|a|DT|_ type|type|NN|_ T|t|NN|_ thermocouple|thermocouple|NN|_ connected|connect|VBN|_ to|to|TO|_ a|a|DT|_ MultiPaq|MultiPaq|NNP|_ 21|21|CD|_ datalogger|datalogger|NN|_ -LRB-|-lrb-|-LRB-|_ Datapaq|Datapaq|NNP|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ temperature|temperature|NN|_ profile|profile|NN|_ and|and|CC|_ the|the|DT|_ process|process|NN|_ lethality|lethality|NN|_ values|value|NNS|_ monitoring|monitor|VBG|_ in|in|IN|_ real|real|JJ|_ time|time|NN|_ .|.|.|_ Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ were|be|VBD|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ process|process|NN|_ lethality|lethality|NN|_ values|value|NNS|_ of|of|IN|_ 2|2|CD|_ and|and|CC|_ 3|3|CD|_ ,|,|,|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ ,|,|,|_ or|or|CC|_ until|until|IN|_ a|a|DT|_ temperature|temperature|NN|_ of|of|IN|_ 71|71|CD|_ °C|°c|NN|_ was|be|VBD|_ reached|reach|VBN|_ .|.|.|_ Just|just|RB|_ after|after|IN|_ heating|heating|NN|_ ,|,|,|_ cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ cooled|cool|VBN|_ in|in|IN|_ an|a|DT|_ iced|iced|JJ|_ water|water|NN|_ bath|bath|NN|_ under|under|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ -LRB-|-lrb-|-LRB-|_ 150|150|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ the|the|DT|_ temperature|temperature|NN|_ dropped|drop|VBD|_ back|back|RB|_ to|to|TO|_ no|no|DT|_ less|less|JJR|_ than|than|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ order|order|NN|_ to|to|TO|_ avoid|avoid|VB|_ cold|cold|JJ|_ stress|stress|NN|_ .|.|.|_ Cell|cell|NN|_ suspensions|suspension|NNS|_ were|be|VBD|_ then|then|RB|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ the|the|DT|_ remaining|remain|VBG|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNA|rna|NN|_ protect|protect|VBP|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ prior|prior|RB|_ to|to|TO|_ freezing|freezing|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Bacteria|bacterium|NNS|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ F|f|NN|_ =|=|JJ|_ 2|2|CD|_
Bacteria|bacterium|NNS|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ F|f|NN|_ =|=|JJ|_ 3|3|CD|_
Bacteria|bacterium|NNS|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ F|f|NN|_ =|=|JJ|_ 3|3|CD|_
Bacteria|bacterium|NNS|_ at|at|IN|_ 71|71|CD|_ °C|°c|NN|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 2|2|CD|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 2|2|CD|_ -|-|:|_ Replicate|replicate|VB|_ 2|2|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 2|2|CD|_ -|-|:|_ Replicate|replicate|VB|_ 3|3|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 2|2|CD|_ -|-|:|_ Replicate|replicate|VB|_ 4|4|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 2|2|CD|_ -|-|:|_ Replicate|replicate|VB|_ 5|5|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 2|2|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 3|3|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 4|4|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 2|2|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 3|3|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ at|at|IN|_ 60|60|CD|_ °C|°c|NN|_ to|to|TO|_ a|a|DT|_ process|process|NN|_ lethality|lethality|NN|_ value|value|NN|_ of|of|IN|_ 3|3|CD|_ -|-|:|_ Replicate|replicate|VB|_ 4|4|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ to|to|TO|_ a|a|DT|_ core|core|NN|_ temperature|temperature|NN|_ of|of|IN|_ 71|71|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 1|1|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ to|to|TO|_ a|a|DT|_ core|core|NN|_ temperature|temperature|NN|_ of|of|IN|_ 71|71|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 2|2|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ to|to|TO|_ a|a|DT|_ core|core|NN|_ temperature|temperature|NN|_ of|of|IN|_ 71|71|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 3|3|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ to|to|TO|_ a|a|DT|_ core|core|NN|_ temperature|temperature|NN|_ of|of|IN|_ 71|71|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 4|4|CD|_
Bacteria|bacterium|NNS|_ suspension|suspension|NN|_ heated|heat|VBN|_ to|to|TO|_ a|a|DT|_ core|core|NN|_ temperature|temperature|NN|_ of|of|IN|_ 71|71|CD|_ °C|°c|NN|_ -|-|:|_ Replicate|replicate|VB|_ 5|5|CD|_
Control|Control|NNP|_ bacteria|bacterium|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ common|common|JJ|_ reference|reference|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ 5|5|CD|_ indepedent|indepedent|NN|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pool|VBN|_ after|after|IN|_ cDNA|cdna|NN|_ labeling|labeling|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ replicate|replicate|VB|_ ,|,|,|_ frozen|frozen|JJ|_ aliquots|aliquot|NNS|_ -LRB-|-lrb-|-LRB-|_ 500μl|500μl|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ stock|stock|NN|_ cultures|culture|NNS|_ were|be|VBD|_ subcultured|subculture|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ of|of|IN|_ Brain|brain|NN|_ Heart|Heart|NNP|_ Infusion|Infusion|NNP|_ -LRB-|-lrb-|-LRB-|_ BHI|BHI|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ sub-cultured|sub-cultured|JJ|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ %|%|NN|_ v|v|LS|_
Frozen|frozen|JJ|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lyzed|lyze|VBN|_ with|with|IN|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K|k|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ cell|cell|NN|_ lysates|lysate|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Midi|Midi|NNP|_ Kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Life|Life|NNP|_ technologies|technology|NNS|_ -RRB-|-rrb-|-RRB-|_ before|before|IN|_ a|a|DT|_ phenol|phenol|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD600nm|od600nm|NN|_ of|of|IN|_ 0.9|0.9|CD|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Controls|Controls|NNP|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ optimal|optimal|JJ|_ temperature|temperature|NN|_ of|of|IN|_ 37|37|CD|_ °C|°c|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Treatment|treatment|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ 58|58|CD|_ °C|°c|NN|_ F|f|NN|_ =|=|JJ|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Treatment|treatment|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ 58|58|CD|_ °C|°c|NN|_ F|f|NN|_ =|=|JJ|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Treatment|treatment|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ 60|60|CD|_ °C|°c|NN|_ F|f|NN|_ =|=|JJ|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Treatment|treatment|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ core|core|NN|_ temperature|temperature|NN|_ of|of|IN|_ 71|71|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_
LOWESS|lowess|NN|_ normalized|normalize|VBD|_ data|datum|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ log2|log2|NN|_ of|of|IN|_ processed|process|VBN|_ Red|red|JJ|_ signal|signal|NN|_ -LRB-|-lrb-|-LRB-|_ treated|treat|VBN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ strain|strain|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ MG1655|mg1655|NN|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_ 10.10.1.1|10.10.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 2.5|2.5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 80|80|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 2.5|2.5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 80|80|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ prior|prior|RB|_ to|to|TO|_ CORM-3|corm-3|NN|_ addition|addition|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 2.5|2.5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 80|80|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 2.5|2.5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 80|80|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ prior|prior|RB|_ to|to|TO|_ CORM-3|corm-3|NN|_ addition|addition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Slide|slide|NN|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|Slide|NNP|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 10|10|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 11|11|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|Slide|NNP|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 12|12|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 18|18|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 19|19|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 20|20|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 25|25|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 26|26|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 27|27|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 28|28|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 29|29|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 30|30|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|SYM|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
strain|strain|NN|_ :|:|:|_ Wild|Wild|NNP|_ type|type|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_
dpiA|dpia|NN|GEN 2x|2x|NN|_ Overexpression|overexpression|NN|_ pHI1429|phi1429|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Phase|phase|NN|_
dpiAoverexpressor|dpiaoverexpressor|NN|_
ecd3-c-0081429|ecd3-c-0081429|NN|_ wt|wt|JJ|_ vs|vs|CC|_ dpiAoverexpressor|dpiaoverexpressor|JJ|_
ecd3-c-0101429|ecd3-c-0101429|NN|_ wt|wt|JJ|_ vs|vs|CC|_ dpiAoverexpressor|dpiaoverexpressor|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
VALUE|value|NN|_ is|be|VBZ|_ Log|log|NN|_ -LRB-|-lrb-|-LRB-|_ base|base|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ Channel|Channel|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 635|635|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ Channel|Channel|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ usually|usually|RB|_ 532|532|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_
WT1088|wt1088|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Phase|phase|NN|_
WT1088|wt1088|NN|_ vs.|vs.|CC|_ dpiA|dpia|NN|GEN 2x|2x|NN|_ Overexpression|overexpression|NN|_ pHI1429|phi1429|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Phase|phase|NN|_ Trial|trial|NN|_ A|a|NN|_
WT1088|wt1088|NN|_ vs.|vs.|CC|_ dpiA|dpia|NN|GEN 2x|2x|NN|_ Overexpression|overexpression|NN|_ pHI1429|phi1429|NN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ Mid|Mid|NNP|_ Log|Log|NNP|_ Phase|phase|NN|_ Trial|trial|NN|_ B|b|NN|_
antibody|antibody|NN|_ :|:|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ FNR|fnr|NN|TF antibody|antibody|NN|_
antibody|antibody|NN|_ :|:|:|_ Pre-cleared|pre-cleared|JJ|_ FNR|fnr|NN|TF antibody|antibody|NN|_
antibody|antibody|NN|_ :|:|:|_ Pre-cleared|pre-cleared|JJ|_ H-NS|h-ns|NN|_ polyclonal|polyclonal|JJ|_ antibody|antibody|NN|_
antibody|antibody|NN|_ :|:|:|_ Pre-cleared|pre-cleared|JJ|_ IHF|ihf|NN|TF polyclonal|polyclonal|JJ|_ antibody|antibody|NN|_
antibody|antibody|NN|_ :|:|:|_ RNA|rna|NN|_ Polymerase|polymerase|NN|_ ß|ß|NN|_ monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ from|from|IN|_ NeoClone|NeoClone|NNP|_ -LRB-|-lrb-|-LRB-|_ W0002|w0002|NN|_ -RRB-|-rrb-|-RRB-|_
Arrays|array|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Nimblegen|Nimblegen|NNP|_ 's|'s|POS|_ standard|standard|JJ|_ protocol|protocol|NN|_ for|for|IN|_ Nimblescan|nimblescan|JJ|_ 2.4|2.4|CD|_ ChIP|chip|NN|_ data|datum|NNS|_ extraction|extraction|NN|_ .|.|.|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250ul|250ul|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 25|25|CD|_ %|%|NN|_ O2|o2|CD|_ ,|,|,|_ 70|70|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.35|0.35|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ with|with|IN|_ 16|16|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ and|and|CC|_ 300|300|CD|_ µL|µl|NN|_ Cm20|cm20|NN|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ with|with|IN|_ 4|4|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ and|and|CC|_ 300|300|CD|_ µL|µl|NN|_ Cm20|cm20|NN|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ with|with|IN|_ 8|8|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_ and|and|CC|_ 300|300|CD|_ µL|µl|NN|_ Cm20|cm20|NN|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655star|mg1655star|JJ|_
FNR|fnr|SYM|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ A|a|NN|_
FNR|fnr|SYM|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ -|-|:|_ A|a|NN|_
FNR|fnr|SYM|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ -|-|:|_ B|b|NN|_
FNR|fnr|SYM|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ B|b|NN|_
FNR|fnr|SYM|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ C|c|NN|_
∆|∆|CD|_ fnr|fnr|SYM|GEN -|-|:|_ Anaeroibc|Anaeroibc|NNP|_
FNR|FNR|NNP|TF ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ ∆|∆|CD|_ hns|hn|NNS|GEN
∆|∆|CD|_ fnr|fnr|NN|GEN ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ PK4854|pk4854|NN|_
FNR|fnr|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherchia|Escherchia|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_
FNR|fnr|SYM|TF -|-|:|_ ∆|∆|SYM|_ hns|hn|VBZ|GEN ∆|∆|SYM|_ stpA|stpa|NN|GEN A|a|NN|_
FNR|fnr|SYM|TF -|-|:|_ ∆|∆|SYM|_ hns|hn|VBZ|GEN ∆|∆|SYM|_ stpA|stpa|NN|GEN B|b|NN|_
FNR|fnr|NN|TF INPUT|input|NN|_ from|from|IN|_ PK8263|pk8263|NN|_ with|with|IN|_ 16|16|CD|_ µM|µm|NN|_ INPUTTG|inputtg|NN|_
FNR|fnr|NN|TF INPUT|input|NN|_ from|from|IN|_ PK8263|pk8263|NN|_ with|with|IN|_ 4|4|CD|_ µM|µm|NN|_ INPUTTG|inputtg|NN|_
FNR|fnr|NN|TF INPUT|input|NN|_ from|from|IN|_ PK8263|pk8263|NN|_ with|with|IN|_ 8|8|CD|_ µM|µm|NN|_ INPUTTG|inputtg|NN|_
FNR|fnr|NN|TF INPUT|input|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
FNR|fnr|NN|TF IP|IP|NNP|_ from|from|IN|_ PK8263|pk8263|NN|_ with|with|IN|_ 16|16|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
FNR|fnr|NN|TF IP|IP|NNP|_ from|from|IN|_ PK8263|pk8263|NN|_ with|with|IN|_ 4|4|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
FNR|fnr|NN|TF IP|IP|NNP|_ from|from|IN|_ PK8263|pk8263|NN|_ with|with|IN|_ 8|8|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
FNR|fnr|NN|TF IP|IP|NNP|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ 16|16|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ 4|4|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ 8|8|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Aerobic|aerobic|JJ|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_
HNS|hns|SYM|_ -|-|:|_ Aerobic|aerobic|JJ|_ A|a|NN|_
HNS|hns|SYM|_ -|-|:|_ Aerobic|aerobic|JJ|_ B|b|NN|_
HNS|hns|SYM|_ -|-|:|_ Anaerobic|anaerobic|JJ|_ A|a|NN|_
HNS|hns|SYM|_ -|-|:|_ Anaerobic|anaerobic|JJ|_ B|b|NN|_
HNS|hn|VBZ|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
HNS|hn|VBZ|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ Replicate|replicate|VB|_ B|b|NN|_
IHF|ihf|SYM|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ A|a|NN|_
IHF|ihf|SYM|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ B|b|NN|_
IHF|ihf|NN|TF ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
IHF|ihf|VBP|TF ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ Replicate|replicate|VB|_ B|b|NN|_
INPUT|input|VBP|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ ∆|∆|CD|_ hns|hn|NNS|GEN
INPUT|input|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherchia|Escherchia|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_ ,|,|,|_ no|no|DT|_ antibody|antibody|NN|_ control|control|NN|_
INPUT|INPUT|NNP|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherchia|Escherchia|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_ ,|,|,|_ no|no|DT|_ antibody|antibody|NN|_ control|control|NN|_ ,|,|,|_ Replicate|replicate|VB|_ B|b|NN|_
INPUT|input|VBP|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WTPK4854|wtpk4854|NN|_ ,|,|,|_ no|no|DT|_ antibody|antibody|NN|_ control|control|NN|_
Ptac|ptac|NN|_ :|:|:|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ A|a|NN|_ -|-|:|_ 16|16|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
Ptac|ptac|NN|_ :|:|:|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ A|a|NN|_ -|-|:|_ 4|4|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
Ptac|ptac|NN|_ :|:|:|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ A|a|NN|_ -|-|:|_ 8|8|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
Ptac|ptac|NN|_ :|:|:|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ B|b|NN|_ -|-|:|_ 16|16|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
Ptac|ptac|NN|_ :|:|:|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ B|b|NN|_ -|-|:|_ 4|4|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
Ptac|ptac|NN|_ :|:|:|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ B|b|NN|_ -|-|:|_ 8|8|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
Ptac|ptac|NN|_ :|:|:|_ :|:|:|_ fnr|fnr|SYM|GEN -|-|:|_ C|c|NN|_ -|-|:|_ 16|16|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
ß|ß|SYM|_ -|-|:|_ Aerobic|aerobic|JJ|_ -|-|:|_ A|a|NN|_
ß|ß|SYM|_ -|-|:|_ Aerobic|aerobic|JJ|_ -|-|:|_ B|b|NN|_
ß|ß|SYM|_ -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ A|a|NN|_
ß|ß|SYM|_ -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ B|b|NN|_
ß|ß|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
strain|strain|NN|_ :|:|:|_ ∆|∆|CD|_ hns|hn|NNS|GEN
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_ WT|wt|JJ|_
strain|strain|NN|_ :|:|:|_ PK4854|pk4854|NN|_
strain|strain|NN|_ :|:|:|_ PK8263|pk8263|NN|_
tag|tag|NN|GEN :|:|:|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_ WT|wt|JJ|_
10|10|CD|_ ng|ng|NN|_ of|of|IN|_ DNA|dna|NN|_ were|be|VBD|_ submitted|submit|VBN|_ to|to|TO|_ the|the|DT|_ University|University|NNP|_ of|of|IN|_ Wisconsin-Madison|Wisconsin-Madison|NNP|_ DNA|DNA|NNP|_ Sequencing|sequencing|NN|_ Facility|facility|NN|_ for|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ sheared|shear|VBN|_ to|to|TO|_ 200-500|200-500|CD|_ nt|nt|NNS|_ during|during|IN|_ the|the|DT|_ IP|IP|NNP|_ process|process|NN|_ to|to|TO|_ facilitate|facilitate|VB|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ All|all|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ reagents|reagent|NNS|_ from|from|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Paired|Paired|NNP|_ End|End|NNP|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ ``|``|``|_ Preparing|prepare|VBG|_ Samples|sample|NNS|_ for|for|IN|_ ChIP|chip|NN|_ Sequencing|sequencing|NN|_ of|of|IN|_ DNA|dna|NN|_ ''|''|''|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ part|part|NN|_ #|#|#|_ 11257047|11257047|CD|_ RevA|reva|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ except|except|IN|_ products|product|NNS|_ of|of|IN|_ the|the|DT|_ ligation|ligation|NN|_ reaction|reaction|NN|_ were|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ using|use|VBG|_ 2|2|CD|_ %|%|NN|_ SizeSelect|sizeselect|NN|_ agarose|agarose|NN|_ gels|gel|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ targeting|target|VBG|_ either|either|CC|_ 275|275|CD|_ bp|bp|NN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ s70|s70|NN|_ libraries|library|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 400|400|CD|_ bp|bp|NN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ FNR|fnr|NN|TF libraries|library|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ amplification|amplification|NN|_ ,|,|,|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ were|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|agilent|JJ|_ DNA|dna|NN|_ 1000|1000|CD|_ series|series|NN|_ chip|chip|NN|_ assay|assay|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ QuantIT|quantit|NN|_ PicoGreen|picogreen|NN|_ dsDNA|dsdna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ and|and|CC|_ libraries|library|NNS|_ were|be|VBD|_ standardized|standardized|JJ|_ to|to|TO|_ 10μM|10μm|NN|_ .|.|.|_ Cluster|cluster|NN|_ generation|generation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ cBot|cBot|NNP|_ Single|single|JJ|_ Read|Read|NNP|_ Cluster|Cluster|NNP|_ Generation|Generation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ placed|place|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ cBot|cBot|NNP|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ read|read|NN|_ ,|,|,|_ 36|36|CD|_ bp|bp|NN|_ run|run|NN|_ was|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ SBS|SBS|NNP|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ SCS|scs|NN|_ 2.6|2.6|CD|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ IIx|IIx|NNP|_ .|.|.|_ A|a|DT|_ paired|paired|JJ|_ read|read|NN|_ ,|,|,|_ 100|100|CD|_ bp|bp|NN|_ runs|run|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ one|one|CD|_ replicate|replicate|VB|_ of|of|IN|_ each|each|DT|_ s70|s70|NN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ conditions|condition|NNS|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ SBS|SBS|NNP|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ SCS|scs|NN|_ 2.6|2.6|CD|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ .|.|.|_ Basecalling|basecall|VBG|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ Pipeline|Pipeline|NNP|_ version|version|NN|_ 1.6|1.6|CD|_ .|.|.|_
Aerobic|Aerobic|NNP|_ Cultures|Cultures|NNP|_
aerobic|aerobic|JJ|_ INPUT|input|NN|_ DNA|dna|NN|_
Anaerobic|anaerobic|JJ|_ Cultures|culture|NNS|_
anaerobic|anaerobic|JJ|_ INPUT|input|NN|_ DNA|dna|NN|_
Antibodies|antibody|NNS|_ for|for|IN|_ beta|beta|NN|_ of|of|IN|_ RNAP|rnap|NN|_ -|-|:|_ NeoClone|NeoClone|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ Number|number|NN|_ :|:|:|_ W0002|w0002|NN|_ ,|,|,|_ Lot|lot|NN|_ Number|number|NN|_ :|:|:|_ 2008L10-001|2008l10-001|NN|_ Antibodies|antibody|NNS|_ for|for|IN|_ sigma70|sigma70|NN|_ of|of|IN|_ RNAP|rnap|NN|_ -|-|:|_ NeoClone|NeoClone|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ Number|number|NN|_ :|:|:|_ W0004|w0004|NN|_ ,|,|,|_ Lot|lot|NN|_ Number|number|NN|_ :|:|:|_ 2008K12-001|2008k12-001|NN|_ All|all|DT|_ other|other|JJ|_ antibodies|antibody|NNS|_ -LRB-|-lrb-|-LRB-|_ FNR|fnr|NN|TF ,|,|,|_ H-NS|h-ns|NN|_ ,|,|,|_ IHF|ihf|NN|TF -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ produced|produce|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ and|and|CC|_ are|be|VBP|_ not|not|RB|_ commercially|commercially|RB|_ available|available|JJ|_ .|.|.|_
antibody|antibody|NN|_ :|:|:|_ Affinity|affinity|NN|_ purified|purify|VBN|_ FNR|fnr|NN|TF polyclonal|polyclonal|JJ|_ antibody|antibody|NN|_
antibody|antibody|NN|_ :|:|:|_ INPUT|INPUT|NNP|_
antibody|antibody|NN|_ :|:|:|_ RNA|rna|NN|_ Polymerase|polymerase|NN|_ σ70|σ70|NN|_ monoclonal|monoclonal|JJ|_ antibody|antibody|NN|_ from|from|IN|_ NeoClone|NeoClone|NNP|_ -LRB-|-lrb-|-LRB-|_ W0004|w0004|NN|_ -RRB-|-rrb-|-RRB-|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250ul|250ul|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
ChIP-Seq|chip-seq|NN|_
DNA|dna|NN|_ were|be|VBD|_ submitted|submit|VBN|_ to|to|TO|_ the|the|DT|_ Joint|Joint|NNP|_ Genome|Genome|NNP|_ Institute|Institute|NNP|_ for|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ sheared|shear|VBN|_ to|to|TO|_ 200-500|200-500|CD|_ nt|nt|NNS|_ during|during|IN|_ the|the|DT|_ IP|IP|NNP|_ process|process|NN|_ to|to|TO|_ facilitate|facilitate|VB|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ All|all|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ reagents|reagent|NNS|_ from|from|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Paired|Paired|NNP|_ End|End|NNP|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ ``|``|``|_ Preparing|prepare|VBG|_ Samples|sample|NNS|_ for|for|IN|_ ChIP|chip|NN|_ Sequencing|sequencing|NN|_ of|of|IN|_ DNA|dna|NN|_ ''|''|''|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ part|part|NN|_ #|#|#|_ 11257047|11257047|CD|_ RevA|reva|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ except|except|IN|_ products|product|NNS|_ of|of|IN|_ the|the|DT|_ ligation|ligation|NN|_ reaction|reaction|NN|_ were|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ using|use|VBG|_ 2|2|CD|_ %|%|NN|_ SizeSelect|sizeselect|NN|_ agarose|agarose|NN|_ gels|gel|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ targeting|target|VBG|_ either|either|CC|_ 275|275|CD|_ bp|bp|NN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ s70|s70|NN|_ libraries|library|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ amplification|amplification|NN|_ ,|,|,|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ were|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|agilent|JJ|_ DNA|dna|NN|_ 1000|1000|CD|_ series|series|NN|_ chip|chip|NN|_ assay|assay|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ QuantIT|quantit|NN|_ PicoGreen|picogreen|NN|_ dsDNA|dsdna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ and|and|CC|_ libraries|library|NNS|_ were|be|VBD|_ standardized|standardized|JJ|_ to|to|TO|_ 10μM|10μm|NN|_ .|.|.|_ Cluster|cluster|NN|_ generation|generation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ cBot|cBot|NNP|_ Single|single|JJ|_ Read|Read|NNP|_ Cluster|Cluster|NNP|_ Generation|Generation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ placed|place|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ cBot|cBot|NNP|_ .|.|.|_ A|a|DT|_ single|single|JJ|_ read|read|NN|_ ,|,|,|_ 36|36|CD|_ bp|bp|NN|_ run|run|NN|_ was|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ SBS|SBS|NNP|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ SCS|scs|NN|_ 2.6|2.6|CD|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ IIx|IIx|NNP|_ .|.|.|_ Basecalling|basecall|VBG|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ Pipeline|Pipeline|NNP|_ version|version|NN|_ 1.6|1.6|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655star|mg1655star|JJ|_
FNR|fnr|NN|TF IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Anaerobic|Anaerobic|NNP|_ A|A|NNP|_
FNR|FNR|NNP|TF _|_|SYM|_ IP|IP|NNP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ A|a|DT|_ _|_|NN|_ WIG.wig|wig.wig|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
FNR|fnr|NN|TF IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Anaerobic|anaerobic|JJ|_ B|b|NN|_
FNR|fnr|NN|TF _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ WIG.wig|wig.wig|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Aerobic|Aerobic|NNP|_ Cultures|Cultures|NNP|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ Cultures|culture|NNS|_
INPUT|input|VBP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_ _|_|NNP|_ Aerobic|Aerobic|NNP|_ _|_|SYM|_ WIG.wig|WIG.wig|NNP|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
INPUT|input|VBP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ WIG.wig|wig.wig|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
INPUT|input|NN|_ DNA|dna|NN|_ B|b|NN|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ published|publish|VBN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ software|software|NN|_ packages|package|NNS|_ SOAP|soap|NN|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ELAND|ELAND|NNP|_ -LRB-|-lrb-|-LRB-|_ within|within|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ Software|Software|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ allowing|allow|VBG|_ at|at|IN|_ most|most|JJS|_ two|two|CD|_ mismatches|mismatch|NNS|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ with|with|IN|_ sequences|sequence|NNS|_ that|that|WDT|_ did|do|VBD|_ not|not|RB|_ align|align|VB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ aligned|align|VBN|_ to|to|TO|_ multiple|multiple|JJ|_ locations|location|NNS|_ on|on|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ or|or|CC|_ contained|contain|VBD|_ more|more|JJR|_ than|than|IN|_ two|two|CD|_ mismatches|mismatch|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ from|from|IN|_ further|further|JJ|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 10|10|CD|_ %|%|NN|_ of|of|IN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Supplemental|Supplemental|NNP|_ Files|Files|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ visualization|visualization|NN|_ the|the|DT|_ raw|raw|JJ|_ tag|tag|NN|GEN density|density|NN|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ QuEST|quest|NN|_ -LRB-|-lrb-|-LRB-|_ Valouev|Valouev|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ normalized|normalize|VBD|_ as|as|IN|_ tag|tag|NN|GEN density|density|NN|_ per|per|IN|_ million|million|CD|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ .|.|.|_
Sigma70|sigma70|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_ _|_|NNP|_ Aerobic|Aerobic|NNP|_ _|_|SYM|_ A|a|DT|_ _|_|JJ|_ SET|SET|NNP|_ _|_|SYM|_ WIG.wig|WIG.wig|NNP|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Sigma70|sigma70|NN|_ _|_|CD|_ IP|IP|NNP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ A|a|DT|_ _|_|JJ|_ SET|SET|NNP|_ _|_|SYM|_ WIG.wig|WIG.wig|NNP|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
strain|strain|NN|_ :|:|:|_ Wild|Wild|NNP|_ Type|type|NN|_ K-12|k-12|NN|_
σ70|σ70|NN|_ IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Aerobic|Aerobic|NNP|_ A|A|NNP|_
σ70|σ70|NN|_ IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Aerobic|Aerobic|NNP|_ B|B|NNP|_
σ70|σ70|NN|_ IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Anaerobic|Anaerobic|NNP|_ A|A|NNP|_
σ70|σ70|NN|_ IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Anaerobic|anaerobic|JJ|_ B|b|NN|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ a|a|DT|_ stop|stop|NN|_ solution|solution|NN|_ of|of|IN|_ Phenol|phenol|NN|_ and|and|CC|_ Ethanol|ethanol|NN|_ ,|,|,|_ spun|spin|VBD|_ down|down|RB|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ ref|ref|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ ref|ref|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ bioanalyzer|bioanalyzer|NN|_ and|and|CC|_ quantity|quantity|NN|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ .|.|.|_ To|to|TO|_ enrich|enrich|VB|_ for|for|IN|_ mRNA|mrna|NN|_ ,|,|,|_ the|the|DT|_ 23S|23s|NN|_ and|and|CC|_ 16S|16s|NN|_ rRNA|rrna|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ guidelines|guideline|NNS|_ ,|,|,|_ except|except|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ the|the|DT|_ rRNA|rrna|NN|_ oligonucleotides|oligonucleotide|NNS|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ instead|instead|RB|_ of|of|IN|_ 15|15|CD|_ minutes|minute|NNS|_ .|.|.|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ dFNR|dfnr|NN|_ _|_|CD|_ rep1|rep1|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ dFNR|dfnr|NN|_ _|_|CD|_ rep2|rep2|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wild-type|wild-type|JJ|_ _|_|NN|_ rep1|rep1|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ wild-type|wild-type|JJ|_ _|_|NN|_ rep2|rep2|NN|_ _|_|CD|_ anaerobic|anaerobic|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ dFNR|dfnr|NN|_ -LRB-|-lrb-|-LRB-|_ PK4854|pk4854|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ WT|WT|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ WT|wt|NN|_ and|and|CC|_ ∆|∆|NN|_ fnr|fnr|NN|GEN were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ anerobically|anerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ MOPS|MOPS|NNP|MED +0.2|+0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ Ref|ref|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655star|mg1655star|JJ|_
FNR|fnr|SYM|TF -|-|:|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ Tag|tag|NN|_ _|_|CD|_ Count.txt|count.txt|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
FNR|fnr|SYM|TF -|-|:|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ WIG.wig|wig.wig|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
FNR|fnr|SYM|TF -|-|:|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ Tag|tag|NN|_ _|_|CD|_ Count.txt|count.txt|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
FNR|fnr|SYM|TF -|-|:|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ WIG.wig|wig.wig|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
genoype|genoype|NN|_ :|:|:|_ dFNR|dfnr|NN|_
genoype|genoype|NN|_ :|:|:|_ Wild-Type|wild-type|JJ|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
phenotype|phenotype|NN|_ :|:|:|_ lacking|lack|VBG|_ FNR|fnr|NN|TF protein|protein|NN|_
phenotype|phenotype|NN|_ :|:|:|_ normal|normal|JJ|_
Resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ published|publish|VBN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ software|software|NN|_ package|package|NN|_ SOAP|soap|NN|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ allowing|allow|VBG|_ no|no|RB|_ more|more|JJR|_ than|than|IN|_ two|two|CD|_ mismatches|mismatch|NNS|_ -LRB-|-lrb-|-LRB-|_ Supplemental|Supplemental|NNP|_ File|File|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ repeated|repeated|JJ|_ elements|element|NNS|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ e.g.|e.g.|FW|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ reads|read|VBZ|_ that|that|IN|_ had|have|VBD|_ no|no|DT|_ mapping|mapping|NN|_ locations|location|NNS|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ 36|36|CD|_ bp|bp|NN|_ ,|,|,|_ the|the|DT|_ 3-30|3-30|CD|_ bp|bp|NN|_ subsequences|subsequence|NNS|_ were|be|VBD|_ used|use|VBN|_ in|in|IN|_ the|the|DT|_ subsequent|subsequent|JJ|_ mapping|mapping|NN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ .|.|.|_ Reads|read|NNS|_ that|that|WDT|_ had|have|VBD|_ unique|unique|JJ|_ mapping|mapping|NN|_ locations|location|NNS|_ and|and|CC|_ did|do|VBD|_ not|not|RB|_ match|match|VB|_ annotated|annotated|JJ|_ rRNA|rrna|NN|_ genes|gene|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ gene|gene|NN|_ ,|,|,|_ the|the|DT|_ tag|tag|NN|GEN density|density|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ as|as|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ aligned|align|VBN|_ sequencing|sequencing|NN|_ tags|tag|NNS|_ divided|divide|VBN|_ by|by|IN|_ gene|gene|NN|_ size|size|NN|_ in|in|IN|_ kb|kb|NN|_ .|.|.|_ Per-gene|per-gene|JJ|_ tag|tag|NN|GEN density|density|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Supplemental|Supplemental|NNP|_ Files|Files|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ tag|tag|NN|GEN density|density|NN|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ statistically|statistically|RB|_ significant|significant|JJ|_ differential|differential|JJ|_ expression|expression|NN|_ using|use|VBG|_ BaySeq|BaySeq|NNP|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|Hardcastle|NNP|_ &|&|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ FDR|FDR|NNP|_ of|of|IN|_ 0.01|0.01|CD|_ ,|,|,|_ and|and|CC|_ genes|gene|NNS|_ were|be|VBD|_ organized|organize|VBN|_ into|into|IN|_ operons|operon|NNS|_ using|use|VBG|_ data|datum|NNS|_ from|from|IN|_ EcoCyc|EcoCyc|NNP|_ -LRB-|-lrb-|-LRB-|_ Keseler|Keseler|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
The|the|DT|_ RNAs|rna|NNS|_ were|be|VBD|_ chemically|chemically|RB|_ fragmented|fragment|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ the|the|DT|_ size|size|NN|_ range|range|NN|_ of|of|IN|_ 200-250|200-250|CD|_ bp|bp|NN|_ using|use|VBG|_ 1x|1x|NN|_ fragmentation|fragmentation|NN|_ solution|solution|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ SuperScript|SuperScript|NNP|_ Double-Stranded|Double-Stranded|NNP|_ cDNA|cdna|NN|_ Synthesis|synthesis|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ Illumina|Illumina|NNP|_ Paired|Paired|NNP|_ End|End|NNP|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ kit|kit|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ Illumina|Illumina|NNP|_ RNA-seq|RNA-seq|NNP|_ library|library|NN|_ creation|creation|NN|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ the|the|DT|_ fragmented|fragmented|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ end|end|NN|_ repaired|repair|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ Illumina|Illumina|NNP|_ specific|specific|JJ|_ adapters|adapter|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ with|with|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ SR|sr|JJ|_ Cluster|Cluster|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Single-end|single-end|JJ|_ 36|36|CD|_ bp|bp|NN|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ sequencing|sequencing|NN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ IIx|IIx|NNP|_ ,|,|,|_ using|use|VBG|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ SBS|SBS|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ v5|v5|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
WT|wt|SYM|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ Tag|tag|NN|_ _|_|CD|_ Count.txt|count.txt|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
WT|wt|VBD|_ _|_|CD|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ WIG.wig|wig.wig|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
WT|wt|VBD|_ _|_|CD|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ Tag|tag|NN|_ _|_|CD|_ Count.txt|count.txt|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
WT|wt|VBD|_ _|_|CD|_ Anaerobic|anaerobic|JJ|_ _|_|NN|_ RNAseq|rnaseq|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ WIG.wig|wig.wig|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250ul|250ul|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ concentration|concentration|NN|_ with|with|IN|_ continued|continued|JJ|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ before|before|IN|_ quenching|quench|VBG|_ with|with|IN|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP final|final|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 37|37|CD|_ oC|oc|NN|_ in|in|IN|_ gas-sparged|gas-sparged|JJ|_ Roux|Roux|NNP|_ bottles|bottle|NNS|_ or|or|CC|_ shaking|shake|VBG|_ flasks|flask|NNS|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3-0.4|0.3-0.4|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-b|anti-b|JJ|_ -LRB-|-lrb-|-LRB-|_ RNAP|rnap|NN|_ -RRB-|-rrb-|-RRB-|_ NT63|nt63|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-H-NS|anti-h-ns|JJ|_
chip|chip|NN|_ antibody|antibody|NN|_ cat|cat|NN|_ .|.|.|_ #|#|#|_ :|:|:|_ W0002|w0002|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ vendor|vendor|NN|_ :|:|:|_ Neoclone|Neoclone|NNP|_
Datasets|Datasets|NNPS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ locally|locally|RB|_ weighted|weighted|JJ|_ linear|linear|JJ|_ regression|regression|NN|_ -LRB-|-lrb-|-LRB-|_ LOWESS|lowess|NN|_ -RRB-|-rrb-|-RRB-|_ normalization|normalization|NN|_ on|on|IN|_ raw|raw|JJ|_ Cy3|cy3|NN|_ and|and|CC|_ Cy5|cy5|NN|_ signals|signal|NNS|_ to|to|TO|_ correct|correct|VB|_ for|for|IN|_ intensity-dependent|intensity-dependent|JJ|_ dye|dye|VB|_ effects|effect|NNS|_ within|within|IN|_ each|each|DT|_ array|array|NN|_ using|use|VBG|_ the|the|DT|_ ``|``|``|_ normalizeWithinArrays|normalizewithinarrays|NN|_ ''|''|''|_ function|function|NN|_ in|in|IN|_ the|the|DT|_ limma|limma|NN|_ package|package|NN|_ for|for|IN|_ the|the|DT|_ statistical|statistical|JJ|_ program|program|NN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 2.14.2|2.14.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
genotype|genotype|NN|_
H-NS|h-ns|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ MDS42|mds42|NN|_ cells|cell|NNS|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ MDS42|mds42|NN|_ ΔnusA|δnusa|NN|_ *|*|SYM|_ cells|cell|NNS|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ MDS42|mds42|NN|_ ΔnusG|δnusg|NN|_ cells|cell|NNS|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ Δhns|δhns|NN|_ cells|cell|NNS|_
MDS42|mds42|NN|_ RNAP|rnap|NN|_ 1|1|CD|_
MDS42|mds42|NN|_ RNAP|rnap|NN|_ 2|2|CD|_
MDS42|mds42|NN|_ ΔnusA|δnusa|NN|_ *|*|SYM|_ RNAP|rnap|NN|_ 1|1|CD|_
MDS42|mds42|NN|_ ΔnusA|δnusa|NN|_ *|*|SYM|_ RNAP|rnap|NN|_ 2|2|CD|_
MDS42|mds42|NN|_ ΔnusG|δnusg|NN|_ RNAP|rnap|NN|_ 1|1|CD|_
MDS42|mds42|NN|_ ΔnusG|δnusg|NN|_ RNAP|rnap|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ H-NS|h-ns|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ H-NS|h-ns|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ RNAP|rnap|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ RNAP|rnap|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ Δhns|δhns|NNS|_ RNAP|rnap|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ Δhns|δhns|NNS|_ RNAP|rnap|NN|_ 2|2|CD|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MDS42|mds42|NN|_ cells|cell|NNS|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MDS42|mds42|NN|_ ΔnusA|δnusa|NN|_ *|*|NN|_ cells|cell|NNS|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MDS42|mds42|NN|_ ΔnusG|δnusg|NN|_ cells|cell|NNS|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ cells|cell|NNS|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ MG1655|mg1655|NN|_ Δhns|δhns|NN|_ cells|cell|NNS|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ input|input|NN|_ DNA|dna|NN|_
strain|strain|NN|_ :|:|:|_ MDS42|mds42|NN|_ -LRB-|-lrb-|-LRB-|_ RL1961|rl1961|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ RL1655|rl1655|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ RL2673|rl2673|NN|_
strain|strain|NN|_ :|:|:|_ RSW421|rsw421|NN|_ -LRB-|-lrb-|-LRB-|_ RL1962|rl1962|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ RSW422|rsw422|NN|_ -LRB-|-lrb-|-LRB-|_ RL1963|rl1963|NN|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 37|37|CD|_ oC|oc|NN|_ in|in|IN|_ gas-sparged|gas-sparged|JJ|_ Roux|Roux|NNP|_ bottles|bottle|NNS|_ or|or|CC|_ shaking|shake|VBG|_ flasks|flask|NNS|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3-0.4|0.3-0.4|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ transferred|transfer|VBN|_ directly|directly|RB|_ into|into|IN|_ an|a|DT|_ ice-cold|ice-cold|JJ|_ ethanol|ethanol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
genotype|genotype|NN|_
MDS42|mds42|NN|_
MDS42|mds42|NN|_ 1|1|CD|_
MDS42|mds42|NN|_ 2|2|CD|_
MDS42|mds42|NN|_ +|+|CC|_ 20|20|CD|_ ug|ug|NN|_
MDS42|mds42|NN|_ ΔnusA|δnusa|NN|_ *|*|SYM|_
MDS42|mds42|NN|_ ΔnusA|δnusa|NN|_ *|*|SYM|_ 1|1|CD|_
MDS42|mds42|NN|_ ΔnusA|δnusa|NN|_ *|*|SYM|_ 2|2|CD|_
MDS42|mds42|NN|_ ΔnusG|δnusg|NN|_
MDS42|mds42|NN|_ ΔnusG|δnusg|NN|_ 1|1|CD|_
MDS42|mds42|NN|_ ΔnusG|δnusg|NN|_ 2|2|CD|_
Raw|raw|NN|_ probe|probe|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ across|across|IN|_ samples|sample|NNS|_ using|use|VBG|_ RMA|rma|NN|_ analysis|analysis|NN|_ implemented|implement|VBD|_ in|in|IN|_ the|the|DT|_ NimbleScan|NimbleScan|NNP|_ software|software|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 2.4|2.4|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MDS42|mds42|NN|_ -LRB-|-lrb-|-LRB-|_ RL1961|rl1961|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ RSW421|rsw421|NN|_ -LRB-|-lrb-|-LRB-|_ RL1962|rl1962|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ RSW421|rsw421|NN|_ -LRB-|-lrb-|-LRB-|_ RL1967|rl1967|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ RSW422|rsw422|NN|_ -LRB-|-lrb-|-LRB-|_ RL1963|rl1963|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ RSW472|rsw472|NN|_ -LRB-|-lrb-|-LRB-|_ RL1966|rl1966|NN|_ -RRB-|-rrb-|-RRB-|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ by|by|IN|_ hot|hot|JJ|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ microchannel|microchannel|NN|_ electrophoretograms|electrophoretogram|NNS|_ .|.|.|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 20|20|CD|_ ug|ug|NN|_
Δrac|δrac|JJ|_
Δrac|δrac|NN|_ 1|1|CD|_
Δrac|δrac|NN|_ 2|2|CD|_
Δrac|δrac|NN|_ +|+|CC|_ 20|20|CD|_ ug|ug|NN|_
Δrac|δrac|NN|_ ΔnusG|δnusg|NN|_
Δrac|δrac|NN|_ ΔnusG|δnusg|NN|_ 1|1|CD|_
Δrac|δrac|NN|_ ΔnusG|δnusg|NN|_ 2|2|CD|_
Base|Base|NNP|_ calling|call|VBG|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ the|the|DT|_ DOE|DOE|NNP|_ Joint|Joint|NNP|_ Genome|Genome|NNP|_ Institute|Institute|NNP|_ using|use|VBG|_ Illumina|Illumina|NNP|_ software|software|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 37|37|CD|_ oC|oc|NN|_ in|in|IN|_ gas-sparged|gas-sparged|JJ|_ Roux|Roux|NNP|_ bottles|bottle|NNS|_ or|or|CC|_ shaking|shake|VBG|_ flasks|flask|NNS|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3-0.4|0.3-0.4|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Counts|count|VBZ|_ per|per|IN|_ million|million|CD|_ unique|unique|JJ|_ reads|read|VBZ|_ were|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ transferred|transfer|VBN|_ directly|directly|RB|_ into|into|IN|_ an|a|DT|_ ice-cold|ice-cold|JJ|_ ethanol|ethanol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
genotype|genotype|NN|_
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ +|+|CC|_ 20|20|CD|_ ug|ug|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ ribosome-depeleted|ribosome-depeleted|JJ|_ RNA|rna|NN|_
RNA-Seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ the|the|DT|_ DOE|DOE|NNP|_ Joint|Joint|NNP|_ Genome|Genome|NNP|_ Institute|Institute|NNP|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ ribosome-depleted|ribosome-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ in|in|IN|_ a|a|DT|_ buffered|buffer|VBN|_ zinc|zinc|NN|_ solution|solution|NN|_ ,|,|,|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ AMPure|ampure|NN|_ SPRI|spri|NN|_ beads|bead|NNS|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNAs|cdna|NNS|_ were|be|VBD|_ then|then|RB|_ synthesized|synthesize|VBN|_ from|from|IN|_ the|the|DT|_ fragmented|fragmented|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ II|II|NNP|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ a|a|DT|_ second|second|JJ|_ bead|bead|NN|_ purification|purification|NN|_ .|.|.|_ dUTP|dutp|NN|_ was|be|VBD|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ reaction|reaction|NN|_ in|in|IN|_ addition|addition|NN|_ to|to|TO|_ dTTP|dttp|NN|_ to|to|TO|_ chemically|chemically|RB|_ mark|mark|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ .|.|.|_ Two|two|CD|_ further|further|JJ|_ bead|bead|NN|_ purification|purification|NN|_ steps|step|NNS|_ using|use|VBG|_ different|different|JJ|_ ratios|ratio|NNS|_ of|of|IN|_ beads|bead|NNS|_ to|to|TO|_ cDNA|cdna|NN|_ -LRB-|-lrb-|-LRB-|_ 85|85|CD|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ ,|,|,|_ the|the|DT|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ SOAP|soap|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ CPM|CPM|NNP|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ by|by|IN|_ hot|hot|JJ|_ phenol|phenol|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ or|or|CC|_ microchannel|microchannel|NN|_ electrophoretograms|electrophoretogram|NNS|_ .|.|.|_ 16S|16s|NN|_ and|and|CC|_ 23S|23s|NN|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ prior|prior|RB|_ to|to|TO|_ construction|construction|NN|_ of|of|IN|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ using|use|VBG|_ MICROBExpress|microbexpress|NN|_ reagents|reagent|NNS|_ .|.|.|_
1|1|CD|_ ml|ml|NN|_ of|of|IN|_ VWPE|VWPE|NNP|_ extract|extract|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mg|mg|NN|_
agent|agent|NN|_ :|:|:|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED added|add|VBD|_ -RRB-|-rrb-|-RRB-|_
agent|agent|NN|_ :|:|:|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ added|add|VBD|_ -RRB-|-rrb-|-RRB-|_
agent|agent|NN|_ :|:|:|_ polyphenols|polyphenol|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ OVWPE|ovwpe|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ added|add|VBD|_ -RRB-|-rrb-|-RRB-|_
Data|Data|NNP|_ processed|process|VBN|_ with|with|IN|_ FeatureExtraction|FeatureExtraction|NNP|_ v9|v9|NN|_ .5.1|.5.1|NN|_ and|and|CC|_ quantile|quantile|NN|_ normalized|normalize|VBD|_ using|use|VBG|_ R2|r2|NN|_ .6.1|.6.1|CD|_ statistical|statistical|JJ|_ software|software|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|JJ|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ repA|repa|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repA|repa|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repA|repa|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repB|repb|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repB|repb|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repB|repb|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repC|repc|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repC|repc|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ control|control|NN|_ _|_|CD|_ repC|repc|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ A|a|DT|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ B|b|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ culture|culture|NN|_ with|with|IN|_ VWPE|vwpe|NN|_ extract|extract|NN|_ diluted|dilute|VBN|_ in|in|IN|_ ethanol|ethanol|NN|_ 20|20|CD|_ %|%|NN|_ ,|,|,|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ replicate|replicate|VB|_ C|c|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repA|repa|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repA|repa|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repA|repa|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repB|repb|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repB|repb|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repB|repb|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repC|repc|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repC|repc|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ ethanol|ethanol|NN|_ _|_|NN|_ repC|repc|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ was|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repA|repa|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|SYM|_ repA|repA|NNP|_ _|_|SYM|_ t2|t2|FW|_
E.coli|e.coli|FW|_ _|_|SYM|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repA|repa|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repB|repb|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repB|repb|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repB|repb|NN|_ _|_|CD|_ t3|t3|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repC|repc|NN|_ _|_|CD|_ t1|t1|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repC|repc|NN|_ _|_|CD|_ t2|t2|NN|_
E.coli|e.coli|NNS|_ _|_|VBP|_ polyphenols|polyphenol|NNS|_ _|_|VBP|_ repC|repc|NN|_ _|_|CD|_ t3|t3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ according|accord|VBG|_ to|to|TO|_ QiAgen|QiAgen|NNP|_ RNeasy|RNeasy|NNP|_ MiniKit|MiniKit|NNP|_ protocol|protocol|NN|_ for|for|IN|_ bacterial|bacterial|JJ|_ samples|sample|NNS|_
time|time|NN|_ :|:|:|_ 20|20|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_
time|time|NN|_ :|:|:|_ 40|40|CD|_ minutes|minute|NNS|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_ after|after|IN|_ treatment|treatment|NN|_
time|time|NN|_ :|:|:|_ at|at|IN|_ time|time|NN|_ of|of|IN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
genotype|genotype|NN|_ :|:|:|_ yajL|yajl|NN|GEN mutant|mutant|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
Intensity|intensity|NN|_ measures|measure|NNS|_ in|in|IN|_ wild|wild|JJ|_ type|type|NN|_ strain|strain|NN|_ ,|,|,|_ replicate|replicate|VBP|_ 1|1|CD|_
Intensity|intensity|NN|_ measures|measure|NNS|_ in|in|IN|_ wild|wild|JJ|_ type|type|NN|_ strain|strain|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
Intensity|intensity|NN|_ measures|measure|NNS|_ in|in|IN|_ yajL|yajl|NN|GEN mutant|mutant|JJ|_ strain|strain|NN|_ ,|,|,|_ replicate|replicate|VBP|_ 1|1|CD|_
Intensity|intensity|NN|_ measures|measure|NNS|_ in|in|IN|_ yajL|yajl|NN|GEN mutant|mutant|JJ|_ strain|strain|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
Luria|Luria|NNP|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ under|under|IN|_ aeration|aeration|NN|_ ,|,|,|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ .|.|.|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ phenol|phenol|NN|_ treatment|treatment|NN|_ .|.|.|_
strain|strain|NN|_
The|the|DT|_ CEL|cel|NN|_ files|file|VBZ|_ generated|generate|VBN|_ for|for|IN|_ each|each|DT|_ array|array|NN|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Console|console|NN|_ software|software|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
Untreated|untreated|JJ|_ wild|wild|JJ|_ type|type|NN|_ versus|versus|CC|_ untreated|untreated|JJ|_ yajL|yajl|NN|GEN mutant|mutant|NN|_ .|.|.|_
wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_
yajL|yajl|NN|GEN mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ genetic|genetic|JJ|_ background|background|NN|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_
At|at|IN|_ OD600|od600|NN|_ of|of|IN|_ 0.5|0.5|CD|_ ,|,|,|_ cell|cell|NN|_ cultures|culture|NNS|_ were|be|VBD|_ separated|separate|VBN|_ into|into|IN|_ two|two|CD|_ flasks|flask|NNS|_ .|.|.|_ D-galactose|d-galactose|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ 0.3|0.3|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ one|one|CD|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 1.5|1.5|CD|_ h|h|NN|_ further|further|RB|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ placed|place|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ RNAprotect|rnaprotect|NN|_ ™|™|NN|_ bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ stabilize|stabilize|VB|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ Total|total|JJ|_ RNAs|rna|NNS|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Isolated|isolate|VBN|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ random|random|JJ|_ primer|primer|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ ,|,|,|_ 18064|18064|CD|_ --|--|:|_ 071|071|CD|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ mixture|mixture|NN|_ was|be|VBD|_ then|then|RB|_ subsequently|subsequently|RB|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ N|n|NN|_ NaOH|naoh|NN|_ to|to|TO|_ degrade|degrade|VB|_ any|any|DT|_ remaining|remain|VBG|_ RNA|rna|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ N|n|NN|_ HCl|hcl|NN|_ to|to|TO|_ neutralize|neutralize|VB|_ the|the|DT|_ NaOH|naoh|NN|_ .|.|.|_ Synthesized|synthesize|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ MiniElute|MiniElute|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ columns|column|NNS|_ ,|,|,|_ 28004|28004|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Purified|purify|VBN|_ cDNA|cdna|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ fragmented|fragmented|JJ|_ to|to|TO|_ between|between|IN|_ 50|50|CD|_ and|and|CC|_ 200|200|CD|_ bps|bp|NNS|_ by|by|IN|_ 0.6|0.6|CD|_ U|U|NNP|_
Computation|Computation|NNP|_ of|of|IN|_ genomic|genomic|JJ|_ intervals|interval|NNS|_ based|base|VBN|_ on|on|IN|_ computed|computed|JJ|_ signal|signal|NN|_ and|and|CC|_ p-values|p-values|JJ|_
Computation|computation|NN|_ of|of|IN|_ summary|summary|NN|_ statistics|statistics|NNS|_
E.|e.|FW|_ coli|coli|FW|_ galT|galt|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 125-mL|125-ml|NN|_ corning|corning|NN|_ flasks|flask|NNS|_ containing|contain|VBG|_ 30|30|CD|_ mL|ml|NN|_ of|of|IN|_ M63|m63|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ plus|plus|CC|_ glycerol|glycerol|NN|SUPP -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ 0.3|0.3|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ galT|galt|NN|GEN mutant|mutant|NN|_ with|with|IN|_ galactose|galactose|NN|_
E.|E.|NNP|_ coli|coli|NN|_ galT|galt|NN|GEN mutant|mutant|NN|_ without|without|IN|_ galactose|galactose|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
Signal|signal|NN|_ and|and|CC|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ interrogated|interrogate|VBN|_ .|.|.|_
The|the|DT|_ program|program|NN|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ bed|bed|NN|_
The|the|DT|_ TAS|tas|NN|_ software|software|NN|_ provides|provide|VBZ|_ analysis|analysis|NN|_ capabilities|capability|NNS|_ specifically|specifically|RB|_ for|for|IN|_ the|the|DT|_ GeneChip|GeneChip|NNP|_ ®|®|NNP|_ Tiling|Tiling|NNP|_ Arrays|Arrays|NNPS|_ .|.|.|_ TAS|tas|NN|_ analyzes|analyze|VBZ|_ feature|feature|NN|_ intensity|intensity|NN|_ data|datum|NNS|_ stored|store|VBN|_ in|in|IN|_ GCOS|gcos|NN|_ output|output|NN|_ .|.|.|_ CEL|CEL|NNP|_ files|file|NNS|_ and|and|CC|_ produces|produce|VBZ|_ :|:|:|_
Visualizations|visualization|NNS|_ for|for|IN|_ assessing|assess|VBG|_ the|the|DT|_ quality|quality|NN|_ of|of|IN|_ the|the|DT|_ array|array|NN|_ data|datum|NNS|_
with|with|IN|_ D-galactose|d-galactose|JJ|_
without|without|IN|_ D-galactose|d-galactose|JJ|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBD|_ 0|0|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBD|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 2.5|2.5|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
Culture|culture|NN|_ samples|sample|NNS|_ for|for|IN|_ microarray|microarray|NN|_ analysis|analysis|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ solution|solution|NN|_ ,|,|,|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 6,600|6,600|CD|_ g|g|NN|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ N2|n2|NN|_ before|before|IN|_ storing|store|VBG|_ at|at|IN|_ -80|-80|CD|_ degrees|degree|NNS|_ C|c|NN|_ until|until|IN|_ required|require|VBN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ stored|store|VBN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ ,|,|,|_ and|and|CC|_ labeled|label|VBN|_ Cy3|cy3|NN|_ and|and|CC|_ Cy5|cy5|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ 16|16|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ with|with|IN|_ 10|10|CD|_ ug|ug|NN|_ random|random|JJ|_ hexamer|hexamer|NN|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Coralville|Coralville|NNP|_ ,|,|,|_ IA|IA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Data|Data|NNP|_ filtered|filter|VBD|_ for|for|IN|_ PCR|pcr|NN|_ success|success|NN|_ ,|,|,|_ >|>|JJR|_ 3x|3x|NN|_ local|local|JJ|_ background|background|NN|_ and|and|CC|_ spot|spot|NN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ GenePix|GenePix|NNP|_ Flag|Flag|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Normalized|normalize|VBN|_ using|use|VBG|_ Lowess|Lowess|NNP|_ smoothing|smooth|VBG|_ from|from|IN|_ MA|MA|NNP|_ plot|plot|NN|_
EC18n122|ec18n122|NN|_ RpoH|rpoh|NN|_ 10|10|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 4|4|CD|_
EC18n167|ec18n167|NN|_ RpoH|rpoh|NN|_ 0|0|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC18n168|ec18n168|NN|_ RpoH|rpoh|NN|_ 2.5|2.5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC18n169|ec18n169|NN|_ RpoH|rpoh|NN|_ 5|5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC18n170|ec18n170|NN|_ RpoH|rpoh|NN|_ 10|10|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC18n171|ec18n171|NN|_ RpoH|rpoh|NN|_ 20|20|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 2|2|CD|_
EC18n177|ec18n177|NN|_ RpoH|rpoh|NN|_ 0|0|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC18n178|ec18n178|NN|_ RpoH|rpoh|NN|_ 2.5|2.5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC18n179|ec18n179|NN|_ RpoH|rpoh|NN|_ 5|5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC18n180|ec18n180|NN|_ RpoH|rpoh|NN|_ 10|10|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC18n181|ec18n181|NN|_ RpoH|rpoh|NN|_ 20|20|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 1|1|CD|_
EC18n182|ec18n182|NN|_ RpoH|rpoh|NN|_ 0|0|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC18n183|ec18n183|NN|_ RpoH|rpoh|NN|_ 2.5|2.5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC18n184|ec18n184|NN|_ RpoH|rpoh|NN|_ 5|5|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC18n185|ec18n185|NN|_ RpoH|rpoh|NN|_ 10|10|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
EC18n186|ec18n186|NN|_ RpoH|rpoh|NN|_ 20|20|CD|_ min|min|NN|_ Time|Time|NNP|_ course|course|NN|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
M9|m9|NN|_ minimal|minimal|JJ|_ complete|complete|JJ|_ media|media|NNS|_ ,|,|,|_ cultures|culture|NNS|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ in|in|IN|_ a|a|DT|_ gyratory|gyratory|JJ|_ water|water|NN|_ bath|bath|NN|_ shaking|shake|VBG|_ at|at|IN|_ 240|240|CD|_ rpm|rpm|NN|_
MG1655|mg1655|NN|_ PhtpG|phtpg|NN|_ :|:|:|_ :|:|:|_ lacZ|lacz|NN|GEN delta|delta|NN|_ lacX74|lacx74|NN|_
RpoH|rpoh|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoH|rpoh|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoH|rpoh|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoH|rpoh|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
RpoH|rpoh|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 0|0|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ampicillin|ampicillin|NN|_ treatment|treatment|NN|_ T1|t1|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Ampicillin|Ampicillin|NNP|_ treatment|treatment|NN|_ T2|t2|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Ampicillin|Ampicillin|NNP|_ treatment|treatment|NN|_ T3|t3|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Ampicillin|Ampicillin|NNP|_ treatment|treatment|NN|_ T4|t4|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Ampicillin|Ampicillin|NNP|_ treatment|treatment|NN|_ T5|t5|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Ampicillin|Ampicillin|NNP|_ treatment|treatment|NN|_ T6|t6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 40|40|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 50|50|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ after|after|IN|_ Ampicillin|Ampicillin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ CaCl2|cacl2|NN|_ wash|wash|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ CaCl2|cacl2|NN|_ wash|wash|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ CaCl2|cacl2|NN|_ wash|wash|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ CaCl2|cacl2|NN|_ wash|wash|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ CaCl2|cacl2|NN|_ wash|wash|NN|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ CaCl2|cacl2|NN|_ wash|wash|NN|_ T6|t6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.43|0.43|CD|_ LB|lb|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Sample|sample|NN|_ washed|wash|VBN|_ in|in|IN|_ 0.1|0.1|CD|_ M|m|NN|_ CaCl2|cacl2|NN|_ +|+|CC|_ 15|15|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP vs|vs|CC|_ before|before|IN|_ washing|wash|VBG|_ OD|od|NN|_ 0.43|0.43|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ timepoint|timepoint|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Sample|sample|NN|_ washed|wash|VBN|_ in|in|IN|_ 0.1|0.1|CD|_ M|m|NN|_ CaCl2|cacl2|NN|_ +|+|CC|_ 15|15|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP vs|vs|CC|_ before|before|IN|_ washing|wash|VBG|_ OD|od|NN|_ 0.43|0.43|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ timepoint|timepoint|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Sample|sample|NN|_ washed|wash|VBN|_ in|in|IN|_ 0.1|0.1|CD|_ M|m|NN|_ CaCl2|cacl2|NN|_ +|+|CC|_ 15|15|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP vs|vs|CC|_ before|before|IN|_ washing|wash|VBG|_ OD|od|NN|_ 0.43|0.43|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ timepoint|timepoint|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Sample|sample|NN|_ washed|wash|VBN|_ in|in|IN|_ 0.1|0.1|CD|_ M|m|NN|_ CaCl2|cacl2|NN|_ +|+|CC|_ 15|15|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP vs|vs|CC|_ before|before|IN|_ washing|wash|VBG|_ OD|od|NN|_ 0.43|0.43|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 40|40|CD|_ min|min|NN|_ timepoint|timepoint|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Sample|sample|NN|_ washed|wash|VBN|_ in|in|IN|_ 0.1|0.1|CD|_ M|m|NN|_ CaCl2|cacl2|NN|_ +|+|CC|_ 15|15|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP vs|vs|CC|_ before|before|IN|_ washing|wash|VBG|_ OD|od|NN|_ 0.43|0.43|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ timepoint|timepoint|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Sample|sample|NN|_ washed|wash|VBN|_ in|in|IN|_ 0.1|0.1|CD|_ M|m|NN|_ CaCl2|cacl2|NN|_ +|+|CC|_ 15|15|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP vs|vs|CC|_ before|before|IN|_ washing|wash|VBG|_ OD|od|NN|_ 0.43|0.43|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ timepoint|timepoint|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Early|Early|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T1|t1|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Early|Early|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T2|t2|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Early|Early|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T3|t3|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Early|Early|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T4|t4|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Early|Early|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T5|T5|NNP|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Early|Early|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T6|T6|NNP|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Early|Early|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T7|T7|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ OD|OD|NNP|_ ~|~|SYM|_ 0.5|0.5|CD|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ Indol-acrylate|indol-acrylate|JJ|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Kanamycin|kanamycin|NN|_ treatment|treatment|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Kanamycin|kanamycin|NN|_ treatment|treatment|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Kanamycin|kanamycin|NN|_ treatment|treatment|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Kanamycin|kanamycin|NN|_ treatment|treatment|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Kanamycin|kanamycin|NN|_ treatment|treatment|NN|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Kanamycin|kanamycin|NN|_ treatment|treatment|NN|_ T6|t6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 40|40|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 50|50|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ after|after|IN|_ Kanamycin|Kanamycin|NNP|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T10|t10|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T11|t11|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T6|t6|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T7|t7|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T8|t8|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ LB|lb|NN|_ growth|growth|NN|_ T9|t9|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 105|105|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 133|133|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 1440|1440|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 163|163|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 191|191|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 218|218|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 261|261|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 313|313|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 443|443|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 78|78|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glc|glc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ OD|OD|NNP|_ ~|~|SYM|_ 0.5|0.5|CD|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Late|Late|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T1|t1|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Late|Late|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T2|t2|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Late|Late|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T3|t3|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Late|Late|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T4|t4|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Late|Late|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T5|T5|NNP|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Late|Late|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T6|T6|NNP|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Late|Late|NNP|_ Recovery|Recovery|NNP|_ in|in|IN|_ LB|LB|NNP|_ T7|T7|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP at|at|IN|_ OD|od|NN|_ 1.0|1.0|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ OD|OD|NNP|_ ~|~|SYM|_ 0.5|0.5|CD|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ NOX|nox|NN|_ +|+|CC|_ _|_|NN|_ balanced|balanced|JJ|_ growth|growth|NN|_ at|at|IN|_ OD|OD|NNP|_ 0.13|0.13|CD|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ NOX|nox|NN|_ +|+|CC|_ _|_|NN|_ balanced|balanced|JJ|_ growth|growth|NN|_ at|at|IN|_ OD|OD|NNP|_ 0.21|0.21|CD|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ NOX|nox|NN|_ +|+|CC|_ _|_|NN|_ balanced|balanced|JJ|_ growth|growth|NN|_ at|at|IN|_ OD|OD|NNP|_ 0.28|0.28|CD|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ NOX|nox|NN|_ +|+|CC|_ _|_|NN|_ balanced|balanced|JJ|_ growth|growth|NN|_ at|at|IN|_ OD|OD|NNP|_ 0.34|0.34|CD|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ NOX|nox|NN|_ +|+|CC|_ _|_|NN|_ balanced|balanced|JJ|_ growth|growth|NN|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecoli|JJ|_ _|_|SYM|_ NOX|nox|SYM|_ -|-|:|_ _|_|NN|_ balanced|balanced|JJ|_ groNOX-h|gronox-h|NN|_ at|at|IN|_ OD|OD|NNP|_ 0.19|0.19|CD|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ NOX|NOX|NNP|_ -|-|:|_ _|_|NN|_ balanced|balanced|JJ|_ groNOX-h|gronox-h|NN|_ at|at|IN|_ OD|od|NN|_ 0.3|0.3|CD|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ NOX|NOX|NNP|_ -|-|:|_ _|_|NN|_ balanced|balanced|JJ|_ groNOX-h|gronox-h|NN|_ at|at|IN|_ OD|OD|NNP|_ 0.41|0.41|CD|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ NOX|NOX|NNP|_ -|-|:|_ _|_|NN|_ balanced|balanced|JJ|_ groNOX-h|gronox-h|NN|_ at|at|IN|_ OD|OD|NNP|_ 0.49|0.49|CD|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ NOX|NOX|NNP|_ -|-|:|_ _|_|NN|_ balanced|balanced|JJ|_ groNOX-h|gronox-h|NN|_ at|at|IN|_ OD|od|NN|_ 0.6|0.6|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Norfloxacin|norfloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ ,|,|,|_ LB|lb|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ gyrArparCr|gyrarparcr|NN|_ _|_|CD|_ Norfloxacin|norfloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 15|15|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ LB|lb|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ gyrArparCr|gyrarparcr|NN|_ _|_|CD|_ Norfloxacin|norfloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Norfloxacin|Norfloxacin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ LB|lb|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism C600|c600|NN|_ -LRB-|-lrb-|-LRB-|_ gyrArparCr|gyrarparcr|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ T6|t6|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ T7|t7|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ OD|OD|NNP|_ ~|~|SYM|_ 0.5|0.5|CD|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP T6|t6|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP T7|t7|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 75|75|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10mM|10mm|NN|_ Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_ recovery|recovery|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Na-P|na-p|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ OD|OD|NNP|_ ~|~|SYM|_ 0.5|0.5|CD|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Sodium|sodium|NN|_ Azide|azide|NN|_ treatment|treatment|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Sodium|sodium|NN|_ Azide|azide|NN|_ treatment|treatment|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Sodium|sodium|NN|_ Azide|azide|NN|_ treatment|treatment|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Sodium|sodium|NN|_ Azide|azide|NN|_ treatment|treatment|NN|_ T4|t4|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110|w3110|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_ ,|,|,|_ Bonner-Vogel|Bonner-Vogel|NNP|_ +|+|CC|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110|w3110|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_ in|in|IN|_ Bonner-Vogel|Bonner-Vogel|NNP|_ +|+|CC|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110|w3110|NN|_ ,5|,5|CD|_ min|min|NN|_ 0.01|0.01|CD|_ M|m|NN|_ Sodium|sodium|NN|_ Azide|azide|NN|_ treatment|treatment|NN|_ vs|vs|CC|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_ in|in|IN|_ Bonner-Vogel|Bonner-Vogel|NNP|_ +|+|CC|_ 50|50|CD|_ ug|ug|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T6|t6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.03|0.03|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.2|0.2|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.35|0.35|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.6|0.6|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.9|0.9|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_ reference|reference|NN|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ T6|t6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.05|0.05|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.21|0.21|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.43|0.43|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.7|0.7|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 1.2|1.2|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Normalized|normalize|VBD|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T6|t6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ Aerobic|aerobic|JJ|_ growth|growth|NN|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ Aerobic|aerobic|JJ|_ growth|growth|NN|_ on|on|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.08|0.08|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.15|0.15|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.34|0.34|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.73|0.73|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 1.02|1.02|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 1.27|1.27|CD|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP ,|,|,|_
Normalized|normalize|VBD|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T5|t5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP vs|vs|CC|_ Aerobic|aerobic|JJ|_ OD|od|NN|_ 0.4|0.4|CD|_ T6|t6|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ Aerobic|aerobic|JJ|_ growth|growth|NN|_ on|on|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_ OD|od|NN|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.15|0.15|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.30|0.30|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.63|0.63|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 0.85|0.85|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 1.07|1.07|CD|_ ,|,|,|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ OD|od|NN|_ 1.29|1.29|CD|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ in|in|IN|_ M9|m9|NN|_ +|+|CC|_ glucose|glucose|NN|SUPP +|+|CC|_ fumarate|fumarate|NN|SUPP ,|,|,|_
Normalized|normalize|VBD|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ T5|t5|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_ ,|,|,|_ Davis|Davis|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ in|in|IN|_ Davis|Davis|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ in|in|IN|_ Davis|Davis|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 40|40|CD|_ min|min|NN|_ after|after|IN|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ in|in|IN|_ Davis|Davis|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ in|in|IN|_ Davis|Davis|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ Gamma|gamma|NN|_ treatment|treatment|NN|_ in|in|IN|_ Davis|Davis|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Davis|Davis|NNP|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Novobiocin|novobiocin|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ ug|ug|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Novobiocin|Novobiocin|NNP|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ ug|ug|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Novobiocin|Novobiocin|NNP|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Novobiocin|Novobiocin|NNP|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism LE234|le234|NN|_ acrD|acrd|NN|GEN -|-|:|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_ in|in|IN|_ LB|LB|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism LE234|le234|NN|_ acrD|acrd|NN|GEN -|-|:|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Novobiocin|Novobiocin|NNP|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism LE234|le234|NN|_ acrD|acrd|NN|GEN -|-|:|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Novobiocin|Novobiocin|NNP|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism LE234|le234|NN|_ acrD|acrd|NN|GEN -|-|:|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Novobiocin|Novobiocin|NNP|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism LE234|le234|NN|_ acrD|acrd|NN|GEN -|-|:|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ Novobiocin|Novobiocin|NNP|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism LE234|le234|NN|_ acrD|acrd|NN|GEN -|-|:|_ ,|,|,|_ LB|LB|NNP|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ before|before|IN|_ treatment|treatment|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ pUC|puc|NN|_ expression|expression|NN|_ OD|od|NN|_ 0.2|0.2|CD|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ pUC|puc|NN|_ expression|expression|NN|_ OD|od|NN|_ 0.5|0.5|CD|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ pUC|puc|NN|_ expression|expression|NN|_ OD|od|NN|_ 0.9|0.9|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5alpha|dh5alpha|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ OD|od|NN|_ 0.2|0.2|CD|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ Amp|amp|NN|_ ,|,|,|_ pUC|puc|NN|_ expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5alpha|dh5alpha|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ OD|od|NN|_ 0.2|0.2|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ no|no|DT|_ pUC|puc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5alpha|dh5alpha|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ OD|od|NN|_ 0.5|0.5|CD|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ Amp|amp|NN|_ ,|,|,|_ pUC|puc|NN|_ expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5alpha|dh5alpha|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ OD|od|NN|_ 0.5|0.5|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ no|no|DT|_ pUC|puc|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5alpha|dh5alpha|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ OD|od|NN|_ 0.9|0.9|CD|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ Amp|amp|NN|_ ,|,|,|_ pUC|puc|NN|_ expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism DH5alpha|dh5alpha|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ OD|od|NN|_ 0.9|0.9|CD|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ no|no|DT|_ pUC|puc|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ T1|t1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ T2|t2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ T3|t3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ T4|t4|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|LB|NNP|_ T5|T5|NNP|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Stationary|Stationary|NNP|_ phase|phase|NN|_ in|in|IN|_ LB|LB|NNP|_ T6|T6|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ OD|od|NN|_ 2.4|2.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ OD|od|NN|_ 2.8|2.8|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ OD|od|NN|_ 3.1|3.1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ OD|od|NN|_ 3.1|3.1|CD|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ Stationary|stationary|JJ|_ phase|phase|NN|_ in|in|IN|_ LB|lb|NN|_ OD|od|NN|_ 3.1|3.1|CD|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ ,|,|,|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ LB|lb|NN|_ ,|,|,|_ OD|od|NN|_ 3.1|3.1|CD|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Temperature|temperature|NN|_ upshift|upshift|NN|_ in|in|IN|_ gyrBT|gyrBT|NNP|_ mutant|mutant|JJ|_ T1|t1|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Temperature|Temperature|NNP|_ upshift|upshift|NN|_ in|in|IN|_ gyrBT|gyrBT|NNP|_ mutant|mutant|JJ|_ T2|t2|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Temperature|Temperature|NNP|_ upshift|upshift|NN|_ in|in|IN|_ gyrBT|gyrBT|NNP|_ mutant|mutant|JJ|_ T3|t3|NN|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ Temperature|Temperature|NNP|_ upshift|upshift|NN|_ in|in|IN|_ gyrBT|gyrBT|NNP|_ mutant|mutant|JJ|_ T4|t4|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110gyrb234|w3110gyrb234|NN|_ ,|,|,|_ LB|lb|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110gyrb234|w3110gyrb234|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ upshift|upshift|NN|_ to|to|TO|_ 42|42|CD|_ C|c|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110gyrb234|w3110gyrb234|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ upshift|upshift|NN|_ to|to|TO|_ 42|42|CD|_ C|c|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110gyrb234|w3110gyrb234|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ after|after|IN|_ upshift|upshift|NN|_ to|to|TO|_ 42|42|CD|_ C|c|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism W3110gyrb234|w3110gyrb234|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ upshift|upshift|NN|_ to|to|TO|_ 42|42|CD|_ C|c|NN|_
Normalized|normalize|VBN|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ratio|ratio|NN|_ of|of|IN|_ Cy5|cy5|NN|_
CCCP-1|cccp-1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
CCCP-2|cccp-2|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
CCCP-3|cccp-3|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
Control-1|control-1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
Control-2|control-2|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Control-3|control-3|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ CCCP|CCCP|NNP|_ _|_|SYM|_ 15|15|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ _|_|NN|_ gentamicin|gentamicin|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ -LRB-|-lrb-|-LRB-|_ OD660|od660|NN|_ nm|nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ control|control|NN|_ protein|protein|NN|_ or|or|CC|_ antibacterial|antibacterial|JJ|_ preparations|preparation|NNS|_ in|in|IN|_ 5|5|CD|_ mM|mm|NN|KWSUPP TRIS|tris|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.6|7.6|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 150|150|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 10|10|CD|_ µM|µm|NN|_ ZnSO4|znso4|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ %|%|NN|_ LB|lb|NN|_ ,|,|,|_ at|at|IN|_ 37oC|37oc|NN|_ aerobically|aerobically|RB|_ with|with|IN|_ shaking|shake|VBG|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ _|_|SYM|_ PGRP|pgrp|SYM|_ _|_|SYM|_ 30|30|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ was|be|VBD|_ treated|treat|VBN|_ at|at|IN|_ 37C|37c|NN|_ aerobically|aerobically|RB|_ with|with|IN|_ shaking|shake|VBG|_ with|with|IN|_ BSA|bsa|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ ,|,|,|_ 100|100|CD|_ µg|µg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Gentamicin-1|gentamicin-1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
Gentamicin-2|gentamicin-2|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Gentamicin-3|gentamicin-3|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ logarithmic|logarithmic|JJ|_ growth|growth|NN|_
PGRP-1|pgrp-1|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
PGRP-2|pgrp-2|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
PGRP-3|pgrp-3|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ RiboPureTM-bacteria|RiboPureTM-bacteria|NNP|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Signal|signal|NN|_ intensities|intensity|NNS|_ with|with|IN|_ all|all|DT|_ probes|probe|NNS|_ are|be|VBP|_ shown|show|VBN|_ in|in|IN|_ Sample|Sample|NNP|_ data|datum|NNS|_ table|table|NN|_ .|.|.|_ The|the|DT|_ `|`|``|_ expressed_present_probes.txt|expressed_present_probes.txt|NN|_ -LRB-|-lrb-|-LRB-|_ available|available|JJ|_ on|on|IN|_ Series|Series|NNP|_ records|record|NNS|_ -RRB-|-rrb-|-RRB-|_ contains|contain|VBZ|_ Signal|signal|NN|_ intensities|intensity|NNS|_ with|with|IN|_ present|present|JJ|_ probes|probe|NNS|_ .|.|.|_ Average|average|JJ|_ signal|signal|NN|_ intensities|intensity|NNS|_ from|from|IN|_ 3|3|CD|_ experiments|experiment|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ fold|fold|JJ|_ increases|increase|NNS|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ treated|treated|JJ|_ and|and|CC|_ control|control|JJ|_ groups|group|NNS|_ ,|,|,|_ with|with|IN|_ signal|signal|NN|_ intensity|intensity|NN|_ of|of|IN|_ 39|39|CD|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ minimum|minimum|JJ|_ intensity|intensity|NN|_ ,|,|,|_ using|use|VBG|_ the|the|DT|_ formula|formula|NN|_ :|:|:|_ average|average|JJ|_ intensity|intensity|NN|_ in|in|IN|_ treated|treated|JJ|_ group|group|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substrain|substrain|NN|_ MG1655|mg1655|NN|_
The|the|DT|_ hybridization|hybridization|NN|_ intensity|intensity|NN|_ data|datum|NNS|_ signals|signal|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ ,|,|,|_ normalized|normalize|VBD|_ ,|,|,|_ and|and|CC|_ corrected|correct|VBN|_ for|for|IN|_ batch|batch|NN|_ effect|effect|NN|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ GeneChip|GeneChip|NNP|_ ®|®|NNP|_ Command|command|NN|_ Console|Console|NNP|_ ®|®|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ AGCC|AGCC|NNP|_ v.|v.|CC|_ 3.0|3.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Signal|signal|NN|_ average|average|NN|_ ,|,|,|_ noise|noise|NN|_ average|average|NN|_ ,|,|,|_ scaling|scaling|NN|_ factor|factor|NN|_ ,|,|,|_ %|%|NN|_ present|present|JJ|_ ,|,|,|_ and|and|CC|_ %|%|NN|_ absent|absent|JJ|_ were|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ each|each|DT|_ probe|probe|NN|_ ,|,|,|_ from|from|IN|_ which|which|WDT|_ the|the|DT|_ signal|signal|NN|_ intensity|intensity|NN|_ of|of|IN|_ >|>|JJR|_ 39|39|CD|_ was|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ reliable|reliable|JJ|_ expression|expression|NN|_ .|.|.|_ Using|use|VBG|_ this|this|DT|_ cutoff|cutoff|NN|_ ,|,|,|_ 5531|5531|CD|_ probes|probe|NNS|_ were|be|VBD|_ classified|classify|VBN|_ as|as|IN|_ present|present|JJ|_ out|out|IN|_ of|of|IN|_ total|total|JJ|_ 10208|10208|CD|_ probes|probe|NNS|_ on|on|IN|_ the|the|DT|_ array|array|NN|_ -LRB-|-lrb-|-LRB-|_ full_expressed_data.txt|full_expressed_data.txt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
tissue|tissue|NN|_ :|:|:|_ entire|entire|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 100|100|CD|_ µg|µg|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 5|5|CD|_ µg|µg|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 800|800|CD|_ µM|µm|NN|_ CCCP|cccp|NN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_
BWG|bwg|NN|_ _|_|CD|_ butanol|butanol|NN|_ _|_|CD|_ 3passages|3passage|NNS|_
BWG|bwg|NN|_ _|_|NN|_ replicated|replicate|VBN|_
BWY|bwy|NN|_ _|_|NN|_ butanol|butanol|NN|_ _|_|CD|_ 3passages|3passage|NNS|_
BWY|bwy|NN|_ _|_|NN|_ replicated|replicate|VBD|_
Data|Data|NNP|_ were|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ GenePix|GenePix|NNP|_ 4100A|4100a|CD|_ scanning|scanning|NN|_ software|software|NN|_ and|and|CC|_ normalized|normalize|VBD|_ using|use|VBG|_ the|the|DT|_ lowess|lowess|NN|_ method|method|NN|_ implemented|implement|VBN|_ in|in|IN|_ TM4|tm4|NN|_ MIDAS|MIDAS|NNP|_
Donor|Donor|NNP|_ was|be|VBD|_ transformed|transform|VBN|_ with|with|IN|_ a|a|DT|_ random|random|JJ|_ genomic|genomic|JJ|_ library|library|NN|_ made|make|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ stored|store|VBN|_ as|as|IN|_ glycerol|glycerol|NN|SUPP stocks|stock|NNS|_ .|.|.|_ The|the|DT|_ library|library|NN|_ was|be|VBD|_ revived|revive|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ four|four|CD|_ recipient|recipient|JJ|_ strains|strain|NNS|_ using|use|VBG|_ conjugation|conjugation|NN|_ ;|;|:|_ the|the|DT|_ donor|donor|NN|_ was|be|VBD|_ miniprepped|miniprepp|VBN|_ at|at|IN|_ this|this|DT|_ time|time|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ recipients|recipient|NNS|_ were|be|VBD|_ miniprepped|miniprepp|VBN|_ after|after|IN|_ outgrowth|outgrowth|NN|_ under|under|IN|_ dual|dual|JJ|_ selection|selection|NN|_ .|.|.|_ Two|two|CD|_ recipient|recipient|JJ|_ libraries|library|NNS|_ in|in|IN|_ BWG|bwg|NN|_ and|and|CC|_ BWY|bwy|NN|_ were|be|VBD|_ propagated|propagate|VBN|_ under|under|IN|_ n-butanol|n-butanol|JJ|_ stress|stress|NN|_ for|for|IN|_ three|three|CD|_ days|day|NNS|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ miniprepped|miniprepp|VBD|_ as|as|RB|_ well|well|RB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Library|Library|NNP|_ minipreps|miniprep|NNS|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Zyppy|Zyppy|NNP|_ Miniprep|Miniprep|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ dsDNA|dsDNA|NNP|_ BR|BR|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_
MG6|mg6|NN|_ _|_|NN|_ replicated|replicate|VBN|_
MY4|my4|NN|_ _|_|NN|_ replicated|replicate|VBN|_
Plasmid|plasmid|NN|_ DNA|dna|NN|_ ,|,|,|_ after|after|IN|_ n-butanol|n-butanol|NN|_ selection|selection|NN|_
Plasmid|plasmid|NN|_ DNA|dna|NN|_ ,|,|,|_ BWG|BWG|NNP|_ post|post|NN|_ conjugation|conjugation|NN|_
Plasmid|plasmid|NN|_ DNA|dna|NN|_ ,|,|,|_ BWY|BWY|NNP|_ post|post|NN|_ conjugation|conjugation|NN|_
Plasmid|plasmid|NN|_ DNA|dna|NN|_ ,|,|,|_ donor|donor|NN|_ ,|,|,|_ XL1-Blue|xl1-blue|JJ|_
Plasmid|plasmid|NN|_ DNA|dna|NN|_ ,|,|,|_ post|post|NN|_ conjugation|conjugation|NN|_
plasmid|plasmid|NN|_ :|:|:|_ Donor|Donor|NNP|_ Library|Library|NNP|_
plasmid|plasmid|NN|_ :|:|:|_ Initial|initial|JJ|_ Recipient|Recipient|NNP|_ Library|Library|NNP|_ -LRB-|-lrb-|-LRB-|_ BWG|BWG|NNP|_ -RRB-|-rrb-|-RRB-|_
plasmid|plasmid|NN|_ :|:|:|_ Initial|initial|JJ|_ Recipient|Recipient|NNP|_ Library|Library|NNP|_ -LRB-|-lrb-|-LRB-|_ BWY|BWY|NNP|_ -RRB-|-rrb-|-RRB-|_
plasmid|plasmid|NN|_ source|source|NN|_ :|:|:|_ Initial|initial|JJ|_ Recipient|Recipient|NNP|_ Library|Library|NNP|_
plasmid|plasmid|NN|_ source|source|NN|_ :|:|:|_ Post|Post|NNP|_ Selection|selection|NN|_ Library|Library|NNP|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Persister|persister|NN|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
furanone-free|furanone-free|JJ|_ control|control|NN|_
GeneChip|GeneChip|NNP|_ Operating|Operating|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ MAS|MAS|NNP|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ ,|,|,|_ genes|gene|NNS|_ with|with|IN|_ a|a|DT|_ p-value|p-value|NN|_ of|of|IN|_ less|less|JJR|_ than|than|IN|_ 0.0025|0.0025|CD|_ or|or|CC|_ greater|greater|JJR|_ than|than|IN|_ 0.9975|0.9975|CD|_ were|be|VBD|_ considered|consider|VBN|_ statistically|statistically|RB|_ significant|significant|JJ|_ based|base|VBN|_ on|on|IN|_ Wilcoxon|Wilcoxon|NNP|_ signed|sign|VBD|_ rank|rank|JJ|_ test|test|NN|_ and|and|CC|_ Tukey|tukey|NN|_ Byweight|byweight|NN|_ ,|,|,|_ labeled|label|VBN|_ as|as|IN|_ I|I|PRP|_ and|and|CC|_ D|d|NN|_ in|in|IN|_ the|the|DT|_ attached|attach|VBN|_ txt|txt|NN|_ file|file|NN|_ .|.|.|_ To|to|TO|_ ensure|ensure|VB|_ the|the|DT|_ significance|significance|NN|_ of|of|IN|_ microarray|microarray|NN|_ data|datum|NNS|_ ,|,|,|_ an|a|DT|_ additional|additional|JJ|_ criterion|criterion|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ only|only|RB|_ select|select|VB|_ the|the|DT|_ genes|gene|NNS|_ with|with|IN|_ an|a|DT|_ expression|expression|NN|_ ratio|ratio|NN|_ of|of|IN|_ 2|2|CD|_ or|or|CC|_ high|high|JJ|_ from|from|IN|_ this|this|DT|_ group|group|NN|_ as|as|IN|_ induced|induce|VBN|_ and|and|CC|_ repressed|repress|VBN|_ genes|gene|NNS|_ .|.|.|_
RNeasy|rneasy|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Austin|Austin|NNP|_ ,|,|,|_ TX|TX|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ RNase-Free|rnase-free|JJ|_ DNase|dnase|NN|_ Set|set|VB|_ ,|,|,|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RP437|rp437|NN|_ persisters|persister|NNS|_ treated|treat|VBN|_ with|with|IN|_ BF8|bf8|NN|_ at|at|IN|_ 5|5|CD|_ µg|µg|NN|_
RP437|rp437|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 100|100|CD|_ mL|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 18|18|CD|_ h|h|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ ,|,|,|_ 37oC|37oc|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Persister|persister|NN|_ cells|cell|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ lysing|lyse|VBG|_ the|the|DT|_ normal|normal|JJ|_ cells|cell|NNS|_ with|with|IN|_ 5|5|CD|_ µg|µg|NN|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ RP437|rp437|NN|_
The|the|DT|_ isolated|isolate|VBN|_ persisters|persister|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ rpm|rpm|NN|_ ,|,|,|_ 37oC|37oc|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ or|or|CC|_ without|without|IN|_ 5|5|CD|_ µg|µg|NN|_
Cells|cell|NNS|_ of|of|IN|_ each|each|DT|_ evolved|evolve|VBD|_ colony|colony|NN|_ type|type|NN|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 13,000|13,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ were|be|VBD|_ immediately|immediately|RB|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ with|with|IN|_ NucleoSpin|nucleospin|NN|_ RNA|rna|NN|_ II|ii|CD|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Macherey|macherey|NN|_ --|--|:|_ Nagel|Nagel|NNP|_ ,|,|,|_ Biokè|Biokè|NNP|_ ,|,|,|_ Leiden|Leiden|NNP|_ ,|,|,|_ the|the|DT|_ Netherlands|Netherlands|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
culture|culture|NN|_ type|type|NN|_ :|:|:|_ Ancestor|Ancestor|NNP|_
culture|culture|NN|_ type|type|NN|_ :|:|:|_ evolved|evolve|VBD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Growth|growth|NN|_ curves|curve|NNS|_ of|of|IN|_ all|all|DT|_ selected|select|VBN|_ evolved|evolve|VBD|_ colony|colony|NN|_ types|type|NNS|_ and|and|CC|_ the|the|DT|_ ancestor|ancestor|NN|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ growing|grow|VBG|_ them|they|PRP|_ under|under|IN|_ their|they|PRP$|_ evolved|evolve|VBN|_ environmental|environmental|JJ|_ conditions|condition|NNS|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED until|until|IN|_ Log-phase|log-phase|NN|_ .|.|.|_ For|for|IN|_ this|this|DT|_ ,|,|,|_ optical|optical|JJ|_ density|density|NN|_ was|be|VBD|_ recorded|record|VBN|_ at|at|IN|_ 600nm|600nm|CD|_ at|at|IN|_ a|a|DT|_ value|value|NN|_ of|of|IN|_ 0.6|0.6|CD|_ to|to|TO|_ 0.7|0.7|CD|_ .|.|.|_
morphology|morphology|NN|_ :|:|:|_ a|a|DT|_
morphology|morphology|NN|_ :|:|:|_ b|b|NN|_
morphology|morphology|NN|_ :|:|:|_ c|c|NN|_
oxygen|oxygen|NN|_ regime|regime|NN|_ :|:|:|_ daily|daily|JJ|_ shift|shift|NN|_ between|between|IN|_ shaking|shake|VBG|_ and|and|CC|_ static|static|JJ|_ -LRB-|-lrb-|-LRB-|_ no|no|DT|_ shaking|shake|VBG|_ -RRB-|-rrb-|-RRB-|_ conditions|condition|NNS|_
oxygen|oxygen|NN|_ regime|regime|NN|_ :|:|:|_ transfers|transfer|NNS|_ in|in|IN|_ constant|constant|JJ|_ static|static|JJ|_ conditions|condition|NNS|_
oxygen|oxygen|NN|_ regime|regime|NN|_ :|:|:|_ transfers|transfer|NNS|_ under|under|IN|_ constant|constant|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 200rpm|200rpm|NN|_ -RRB-|-rrb-|-RRB-|_
population|population|NN|_ :|:|:|_ 1|1|CD|_
population|population|NN|_ :|:|:|_ 2|2|CD|_
population|population|NN|_ :|:|:|_ 3|3|CD|_
population|population|NN|_ :|:|:|_ 4|4|CD|_
population|population|NN|_ :|:|:|_ 5|5|CD|_
population|population|NN|_ :|:|:|_ 6|6|CD|_
population|population|NN|_ :|:|:|_ 7|7|CD|_
Pure|pure|JJ|_ culture|culture|NN|_ in|in|IN|_ LB|LB|NNP|_
Statistical|statistical|JJ|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ R|r|NN|_ Limma|limma|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ Linear|linear|JJ|_ Models|model|NNS|_ for|for|IN|_ Microarrays|Microarrays|NNP|_ Data|Data|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Smyth|Smyth|NNP|_ 2004|2004|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ where|where|WRB|_ the|the|DT|_ two|two|CD|_ microarrays|microarray|NNS|_ per|per|IN|_ sample|sample|NN|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ lowess|lowess|JJ|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ Multiple-gene|multiple-gene|JJ|_ probes|probe|NNS|_ results|result|NNS|_ were|be|VBD|_ merged|merge|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ MA|MA|NNP|_ table|table|NN|_ conversion|conversion|NN|_ tool|tool|NN|_ available|available|JJ|_ on|on|IN|_ the|the|DT|_ MOLGEN|MOLGEN|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ Server|server|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
strain|strain|NN|_ :|:|:|_ MC1000|mc1000|NN|_
Treatment|treatment|NN|_ A|a|NN|_ Population|Population|NNP|_ 1|1|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 1|1|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 1|1|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 1|1|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 1|1|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 1|1|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 2|2|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 2|2|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 2|2|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 2|2|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 2|2|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ A|a|DT|_ Population|Population|NNP|_ 2|2|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 3|3|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 3|3|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 3|3|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 3|3|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 3|3|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 3|3|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 4|4|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 4|4|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 4|4|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 4|4|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 4|4|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 4|4|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 5|5|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 5|5|CD|_ Colony|Colony|NNP|_ a|a|DT|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 5|5|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 5|5|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 5|5|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ B|b|NN|_ Population|Population|NNP|_ 5|5|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 6|6|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 6|6|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 6|6|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 6|6|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 7|7|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 7|7|CD|_ Colony|Colony|NNP|_ b|b|NN|_ replica|replica|NN|_ 2|2|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 7|7|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 1|1|CD|_
Treatment|treatment|NN|_ C|c|NN|_ Population|Population|NNP|_ 7|7|CD|_ Colony|Colony|NNP|_ c|c|NN|_ replica|replica|NN|_ 2|2|CD|_
100ng|100ng|CD|_ 16S|16s|NN|_ rRNA|rrna|NN|_ gene|gene|NN|_ amplicon|amplicon|NN|_ of|of|IN|_ a|a|DT|_ mock|mock|JJ|_ community|community|NN|_
Bacteroides|Bacteroides|NNPS|_ fragilis|fragili|VBZ|_
Blautia|Blautia|NNP|_ coccoides|coccoide|VBZ|_
-LSB-|-lsb-|-LRB-|_ Clostridium|clostridium|NN|_ -RSB-|-rsb-|-RRB-|_ leptum|leptum|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Faecal|faecal|JJ|_ samples|sample|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ the|the|DT|_ Department|Department|NNP|_ of|of|IN|_ Microbiology|Microbiology|NNP|_ and|and|CC|_ Alimentary|Alimentary|NNP|_ Pharmabiotic|Pharmabiotic|NNP|_ Centre|Centre|NNP|_ -LRB-|-lrb-|-LRB-|_ Cork|Cork|NNP|_ ,|,|,|_ Ireland|Ireland|NNP|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ three|three|CD|_ elderly|elderly|JJ|_ patients|patient|NNS|_ -LRB-|-lrb-|-LRB-|_ 176|176|CD|_ ,|,|,|_ 204|204|CD|_ and|and|CC|_ 205|205|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ mock|mock|JJ|_ community|community|NN|_ was|be|VBD|_ performed|perform|VBN|_ after|after|IN|_ culture|culture|NN|_ of|of|IN|_ each|each|DT|_ individual|individual|JJ|_ bacterial|bacterial|JJ|_ strain|strain|NN|_ in|in|IN|_ their|they|PRP$|_ reference|reference|NN|_ medium|medium|NN|_ at|at|IN|_ their|they|PRP$|_ optimal|optimal|JJ|_ temperature|temperature|NN|_ for|for|IN|_ several|several|JJ|_ days|day|NNS|_ .|.|.|_
Lactobacillus|lactobacillus|NN|_ acidophilus|acidophilus|NN|_
Mock|Mock|NNP|_ community|community|NN|_
No|No|NNP|_ treatment|treatment|NN|_ were|be|VBD|_ studied|study|VBN|_ in|in|IN|_ this|this|DT|_ experience|experience|NN|_
Pixel|Pixel|NNP|_ intensities|intensity|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ ``|``|``|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ ''|''|''|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Palo|Palo|NNP|_ Alto|Alto|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ No|no|DT|_ normalization|normalization|NN|_ step|step|NN|_ was|be|VBD|_ performed|perform|VBN|_ and|and|CC|_ the|the|DT|_ retained|retain|VBN|_ intensity|intensity|NN|_ value|value|NN|_ for|for|IN|_ each|each|DT|_ probe|probe|NN|_ was|be|VBD|_ the|the|DT|_ ratio|ratio|NN|_ between|between|IN|_ the|the|DT|_ spot|spot|NN|_ 's|'s|POS|_ median|median|JJ|_ intensity|intensity|NN|_ signals|signal|NNS|_ and|and|CC|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ background|background|NN|_ signals|signal|NNS|_ .|.|.|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ mock|mock|JJ|_ community|community|NN|_ -LSB-|-lsb-|-LRB-|_ artificial|artificial|JJ|_ bacterial|bacterial|JJ|_ DNA|dna|NN|_ mix|mix|NN|_ -RSB-|-rsb-|-RRB-|_
Total|total|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ three|three|CD|_ human|human|JJ|_ faecal|faecal|JJ|_ samples|sample|NNS|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ DNA|dna|NN|_ Stool|Stool|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ West|West|NNP|_ Sussex|Sussex|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ pure|pure|JJ|_ bacterial|bacterial|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ DNeasy|dneasy|JJ|_ Blood|blood|NN|_ and|and|CC|_ Tissue|tissue|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ West|West|NNP|_ Sussex|Sussex|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 10ng|10ng|NN|_ of|of|IN|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ used|use|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ .|.|.|_ 16S|16s|CD|_ rRNA|rrna|NN|_ genes|gene|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ using|use|VBG|_ universal|universal|JJ|_ primers|primer|NNS|_ 27F|27f|NN|_ -LRB-|-lrb-|-LRB-|_ AGAGTTTGATCMTGGCTCAG|agagtttgatcmtggctcag|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 1492R|1492r|NN|_ -LRB-|-lrb-|-LRB-|_ TACGGYTACCTTGTTACGACT|tacggytaccttgttacgact|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ PCR|pcr|NN|_ reactions|reaction|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ a|a|DT|_ 50µl|50µl|JJ|_ volume|volume|NN|_ ,|,|,|_ using|use|VBG|_ DreamTaq|DreamTaq|NNP|_ DNA|DNA|NNP|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|Fermentas|NNP|_ ,|,|,|_ St.|St.|NNP|_ Leon-Rot|Leon-Rot|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ PCR|pcr|NN|_ reaction|reaction|NN|_ consisted|consist|VBD|_ of|of|IN|_ an|a|DT|_ initial|initial|JJ|_ denaturation|denaturation|NN|_ step|step|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ followed|follow|VBN|_ by|by|IN|_ 35|35|CD|_ cycles|cycle|NNS|_ of|of|IN|_ denaturation|denaturation|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 30|30|CD|_ s|s|NNS|_ ,|,|,|_ annealing|annealing|NN|_ at|at|IN|_ 58|58|CD|_ °C|°c|NN|_ for|for|IN|_ 40|40|CD|_ s|s|NNS|_ and|and|CC|_ elongation|elongation|NN|_ at|at|IN|_ 72|72|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ .|.|.|_ A|a|DT|_ final|final|JJ|_ extension|extension|NN|_ step|step|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 72|72|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ PCR|pcr|NN|_ product|product|NN|_ size|size|NN|_ was|be|VBD|_ verified|verify|VBN|_ by|by|IN|_ electrophoresis|electrophoresis|NN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w|w|NN|_
All|all|DT|_ RNA|rna|NN|_ data|datum|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Xuzhou21|xuzhou21|NN|_ using|use|VBG|_ SOAP2|soap2|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
For|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_ the|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 16|16|CD|_ h.|h.|NN|_ 50|50|CD|_ µl|µl|NN|_ of|of|IN|_ the|the|DT|_ above|above|JJ|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ the|the|DT|_ culture|culture|NN|_ was|be|VBD|_ shaken|shake|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ about|about|IN|_ 2.5|2.5|CD|_ h|h|NN|_ until|until|IN|_ the|the|DT|_ OD600|od600|NN|_ reached|reach|VBD|_ 0.6|0.6|CD|_ .|.|.|_ 500|500|CD|_ µl|µl|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ RNA|rna|NN|_ protect|protect|VBP|_ bacterial|bacterial|JJ|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
genotype|genotype|NN|_ :|:|:|_ plasmid|plasmid|NN|_ cured|cure|VBD|_ strain|strain|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Isolated|isolate|VBN|_ from|from|IN|_ feces|fece|NNS|_ of|of|IN|_ a|a|DT|_ HUS|hus|NN|_ patient|patient|NN|_ from|from|IN|_ an|a|DT|_ outbreak|outbreak|NN|_ in|in|IN|_ China|China|NNP|_ in|in|IN|_ 1999|1999|CD|_
plasmid|plasmid|NN|_ cured|cure|VBD|_ rep1|rep1|NN|_
plasmid|plasmid|NN|_ cured|cure|VBD|_ rep2|rep2|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Xuzhou21|xuzhou21|NN|_
strain|strain|NN|_ :|:|:|_ Xuzhou21m|xuzhou21m|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
The|The|NNP|_ bacteria|bacterium|NNS|_ were|be|VBD|_ routinely|routinely|RB|_ grown|grow|VBN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ or|or|CC|_ on|on|IN|_ LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.2|7.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ distribution|distribution|NN|_ of|of|IN|_ reads|read|VBZ|_ was|be|VBD|_ plotted|plot|VBN|_ by|by|IN|_ its|its|PRP$|_ location|location|NN|_ in|in|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ divided|divide|VBN|_ into|into|IN|_ gene|gene|NN|_ region|region|NN|_ and|and|CC|_ intergenic|intergenic|JJ|_ region|region|NN|_ .|.|.|_ Genome|Genome|NNP|_ and|and|CC|_ gene|gene|NN|_ coverage|coverage|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ counting|count|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ and|and|CC|_ individual|individual|JJ|_ genes|gene|NNS|_ respectively|respectively|RB|_ .|.|.|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ the|the|DT|_ RPKM|rpkm|NN|_ method|method|NN|_
The|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ Xuzhou21|xuzhou21|NN|_ and|and|CC|_ Xuzhou21m|xuzhou21m|NN|_ were|be|VBD|_ first|first|JJ|_ treated|treat|VBN|_ with|with|IN|_ Ribo-Zero|ribo-zero|NN|_ ™|™|CD|_ rRNA|rrna|NN|_ Removal|removal|NN|_ kit|kit|NN|_ to|to|TO|_ remove|remove|VB|_ rRNA|rrna|NN|_ .|.|.|_ The|the|DT|_ mRNA|mrna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ produced|produce|VBD|_ cDNA|cdna|NN|_ libraries|library|NNS|_ primed|prime|VBN|_ with|with|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ selected|select|VBN|_ by|by|IN|_ size|size|NN|_ ,|,|,|_ amplificated|amplificate|VBN|_ using|use|VBG|_ PCR|pcr|NN|_ and|and|CC|_ and|and|CC|_ then|then|RB|_ sent|send|VBD|_ to|to|TO|_ sequencing|sequencing|NN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ HiseqTM|HiseqTM|NNP|_ 2000|2000|CD|_ commercially|commercially|RB|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ were|be|VBD|_ then|then|RB|_ isolated|isolate|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ both|both|DT|_ Xuzhou21|xuzhou21|NN|_ and|and|CC|_ Xuzhou21m|xuzhou21m|NN|_ using|use|VBG|_ Wizard|Wizard|NNP|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|Promega|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocols|protocol|NNS|_ .|.|.|_
WT|WT|NNP|_ rep1|rep1|NN|_
WT|wt|JJ|_ rep2|rep2|NN|_
Xuzhou21|xuzhou21|NN|_ cured|cure|VBD|_ of|of|IN|_ the|the|DT|_ pO157|po157|NN|_ _|_|CD|_ Sal|Sal|NNP|_ plasmid|plasmid|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
BL21|bl21|NN|_ _|_|NN|_ 1|1|CD|_
BL21|bl21|NN|_ _|_|NN|_ 2|2|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ fermenter|fermenter|NN|_ containing|contain|VBG|_ 100|100|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 3|3|CD|_ g|g|NN|_
condition|condition|NN|_ :|:|:|_ LB|lb|NN|_ +3|+3|CD|_ g|g|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
First|First|NNP|_ and|and|CC|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ Ovation|Ovation|NNP|_ ®|®|NNP|_ Prokaryotic|Prokaryotic|NNP|_ RNA-Seq|RNA-Seq|NNP|_ System|System|NNP|_ -LRB-|-lrb-|-LRB-|_ NuGEN|NuGEN|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ San|San|NNP|_ Carlos|Carlos|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ NuGEN|nugen|NN|_ 's|'s|POS|_ Encore|encore|NN|_ NGS|ngs|NN|_ Library|Library|NNP|_ System|System|NNP|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ construct|construct|VB|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ for|for|IN|_ the|the|DT|_ IlluminaHiSeq|IlluminaHiSeq|NNP|_ platform|platform|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ gi|gi|NN|_ ||||SYM|_ 387825439|387825439|CD|_
genotype|genotype|NN|_ :|:|:|_ Pck|pck|NN|_ over-expressed|over-expressed|JJ|_
genotype|genotype|NN|_ :|:|:|_ wild-type|wild-type|JJ|_
PCK|pck|NN|_ over|over|IN|_
Raw|raw|NN|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ FASTQ|fastq|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ processed|process|VBN|_ by|by|IN|_ Xpression|xpression|NN|_ and|and|CC|_ only|only|RB|_ the|the|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
Reference|Reference|NNP|_ files|file|VBZ|_ for|for|IN|_ the|the|DT|_ genome|genome|NN|_ sequence|sequence|NN|_ being|be|VBG|_ queried|query|VBN|_ ,|,|,|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 012971|012971|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ uploaded|upload|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ overlapping|overlap|VBG|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ recorded|record|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ based|base|VBN|_ on|on|IN|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ uniquely|uniquely|RB|_ mapped|map|VBD|_ reads|read|VBZ|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ C.|C.|NNP|_ glutamicum|glutamicum|NN|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ ®|®|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|NNP|_ -LRB-|-lrb-|-LRB-|_ Macherey-Nagel|Macherey-Nagel|NNP|_ ,|,|,|_ Düren|Düren|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ resuspended|resuspend|VBN|_ in|in|IN|_ TRIzol|trizol|NN|_ ®|®|NN|_ reagent|reagent|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ a|a|DT|_ vial|vial|NN|_ containing|contain|VBG|_ Lysing|lyse|VBG|_ Matrix|Matrix|NNP|_ B|B|NNP|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedicals|biomedical|NNS|_ ,|,|,|_ Solon|Solon|NNP|_ ,|,|,|_ OH|oh|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ lysis|lysis|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ a|a|DT|_ NucleoSpin|NucleoSpin|NNP|_ ®|®|NN|_ RNA|rna|NN|_ II|ii|CD|_ kit|kit|NN|_ for|for|IN|_ purification|purification|NN|_ .|.|.|_
Xpression|xpression|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
Xpression|xpression|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ filtering|filter|VBG|_ and|and|CC|_ trimming|trim|VBG|_ reads|read|VBZ|_ .|.|.|_
control|control|VBP|_ 12h|12h|JJ|_
control|control|VBP|_ 24h|24h|JJ|_
control|control|VBP|_ 6h|6h|JJ|_
Cy3|cy3|NN|_ and|and|CC|_ Cy5|cy5|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ scaling|scale|VBG|_ so|so|RB|_ that|that|IN|_ the|the|DT|_ 75th|75th|JJ|_ percentile|percentile|NN|_ in|in|IN|_ the|the|DT|_ Cy3|cy3|NN|_ and|and|CC|_ Cy5|cy5|NN|_ channels|channel|NNS|_ were|be|VBD|_ equal|equal|JJ|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
expose|expose|VBP|_ Bacillus|bacillus|NN|_ VOC|voc|NN|_ 12h|12h|VBP|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-12h|voc-12h|JJ|_ rep1|rep1|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-12h|voc-12h|JJ|_ rep2|rep2|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-12h|voc-12h|JJ|_ rep3|rep3|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-12h|voc-12h|JJ|_ rep4|rep4|NN|_
expose|expose|VBP|_ Bacillus|bacillus|NN|_ VOC24h|voc24h|JJ|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-24h|voc-24h|JJ|_ rep1|rep1|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-24h|voc-24h|JJ|_ rep2|rep2|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-24h|voc-24h|JJ|_ rep3|rep3|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-24h|voc-24h|JJ|_ rep4|rep4|NN|_
expose|expose|VBP|_ Bacillus|bacillus|NN|_ VOC|voc|NN|_ 6h|6h|VBP|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-6h|voc-6h|JJ|_ rep1|rep1|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-6h|voc-6h|JJ|_ rep2|rep2|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-6h|voc-6h|JJ|_ rep3|rep3|NN|_
Expose|expose|VB|_ Bacillus|bacillus|NN|_ VOC-6h|voc-6h|JJ|_ rep4|rep4|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
time|time|NN|_ :|:|:|_ 12|12|CD|_ h|h|NN|_
time|time|NN|_ :|:|:|_ 24|24|CD|_ h|h|NN|_
time|time|NN|_ :|:|:|_ 6|6|CD|_ h|h|NN|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ manufacture|manufacture|NN|_ 's|'s|POS|_ instruction|instruction|NN|_
treatment|treatment|NN|_ :|:|:|_ Bacillus|bacillus|NN|_ volatile|volatile|JJ|_ organic|organic|JJ|_ compounds|compound|NNS|_ -LRB-|-lrb-|-LRB-|_ VOCs|voc|NNS|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ control|control|NN|_
Aerobic|aerobic|JJ|_ growth|growth|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ specified|specify|VBN|_ media|media|NNS|_
Cells|cell|NNS|_ treated|treat|VBN|_ during|during|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
CV108|cv108|NN|_ _|_|CD|_ minus|minus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 1|1|CD|_
CV108|cv108|NN|_ _|_|CD|_ minus|minus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 2|2|CD|_
CV108|cv108|NN|_ _|_|CD|_ minus|minus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 3|3|CD|_
CV108|cv108|NN|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 1|1|CD|_
CV108|cv108|NN|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 2|2|CD|_
CV108|cv108|NN|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Galaxy1|galaxy1|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pHDB3|phdb3|NN|_ _|_|CD|_ 5|5|CD|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_
Galaxy2|galaxy2|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pLCV1|plcv1|NN|_ _|_|CD|_ 5|5|CD|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_
Galaxy3|galaxy3|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pLCV1|plcv1|NN|_ _|_|NN|_ 10|10|CD|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_
Galaxy4|galaxy4|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pHDB3|phdb3|NN|_ _|_|CD|_ 20|20|CD|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_
Galaxy5|galaxy5|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pLCV1|plcv1|NN|_ _|_|CD|_ 20|20|CD|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_
Galaxy6|galaxy6|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pHDB3|phdb3|NN|_ _|_|NN|_ 10|10|CD|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ CV108|cv108|NN|_
genotype|genotype|NN|_ :|:|:|_ Galaxy1|galaxy1|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pHDB3|phdb3|NN|_ _|_|CD|_ 5|5|CD|_ -RSB-|-rsb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ Galaxy2|galaxy2|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pLCV1|plcv1|NN|_ _|_|CD|_ 5|5|CD|_ -RSB-|-rsb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ Galaxy3|galaxy3|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pLCV1|plcv1|NN|_ _|_|NN|_ 10|10|CD|_ -RSB-|-rsb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ Galaxy4|galaxy4|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pHDB3|phdb3|NN|_ _|_|CD|_ 20|20|CD|_ -RSB-|-rsb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ Galaxy5|galaxy5|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pLCV1|plcv1|NN|_ _|_|CD|_ 20|20|CD|_ -RSB-|-rsb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ Galaxy6|galaxy6|NN|_ -|-|:|_ -LSB-|-lsb-|-LRB-|_ CV104|cv104|NN|_ _|_|CD|_ pHDB3|phdb3|NN|_ _|_|NN|_ 10|10|CD|_ -RSB-|-rsb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ pHDB3|phdb3|NN|_
genotype|genotype|NN|_ :|:|:|_ pLCV1|plcv1|NN|_
genotype|genotype|NN|_ :|:|:|_ SgrR|sgrr|NN|TF
genotype|genotype|NN|_ :|:|:|_ sgrS|sgrs|NN|GEN
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
Hot|Hot|NNP|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ .|.|.|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugghe|Crombrugghe|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p.|p.|NN|_ 11905-11910|11905-11910|CD|_ .|.|.|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ 2-DG|2-dg|JJ|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Minimal|minimal|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ Glucose|glucose|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_
media|media|NNS|_ :|:|:|_ Defined|define|VBN|_ MOPS|mop|NNS|MED Rich|rich|JJ|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ Glycerol|glycerol|NN|_ +0.5|+0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_ +|+|CC|_ 0.5|0.5|CD|_ %|%|NN|_ aMG|amg|NN|_
MG1655-aMG|mg1655-amg|NN|_ _|_|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ +|+|CC|_ aMG|amg|NN|_ _|_|NN|_ 1|1|CD|_
MG1655-aMG|mg1655-amg|NN|_ _|_|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ +|+|CC|_ aMG|amg|NN|_ _|_|NN|_ 2|2|CD|_
MG1655-aMG|mg1655-amg|NN|_ _|_|CD|_ 3|3|CD|_
MG1655|mg1655|NN|_ +|+|CC|_ aMG|amg|NN|_ _|_|CD|_ 3|3|CD|_
MG1655|mg1655|NN|_ _|_|CD|_ minus|minus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 1|1|CD|_
MG1655|mg1655|NN|_ _|_|CD|_ minus|minus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 2|2|CD|_
MG1655|mg1655|NN|_ _|_|CD|_ minus|minus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 3|3|CD|_
MG1655|mg1655|NN|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 1|1|CD|_
MG1655|mg1655|NN|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 2|2|CD|_
MG1655|mg1655|NN|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ aMG|aMG|NNP|_ _|_|SYM|_ 3|3|CD|_
pHDB3|phdb3|NN|_ _|_|NN|_ 1|1|CD|_
pHDB3|phdb3|NN|_ _|_|NN|_ 2|2|CD|_
pHDB3|phdb3|NN|_ _|_|CD|_ 3|3|CD|_
pLCV1|plcv1|NN|_ _|_|NN|_ 1|1|CD|_
pLCV1|plcv1|NN|_ _|_|NN|_ 2|2|CD|_
pLCV1|plcv1|NN|_ _|_|CD|_ 3|3|CD|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ first|first|JJ|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ kit|kit|NN|_ .|.|.|_ Enriched|enriched|JJ|_ mRNAs|mrna|NNS|_ were|be|VBD|_ then|then|RB|_ converted|convert|VBN|_ into|into|IN|_ indexed|index|VBN|_ libraries|library|NNS|_ using|use|VBG|_ the|the|DT|_ into|into|IN|_ ScriptSeqTM|scriptseqtm|NN|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
RNA-Seq|rna-seq|NN|_
Rockhopper|rockhopper|NN|_ version|version|NN|_ 1.20|1.20|CD|_ -LRB-|-lrb-|-LRB-|_ manuscript|manuscript|NN|_ submitted|submit|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ available|available|JJ|_ for|for|IN|_ download|download|NN|_ from|from|IN|_ http|http|NN|_ :|:|:|_
SgrR|sgrr|NN|TF _|_|NN|_ 1|1|CD|_
SgrR|sgrr|NN|TF _|_|NN|_ 2|2|CD|_
SgrR|sgrr|NN|TF _|_|CD|_ 3|3|CD|_
sgrS|sgrs|NN|GEN _|_|CD|_ T|t|NN|_ _|_|NN|_ 1|1|CD|_
sgrS|sgrs|NN|GEN _|_|CD|_ T|t|NN|_ _|_|NN|_ 2|2|CD|_
sgrS|sgrs|NN|GEN _|_|CD|_ T|t|NN|_ _|_|NN|_ 3|3|CD|_
sgrS|sgrs|NN|GEN _|_|CD|_ un|un|NN|_ _|_|NN|_ 1|1|CD|_
sgrS|sgrs|NN|GEN _|_|CD|_ un|un|NN|_ _|_|NN|_ 2|2|CD|_
sgrS|sgrs|NN|GEN _|_|CD|_ un|un|NN|_ _|_|NN|_ 3|3|CD|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab|tab|NN|_ delimited|delimit|VBN|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ transcription|transcription|NN|_ coordinates|coordinate|VBZ|_ and|and|CC|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
WT|wt|JJ|_ _|_|NN|_ 1|1|CD|_
WT|wt|JJ|_ _|_|NN|_ 2|2|CD|_
WT|wt|JJ|_ _|_|NN|_ 3|3|CD|_
WT|wt|JJ|_ _|_|NN|_ minus|minus|CC|_ _|_|SYM|_ 2DG|2dg|CD|_ _|_|NN|_ 1|1|CD|_
WT|wt|JJ|_ _|_|NN|_ minus|minus|CC|_ _|_|SYM|_ 2DG|2dg|CD|_ _|_|NN|_ 2|2|CD|_
WT|wt|JJ|_ _|_|NN|_ minus|minus|CC|_ _|_|SYM|_ 2DG|2dg|CD|_ _|_|SYM|_ 3|3|CD|_
WT|wt|JJ|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ 2DG|2dg|CD|_ _|_|NN|_ 1|1|CD|_
WT|wt|JJ|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ 2DG|2dg|CD|_ _|_|NN|_ 2|2|CD|_
WT|wt|JJ|_ _|_|NN|_ plus|plus|CC|_ _|_|SYM|_ 2DG|2dg|CD|_ _|_|SYM|_ 3|3|CD|_
wt|wt|JJ|_ _|_|NN|_ T|t|NN|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|NN|_ T|t|NN|_ _|_|NN|_ 2|2|CD|_
wt|wt|JJ|_ _|_|NN|_ T|t|NN|_ _|_|CD|_ 3|3|CD|_
wt|wt|JJ|_ _|_|NN|_ un|un|NN|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|NN|_ un|un|NN|_ _|_|NN|_ 2|2|CD|_
wt|wt|JJ|_ _|_|NN|_ un|un|NN|_ _|_|NN|_ 3|3|CD|_
Chemostat|chemostat|NN|_ 1|1|CD|_ h|h|NN|_ irradiated|irradiated|JJ|_
Chemostat|chemostat|NN|_ 1h|1h|NN|_ irradiated|irradiated|JJ|_
Chemostat|chemostat|NN|_ 50|50|CD|_ h|h|NN|_ irradiated|irradiated|JJ|_
Control|Control|NNP|_ chemostat|chemostat|NN|_ 1|1|CD|_ h|h|NN|_ not|not|RB|_ irradiated|irradiated|JJ|_
Control|Control|NNP|_ chemostat|chemostat|NN|_ 1h|1h|NN|_ not|not|RB|_ irradiated|irradiated|JJ|_
Control|Control|NNP|_ chemostat|chemostat|NN|_ 50|50|CD|_ h|h|NN|_ not|not|RB|_ irradiated|irradiated|JJ|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Jaguar|Jaguar|NNP|_
UVA|UVA|NNP|_ irradiated|irradiate|VBD|_ chemostat|chemostat|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ run|run|VBP|_ 1|1|CD|_
UVA|uva|NN|_ irradiated|irradiated|JJ|_ chemostat|chemostat|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ run|run|NN|_ 2|2|CD|_
UVA|uva|NN|_ irradiated|irradiated|JJ|_ chemostat|chemostat|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ run|run|NN|_ 2|2|CD|_ dye|dye|VBP|_ swap|swap|NN|_
UVA|uva|NN|_ irradiated|irradiated|JJ|_ chemostat|chemostat|NN|_ for|for|IN|_ 1|1|CD|_ h|h|NN|_ ,|,|,|_ run|run|VBP|_ 3|3|CD|_
UVA|uva|NN|_ irradiated|irradiated|JJ|_ chemostat|chemostat|NN|_ for|for|IN|_ 50|50|CD|_ h|h|NN|_ ,|,|,|_ run|run|VBP|_ 1|1|CD|_
UVA|uva|NN|_ irradiated|irradiated|JJ|_ chemostat|chemostat|NN|_ for|for|IN|_ 50|50|CD|_ h|h|NN|_ ,|,|,|_ run|run|NN|_ 2|2|CD|_
UVA|uva|NN|_ irradiated|irradiated|JJ|_ chemostat|chemostat|NN|_ for|for|IN|_ 50|50|CD|_ h|h|NN|_ ,|,|,|_ run|run|VBP|_ 3|3|CD|_
e.coli|e.coli|JJ|_ culture|culture|NN|_ protocol|protocol|NN|_ :|:|:|_ conditioned|condition|VBN|_ Caco-2|caco-2|NN|_ cell|cell|NN|_ medium|medium|NN|_
e.coli|e.coli|JJ|_ culture|culture|NN|_ protocol|protocol|NN|_ :|:|:|_ fresh|fresh|JJ|_ medium|medium|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
STEC|stec|NN|_ EC472|ec472|NN|_
STEC|STEC|NNP|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 4|4|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EC472|ec472|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 4|4|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 4|4|CD|_ -LSB-|-lsb-|-LRB-|_ COND|cond|NN|_ -RSB-|-rsb-|-RRB-|_
STEC|stec|NN|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EH41|eh41|NN|_ after|after|IN|_ 3|3|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ ,|,|,|_ replicate|replicate|VB|_ 4|4|CD|_ -LSB-|-lsb-|-LRB-|_ FRESH|fresh|JJ|_ -RSB-|-rsb-|-RRB-|_
STEC|STEC|NNP|_ EH41|eh41|NN|_ ,|,|,|_ conditioned|conditioned|JJ|_ medium|medium|NN|_
STEC|STEC|NNP|_ EH41|eh41|NN|_ ,|,|,|_ fresh|fresh|JJ|_ medium|medium|NN|_
STEC|STEC|NNP|_ strains|strain|NNS|_ were|be|VBD|_ lysate|lysate|NN|_ using|use|VBG|_ lysozyme|lysozyme|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mg|mg|NN|_
strain|strain|NN|_ :|:|:|_ EC472|ec472|NN|_
strain|strain|NN|_ :|:|:|_ EH41|eh41|NN|_ -LRB-|-lrb-|-LRB-|_ isolated|isolate|VBN|_ from|from|IN|_ patient|patient|NN|_ with|with|IN|_ HUS|hus|NN|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ conditioned|conditioned|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ the|the|DT|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ containing|contain|VBG|_ 10|10|CD|_ %|%|NN|_ FBS|fbs|NN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ recovered|recover|VBN|_ after|after|IN|_ 24|24|CD|_ hrs|hr|NNS|_ incubation|incubation|NN|_ with|with|IN|_ differentiated|differentiate|VBN|_ Caco-2|caco-2|NN|_ cells|cell|NNS|_ .|.|.|_ 400|400|CD|_ µL|µl|NN|_ of|of|IN|_ STEC|stec|NN|_ culture|culture|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 4|4|CD|_ mL|ml|NN|_ of|of|IN|_ C|c|NN|_ medium|medium|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 3|3|CD|_ hrs|hr|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ this|this|DT|_ period|period|NN|_ the|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 5000|5000|CD|_ xg|xg|NN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ ressuspended|ressuspend|VBN|_ in|in|IN|_ 600|600|CD|_ µL|µl|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ cat|cat|NN|_ .|.|.|_ no.|no.|RB|_ 76506|76506|CD|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
The|the|DT|_ fresh|fresh|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ F|f|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ the|the|DT|_ DMEM|DMEM|NNP|_ medium|medium|NN|_ containing|contain|VBG|_ 10|10|CD|_ %|%|NN|_ FBS|fbs|NN|_ without|without|IN|_ antibiotics|antibiotic|NNS|_ .|.|.|_ 400|400|CD|_ µL|µl|NN|_ of|of|IN|_ STEC|stec|NN|_ culture|culture|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ in|in|IN|_ 4|4|CD|_ mL|ml|NN|_ of|of|IN|_ F|f|NN|_ medium|medium|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 3|3|CD|_ hrs|hr|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ this|this|DT|_ period|period|NN|_ the|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 5000|5000|CD|_ xg|xg|NN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ ressuspended|ressuspend|VBN|_ in|in|IN|_ 600|600|CD|_ µL|µl|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ cat|cat|NN|_ .|.|.|_ no.|no.|RB|_ 76506|76506|CD|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
The|the|DT|_ scanned|scan|VBN|_ images|image|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ version|version|NN|_ 9.5.3.1|9.5.3.1|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ -LRB-|-lrb-|-LRB-|_ protocol|protocol|NN|_ GE1-v5|ge1-v5|NN|_ _|_|CD|_ 95|95|CD|_ and|and|CC|_ Grid|Grid|NNP|_ :|:|:|_ 020097|020097|CD|_ _|_|NN|_ D|d|NN|_ _|_|CD|_ F|f|NN|_ _|_|SYM|_ 20080627|20080627|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ background|background|NN|_ subtracted|subtract|VBN|_ and|and|CC|_ spatially|spatially|RB|_ detrended|detrend|VBD|_ Processed|processed|JJ|_ Signal|signal|NN|_ intensities|intensity|NNS|_ but|but|CC|_ not|not|RB|_ included|include|VBD|_ the|the|DT|_ normalization|normalization|NN|_ process|process|NN|_ .|.|.|_ Features|feature|NNS|_ flagged|flag|VBD|_ in|in|IN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ as|as|IN|_ Feature|Feature|NNP|_ Non-uniform|non-uniform|JJ|_ outliers|outlier|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ .|.|.|_
antibody|antibody|NN|_ :|:|:|_ polycolonal|polycolonal|JJ|_ antiserum|antiserum|NN|_ was|be|VBD|_ raised|raise|VBN|_ against|against|IN|_ His6-ArcA|his6-arca|NN|_ then|then|RB|_ Affinity|Affinity|NNP|_ Purified|purify|VBN|_ against|against|IN|_ ArcA|arca|NN|TF to|to|TO|_ yield|yield|VB|_ the|the|DT|_ polyclonal|polyclonal|JJ|_ antibodies|antibody|NNS|_ used|use|VBN|_ for|for|IN|_ ChIP|chip|NN|_
ArcA|arca|NN|TF -|-|:|_ Aerobic|aerobic|JJ|_ -|-|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ -|-|:|_ A|a|NN|_
ArcA|arca|NN|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ -|-|:|_ biological|biological|JJ|_ rep|rep|NN|GEN A|a|DT|_
ArcA|arca|NN|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ -|-|:|_ biological|biological|JJ|_ rep|rep|NN|GEN B|b|NN|_
∆|∆|CD|_ ArcA|arca|NN|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ -|-|:|_ technical|technical|JJ|_ rep|rep|NN|GEN A|a|DT|_
∆|∆|CD|_ ArcA|arca|NN|TF -|-|:|_ Anaerobic|anaerobic|JJ|_ -|-|:|_ Affinity|affinity|NN|_ Purified|purify|VBN|_ -|-|:|_ technical|technical|JJ|_ rep|rep|NN|GEN B|b|NN|_
ArcA|arca|NN|TF INPUT|input|NN|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherchia|Escherchia|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_ ,|,|,|_ no|no|DT|_ antibody|antibody|NN|_ control|control|NN|_
ArcA|arca|NN|TF INPUT|input|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
∆|∆|CD|_ arcA|arcA|NNP|GEN IP|IP|NNP|_ DNA|dna|NN|_ from|from|IN|_ PK9416|pk9416|NN|_
ArcA|arca|NN|TF IP|IP|NNP|_ DNA|dna|NN|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
ArcA|arca|NN|TF IP|IP|NNP|_ from|from|IN|_ WT|WT|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_
Arrays|array|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Nimblegen|Nimblegen|NNP|_ 's|'s|POS|_ standard|standard|JJ|_ protocol|protocol|NN|_ for|for|IN|_ Nimblescan|nimblescan|JJ|_ 2.4|2.4|CD|_ ChIP|chip|NN|_ data|datum|NNS|_ extraction|extraction|NN|_ .|.|.|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250ul|250ul|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 25|25|CD|_ %|%|NN|_ O2|o2|CD|_ ,|,|,|_ 70|70|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.35|0.35|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
INPUT|input|VBP|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ PK9416|pk9416|NN|_ ,|,|,|_ no|no|DT|_ ArcA|arca|NN|TF control|control|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_ WT|wt|JJ|_
strain|strain|NN|_ :|:|:|_ PK9416|pk9416|NN|_
10|10|CD|_ ng|ng|NN|_ of|of|IN|_ DNA|dna|NN|_ were|be|VBD|_ submitted|submit|VBN|_ to|to|TO|_ the|the|DT|_ University|University|NNP|_ of|of|IN|_ Wisconsin-Madison|Wisconsin-Madison|NNP|_ DNA|DNA|NNP|_ Sequencing|sequencing|NN|_ Facility|facility|NN|_ for|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ sheared|shear|VBN|_ to|to|TO|_ 200-500|200-500|CD|_ nt|nt|NNS|_ during|during|IN|_ the|the|DT|_ IP|IP|NNP|_ process|process|NN|_ to|to|TO|_ facilitate|facilitate|VB|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ All|all|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ reagents|reagent|NNS|_ from|from|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Paired|Paired|NNP|_ End|End|NNP|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ ``|``|``|_ Preparing|prepare|VBG|_ Samples|sample|NNS|_ for|for|IN|_ ChIP|chip|NN|_ Sequencing|sequencing|NN|_ of|of|IN|_ DNA|dna|NN|_ ''|''|''|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ part|part|NN|_ #|#|#|_ 11257047|11257047|CD|_ RevA|reva|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ except|except|IN|_ products|product|NNS|_ of|of|IN|_ the|the|DT|_ ligation|ligation|NN|_ reaction|reaction|NN|_ were|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ using|use|VBG|_ 2|2|CD|_ %|%|NN|_ SizeSelect|sizeselect|NN|_ agarose|agarose|NN|_ gels|gel|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ targeting|target|VBG|_ 400|400|CD|_ bp|bp|NN|_ fragments|fragment|NNS|_ .|.|.|_ After|after|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ amplification|amplification|NN|_ ,|,|,|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ were|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|agilent|JJ|_ DNA|dna|NN|_ 1000|1000|CD|_ series|series|NN|_ chip|chip|NN|_ assay|assay|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ QuantIT|quantit|NN|_ PicoGreen|picogreen|NN|_ dsDNA|dsdna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ and|and|CC|_ libraries|library|NNS|_ were|be|VBD|_ standardized|standardized|JJ|_ to|to|TO|_ 10μM|10μm|NN|_ .|.|.|_ Cluster|cluster|NN|_ generation|generation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ cBot|cBot|NNP|_ Single|single|JJ|_ Read|Read|NNP|_ Cluster|Cluster|NNP|_ Generation|Generation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ placed|place|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ cBot|cBot|NNP|_ .|.|.|_ Single|single|JJ|_ read|read|NN|_ ,|,|,|_ 75|75|CD|_ bp|bp|NN|_ -LRB-|-lrb-|-LRB-|_ rep|rep|NN|GEN A|a|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 36|36|CD|_ bp|bp|NN|_ -LRB-|-lrb-|-LRB-|_ rep|rep|NN|GEN B|b|NN|_ -RRB-|-rrb-|-RRB-|_ runs|run|NNS|_ were|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ SBS|SBS|NNP|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ SCS|scs|NN|_ 2.6|2.6|CD|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ IIx|IIx|NNP|_ .|.|.|_ Basecalling|basecall|VBG|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ Pipeline|Pipeline|NNP|_ version|version|NN|_ 1.6|1.6|CD|_ .|.|.|_
Anaerobic|anaerobic|JJ|_ Cultures|culture|NNS|_
antibody|antibody|NN|_ :|:|:|_ polyclonal|polyclonal|JJ|_ antiserum|antiserum|NN|_ was|be|VBD|_ raised|raise|VBN|_ against|against|IN|_ His6-ArcA|his6-arca|NN|_ then|then|RB|_ Affinity|Affinity|NNP|_ Purified|purify|VBN|_ using|use|VBG|_ purified|purify|VBN|_ ArcA|arca|NN|TF to|to|TO|_ yield|yield|VB|_ the|the|DT|_ polyclonal|polyclonal|JJ|_ antibodies|antibody|NNS|_ used|use|VBN|_ for|for|IN|_ ChIP|chip|NN|_
ArcA|arca|NN|TF _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ ChIP-seq|ChIP-seq|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|SYM|_ A.wig|A.wig|NNP|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
ArcA|arca|NN|TF _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ ChIP-seq|ChIP-seq|NNP|_ _|_|NNP|_ IP|IP|NNP|_ _|_|NNP|_ B.wig|B.wig|NNP|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
ArcA|arca|NN|TF IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Anaerobic|Anaerobic|NNP|_ Biological|Biological|NNP|_ replicate|replicate|VB|_ 1|1|CD|_
ArcA|arca|NN|TF IP|IP|NNP|_ ChIP-seq|ChIP-seq|NNP|_ Anaerobic|Anaerobic|NNP|_ Biological|Biological|NNP|_ replicate|replicate|VB|_ 2|2|CD|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250ul|250ul|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ volumen|voluman|NNS|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ ten|ten|CD|_ minutes|minute|NNS|_ .|.|.|_ Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
ChIP-Seq|chip-seq|NN|_
culture|culture|NN|_ condition|condition|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ Cultures|culture|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ Build|Build|NNP|_ :|:|:|_
genome|genome|NN|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ published|publish|VBN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ software|software|NN|_ packages|package|NNS|_ SOAP|soap|NN|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ELAND|ELAND|NNP|_ -LRB-|-lrb-|-LRB-|_ within|within|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ Pipeline|Pipeline|NNP|_ Software|Software|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ allowing|allow|VBG|_ at|at|IN|_ most|most|JJS|_ two|two|CD|_ mismatches|mismatch|NNS|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ with|with|IN|_ sequences|sequence|NNS|_ that|that|WDT|_ did|do|VBD|_ not|not|RB|_ align|align|VB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ aligned|align|VBN|_ to|to|TO|_ multiple|multiple|JJ|_ locations|location|NNS|_ on|on|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ or|or|CC|_ contained|contain|VBD|_ more|more|JJR|_ than|than|IN|_ two|two|CD|_ mismatches|mismatch|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ from|from|IN|_ further|further|JJ|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ <|<|JJR|_ 10|10|CD|_ %|%|NN|_ of|of|IN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Supplemental|Supplemental|NNP|_ Files|Files|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ visualization|visualization|NN|_ the|the|DT|_ raw|raw|JJ|_ tag|tag|NN|GEN density|density|NN|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ QuEST|quest|NN|_ -LRB-|-lrb-|-LRB-|_ Valouev|Valouev|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ normalized|normalize|VBD|_ as|as|IN|_ tag|tag|NN|GEN density|density|NN|_ per|per|IN|_ million|million|CD|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ Wild|Wild|NNP|_ Type|type|NN|_ K-12|k-12|NN|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|CD|_ adhE|adhe|NN|GEN mutant|mutant|JJ|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ adhE|adhe|NN|GEN mutant|mutant|JJ|_
B|b|NN|_ strain|strain|NN|_ _|_|RB|_ wild|wild|JJ|_ type|type|NN|_
B|b|NN|_ strain|strain|NN|_ ,|,|,|_ wild|wild|JJ|_ type|type|NN|_
BW25113|bw25113|NN|_ _|_|CD|_ adhE|adhe|NN|GEN mutant|mutant|JJ|_
BW25113|bw25113|NN|_ ,|,|,|_ adhE|adhe|NN|GEN mutant|mutant|JJ|_
Data|Data|NNP|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ software|software|NN|_ 9.3.2.1|9.3.2.1|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technology|Technology|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ average|average|JJ|_ fluorescence|fluorescence|NN|_ intensity|intensity|NN|_ for|for|IN|_ each|each|DT|_ spot|spot|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ and|and|CC|_ local|local|JJ|_ background|background|NN|_ was|be|VBD|_ subtracted|subtract|VBN|_ .|.|.|_ All|all|DT|_ data|datum|NNS|_ normalization|normalization|NN|_ and|and|CC|_ selection|selection|NN|_ of|of|IN|_ fold-changed|fold-changed|JJ|_ genes|gene|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ GeneSpringGX|GeneSpringGX|NNP|_ 7.3.1|7.3.1|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technology|Technology|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Normalization|normalization|NN|_ for|for|IN|_ Agilent|Agilent|NNP|_ one-color|one-color|JJ|_ method|method|NN|_ was|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ Data|Data|NNP|_ transformation|transformation|NN|_ .|.|.|_ Set|set|VB|_ measurements|measurement|NNS|_ less|less|JJR|_ than|than|IN|_ 5.0|5.0|CD|_ to|to|TO|_ 5.0|5.0|CD|_ and|and|CC|_ Per|per|IN|_ Chip|chip|NN|_ :|:|:|_ Normalize|normalize|VB|_ to|to|TO|_ 50th|50th|JJ|_ percentage|percentage|NN|_ .|.|.|_ Reliable|reliable|JJ|_ genes|gene|NNS|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ flag|flag|NN|_ as|as|IN|_ following|follow|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ manual|manual|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
For|for|IN|_ control|control|NN|_ and|and|CC|_ test|test|NN|_ RNAs|rna|NNS|_ ,|,|,|_ the|the|DT|_ synthesis|synthesis|NN|_ of|of|IN|_ target|target|NN|_ cRNA|crna|NN|_ probes|probe|NNS|_ and|and|CC|_ hybridization|hybridization|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ 's|'s|POS|_ Low|low|JJ|_ Input|Input|NNP|_ Quick|Quick|NNP|_ Amp|Amp|NNP|_ WT|WT|NNP|_ Labeling|label|VBG|_ Kit|kit|NN|_ ,|,|,|_ one|one|CD|_ color|color|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technology|Technology|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ each|each|DT|_ 0.2|0.2|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ WT|wt|JJ|_ primer|primer|NN|_ mix|mix|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 65ºC|65ºc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ cDNA|cdna|NN|_ master|master|NN|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ 5X|5x|NN|_ First|first|JJ|_ strand|strand|NN|_ buffer|buffer|NN|_ ,|,|,|_ 0.1|0.1|CD|_ M|m|NN|_ DTT|dtt|NN|_ ,|,|,|_ 10mM|10mm|NN|_ dNTP|dntp|NN|_ mix|mix|NN|_ ,|,|,|_ RNase-Out|rnase-out|NN|_ ,|,|,|_ and|and|CC|_ MMLV-RT|mmlv-rt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ prepared|prepare|VBN|_ and|and|CC|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ reaction|reaction|NN|_ mixer|mixer|NN|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 40ºC|40ºc|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ and|and|CC|_ then|then|RB|_ the|the|DT|_ RT|rt|NN|_ and|and|CC|_ dsDNA|dsdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ terminated|terminate|VBN|_ by|by|IN|_ incubating|incubate|VBG|_ at|at|IN|_ 70ºC|70ºC|NNP|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ .|.|.|_
genotype|genotype|NN|_
K-12|k-12|NN|_ strain|strain|NN|_ _|_|RB|_ wild|wild|JJ|_ type|type|NN|_
K-12|k-12|NN|_ strain|strain|NN|_ ,|,|,|_ wild|wild|JJ|_ type|type|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ B|b|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ K-12|k-12|NN|_
The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ six|six|CD|_ hours|hour|NNS|_ under|under|IN|_ anaerobic|anaerobic|JJ|_ growth|growth|NN|_ condition|condition|NN|_ in|in|IN|_ glucose-containing|glucose-containing|JJ|_ complex|complex|JJ|_ medium|medium|NN|_ .|.|.|_
The|the|DT|_ microarray|microarray|NN|_ experiment|experiment|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ two|two|CD|_ serotypes|serotype|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ and|and|CC|_ their|they|PRP$|_ adhE|adhE|NNP|GEN mutants|mutant|NNS|_ :|:|:|_ -LRB-|-lrb-|-LRB-|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_ K-12|k-12|NN|_ strain|strain|NN|_ ,|,|,|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ -LRB-|-lrb-|-LRB-|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ B|b|NN|_ strain|strain|NN|_ ,|,|,|_ wild|wild|JJ|_ type|type|NN|_ ;|;|:|_ -LRB-|-lrb-|-LRB-|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_ BW25113|bw25113|NN|_ ,|,|,|_ adhE|adhe|NN|GEN mutants|mutant|NNS|_ ;|;|:|_ -LRB-|-lrb-|-LRB-|_ 4|4|LS|_ -RRB-|-rrb-|-RRB-|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ adhE|adhe|NN|GEN mutants|mutant|NNS|_ .|.|.|_
A|a|NN|_ single|single|JJ|_ large|large|JJ|_ fastq|fastq|NN|_ format|format|NN|_ file|file|NN|_ of|of|IN|_ high|high|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ Q|Q|NNP|_ ≥|≥|SYM|_ 30|30|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ split|split|VBN|_ into|into|IN|_ about|about|IN|_ 10|10|CD|_ smaller|smaller|JJR|_ files|file|NNS|_ by|by|IN|_ using|use|VBG|_ a|a|DT|_ shell|shell|NN|_ script|script|NN|_ splitReads.sh|splitreads.sh|JJ|_
CASAVA|casava|NN|_ version|version|NN|_ 1.4|1.4|CD|_
Cells|cell|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED containing|contain|VBG|_ ampicillin|ampicillin|NN|_ at|at|IN|_ 28|28|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ overnight|overnight|JJ|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ the|the|DT|_ fresh|fresh|JJ|_ medium|medium|NN|_ at|at|IN|_ 1|1|CD|_
Each|each|DT|_ type|type|NN|_ of|of|IN|_ error|error|NN|_ rates|rate|NNS|_ per|per|IN|_ position|position|NN|_ was|be|VBD|_ determined|determine|VBN|_ as|as|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ with|with|IN|_ a|a|DT|_ particular|particular|JJ|_ type|type|NN|_ of|of|IN|_ base-substitution|base-substitution|NN|_ divided|divide|VBN|_ by|by|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ with|with|IN|_ the|the|DT|_ reference|reference|NN|_ base|base|NN|_ in|in|IN|_ each|each|DT|_ DNA|dna|NN|_ position|position|NN|_ .|.|.|_
E.coli|e.coli|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_
error-prone|error-prone|NN|_ in|in|FW|_ vitro|vitro|FW|_ -LRB-|-lrb-|-LRB-|_ Mn2|mn2|NN|_ +|+|CC|_ -RRB-|-rrb-|-RRB-|_
error-prone|error-prone|JJ|_ in|in|FW|_ vitro|vitro|FW|_ MnCl2|mncl2|NN|SUPP
error-proof|error-proof|JJ|_ in|in|FW|_ vitro|vitro|FW|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ GreAB|greab|NN|_
error-proof|error-proof|JJ|_ in|in|FW|_ vitro|vitro|FW|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ GreAB|greab|NN|_
error-proof|error-proof|JJ|_ in|in|FW|_ vitro|vitro|FW|_ MgCl2|mgcl2|NN|_ +|+|CC|_ GreAB|greab|NN|_
error-proof|error-proof|JJ|_ in|in|FW|_ vitro|vitro|FW|_ MnCl2|mncl2|NN|SUPP +|+|CC|_ GreAB|greab|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ pPR9|ppr9|NN|_ plasmid|plasmid|NN|_ -LRB-|-lrb-|-LRB-|_ ref|ref|NN|_ is|be|VBZ|_ Kashlec|Kashlec|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1989|1989|CD|_ ,|,|,|_ PMID|PMID|NNP|_ :|:|:|_ 2547695|2547695|CD|_ -RRB-|-rrb-|-RRB-|_
In|in|FW|_ vitro|vitro|FW|_ RNA|rna|NN|_ preparation|preparation|NN|_ :|:|:|_ The|the|DT|_ 5.7|5.7|CD|_ kb|kb|NN|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ the|the|DT|_ digested|digest|VBN|_ DNA|dna|NN|_ ,|,|,|_ NTPs|ntp|NNS|_ ,|,|,|_ abortive|abortive|JJ|_ oligo-RNA|oligo-rna|JJ|_ products|product|NNS|_ ,|,|,|_ and|and|CC|_ proteins|protein|NNS|_ by|by|IN|_ Acidic|acidic|JJ|_ phenol|phenol|NN|_ extraction|extraction|NN|_ ,|,|,|_ G50|g50|NN|_ spin|spin|NN|_ column|column|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ EtOH|etoh|NN|_ precipitation|precipitation|NN|_ .|.|.|_
in|in|FW|_ vivo|vivo|FW|_
In|in|FW|_ vivo|vivo|FW|_ RNA|rna|NN|_ preparation|preparation|NN|_ :|:|:|_ The|the|DT|_ cells|cell|NNS|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ culture|culture|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ with|with|IN|_ a|a|DT|_ solution|solution|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ .|.|.|_ The|the|DT|_ suspended|suspend|VBN|_ cells|cell|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ saturated|saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 60|60|CD|_ C|c|NN|_ .|.|.|_ The|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ and|and|CC|_ DNA|dna|NN|_ were|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ ethanol|ethanol|NN|_ from|from|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ DNase|dnase|NN|_ I|i|CD|_ buffer|buffer|NN|_ with|with|IN|_ 10U|10u|NN|_ of|of|IN|_ DNaseI|dnasei|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ separated|separate|VBN|_ from|from|IN|_ the|the|DT|_ digested|digest|VBN|_ DNA|dna|NN|_ by|by|IN|_ acidic|acidic|JJ|_ phenol|phenol|NN|_ extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ G-50|G-50|NNP|_ Micro|Micro|NNP|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ GE|GE|NNP|_ Healthcare|Healthcare|NNP|_ -RRB-|-rrb-|-RRB-|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ precipitated|precipitate|VBD|_ with|with|IN|_ ethanol|ethanol|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ diethylpyrocarbonate-treated|diethylpyrocarbonate-treated|JJ|_ water|water|NN|_ and|and|CC|_ used|use|VBN|_ for|for|IN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ .|.|.|_
mRNA-seq|mrna-seq|NN|_ with|with|IN|_ barcode|barcode|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Index|Index|NNP|_ 1-5|1-5|CD|_ -RRB-|-rrb-|-RRB-|_
mrna|mrna|NN|_ synthesis|synthesis|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_ MgCl2|mgcl2|NN|_
mrna|mrna|NN|_ synthesis|synthesis|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_ MgCl2|mgcl2|NN|_ +|+|CC|_ GreAB|greab|NN|_
mrna|mrna|NN|_ synthesis|synthesis|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_ MnCl2|mncl2|NN|SUPP
mrna|mrna|NN|_ synthesis|synthesis|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_ MnCl2|mncl2|NN|SUPP +|+|CC|_ GreAB|greab|NN|_
mrna|mrna|NN|_ synthesis|synthesis|NN|_ :|:|:|_ in|in|FW|_ vivo|vivo|FW|_
RNA-Seq|rna-seq|NN|_
standard|standard|NN|_ in|in|FW|_ vitro|vitro|FW|_ -LRB-|-lrb-|-LRB-|_ Mg2|mg2|NN|_ +|+|CC|_ -RRB-|-rrb-|-RRB-|_
standard|standard|NN|_ in|in|FW|_ vitro|vitro|FW|_ MgCl2|mgcl2|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ of|of|IN|_ transition|transition|NN|_ error|error|NN|_ rate|rate|NN|_ per|per|IN|_ position|position|NN|_ .|.|.|_ The|the|DT|_ position|position|NN|_ is|be|VBZ|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ \|\|CD|_ Sequenced|sequence|VBN|_ region|region|NN|_ of|of|IN|_ pPR9|ppr9|NN|_ plasmid|plasmid|NN|_ \|\|NN|_ -LRB-|-lrb-|-LRB-|_ one|one|CD|_ of|of|IN|_ the|the|DT|_ attached|attach|VBN|_ txt|txt|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ cells|cell|NNS|_ culture|culture|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ with|with|IN|_ a|a|DT|_ solution|solution|NN|_ containing|contain|VBG|_ 0.5|0.5|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 20|20|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ .|.|.|_ The|the|DT|_ suspended|suspend|VBN|_ cells|cell|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ saturated|saturated|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ pH|ph|NN|_ 5.5|5.5|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 60|60|CD|_ ˚C|˚c|NN|_ .|.|.|_
The|the|DT|_ numbers|number|NNS|_ of|of|IN|_ 4|4|CD|_ bases|basis|NNS|_ A|a|DT|_ ,|,|,|_ T|t|NN|_ ,|,|,|_ G|g|NN|_ ,|,|,|_ C|c|NN|_ ,|,|,|_ and|and|CC|_ N|n|NN|_ were|be|VBD|_ counted|count|VBN|_ in|in|IN|_ each|each|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ mapped|map|VBN|_ reads|read|VBZ|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ program|program|NN|_ SAMtools|samtool|NNS|_ 0.1.18|0.1.18|CD|_ with|with|IN|_ supplemental|supplemental|JJ|_ use|use|NN|_ of|of|IN|_ a|a|DT|_ Perl|Perl|NNP|_ script|script|NN|_ .|.|.|_
The|the|DT|_ obtained|obtain|VBN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ pPR9|ppr9|NN|_ plasmid|plasmid|NN|_ DNA|dna|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 0.12.7|0.12.7|CD|_ .|.|.|_
We|we|PRP|_ established|establish|VBD|_ a|a|DT|_ method|method|NN|_ for|for|IN|_ preparing|prepare|VBG|_ five|five|CD|_ different|different|JJ|_ cDNA|cdna|NN|_ libraries|library|NNS|_ each|each|DT|_ with|with|IN|_ its|its|PRP$|_ own|own|JJ|_ barcode|barcode|NN|_ for|for|IN|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ .|.|.|_ Each|each|DT|_ 6-nt|6-nt|JJ|_ barcode|barcode|NN|_ allows|allow|VBZ|_ multiplexing|multiplex|VBG|_ all|all|DT|_ five|five|CD|_ in|in|FW|_ vitro|vitro|FW|_ and|and|CC|_ in|in|FW|_ vivo|vivo|FW|_ preparations|preparation|NNS|_ in|in|IN|_ a|a|DT|_ single|single|JJ|_ sequencing|sequencing|NN|_ analysis|analysis|NN|_ .|.|.|_ our|we|PRP$|_ method|method|NN|_ introduces|introduce|VBZ|_ internal|internal|JJ|_ control|control|NN|_ sequences|sequence|NNS|_ to|to|TO|_ the|the|DT|_ library|library|NN|_ that|that|WDT|_ are|be|VBP|_ subjected|subject|VBN|_ to|to|TO|_ the|the|DT|_ artifact|artifact|NN|_ errors|error|NNS|_ ,|,|,|_ but|but|CC|_ are|be|VBP|_ not|not|RB|_ for|for|IN|_ RNAP|rnap|NN|_ errors|error|NNS|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ '|'|''|_ fragment|fragment|NN|_ of|of|IN|_ the|the|DT|_ 5.7|5.7|CD|_ kb|kb|NN|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ was|be|VBD|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ to|to|TO|_ make|make|VB|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ PCR|pcr|NN|_ reactions|reaction|NNS|_ that|that|WDT|_ generated|generate|VBD|_ six|six|CD|_ 200|200|CD|_ bp|bp|NN|_ segments|segment|NNS|_ .|.|.|_ The|the|DT|_ primers|primer|NNS|_ contained|contain|VBD|_ a|a|DT|_ specific|specific|JJ|_ barcode|barcode|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ five|five|CD|_ starting|start|VBG|_ preparations|preparation|NNS|_ and|and|CC|_ the|the|DT|_ inner|inner|JJ|_ Illuminasequencing|illuminasequencing|NN|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ 2nd-step|2nd-step|NN|_ of|of|IN|_ PCR|pcr|NN|_ generated|generate|VBD|_ the|the|DT|_ final|final|JJ|_ cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ 1st-step|1st-step|JJ|_ PCR|pcr|NN|_ product|product|NN|_ as|as|IN|_ a|a|DT|_ template|template|NN|_ and|and|CC|_ primers|primer|NNS|_ containing|contain|VBG|_ the|the|DT|_ outer|outer|JJ|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ in|in|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ tails|tail|NNS|_ .|.|.|_
At|at|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ ,|,|,|_ a|a|DT|_ one-eighth|one-eighth|NN|_ volume|volume|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ v|v|LS|_
E.|E.|NNP|_ coli|coli|NN|_ batch|batch|NN|_ culture|culture|NN|_ without|without|IN|_ TAP|tap|NN|_
E.|e.|FW|_ coli|coli|FW|_ batch|batch|NN|_ culture|culture|NN|_ with|with|IN|_ TAP|tap|NN|_
E.|e.|FW|_ coli|coli|FW|_ -|-|:|_ TAP|tap|NN|_
E.|e.|FW|_ coli|coli|FW|_ +|+|CC|_ TAP|tap|FW|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ -LRB-|-lrb-|-LRB-|_ Datsenko|Datsenko|NNP|_ &|&|CC|_ Wanner|Wanner|NNP|_ 2000|2000|CD|_ .|.|.|_ PNAS|PNAS|NNP|_ 97|97|CD|_ :|:|:|_ 6640|6640|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ cultivated|cultivate|VBN|_ in|in|IN|_ 100|100|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Miller|Miller|NNP|_ 1972|1972|CD|_ .|.|.|_ In|in|IN|_ :|:|:|_ Experiments|experiment|NNS|_ in|in|IN|_ molecular|molecular|JJ|_ genetics|genetics|NNS|_ .|.|.|_ Cold|Cold|NNP|_ Spring|Spring|NNP|_ Harbor|Harbor|NNP|_ Laboratory|Laboratory|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ mL|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ an|a|DT|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ 0.6|0.6|CD|_ .|.|.|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ YEME|yeme|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ until|until|IN|_ the|the|DT|_ mycelia|mycelia|NN|_ became|become|VBD|_ pigmented|pigmented|JJ|_ .|.|.|_
For|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 4|4|CD|_ libraries|library|NNS|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ bacterial|bacterial|JJ|_ samples|sample|NNS|_ x|x|CC|_ 2|2|CD|_ treatments|treatment|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ times|time|NNS|_ each|each|DT|_ nucleotide|nucleotide|NN|_ position|position|NN|_ was|be|VBD|_ the|the|DT|_ first|first|JJ|_ in|in|IN|_ a|a|DT|_ sequence|sequence|NN|_ read|read|VBN|_ using|use|VBG|_ a|a|DT|_ simple|simple|JJ|_ script|script|NN|_ -LRB-|-lrb-|-LRB-|_ unpubl|unpubl|NN|_ .|.|.|_ resource|resource|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ were|be|VBD|_ then|then|RB|_ processed|process|VBN|_ separately|separately|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ The|the|DT|_ reference|reference|NN|_ genomes|genome|NNS|_ used|use|VBN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ BW25113|bw25113|NN|_ and|and|CC|_ S.|S.|NNP|_ coelicolor|coelicolor|VBP|_ A3|a3|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ M145|m145|NN|_ were|be|VBD|_ U00096|u00096|NN|_ .2|.2|NN|_ and|and|CC|_ AL645882|al645882|NN|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
genotype|genotype|NN|_ :|:|:|_ wild-type|wild-type|JJ|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -LRB-|-lrb-|-LRB-|_ www.vertis-biotech.com|www.vertis-biotech.com|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ a|a|DT|_ service|service|NN|_ that|that|WDT|_ included|include|VBD|_ treating|treat|VBG|_ an|a|DT|_ aliquot|aliquot|NN|_ of|of|IN|_ each|each|DT|_ RNA|rna|NN|_ sample|sample|NN|_ with|with|IN|_ TAP|tap|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ sequencing|sequencing|NN|_ adaptor|adaptor|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ transcripts|transcript|NNS|_ prior|prior|RB|_ to|to|TO|_ fragmentation|fragmentation|NN|_ ,|,|,|_ thereby|thereby|RB|_ allowing|allow|VBG|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|NNS|_ of|of|IN|_ both|both|DT|_ long|long|JJ|_ and|and|CC|_ short|short|JJ|_ transcripts|transcript|NNS|_ to|to|TO|_ be|be|VB|_ detected|detect|VBN|_ .|.|.|_ Each|each|DT|_ of|of|IN|_ the|the|DT|_ 4|4|CD|_ libraries|library|NNS|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ a|a|DT|_ different|different|JJ|_ barcode|barcode|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ sequences|sequence|NNS|_ from|from|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ two|two|CD|_ differential|differential|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ processed|process|VBN|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ corresponding|corresponding|JJ|_ genomes|genome|NNS|_ as|as|IN|_ a|a|DT|_ service|service|NN|_ provided|provide|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -LRB-|-lrb-|-LRB-|_ www.vertis-biotech.com|www.vertis-biotech.com|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ This|this|DT|_ involved|involved|JJ|_ trimming|trim|VBG|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ masking|mask|VBG|_ for|for|IN|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ .|.|.|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ pellet|pellet|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ using|use|VBG|_ a|a|DT|_ well-established|well-established|JJ|_ ,|,|,|_ published|publish|VBN|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ 2008|2008|CD|_ .|.|.|_ In|in|IN|_ RNA|rna|NN|_ Turnover|turnover|NN|_ in|in|IN|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Archaea|Archaea|NNP|_ and|and|CC|_ Organelles|Organelles|NNP|_ ,|,|,|_ Vol|Vol|NNP|_ 447|447|CD|_ -LRB-|-lrb-|-LRB-|_ ed|ed|VBN|_ .|.|.|_ LE|LE|NNP|_ Maquat|Maquat|NNP|_ ,|,|,|_ CM|cm|NN|_ Arraiano|arraiano|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pp.|pp.|NN|_ 215|215|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ of|of|IN|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ Kirby|Kirby|NNP|_ mix|mix|NN|_ -LRB-|-lrb-|-LRB-|_ Kieser|Kieser|NNP|_ et|et|FW|_ al.|al.|FW|_ 2000|2000|CD|_ .|.|.|_ Practical|Practical|NNP|_ Streptomyces|Streptomyces|NNP|_ Genetics|Genetics|NNP|_ .|.|.|_ The|the|DT|_ John|John|NNP|_ Innes|Innes|NNP|_ Foundation|Foundation|NNP|_ ,|,|,|_ Norwich|Norwich|NNP|_ .|.|.|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ µL|µl|NN|_ per|per|IN|_ 1|1|CD|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ unit|unit|NN|_ ,|,|,|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ Lysing|lyse|VBG|_ Matrix|Matrix|NNP|_ B|B|NNP|_ tubes|tube|NNS|_ containing|contain|VBG|_ fine|fine|JJ|_ silica|silica|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Tubes|tube|NNS|_ were|be|VBD|_ then|then|RB|_ placed|place|VBN|_ in|in|IN|_ a|a|DT|_ high-speed|high-speed|JJ|_ benchtop|benchtop|NN|_ homogenizer|homogenizer|NN|_ -LRB-|-lrb-|-LRB-|_ Fastprep-24|fastprep-24|NN|_ ,|,|,|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ;|;|:|_ set|set|VBN|_ at|at|IN|_ 6.5|6.5|CD|_ M|m|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BedGraphs|bedgraph|NNS|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ TAP|tap|NN|_ treatment|treatment|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_
The|the|DT|_ sample|sample|NN|_ sources|source|NNS|_ of|of|IN|_ individual|individual|JJ|_ reads|read|VBZ|_ were|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ the|the|DT|_ barcoding|barcoding|NN|_ .|.|.|_ The|the|DT|_ barcodes|barcode|NNS|_ for|for|IN|_ the|the|DT|_ minus|minus|NN|_ and|and|CC|_ plus|plus|CC|_ TAP|tap|NN|_ treatments|treatment|NNS|_ were|be|VBD|_ ACTTGA|ACTTGA|NNP|_ and|and|CC|_ CGATGT|CGATGT|NNP|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ for|for|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ RNA|rna|NN|_ ,|,|,|_ and|and|CC|_ CAGATC|CAGATC|NNP|_ and|and|CC|_ ATCACG|ATCACG|NNP|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ for|for|IN|_ the|the|DT|_ S.|S.|NNP|_ coelicolor|coelicolor|NN|_ RNA|rna|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
treatment|treatment|NN|_ :|:|:|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_
Cells|cell|NNS|_ at|at|IN|_ appropriate|appropriate|JJ|_ cell|cell|NN|_ density|density|NN|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ by|by|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 25|25|CD|_ min|min|NN|_ .|.|.|_ Following|follow|VBG|_ quenching|quench|VBG|_ the|the|DT|_ unused|unused|JJ|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 125|125|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ Buffered|buffer|VBN|_ Saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ washed|wash|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ composed|compose|VBN|_ of|of|IN|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ ug|ug|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-c-myc|anti-c-myc|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-FecI|anti-feci|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RpoB|anti-rpob|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RpoD|anti-rpod|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RpoF|anti-rpof|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RpoN|anti-rpon|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RpoS|anti-rpos|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ manufacturer|manufacturer|NN|_ :|:|:|_ Upstate|upstate|JJ|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ -LRB-|-lrb-|-LRB-|_ Upstate|upstate|JJ|_ -RRB-|-rrb-|-RRB-|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ RNAP|rnap|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ anti-RpoB|anti-rpob|JJ|_ antibody|antibody|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ RNAP|rnap|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ using|use|VBG|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ .|.|.|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ FecI|FecI|NNP|_ ChIP|ChIP|NNP|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ FecI|FecI|NNP|_ ChIP|ChIP|NNP|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ FecI|FecI|NNP|_ ChIP|ChIP|NNP|_ DNA|DNA|NNP|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ FecI|FecI|NNP|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ FecI|FecI|NNP|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ FecI|FecI|NNP|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ DelN|deln|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ DelN|deln|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ DelN|deln|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoD|rpod|NN|_ DelN|deln|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoF|rpof|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoF|rpof|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoF|rpof|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoF|rpof|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoF|rpof|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoF|rpof|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Exponential|Exponential|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Glutamine|Glutamine|NNP|_ RpoN|rpon|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Heatshock|Heatshock|NNP|_ RpoH|rpoh|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Iron|Iron|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Iron|Iron|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Iron|Iron|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Iron|Iron|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoB|rpob|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ DelS|dels|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ DelS|dels|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ DelS|dels|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoD|rpod|NN|_ DelS|dels|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ 3|3|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 1|1|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 2|2|CD|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Stationary|Stationary|NNP|_ RpoS|rpos|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ minimal|minimal|JJ|_ M9|m9|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ minimal|minimal|JJ|_ W2|w2|NN|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ rpoH-8myc|rpoh-8myc|NN|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
genotype|genotype|NN|_ :|:|:|_ ΔrpoN|δrpon|NN|_
genotype|genotype|NN|_ :|:|:|_ ΔrpoS|δrpos|NN|_
The|the|DT|_ raw|raw|JJ|_ pair|pair|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ txt|txt|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ per|per|IN|_ channel|channel|NN|_ quantile|quantile|NN|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 19|19|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 185|185|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ IP|IP|NNP|_
Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ media|media|NNS|_ ,|,|,|_ with|with|IN|_ 42oC|42oc|NN|_ heatshock|heatshock|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
Cells|cell|NNS|_ at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ W2|w2|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_
Cells|cell|NNS|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP media|media|NNS|_
E.|e.|FW|_ coli|coli|FW|_ glutamine|glutamine|NN|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ glutamine|glutamine|NN|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ heatshock|heatshock|NN|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ heatshock|heatshock|NN|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ W2|w2|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glutamine|glutamine|NN|_ .|.|.|_ For|for|IN|_ heatshock|heatshock|NN|_ conditions|condition|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 42oC|42oc|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ stationary|stationary|JJ|_ 1|1|CD|_
E.|e.|FW|_ coli|coli|FW|_ stationary|stationary|JJ|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
RNA-Seq|rna-seq|NN|_
Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ counts|count|NNS|_
The|the|DT|_ amplified|amplify|VBN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ .|.|.|_ Sequence|sequence|NN|_ reads|read|VBZ|_ for|for|IN|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ aligned|align|VBN|_ onto|onto|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ ,|,|,|_ using|use|VBG|_ Mosaik|mosaik|NN|_ with|with|IN|_ following|follow|VBG|_ arguments|argument|NNS|_ :|:|:|_ hash|hash|VB|_ size|size|NN|_ =|=|JJ|_ 10|10|CD|_ ,|,|,|_ mismatch|mismatch|NN|_ =|=|JJ|_ 0|0|CD|_ .|.|.|_ Only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ unique|unique|JJ|_ genomic|genomic|JJ|_ location|location|NN|_ were|be|VBD|_ retained|retain|VBN|_ .|.|.|_ Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_ Among|among|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ ,|,|,|_ only|only|RB|_ TSSs|tsss|NNS|_ with|with|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ within|within|IN|_ 10|10|CD|_ bp|bp|NN|_ window|window|NN|_ were|be|VBD|_ kept|keep|VBN|_ to|to|TO|_ remove|remove|VB|_ possible|possible|JJ|_ noise|noise|NN|_ signals|signal|NNS|_ ,|,|,|_ and|and|CC|_ TSSs|tsss|NNS|_ with|with|IN|_ greater|greater|JJR|_ than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ strongest|strongest|JJS|_ signal|signal|NN|_ upstream|upstream|RB|_ of|of|IN|_ an|a|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ considered|consider|VBN|_ as|as|IN|_ multiple|multiple|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ mRNA|mrna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ each|each|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ 5|5|CD|_ '|'|''|_ Phosphate|Phosphate|NNP|_ Dependent|Dependent|NNP|_ Exonuclease|Exonuclease|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ enrich|enrich|VB|_ 5|5|CD|_ '|'|''|_ tri-phosphorylated|tri-phosphorylated|JJ|_ mRNAs|mrna|NNS|_ .|.|.|_ Intact|intact|JJ|_ tri-phosphorylated|tri-phosphorylated|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNA|rna|NN|_ 5|5|CD|_ '|'|''|_ -|-|:|_ Polyphosphatase|polyphosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ 5|5|CD|_ '|'|''|_ -|-|:|_ end|end|VB|_ monophosphorylated|monophosphorylate|VBN|_ RNA|rna|NN|_ for|for|IN|_ ligation|ligation|NN|_ to|to|TO|_ RNA|rna|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ cDNAs|cdna|NNS|_ were|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ the|the|DT|_ adaptor-ligated|adaptor-ligated|JJ|_ mRNAs|mrna|NNS|_ as|as|IN|_ template|template|NN|_ using|use|VBG|_ a|a|DT|_ modified|modify|VBN|_ small|small|JJ|_ RNA|rna|NN|_ RT|rt|NN|_ primer|primer|NN|_ from|from|IN|_ Illumina|Illumina|NNP|_ and|and|CC|_ Superscript|Superscript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ samples|sample|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ ,|,|,|_ and|and|CC|_ size|size|NN|_ fractionated|fractionate|VBN|_ from|from|IN|_ 100|100|CD|_ to|to|TO|_ 300|300|CD|_ bp|bp|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ glutamine|glutamine|NN|_
treatment|treatment|NN|_ :|:|:|_ heat|heat|NN|_ shock|shock|NN|_
treatment|treatment|NN|_ :|:|:|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ processed|process|VBN|_ seperatedly|seperatedly|RB|_ ,|,|,|_ and|and|CC|_ only|only|RB|_ sequence|sequence|NN|_ reads|read|VBZ|_ presented|present|VBN|_ in|in|IN|_ both|both|CC|_ biological|biological|JJ|_ replciates|replciate|NNS|_ were|be|VBD|_ considered|consider|VBN|_ for|for|IN|_ further|further|JJ|_ process|process|NN|_ .|.|.|_ The|the|DT|_ genomic|genomic|JJ|_ coordinates|coordinate|VBZ|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ of|of|IN|_ these|these|DT|_ uniquely|uniquely|RB|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ potential|potential|JJ|_ TSSs|tsss|NNS|_ .|.|.|_
35381|35381|CD|_ _|_|NN|_ 1|1|CD|_
35382|35382|CD|_ _|_|NN|_ 2|2|CD|_
DNA|dna|NN|_ were|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ purified|purify|VBN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ Muniesa|Muniesa|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2003|2003|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Shiga|shiga|NN|_ toxin|toxin|NN|_ 2-converting|2-converting|JJ|_ bacteriophages|bacteriophage|NNS|_ associated|associate|VBN|_ with|with|IN|_ clonal|clonal|JJ|_ variability|variability|NN|_ in|in|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strains|strain|NNS|_ of|of|IN|_ human|human|JJ|_ origin|origin|NN|_ isolated|isolate|VBN|_ from|from|IN|_ a|a|DT|_ single|single|JJ|_ outbreak|outbreak|NN|_ .|.|.|_ Infect|infect|VB|_ Immun|Immun|NNP|_ 71|71|CD|_ ,|,|,|_ 4554-4562|4554-4562|CD|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ 3538|3538|CD|_ #|#|#|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 3538|3538|CD|_ #|#|#|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ 3538|3538|CD|_ _|_|SYM|_ 2x|2x|FW|_ _|_|FW|_ v2|v2|FW|_
E.|e.|FW|_ coli|coli|FW|_ 3538|3538|CD|_ #|#|#|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ 3538|3538|CD|_ _|_|SYM|_ 3x|3x|FW|_ _|_|FW|_ v2|v2|FW|_
ecoli|ecolus|NNS|_ _|_|VBP|_ 3538|3538|CD|_ _|_|SYM|_ 4x|4x|FW|_ _|_|FW|_ v2|v2|FW|_
E.|e.|FW|_ coli|coli|FW|_ D1|d1|NN|_ #|#|#|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ D1|d1|NN|_ #|#|#|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ D1|d1|NN|_ _|_|SYM|_ 2x|2x|FW|_ _|_|FW|_ v2|v2|FW|_
E.|e.|FW|_ coli|coli|FW|_ D1|d1|NN|_ #|#|#|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ D1|d1|NN|_ _|_|SYM|_ 3x|3x|FW|_ _|_|FW|_ v2|v2|FW|_
ecoli|ecolus|NNS|_ _|_|VBP|_ D1|d1|NN|_ _|_|SYM|_ 4x|4x|FW|_ _|_|FW|_ v2|v2|FW|_
E.|e.|FW|_ coli|coli|FW|_ EDL933|edl933|NN|_ #|#|#|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ EDL933|edl933|NN|_ #|#|#|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ EDL933|edl933|NN|_ _|_|SYM|_ 2x|2x|FW|_ _|_|FW|_ v2|v2|FW|_
E.|e.|FW|_ coli|coli|FW|_ EDL933|edl933|NN|_ #|#|#|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ EDL933|edl933|NN|_ _|_|SYM|_ 3x|3x|FW|_ _|_|FW|_ v2|v2|FW|_
ecoli|ecolus|NNS|_ _|_|VBP|_ EDL933|edl933|NN|_ _|_|SYM|_ 4x|4x|FW|_ _|_|FW|_ v2|v2|FW|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ W3110|w3110|NN|_ #|#|#|_ 1|1|CD|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ W3110|w3110|NN|_ #|#|#|_ 2|2|CD|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ W3110|w3110|NN|_ #|#|#|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ phage|phage|NN|_ 3538|3538|CD|_ #|#|#|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ phage|phage|NN|_ 3538|3538|CD|_ #|#|#|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ W3110|w3110|NN|_ _|_|SYM|_ 2x|2x|FW|_ _|_|FW|_ v2|v2|FW|_
ecoli|ecolus|NNS|_ _|_|VBP|_ W3110|w3110|NN|_ _|_|SYM|_ 3x|3x|FW|_ _|_|FW|_ v2|v2|FW|_
ecoli|ecolus|NNS|_ _|_|VBP|_ W3110|w3110|NN|_ _|_|SYM|_ 4x|4x|FW|_ _|_|FW|_ v2|v2|FW|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Induced|induce|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ 3538|3538|CD|_ with|with|IN|_ mitomycin|mitomycin|NN|_ C|c|NN|_
Isolate|isolate|VB|_ W3110|w3110|NN|_ of|of|IN|_ K-12|k-12|NN|_ strain|strain|NN|_
overnight|overnight|JJ|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ with|with|IN|_ continuous|continuous|JJ|_ agitation|agitation|NN|_
phage|phage|NN|_ DNA|dna|NN|_
Qiagen|Qiagen|NNP|_ Genomic|genomic|JJ|_ Tip|tip|NN|_ 500|500|CD|_
serotype|serotype|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
serotype|serotype|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
serotype|serotype|NN|_ O175|o175|NN|_ :|:|:|_ H16|h16|NN|_
Standard|standard|JJ|_ Affymetrix|Affymetrix|NNP|_ procedure|procedure|NN|_
40|40|CD|_ hours|hour|NNS|_ 1|1|CD|_
40|40|CD|_ hours|hour|NNS|_ 2|2|CD|_
40|40|CD|_ hours|hour|NNS|_ 3|3|CD|_
40|40|CD|_ hours|hour|NNS|_ cultivation|cultivation|NN|_ in|in|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ mineral|mineral|JJ|_ medium|medium|NN|_ with|with|IN|_ 100|100|CD|_ mg|mg|NN|_
40|40|CD|_ hours|hour|NNS|_ of|of|IN|_ cultivation|cultivation|NN|_ in|in|IN|_ continuous|continuous|JJ|_ colture|colture|NN|_ -LRB-|-lrb-|-LRB-|_ mineral|mineral|JJ|_ medium|medium|NN|_ with|with|IN|_ 100|100|CD|_ mg|mg|NN|_
500|500|CD|_ hours|hour|NNS|_ 1|1|CD|_
500|500|CD|_ hours|hour|NNS|_ 2|2|CD|_
500|500|CD|_ hours|hour|NNS|_ 3|3|CD|_
500|500|CD|_ hours|hour|NNS|_ of|of|IN|_ cultivation|cultivation|NN|_ in|in|IN|_ continuous|continuous|JJ|_ colture|colture|NN|_ -LRB-|-lrb-|-LRB-|_ mineral|mineral|JJ|_ medium|medium|NN|_ with|with|IN|_ 100|100|CD|_ mg|mg|NN|_
Batch|batch|NN|_ growth|growth|NN|_ in|in|IN|_ mineral|mineral|JJ|_ medium|medium|NN|_ supplied|supply|VBN|_ with|with|IN|_ 4|4|CD|_ g|g|NN|_
control|control|NN|_
Control|Control|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Sample|sample|NN|_
The|the|DT|_ data|datum|NNS|_ provided|provide|VBN|_ are|be|VBP|_ the|the|DT|_ original|original|JJ|_ data|datum|NNS|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ Jaguar|Jaguar|NNP|_ software|software|NN|_ from|from|IN|_ the|the|DT|_ microarray|microarray|NN|_ images|image|NNS|_ .|.|.|_ The|the|DT|_ VALUEs|value|NNS|_ reported|report|VBD|_ represent|represent|VBP|_ log10|log10|NN|_ -LRB-|-lrb-|-LRB-|_ Cy5|cy5|NN|_
Cells|cell|NNS|_ used|use|VBN|_ for|for|IN|_ expression|expression|NN|_ analysis|analysis|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Glansdorff|glansdorff|FW|_ ,|,|,|_ 1965|1965|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ w|w|NN|_
E.Coli|e.coli|NNS|_ ,|,|,|_ strain|strain|NN|_ P4XB2|p4xb2|NN|_ mutant|mutant|NN|_ ,|,|,|_ grown|grow|VBN|_ in|in|IN|_ presence|presence|NN|_ of|of|IN|_ arginine|arginine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
E.Coli|e.coli|NNS|_ ,|,|,|_ strain|strain|NN|_ P4X|p4x|NN|_ ,|,|,|_ grown|grow|VBN|_ in|in|IN|_ presence|presence|NN|_ of|of|IN|_ arginine|arginine|NN|SUPP -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ug|ug|NN|_
E.Coli|e.coli|NNS|_ ,|,|,|_ strain|strain|NN|_ P4X|p4x|NN|_ ,|,|,|_ grown|grow|VBN|_ on|on|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ ,|,|,|_ reference|reference|NN|_ sample|sample|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Initial|initial|JJ|_ data|data|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ GeneChip|GeneChip|NNP|_ ®|®|NNP|_ Operating|Operating|NNP|_ Software|Software|NNP|_ .|.|.|_ Microarray|microarray|NN|_ quality|quality|NN|_ control|control|NN|_ parameters|parameter|NNS|_ were|be|VBD|_ as|as|IN|_ follow|follow|VB|_ :|:|:|_ noise|noise|NN|_ -LRB-|-lrb-|-LRB-|_ RawQ|rawq|NN|_ -RRB-|-rrb-|-RRB-|_ less|less|JJR|_ than|than|IN|_ 5|5|CD|_ ,|,|,|_ background|background|NN|_ signal|signal|NN|_ less|less|JJR|_ than|than|IN|_ 40|40|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ target|target|NN|_ intensity|intensity|NN|_ for|for|IN|_ array|array|NN|_ scaling|scaling|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ consistent|consistent|JJ|_ numbers|number|NNS|_ of|of|IN|_ genes|gene|NNS|_ detected|detect|VBN|_ as|as|IN|_ present|present|JJ|_ across|across|IN|_ arrays|array|NNS|_ .|.|.|_
P4XB2|p4xb2|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Arginine|arginine|NN|_
P4XB2|p4xb2|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ 1993|1993|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Arginine|arginine|NN|_
P4XB2|p4xb2|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ 1994|1994|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Arginine|arginine|NN|_
P4X|p4x|NN|_ Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ 1753|1753|CD|_ -RRB-|-rrb-|-RRB-|_ Reference|Reference|NNP|_
P4X|P4X|NNP|_ Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ 1754|1754|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Arginine|arginine|NN|_
P4X|p4x|NN|_ Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ 1765|1765|CD|_ -RRB-|-rrb-|-RRB-|_ Reference|Reference|NNP|_
P4X|P4X|NNP|_ Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ 1766|1766|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Arginine|arginine|NN|_
P4X|p4x|NN|_ Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ 1989|1989|CD|_ -RRB-|-rrb-|-RRB-|_ Reference|Reference|NNP|_
P4X|P4X|NNP|_ Wild|Wild|NNP|_ Type|type|NN|_ -LRB-|-lrb-|-LRB-|_ 1990|1990|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Arginine|arginine|NN|_
Strain|strain|NN|_ P4X|p4x|NN|_ ,|,|,|_ grown|grow|VBN|_ on|on|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ ,|,|,|_ reference|reference|NN|_ sample|sample|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RNeasy|rneasy|NN|_ ®|®|NN|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ specifications|specification|NNS|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ in|in|IN|_ RNase-free|rnase-free|JJ|_ water|water|NN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ .|.|.|_ RNA|rna|NN|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ UV-spectrometry|uv-spectrometry|NN|_ and|and|CC|_ its|its|PRP$|_ quality|quality|NN|_ controlled|control|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_
BW25113-pCA24N|bw25113-pca24n|NN|_
BW25113-pCA24N|bw25113-pca24n|NN|_ _|_|CD|_ dosP|dosp|NN|GEN
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ -LRB-|-lrb-|-LRB-|_ Biospec|biospec|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ mRNA|mrna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RNALater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ ethanol-dry|ethanol-dry|JJ|_ ice|ice|NN|_ .|.|.|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ GenomeChipOperating|GenomeChipOperating|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ GCOS|GCOS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
genotype|genotype|NN|_
overexpression|overexpression|NN|_ of|of|IN|_ dosP|dosp|NN|GEN -LRB-|-lrb-|-LRB-|_ pCA24N|pca24n|NN|_ _|_|CD|_ dosP|dosp|NN|GEN -RRB-|-rrb-|-RRB-|_
overexpression|overexpression|NN|_ of|of|IN|_ empty|empty|JJ|_ vector|vector|NN|_ -LRB-|-lrb-|-LRB-|_ pCA24N|pca24n|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LBCm30|lbcm30|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_ 16|16|CD|_ h|h|NN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ at|at|IN|_ 1:1000|1:1000|CD|_ into|into|IN|_ fresh|fresh|JJ|_ LBCm30|lbcm30|NN|_ ,|,|,|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ ~|~|NN|_ 1.0|1.0|CD|_ ,|,|,|_ and|and|CC|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ for|for|IN|_ 90|90|CD|_ min|min|NN|_ .|.|.|_
1-butanol|1-butanol|NN|_ was|be|VBD|_ added|add|VBN|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.9|0.9|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol|vol|NN|_
A0-A1|a0-a1|NN|_ _|_|CD|_ rep1|rep1|NN|_ _|_|VBD|_ a|a|DT|_
A0-A1|a0-a1|NN|_ _|_|CD|_ rep1|rep1|NN|_ _|_|NN|_ b|b|NN|_
A0-A1|a0-a1|NN|_ _|_|CD|_ rep2|rep2|NN|_ _|_|VBD|_ a|a|DT|_
A0-A1|a0-a1|NN|_ _|_|CD|_ rep2|rep2|NN|_ _|_|NN|_ b|b|NN|_
A0-A1|a0-a1|NN|_ _|_|CD|_ rep3|rep3|NN|_ _|_|VBD|_ a|a|DT|_
A0-A1|a0-a1|NN|_ _|_|CD|_ rep3|rep3|NN|_ _|_|NN|_ b|b|NN|_
A0-E0|a0-e0|NN|_ _|_|CD|_ rep1|rep1|NN|_ _|_|VBD|_ a|a|DT|_
A0-E0|a0-e0|NN|_ _|_|CD|_ rep1|rep1|NN|_ _|_|NN|_ b|b|NN|_
A0-E0|a0-e0|NN|_ _|_|CD|_ rep2|rep2|NN|_ _|_|VBD|_ a|a|DT|_
A0-E0|a0-e0|NN|_ _|_|CD|_ rep2|rep2|NN|_ _|_|NN|_ b|b|NN|_
A0-E0|a0-e0|NN|_ _|_|CD|_ rep3|rep3|NN|_ _|_|VBD|_ a|a|DT|_
A0-E0|a0-e0|NN|_ _|_|CD|_ rep3|rep3|NN|_ _|_|NN|_ b|b|NN|_
Background|background|NN|_ correction|correction|NN|_ and|and|CC|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ print-tip|print-tip|JJ|_ loess|loess|NN|_ and|and|CC|_ quantile|quantile|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ limma|limma|NN|_ R|r|NN|_ package|package|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED until|until|IN|_ OD600|od600|NN|_ reached|reach|VBD|_ ~|~|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E0-E1|e0-e1|NN|_ _|_|CD|_ rep1|rep1|NN|_ _|_|VBD|_ a|a|DT|_
E0-E1|e0-e1|NN|_ _|_|CD|_ rep1|rep1|NN|_ _|_|NN|_ b|b|NN|_
E0-E1|e0-e1|NN|_ _|_|CD|_ rep2|rep2|NN|_ _|_|VBD|_ a|a|DT|_
E0-E1|e0-e1|NN|_ _|_|CD|_ rep2|rep2|NN|_ _|_|NN|_ b|b|NN|_
E0-E1|e0-e1|NN|_ _|_|CD|_ rep3|rep3|NN|_ _|_|VBD|_ a|a|DT|_
E0-E1|e0-e1|NN|_ _|_|CD|_ rep3|rep3|NN|_ _|_|NN|_ b|b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mutant|mutant|JJ|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ after|after|IN|_ butanol|butanol|NN|_ treatment|treatment|NN|_
mutant|mutant|JJ|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ before|before|IN|_ butanol|butanol|NN|_ treatment|treatment|NN|_
protocol|protocol|NN|_ :|:|:|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ ,|,|,|_ LB|lb|NN|_
protocol|protocol|NN|_ :|:|:|_ late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ ,|,|,|_ LB|lb|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ after|after|IN|_ butanol|butanol|NN|_ treatment|treatment|NN|_
Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ column|column|NN|_
strain|strain|NN|_ :|:|:|_ KCTC|KCTC|NNP|_ 2571|2571|CD|_
strain|strain|NN|_ :|:|:|_ PKH5000|pkh5000|NN|_
wt|wt|JJ|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ after|after|IN|_ butanol|butanol|NN|_ treatment|treatment|NN|_
wt|wt|JJ|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ before|before|IN|_ butanol|butanol|NN|_ treatment|treatment|NN|_
Algorithm|Algorithm|NNP|_ :|:|:|_ ExpressionStat|ExpressionStat|NNP|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ Affymetrix|Affymetrix|NNP|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ Version|Version|NNP|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_
APEC|APEC|NNP|_ strain|strain|NN|_ O08|o08|NN|_
APEC|apec|NN|_ strain|strain|NN|_ SCI-07|sci-07|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O08|o08|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism SCI-07|sci-07|NN|_
growth|growth|NN|_ media|media|NNS|_ :|:|:|_ DMEM|dmem|NN|_ growth|growth|NN|_ media|media|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAeasy|rnaeasy|NN|_ mini-Kit|mini-kit|NN|_ Qiagen|Qiagen|NNP|_ and|and|CC|_ hybridizated|hybridizate|VBN|_ on|on|IN|_ Affymatrix|Affymatrix|NNP|_ microarrays|microarray|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ APEC|apec|NN|_ SCI-07|sci-07|NN|_ -LRB-|-lrb-|-LRB-|_ O|o|NN|_ nontypeable|nontypeable|JJ|_ :|:|:|_ H31|h31|NN|_ -RRB-|-rrb-|-RRB-|_ isolated|isolate|VBN|_ from|from|IN|_ lesions|lesion|NNS|_ -LRB-|-lrb-|-LRB-|_ gelatinous|gelatinous|JJ|_ edema|edema|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ skin|skin|NN|_ of|of|IN|_ the|the|DT|_ head|head|NN|_ and|and|CC|_ periorbital|periorbital|JJ|_ tissues|tissue|NNS|_ from|from|IN|_ a|a|DT|_ laying|lay|VBG|_ hen|hen|NN|_ showing|show|VBG|_ clinical|clinical|JJ|_ signs|sign|NNS|_ of|of|IN|_ swollen|swollen|JJ|_ head|head|NN|_ syndrome|syndrome|NN|_
strain|strain|NN|_ :|:|:|_ O08|o08|NN|_ -LRB-|-lrb-|-LRB-|_ O38|o38|NN|_ :|:|:|_ H10|h10|NN|_ -RRB-|-rrb-|-RRB-|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ yolk|yolk|NN|_ of|of|IN|_ the|the|DT|_ abdomen|abdomen|NN|_ of|of|IN|_ a|a|DT|_ diseased|diseased|JJ|_ 1-day-old|1-day-old|JJ|_ chick|chick|NN|_
Two|two|CD|_ Avian|avian|JJ|_ Pathogenic|pathogenic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strains|strain|NNS|_ -LRB-|-lrb-|-LRB-|_ APEC|apec|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ Dulbecco|Dulbecco|NNP|_ 's|'s|POS|_ Modified|modify|VBN|_ Eagle|Eagle|NNP|_ 's|'s|POS|_ Media|Media|NNP|_ -LRB-|-lrb-|-LRB-|_ DMEM|DMEM|NNP|_ -RRB-|-rrb-|-RRB-|_ media|media|NNS|_ until|until|IN|_ reach|reach|NN|_ O.D|o.d|NN|_ 600|600|CD|_ =|=|JJ|_ 0.8|0.8|CD|_ .|.|.|_
culture|culture|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ _|_|VBP|_ HS15min|hs15min|NN|_
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS30min|hs30min|NN|_
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ HS60min|hs60min|NN|_
E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ _|_|VBP|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ OD|od|NN|_ =|=|JJ|_ 0.87|0.87|CD|_ -RRB-|-rrb-|-RRB-|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ _|_|VBP|_ M-P0h|m-p0h|JJ|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ _|_|VBP|_ M-P2h|m-p2h|JJ|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ _|_|VBP|_ M-P4h|m-p4h|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ GAII|GAII|NNP|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ following|follow|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instruction|instruction|NN|_ using|use|VBG|_ their|they|PRP$|_ Small|small|JJ|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ with|with|IN|_ some|some|DT|_ modifications|modification|NNS|_ .|.|.|_ For|for|IN|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ ,|,|,|_ the|the|DT|_ directional|directional|JJ|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ TruSeq|TruSeq|NNP|_ Small|Small|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ str|str|NN|_ MG1655|mg1655|NN|_
HS15min|hs15min|NN|_ _|_|CD|_ r1|r1|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
HS15min|hs15min|NN|_ _|_|CD|_ r2|r2|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
HS15min|hs15min|NN|_ _|_|CD|_ r3|r3|NN|_ _|_|SYM|_ GAII|gaii|CD|_
HS30min|hs30min|NN|_ _|_|CD|_ r1|r1|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
HS30min|hs30min|NN|_ _|_|CD|_ r2|r2|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
HS60min|hs60min|NN|_ _|_|CD|_ r1|r1|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
HS60min|hs60min|NN|_ _|_|CD|_ r2|r2|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ OD|od|NN|_ =|=|JJ|_ 0.87|0.87|CD|_ -RRB-|-rrb-|-RRB-|_
Merge|merge|VB|_ the|the|DT|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ For|for|IN|_ example|example|NN|_ ,|,|,|_ for|for|IN|_ sample|sample|NN|_ HS15min|hs15min|NN|_ ,|,|,|_ merge|merge|VBP|_ HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN|_ ,|,|,|_ HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN|_ and|and|CC|_ HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN|_ to|to|TO|_ one|one|CD|_ fastq|fastq|NN|_ file|file|NN|_
M-P0h|m-p0h|NN|_ _|_|CD|_ r1|r1|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
M-P0h|m-p0h|NN|_ _|_|CD|_ r2|r2|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
M-P2h|m-p2h|NN|_ _|_|CD|_ r1|r1|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
M-P2h|m-p2h|NN|_ _|_|CD|_ r2|r2|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
M-P4h|m-p4h|NN|_ _|_|CD|_ r1|r1|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
M-P4h|m-p4h|NN|_ _|_|CD|_ r2|r2|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
M-P4h|m-p4h|NN|_ _|_|CD|_ r3|r3|NN|_ _|_|CD|_ HiSeq|hiseq|NN|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v0|v0|NN|_ .12.7|.12.7|CD|_ with|with|IN|_ parameters|parameter|NNS|_ bowtie|bowtie|VBP|_ -|-|:|_ t|t|NN|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 2|2|CD|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWig|BigWig|NNP|_ files|file|VBZ|_ for|for|IN|_ whole-genome|whole-genome|JJ|_ reads|read|VBZ|_ coverage|coverage|NN|_ -LRB-|-lrb-|-LRB-|_ including|include|VBG|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ has|have|VBZ|_ two|two|CD|_ files|file|NNS|_ ,|,|,|_ one|one|CD|_ for|for|IN|_ plus|plus|CC|_ strand|strand|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ other|other|JJ|_ for|for|IN|_ minus|minus|CC|_ strand|strand|NN|_ .|.|.|_ Therefore|therefore|RB|_ ,|,|,|_ there|there|EX|_ are|be|VBP|_ 14|14|CD|_ BigWig|BigWig|NNP|_ files|file|NNS|_ for|for|IN|_ 7|7|CD|_ samples|sample|NNS|_ .|.|.|_
To|to|TO|_ enrich|enrich|VB|_ mRNAs|mrna|NNS|_ and|and|CC|_ other|other|JJ|_ transcripts|transcript|NNS|_ ,|,|,|_ majority|majority|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ a|a|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ RiboPureTM|ribopuretm|NN|_ -|-|:|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Once|once|RB|_ isolated|isolate|VBN|_ ,|,|,|_ ~|~|SYM|_ 10μg|10μg|CD|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 8|8|CD|_ units|unit|NNS|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ twice|twice|RB|_ to|to|TO|_ remove|remove|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
Transform|transform|VB|_ the|the|DT|_ mapped|map|VBN|_ file|file|NN|_ format|format|NN|_ from|from|IN|_ sam|sam|NN|_ to|to|TO|_ sorted|sort|VBN|_ bam|bam|NN|_ which|which|WDT|_ are|be|VBP|_ later|later|RB|_ tranfered|tranfer|VBN|_ to|to|TO|_ bigWig|bigwig|NN|_ ,|,|,|_ and|and|CC|_ separated|separate|VBN|_ by|by|IN|_ the|the|DT|_ strand|strand|NN|_ -LRB-|-lrb-|-LRB-|_ plus|plus|NN|_ and|and|CC|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
basal|basal|JJ|_ media|media|NNS|_ :|:|:|_ M9|m9|NN|_ +|+|CC|_ 4|4|CD|_ g|g|NN|_
cra|cra|NN|GEN KO|ko|NN|_
cra|cra|NN|GEN KO|ko|NN|_ +|+|CC|_ L-trp|l-trp|NN|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ cuffdiff|cuffdiff|JJ|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ primary|primary|JJ|_ carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_ .|.|.|_ Aerobic|aerobic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ anoxic|anoxic|JJ|_ serum|serum|NN|_ bottles|bottle|NNS|_ .|.|.|_ Condition|condition|NN|_ specific|specific|JJ|_ media|media|NNS|_ supplementation|supplementation|NN|_ was|be|VBD|_ added|add|VBN|_ as|as|IN|_ described|describe|VBN|_ else|else|RB|_ where|where|WRB|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
FPKM|fpkm|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ v.|v.|CC|_ 2.0.2|2.0.2|CD|_ with|with|IN|_ upper-quartile|upper-quartile|JJ|_ normalization|normalization|NN|_ and|and|CC|_ fr-firststrand|fr-firststrand|NN|_ for|for|IN|_ library|library|NN|_ type|type|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
genotype|genotype|NN|_
growth|growth|NN|_ stage|stage|NN|_ :|:|:|_ mid|mid|JJ|_ exponetial|exponetial|JJ|_ phase|phase|NN|_
Illumina|Illumina|NNP|_ read|read|VB|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 1|1|CD|_ with|with|IN|_ 2|2|CD|_ mismatches|mismatch|NNS|_ allowed|allow|VBD|_ per|per|IN|_ read|read|NN|_ alignment|alignment|NN|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|SYM|_ cra|cra|FW|GEN KO|ko|FW|_ _|_|SYM|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ aerobic|aerobic|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|SYM|_ cra|cra|FW|GEN KO|ko|FW|_ _|_|SYM|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ +|+|CC|_ L-tryptophan|l-tryptophan|JJ|_ _|_|NN|_ aerobic|aerobic|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ cultures|culture|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNA|rna|NN|_ Protect|protect|VB|_ reagent|reagent|NN|_ following|follow|VBG|_ the|the|DT|_ vendor|vendor|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ for|for|IN|_ <|<|JJR|_ 30|30|CD|_ days|day|NNS|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|CD|_ mntR|mntr|NN|GEN KO|KO|NNP|_ _|_|NNP|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ aerobic|aerobic|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|CD|_ mntR|mntr|NN|GEN KO|KO|NNP|_ _|_|NNP|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|CD|_ nac|nac|NN|GEN KO|KO|NNP|_ _|_|NNP|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ +|+|CC|_ adenine|adenine|JJ|_ _|_|NN|_ aerobic|aerobic|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|CD|_ nac|nac|NN|GEN KO|KO|NNP|_ _|_|NNP|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ aerobic|aerobic|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ +|+|CC|_ adenine|adenine|JJ|_ _|_|NN|_ aerobic|aerobic|JJ|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ aerobic|aerobic|JJ|_ rep1|rep1|NN|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ aerobic|aerobic|JJ|_ rep2|rep2|NN|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ aerobic|aerobic|JJ|_ rep3|rep3|NN|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ rep1|rep1|NN|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ rep2|rep2|NN|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ rep3|rep3|NN|_
Mid|Mid|NNP|_ log|log|NN|_ _|_|NN|_ wildtype|wildtype|JJ|_ _|_|NN|_ glc|glc|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ +|+|CC|_ L-tryptophan|l-tryptophan|JJ|_ _|_|NN|_ aerobic|aerobic|JJ|_
mntR|mntr|NN|GEN KO|ko|NN|_
mntR|mntr|NN|GEN KO|ko|SYM|_ -|-|:|_ O2|o2|CD|_
nac|nac|NN|GEN KO|ko|NN|_
nac|nac|NN|GEN KO|ko|NN|_ +|+|CC|_ ade|ade|NN|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ aerobic|aerobic|JJ|_
oxygen|oxygen|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_
Paired-end|paired-end|NN|_ ,|,|,|_ strand-specific|strand-specific|JJ|_ RNAseq|rnaseq|NN|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LCB-|-lcb-|-LRB-|_ Levin|Levin|NNP|_ JZ|JZ|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RCB-|-rcb-|-RRB-|_ with|with|IN|_ the|the|DT|_ following|follow|VBG|_ modifications|modification|NNS|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ .|.|.|_ Subtracted|subtract|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ 's|'s|POS|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Invitrogen|Invitrogen|NNP|_ 's|'s|POS|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First-Strand|First-Strand|NNP|_ Synthesis|synthesis|NN|_ protocol|protocol|NN|_ with|with|IN|_ random|random|JJ|_ hexamer|hexamer|NN|_ priming|priming|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ csv|csv|NN|_ files|file|NNS|_ ,|,|,|_ FPKM|fpkm|NN|_ values|value|NNS|_ from|from|IN|_ pairwise|pairwise|JJ|_ comparisons|comparison|NNS|_
supplementation|supplementation|NN|_ :|:|:|_ adenine|adenine|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_
supplementation|supplementation|NN|_ :|:|:|_ L-tryptophan|l-tryptophan|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mg|mg|NN|_
supplementation|supplementation|NN|_ :|:|:|_ None|none|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ procedure|procedure|NN|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ Dnase|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WT|WT|NNP|_ +|+|CC|_ ade|ade|JJ|_
WT|wt|NN|_ +|+|CC|_ L-trp|l-trp|JJ|_
WT|wt|SYM|_ -|-|:|_ O2|o2|CD|_
23A1|23a1|NN|_
23B1|23b1|NN|_
23C3|23c3|NN|_
39A1|39a1|NN|_
39B1|39b1|NN|_
39C1|39c1|NN|_
DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ manner|manner|NN|_ as|as|IN|_ described|describe|VBN|_ by|by|IN|_ McNulty|McNulty|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 22030749|22030749|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
ecoli|ecolus|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
genotype|genotype|NN|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ complete|complete|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ version|version|NN|_ 2.0.5|2.0.5|CD|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ count|count|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
WTA1|wta1|NN|_
WTB1|wtb1|NN|_
WTC3|wtc3|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ M63|m63|NN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ cell|cell|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ controlled|control|VBN|_ ~|~|SYM|_ 10|10|CD|_ ^|^|SYM|_ 8|8|CD|_ cells|cell|NNS|_
condition|condition|NN|_ :|:|:|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_
condition|condition|NN|_ :|:|:|_ regular|regular|JJ|_
condition|condition|NN|_ :|:|:|_ starvation|starvation|NN|_
condition|condition|NN|_ :|:|:|_ temperature|temperature|NN|_ change|change|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ NaCl|nacl|NN|_ 0.20|0.20|CD|_ M|m|NN|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.20|0.20|CD|_ M|m|NN|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ NaCl|nacl|NN|_ 0.20|0.20|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.20|0.20|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.20|0.20|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.45|0.45|CD|_ M|m|NN|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.45|0.45|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.45|0.45|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.45|0.45|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.55|0.55|CD|_ M|m|NN|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.55|0.55|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.55|0.55|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ osmotic|osmotic|JJ|_ pressure|pressure|NN|_ ,|,|,|_ NaCl|nacl|NN|_ 0.55|0.55|CD|_ M|m|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ regular|regular|JJ|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ regular|regular|JJ|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ regular|regular|JJ|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ regular|regular|JJ|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ starvation|starvation|NN|_ ,|,|,|_ SHX|shx|NN|_ 100|100|CD|_ ng|ng|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ starvation|starvation|NN|_ ,|,|,|_ SHX|shx|NN|_ 150|150|CD|_ ng|ng|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ starvation|starvation|NN|_ ,|,|,|_ SHX|SHX|NNP|_ 50|50|CD|_ ng|ng|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 40.0|40.0|CD|_ deg|deg|NN|_ C|c|NN|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 40.0|40.0|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 40.0|40.0|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 40.0|40.0|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.5|41.5|CD|_ deg|deg|NN|_ C|c|NN|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.5|41.5|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.5|41.5|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.5|41.5|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.8|41.8|CD|_ deg|deg|NN|_ C|c|NN|_
E.|e.|FW|_ coli|coli|FW|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.8|41.8|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.8|41.8|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MDS42|mds42|NN|_ ,|,|,|_ temperature|temperature|NN|_ change|change|NN|_ ,|,|,|_ 41.8|41.8|CD|_ deg|deg|NN|_ C|c|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ written|write|VBN|_ in|in|IN|_ R|r|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ finite|finite|JJ|_ hybridisation|hybridisation|NN|_ -LRB-|-lrb-|-LRB-|_ FH|fh|NN|_ -RRB-|-rrb-|-RRB-|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Ono|Ono|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ thermodynamic|thermodynamic|JJ|_ model|model|NN|_ of|of|IN|_ non-specific|non-specific|JJ|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ NSB|nsb|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ short|short|JJ|_ nucleotide|nucleotide|NN|_ microarrays|microarray|NNS|_ -LRB-|-lrb-|-LRB-|_ Furusawa|Furusawa|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MDS42|mds42|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ cold|cold|JJ|_ phenol-ethanol|phenol-ethanol|JJ|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ of|of|IN|_ phenol|phenol|NN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ prepared|prepare|VBN|_ in|in|IN|_ advance|advance|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 16,000|16,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Control|Control|NNP|_ Wild|Wild|NNP|_ type|type|NN|_ E.coli|e.coli|NN|_ SE15|se15|NN|_ vs.|vs.|CC|_ LuxS|luxs|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ SE15|se15|NN|_
E.coli|e.coli|NN|_ SE15|se15|NN|_ is|be|VBZ|_ cultured|culture|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ LuxS|luxs|NN|_ E.coli|e.coli|NN|_ SE15|se15|NN|_ is|be|VBZ|_ cultured|culture|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED with|with|IN|_ kanamycine|kanamycine|NN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ and|and|CC|_ in|in|IN|_ 150rpm|150rpm|NN|_ shaking|shake|VBG|_ incubator|incubator|NN|_
E.coli|e.coli|NN|_ SE15|se15|NN|_ is|be|VBZ|_ isolated|isolate|VBN|_ from|from|IN|_ indwelling|indwell|VBG|_ catheter|catheter|NN|_ of|of|IN|_ patient|patient|NN|_ and|and|CC|_ deleted|delete|VBN|_ LuxS|luxs|NN|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ related|related|JJ|_ to|to|TO|_ quorum|quorum|NN|_ sensing|sense|VBG|_ -RRB-|-rrb-|-RRB-|_
E.coli|e.coli|NN|_ SE15|se15|NN|_ isolated|isolate|VBN|_ from|from|IN|_ indwelling|indwell|VBG|_ catheter|catheter|NN|_ of|of|IN|_ patient|patient|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism SE15|se15|NN|_
genotype|genotype|NN|_
Genowiz|genowiz|NN|_ 4.0.5.6|4.0.5.6|CD|_ normalized|normalize|VBD|_ ,|,|,|_ background|background|NN|_ subtracted|subtract|VBD|_ data|datum|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ log2|log2|NN|_ of|of|IN|_ processed|process|VBN|_ Red|red|JJ|_ signal|signal|NN|_
strain|strain|NN|_ :|:|:|_ SE15|se15|NN|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_
Wild|Wild|NNP|_ type|type|NN|_ E.coli|e.coli|NN|_ SE15|se15|NN|_ vs.|vs.|CC|_ LuxS|luxs|NN|_ mutant|mutant|JJ|_ E.coli|e.coli|NN|_ SE15|se15|NN|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ version|version|NN|_ 10.5.1.1|10.5.1.1|CD|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ Anti-FLAG|anti-flag|NN|_ -LRB-|-lrb-|-LRB-|_ sigma-aldrich|sigma-aldrich|JJ|_ cat|cat|NN|_ no|no|DT|_ F3165|f3165|NN|_ -RRB-|-rrb-|-RRB-|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ none|none|NN|_ ,|,|,|_ input|input|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ normal|normal|JJ|_ rabbit|rabbit|NN|_ IgG|igg|NN|_ -LRB-|-lrb-|-LRB-|_ Upstate|upstate|JJ|_ Biotechnology|biotechnology|NN|_ ,|,|,|_ Cat|cat|NN|_ .|.|.|_ no.|no.|RB|_ 12-370|12-370|CD|_ -RRB-|-rrb-|-RRB-|_
CSH50|csh50|NN|_ control|control|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ 90|90|CD|_ min|min|NN|_
CSH50|csh50|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ mock|mock|JJ|_ igG|igg|NN|_ -RRB-|-rrb-|-RRB-|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ replicate|replicate|VB|_ 1|1|CD|_
CSH50|csh50|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ mock|mock|JJ|_ igG|igg|NN|_ -RRB-|-rrb-|-RRB-|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ replicate|replicate|VB|_ 2|2|CD|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 4.5|4.5|CD|_ 90|90|CD|_ min|min|NN|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 4.5|4.5|CD|_ 90|90|CD|_ min|min|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 4.5|4.5|CD|_ 90|90|CD|_ min|min|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 4.5|4.5|CD|_ 90|90|CD|_ min|min|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 7|7|CD|_ 90|90|CD|_ min|min|NN|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 7|7|CD|_ 90|90|CD|_ min|min|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 7|7|CD|_ 90|90|CD|_ min|min|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
CSH50|csh50|NN|_ E-minimal|e-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 7|7|CD|_ 90|90|CD|_ min|min|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
OD600|od600|NN|_ 15|15|CD|_ units|unit|NNS|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ each|each|DT|_ ChIP|chip|NN|_ procedure|procedure|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 8|8|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ PBS|PBS|NNP|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ flask|flask|NN|_ .|.|.|_ DNA-protein|dna-protein|JJ|_ and|and|CC|_ protein-protein|protein-protein|JJ|_ interactions|interaction|NNS|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ by|by|IN|_ adding|add|VBG|_ 1,351|1,351|CD|_ µl|µl|NN|_ of|of|IN|_ formaldehyde|formaldehyde|NN|_ drop-wise|drop-wise|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ %|%|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ with|with|IN|_ stirring|stir|VBG|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_ Glycine|glycine|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.125|0.125|CD|_ M|m|NN|_ with|with|IN|_ stirring|stir|VBG|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4,000|4,000|CD|_ rpm|rpm|NN|_ for|for|IN|_ 8|8|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ supernatant|supernatant|JJ|_ removed|remove|VBN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 0.6|0.6|CD|_ ml|ml|NN|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ containing|contain|VBG|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ 1.4|1.4|CD|_ ml|ml|NN|_ of|of|IN|_ IP|IP|NNP|_ dilution|dilution|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ pH|ph|NN|_ 8.1|8.1|CD|_ ,|,|,|_ 150|150|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ ,|,|,|_ 0.01|0.01|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ Roche|Roche|NNP|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ the|the|DT|_ chromatin|chromatin|NN|_ was|be|VBD|_ sonicated|sonicate|VBN|_ on|on|IN|_ ice|ice|NN|_ in|in|IN|_ a|a|DT|_ 5|5|CD|_ ml|ml|NN|_ tube|tube|NN|_ to|to|TO|_ reduce|reduce|VB|_ the|the|DT|_ DNA|dna|NN|_ length|length|NN|_ to|to|TO|_ an|a|DT|_ average|average|JJ|_ size|size|NN|_ of|of|IN|_ approximately|approximately|RB|_ 500|500|CD|_ bp|bp|NN|_ using|use|VBG|_ the|the|DT|_ Sanyo|Sanyo|NNP|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ then|then|RB|_ equalised|equalise|VBD|_ to|to|TO|_ 0.15|0.15|CD|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ -RRB-|-rrb-|-RRB-|_ units|unit|NNS|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ and|and|CC|_ washed|wash|VBN|_ in|in|IN|_ EG|eg|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.2|7.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ This|this|DT|_ wash|wash|NN|_ step|step|NN|_ was|be|VBD|_ repeated|repeat|VBN|_ twice|twice|RB|_ more|more|RBR|_ with|with|IN|_ centrifugation|centrifugation|NN|_ to|to|TO|_ collect|collect|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ 1X|1x|NN|_ EG|eg|NN|_ minimal|minimal|JJ|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.2|7.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ ~|~|NN|_ 0.5-0.6|0.5-0.6|CD|_ in|in|IN|_ a|a|DT|_ 40|40|CD|_ ml|ml|NN|_ volume|volume|NN|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_
The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ two|two|CD|_ 20-ml|20-ml|JJ|_ volumes|volume|NNS|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ two|two|CD|_ pellets|pellet|NNS|_ were|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ different|different|JJ|_ treatments|treatment|NNS|_ .|.|.|_ One|one|CD|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ 1X|1x|NN|_ EG-minimal|eg-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 7.2|7.2|CD|_ .|.|.|_ The|the|DT|_ second|second|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ 1X|1x|NN|_ EG-minimal|eg-minimal|JJ|_ medium|medium|NN|_ pH|ph|NN|_ 4.5|4.5|CD|_ .|.|.|_ Each|each|DT|_ suspension|suspension|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ ml|ml|NN|_ 1X|1x|NN|_ EG|eg|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ pH|ph|NN|_ in|in|IN|_ a|a|DT|_ 250|250|CD|_ ml|ml|NN|_ flask|flask|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 200|200|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ for|for|IN|_ 90|90|CD|_ min|min|NN|_ before|before|IN|_ harvesting|harvest|VBG|_ for|for|IN|_ analysis|analysis|NN|_ .|.|.|_
5|5|CD|_ ml|ml|NN|_ bacterial|bacterial|JJ|_ cultures|culture|NNS|_ with|with|IN|_ a|a|DT|_ known|known|JJ|_ inoculum|inoculum|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 1.0|1.0|CD|_ ×|×|NN|_ 109|109|CD|_ cfu|cfu|NN|_
cells|cell|NNS|_
E.|e.|FW|_ coli|coli|FW|_ treated|treat|VBN|_ with|with|IN|_ bicontinious|bicontinious|JJ|_ microemulsion|microemulsion|NN|_
E.|E.|NNP|_ coli|coli|NNS|_ treated|treat|VBN|_ with|with|IN|_ o|o|NN|_
E.|E.|NNP|_ coli|coli|NNS|_ treated|treat|VBN|_ with|with|IN|_ w|w|NN|_
E.|E.|NNP|_ coli|coli|NN|_ without|without|IN|_ microemulsion|microemulsion|NN|_ treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Raw|raw|NN|_ microarray|microarray|NN|_ intensity|intensity|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ per|per|IN|_ chip|chip|NN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ mean|mean|NN|_ value|value|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ recommended|recommend|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ CMCC|cmcc|NN|_ -LRB-|-lrb-|-LRB-|_ B|b|NN|_ -RRB-|-rrb-|-RRB-|_ 44102|44102|CD|_
The|the|DT|_ strain|strain|NN|_ E.|e.|FW|_ coli|coli|FW|_ CMCC|cmcc|NN|_ -LRB-|-lrb-|-LRB-|_ B|b|NN|_ -RRB-|-rrb-|-RRB-|_ 44102|44102|CD|_ ,|,|,|_ was|be|VBD|_ provided|provide|VBN|_ by|by|IN|_ Institute|Institute|NNP|_ of|of|IN|_ Microbiology|Microbiology|NNP|_ ,|,|,|_ Chinese|Chinese|NNP|_ Academy|Academy|NNP|_ of|of|IN|_ Sciences|Sciences|NNPS|_ and|and|CC|_ preserved|preserve|VBN|_ at|at|IN|_ the|the|DT|_ Department|Department|NNP|_ of|of|IN|_ Food|Food|NNP|_ Science|Science|NNP|_ and|and|CC|_ Nutrition|Nutrition|NNP|_ ,|,|,|_ Zhejiang|Zhejiang|NNP|_ University|University|NNP|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ maintained|maintain|VBN|_ in|in|IN|_ nutrient|nutrient|NN|_ agar|agar|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NA|na|NN|_ ,|,|,|_ Hangzhou|Hangzhou|NNP|_ Microbiological|Microbiological|NNP|_ Agents|Agents|NNPS|_ Co.|Co.|NNP|_ ,|,|,|_ Ltd.|Ltd.|NNP|_ ,|,|,|_ China|China|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ cultured|culture|VBN|_ in|in|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ TSB|tsb|NN|_ ,|,|,|_ Qingdao|Qingdao|NNP|_ Hope|Hope|NNP|_ Biotechnology|Biotechnology|NNP|_ Co.|Co.|NNP|_ ,|,|,|_ Ltd.|Ltd.|NNP|_ ,|,|,|_ China|China|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ and|and|CC|_ transferred|transfer|VBN|_ every|every|DT|_ 20-24|20-24|CD|_ h|h|NN|_ with|with|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ from|from|IN|_ cells|cell|NNS|_ of|of|IN|_ the|the|DT|_ microemulsion-treated|microemulsion-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ extracted|extract|VBN|_ in|in|IN|_ duplicate|duplicate|VB|_ using|use|VBG|_ an|a|DT|_ RNAiso|rnaiso|NN|_ Plus|plus|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ .|.|.|_ #|#|#|_ 908|908|CD|_ ,|,|,|_ Takara|Takara|NNP|_ ,|,|,|_ Japan|Japan|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_
treatment|treatment|NN|_ :|:|:|_ bicontinious|bicontinious|JJ|_ microemulsion|microemulsion|NN|_
treatment|treatment|NN|_ :|:|:|_ control|control|NN|_
treatment|treatment|NN|_ :|:|:|_ oil|oil|NN|_ in|in|IN|_ water|water|NN|_
treatment|treatment|NN|_ :|:|:|_ water|water|NN|_ in|in|IN|_ oil|oil|NN|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_ 10.10.1.1|10.10.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 0.1|0.1|CD|_ L|l|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 2.5|2.5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 80|80|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 2.5|2.5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 80|80|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 2.5|2.5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ CO|CO|NNP|_ gas|gas|NN|_ at|at|IN|_ 0.1|0.1|CD|_ L|l|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Slide|slide|NN|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|Slide|NNP|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 31|31|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 33|33|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|slide|NN|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|slide|NN|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 37|37|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 39|39|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 53|53|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 53|53|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 53|53|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 53|53|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_ 2|2|CD|_
Slide|Slide|NNP|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|Slide|NNP|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 55|55|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 3|3|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 56|56|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|CD|_ CO|CO|NNP|_ gas|gas|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
strain|strain|NN|_ :|:|:|_ Wild|Wild|NNP|_ type|type|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 2.5|2.5|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 40|40|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 80|80|CD|_ min|min|NN|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_
treatment|treatment|NN|_ :|:|:|_ Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 0.1|0.1|CD|_ L|l|NN|_
treatment|treatment|NN|_ :|:|:|_ Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_
treatment|treatment|NN|_ :|:|:|_ Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ iCORM-3|icorm-3|NN|_
treatment|treatment|NN|_ :|:|:|_ Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 40uM|40um|NN|_ CORM-3|corm-3|NN|_
treatment|treatment|NN|_ :|:|:|_ Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ CO|CO|NNP|_ gas|gas|NN|_ at|at|IN|_ 0.1|0.1|CD|_ L|l|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP to|to|TO|_ 0.8|0.8|CD|_ OD|od|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ to|to|TO|_ 0.8|0.8|CD|_ OD|od|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism was|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ and|and|CC|_ LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ incubator|incubator|NN|_ shaker|shaker|NN|_ at|at|IN|_ 150|150|CD|_ r.p.m.|r.p.m.|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP to|to|TO|_ 0.8|0.8|CD|_ OD|od|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ to|to|TO|_ 0.8|0.8|CD|_ OD|od|NN|_
LB|lb|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
LB|lb|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
LB|lb|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
LB|lb|NN|_ +|+|CC|_ glycerol|glycerol|NN|SUPP ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ culture|culture|NN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini-prep|mini-prep|NN|_ kit.cDNA|kit.cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ using|use|VBG|_ 5-10|5-10|CD|_ µg|µg|NN|_
The|the|DT|_ intensity|intensity|NN|_ cell|cell|NN|_ files|file|NNS|_ were|be|VBD|_ then|then|RB|_ imported|import|VBN|_ ,|,|,|_ normalized|normalize|VBN|_ for|for|IN|_ background|background|NN|_ correction|correction|NN|_ -LRB-|-lrb-|-LRB-|_ used|use|VBN|_ RMA|rma|NN|_ for|for|IN|_ normalization|normalization|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ data|datum|NNS|_ analysed|analyse|VBN|_ using|use|VBG|_ Gene|Gene|NNP|_ Spring|Spring|NNP|_ 11.5|11.5|CD|_ software|software|NN|_ .|.|.|_
To|to|TO|_ study|study|VB|_ gene|gene|NN|_ expression|expression|NN|_ ,|,|,|_ 28|28|CD|_ days|day|NNS|_ old|old|JJ|_ E.coli|e.coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ LB|lb|NN|MED broth|broth|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 10|10|CD|_ %|%|NN|_ v|v|LS|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-FLAG|anti-flag|JJ|_ antibody|antibody|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Cat|Cat|NNP|_ #|#|#|_ :|:|:|_ F3165-1MG|f3165-1mg|NN|_ -RRB-|-rrb-|-RRB-|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ none|none|NN|_
ChIP|chip|NN|_ _|_|CD|_ hns-F|hns-f|NN|_ _|_|SYM|_ bcm|bcm|SYM|_ -|-|:|_ #|#|#|_ 1|1|CD|_
ChIP|chip|NN|_ _|_|CD|_ hns-F|hns-f|NN|_ _|_|CD|_ bcm|bcm|NN|_ +|+|CC|_ #|#|#|_ 1|1|CD|_
ChIP|chip|NN|_ _|_|CD|_ hns-F|hns-f|NN|_ _|_|SYM|_ bcm|bcm|SYM|_ -|-|:|_ #|#|#|_ 2|2|CD|_
ChIP|chip|NN|_ _|_|SYM|_ hns-F|hns-f|JJ|_ _|_|NN|_ bcm|bcm|NN|_ +|+|CC|_ #|#|#|_ 2|2|CD|_
ChIP-Seq|chip-seq|JJ|_
consensus|consensus|NN|_ binding|binding|NN|_ regions|region|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ as|as|IN|_ the|the|DT|_ portion|portion|NN|_ which|which|WDT|_ was|be|VBD|_ covered|cover|VBN|_ by|by|IN|_ replicate|replicate|VB|_ samples|sample|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ each|each|DT|_ co-ordinate|co-ordinate|JJ|_ coverage|coverage|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ which|which|WDT|_ was|be|VBD|_ aligned|align|VBN|_ againist|againist|IN|_ the|the|DT|_ position|position|NN|_ .|.|.|_ The|the|DT|_ coverage|coverage|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ and|and|CC|_ converted|convert|VBN|_ into|into|IN|_ a|a|DT|_ z|z|SYM|_ score|score|NN|_ .|.|.|_ Z|z|NN|_ score|score|NN|_ threshold|threshold|NN|_ of|of|IN|_ 12|12|CD|_ was|be|VBD|_ selected|select|VBN|_ to|to|TO|_ identify|identify|VB|_ H-NS|h-ns|NN|_ binding|binding|NN|_ regions|region|NNS|_ .|.|.|_
genome|genome|NN|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_
H-NS|h-ns|NN|_ flag|flag|NN|_ tagged|tag|VBD|_ cells|cell|NNS|_ with|with|IN|_ bcm|bcm|NN|_ treatment|treatment|NN|_
H-NS|h-ns|NN|_ flag|flag|NN|_ tagged|tag|VBD|_ cells|cell|NNS|_ without|without|IN|_ bcm|bcm|NN|_ treatment|treatment|NN|_
Input|Input|NNP|_ _|_|SYM|_ hns-F|hns-f|JJ|_ _|_|NN|_ bcm|bcm|NN|_ -|-|:|_ #|#|#|_ 1|1|CD|_
Input|Input|NNP|_ _|_|SYM|_ hns-F|hns-f|JJ|_ _|_|NN|_ bcm|bcm|NN|_ +|+|CC|_ #|#|#|_ 1|1|CD|_
Input|Input|NNP|_ _|_|SYM|_ hns-F|hns-f|JJ|_ _|_|NN|_ bcm|bcm|NN|_ -|-|:|_ #|#|#|_ 2|2|CD|_
Input|Input|NNP|_ _|_|SYM|_ hns-F|hns-f|JJ|_ _|_|NN|_ bcm|bcm|NN|_ +|+|CC|_ #|#|#|_ 2|2|CD|_
MG1655|mg1655|NN|_ hns-FLAG|hns-flag|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ and|and|CC|_ without|without|IN|_ bicyclomycin|bicyclomycin|NN|_ -LRB-|-lrb-|-LRB-|_ BCM|bcm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ degree|degree|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200rpm|200rpm|JJ|_
reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ Mg1655|mg1655|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ ,|,|,|_ with|with|IN|_ quality|quality|NN|_ threshold|threshold|NN|_ of|of|IN|_ 20|20|CD|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ locus|locus|NN|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_ The|the|DT|_ mapped|map|VBN|_ position|position|NN|_ obtained|obtain|VBN|_ from|from|IN|_ the|the|DT|_ SAM|SAM|NNP|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ BWA|bwa|NN|_ lists|list|NNS|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ position|position|NN|_ was|be|VBD|_ extended|extend|VBN|_ to|to|TO|_ 280|280|CD|_ bp|bp|NN|_ which|which|WDT|_ is|be|VBZ|_ the|the|DT|_ average|average|JJ|_ length|length|NN|_ of|of|IN|_ DNA|dna|NN|_ fragments|fragment|NNS|_ submitted|submit|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ .|.|.|_
Standard|Standard|NNP|_ illumina|illumina|NNP|_ library|library|NN|_ construction|construction|NN|_ protocol|protocol|NN|_ for|for|IN|_ ChIP|chip|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ contents|contents|NNS|_ :|:|:|_ reference|reference|NN|_ seq,co-ordinate|seq,co-ordinate|JJ|_ start|start|NN|_ position,co-ordinate|position,co-ordinate|JJ|_ end|end|NN|_ position|position|NN|_ ,|,|,|_ counts|count|VBZ|_ for|for|IN|_ the|the|DT|_ position|position|NN|_ ,|,|,|_ mapping|map|VBG|_ quality|quality|NN|_ ,|,|,|_ strand|strand|NN|_ position|position|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ format|format|NN|_ :|:|:|_ bed|bed|NN|_ format|format|NN|_
The|the|DT|_ binding|binding|NN|_ regions|region|NNS|_ were|be|VBD|_ considered|consider|VBN|_ by|by|IN|_ taking|take|VBG|_ into|into|IN|_ account|account|NN|_ base|base|NN|_ position|position|NN|_ with|with|IN|_ z-score|z-score|NN|_ greater|greater|JJR|_ than|than|IN|_ threshold|threshold|NN|_ and|and|CC|_ merging|merge|VBG|_ adjacent|adjacent|JJ|_ binding|binding|NN|_ regions|region|NNS|_ seperated|seperate|VBN|_ by|by|IN|_ a|a|DT|_ distance|distance|NN|_ of|of|IN|_ less|less|JJR|_ than|than|IN|_ 200bo|200bo|CD|_ into|into|IN|_ the|the|DT|_ single|single|JJ|_ binding|binding|NN|_ regions|region|NNS|_
Two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ were|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ samples|sample|NNS|_ with|with|IN|_ and|and|CC|_ without|without|IN|_ treatment|treatment|NN|_ with|with|IN|_ bicyclomycin|bicyclomycin|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ without|without|IN|_ BCM|bcm|NN|_ treatment|treatment|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ OD600|od600|NN|_ ≈|≈|NN|_ 0.8|0.8|CD|_ at|at|IN|_ 370|370|CD|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ with|with|IN|_ BCM|bcm|NN|_ treatment|treatment|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ early|early|JJ|_ log|log|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600|600|CD|_ =|=|JJ|_ 0.1|0.1|CD|_ -RRB-|-rrb-|-RRB-|_ ≈|≈|SYM|_ 1h|1h|VBP|_ at|at|IN|_ 370|370|CD|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ BCM|BCM|NNP|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 25ug|25ug|JJ|_ mL-1|ml-1|NN|_
2xOriT|2xorit|NN|_
A2|a2|NN|_ ,|,|,|_ osmotolerant|osmotolerant|JJ|_ mutant|mutant|JJ|_
A2|a2|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
A2|a2|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
A4|a4|NN|_ ,|,|,|_ osmotolerant|osmotolerant|JJ|_ mutant|mutant|JJ|_
A4|a4|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
A4|a4|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
average|average|JJ|_ fitness|fitness|NN|_ :|:|:|_ 0.196851676684606|0.196851676684606|CD|_
average|average|JJ|_ fitness|fitness|NN|_ :|:|:|_ 0.296737932583603|0.296737932583603|CD|_
average|average|JJ|_ fitness|fitness|NN|_ :|:|:|_ 0.344592279464807|0.344592279464807|CD|_
average|average|JJ|_ fitness|fitness|NN|_ :|:|:|_ 0.353076289611459|0.353076289611459|CD|_
average|average|JJ|_ fitness|fitness|NN|_ :|:|:|_ 0.434286415079969|0.434286415079969|CD|_
average|average|JJ|_ fitness|fitness|NN|_ :|:|:|_ 0.502711019240335|0.502711019240335|CD|_
Data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ LOWESS|LOWESS|NNP|_ algorithm|algorithm|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ for|for|IN|_ statistical|statistical|JJ|_ significance|significance|NN|_ using|use|VBG|_ the|the|DT|_ MeV|mev|NN|_ package|package|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
G2|g2|NN|_ ,|,|,|_ osmotolerant|osmotolerant|JJ|_ mutant|mutant|JJ|_
G2|g2|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
G2|g2|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
G3|g3|NN|_ ,|,|,|_ osmotolerant|osmotolerant|JJ|_ mutant|mutant|JJ|_
G3|g3|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
G3|g3|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
G5|g5|NN|_ ,|,|,|_ osmotolerant|osmotolerant|JJ|_ mutant|mutant|JJ|_
G5|g5|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
G5|g5|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
G6|g6|NN|_ ,|,|,|_ osmotolerant|osmotolerant|JJ|_ mutant|mutant|JJ|_
G6|g6|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
G6|g6|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
genotype|genotype|NN|_
Grown|Grown|NNP|_ in|in|IN|_ glucose|glucose|NN|SUPP M9|m9|NN|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.55|0.55|CD|_ M|m|NN|_ NaCl|nacl|NN|_
Hfr-2xSFX|hfr-2xsfx|NN|_ -|-|:|_
population|population|NN|_ :|:|:|_ A2|a2|NN|_
population|population|NN|_ :|:|:|_ A4|a4|NN|_
population|population|NN|_ :|:|:|_ G2|g2|NN|_
population|population|NN|_ :|:|:|_ G3|g3|NN|_
population|population|NN|_ :|:|:|_ G5|g5|NN|_
population|population|NN|_ :|:|:|_ G6|g6|NN|_
Samples|sample|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid|mid|JJ|GrowthPhase exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD|od|NN|_ approx|approx|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ then|then|RB|_ harvested|harvest|VBN|_ with|with|IN|_ rapid|rapid|JJ|_ filtration|filtration|NN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNALater|rnalater|NN|_ to|to|TO|_ stop|stop|VB|_ RNA|rna|NN|_ degradation|degradation|NN|_ .|.|.|_ The|the|DT|_ Zymo|Zymo|NNP|_ Quick-RNA|quick-rna|NN|_ miniprep|miniprep|NN|_ kit|kit|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ pure|pure|JJ|_ RNA|rna|NN|_ for|for|IN|_ subsequent|subsequent|JJ|_ analysis|analysis|NN|_
strain|strain|NN|_ description|description|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ BW25113|bw25113|NN|_ with|with|IN|_ an|a|DT|_ integrated|integrate|VBN|_ F|f|NN|_ tra|tra|NN|_ operon|operon|NN|_ at|at|IN|_ the|the|DT|_ trp|trp|NN|_ locus|locus|NN|_ ,|,|,|_ plus|plus|CC|_ additional|additional|JJ|_ F|f|NN|_ oriT|orit|NN|_ sequences|sequence|NNS|_ integrated|integrate|VBN|_ at|at|IN|_ mbhA|mbha|NN|_ and|and|CC|_ hyfC|hyfc|NN|GEN
strain|strain|NN|_ description|description|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ BW25113|bw25113|NN|_ with|with|IN|_ F|f|NN|_ oriTs|orit|NNS|_ integrated|integrate|VBN|_ at|at|IN|_ mbhA|mbha|NN|_ and|and|CC|_ hyfC|hyfc|NN|GEN
strain|strain|NN|_ :|:|:|_ unevolved|unevolved|JJ|_ parent|parent|NN|_ strain|strain|NN|_
All|All|NNP|_ samples|sample|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rnasey|Rnasey|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ ,|,|,|_ following|follow|VBG|_ standard|standard|JJ|_ protocol|protocol|NN|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ at|at|IN|_ Purdue|Purdue|NNP|_ using|use|VBG|_ an|a|DT|_ adapted|adapt|VBN|_ SOLiD|SOLiD|NNP|_ Total|Total|NNP|_ RNA-Seq|RNA-Seq|NNP|_ Kit|kit|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ DNase|dnase|NN|_ I|i|CD|_ digested|digest|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ RNase|rnase|NN|_ III|iii|CD|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ labeled|label|VBN|_ as|as|IN|_ TEX|TEX|NNP|_ were|be|VBD|_ also|also|RB|_ subsequently|subsequently|RB|_ digested|digest|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ Exonuclease|Exonuclease|NNP|_ -LRB-|-lrb-|-LRB-|_ TEX|TEX|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Pyrophosphate|pyrophosphate|NN|_ groups|group|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ ′|′|NN|_ terminus|terminus|NN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ an|a|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ ′|′|NN|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ standard|standard|JJ|_ SOLiD|solid|NN|_ 4|4|CD|_ Total|total|JJ|_ RNA-Seq|rna-seq|NN|_ protocol|protocol|NN|_ .|.|.|_ RNA-seq|rna-seq|NN|_ via|via|IN|_ SOLiD|solid|JJ|_ 4|4|CD|_ sequencing|sequencing|NN|_ of|of|IN|_ libraries|library|NNS|_ prepared|prepare|VBN|_ by|by|IN|_ ligation|ligation|NN|_ based|base|VBN|_ chemistry|chemistry|NN|_ to|to|TO|_ provide|provide|VB|_ strand-specific|strand-specific|JJ|_ datasets|dataset|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
For|for|IN|_ alignment|alignment|NN|_ of|of|IN|_ the|the|DT|_ SAET|SAET|NNP|_ reads|read|VBZ|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ RefSeq|refseq|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ short|short|JJ|_ read|read|NN|_ alignment|alignment|NN|_ tool|tool|NN|_ Bowtie|Bowtie|NNP|_ ver|ver|NN|_ .|.|.|_ 1.8|1.8|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ PMID|pmid|NN|_ 19261174|19261174|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ utilized|utilize|VBN|_ in|in|IN|_ three|three|CD|_ consecutive|consecutive|JJ|_ passes|pass|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ dataset|dataset|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ first|first|JJ|_ pass|pass|NN|_ ,|,|,|_ we|we|PRP|_ use|use|VBP|_ paired|paired|JJ|_ end|end|NN|_ color|color|NN|_ space|space|NN|_ mapping|mapping|NN|_ with|with|IN|_ a|a|DT|_ distance|distance|NN|_ cutoff|cutoff|NN|_ of|of|IN|_ 350|350|CD|_ bases|basis|NNS|_ between|between|IN|_ read|read|NN|_ mates|mate|NNS|_ .|.|.|_ Bowtie|Bowtie|NNP|_ parameters|parameter|NNS|_ were|be|VBD|_ set|set|VBN|_ to|to|TO|_ include|include|VB|_ only|only|RB|_ perfect|perfect|JJ|_ matches|match|NNS|_ and|and|CC|_ suppress|suppress|VBP|_ reads|read|VBZ|_ that|that|IN|_ map|map|NN|GEN to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ genome|genome|NN|_ location|location|NN|_ ,|,|,|_ i.e.|i.e.|FW|_ ,|,|,|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ are|be|VBP|_ retained|retain|VBN|_ .|.|.|_ In|in|IN|_ practice|practice|NN|_ we|we|PRP|_ found|find|VBD|_ the|the|DT|_ efficiency|efficiency|NN|_ of|of|IN|_ paired|paired|JJ|_ end|end|NN|_ mapping|mapping|NN|_ was|be|VBD|_ between|between|IN|_ 3|3|CD|_ and|and|CC|_ 10|10|CD|_ %|%|NN|_ .|.|.|_ To|to|TO|_ improve|improve|VB|_ the|the|DT|_ overall|overall|JJ|_ alignment|alignment|NN|_ we|we|PRP|_ mapped|map|VBD|_ the|the|DT|_ orphan|orphan|JJ|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ reads|read|VBZ|_ in|in|IN|_ two|two|CD|_ additional|additional|JJ|_ passes|pass|NNS|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_ The|the|DT|_ output|output|NN|_ of|of|IN|_ the|the|DT|_ three|three|CD|_ passes|pass|VBZ|_ through|through|IN|_ Bowtie|Bowtie|NNP|_ was|be|VBD|_ three|three|CD|_ SAM|SAM|NNP|_ files|file|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Overall|overall|RB|_ ,|,|,|_ we|we|PRP|_ achieved|achieve|VBD|_ 40-60|40-60|CD|_ %|%|NN|_ mapping|mapping|NN|_ efficiency|efficiency|NN|_ with|with|IN|_ this|this|DT|_ three-pass|three-pass|JJ|_ strategy|strategy|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_ ;|;|:|_ Reference|Reference|NNP|_ genome|genome|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ RefSeq|refseq|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Paper|Paper|NNP|_ title|title|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ :|:|:|_ a|a|DT|_ cooperatively|cooperatively|RB|_ developed|develop|VBN|_ annotation|annotation|NN|_ snapshot|snapshot|NN|_ --|--|:|_ 2005|2005|CD|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_ post|post|NN|_ stationary|stationary|JJ|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ 180|180|CD|_ min|min|NN|_ post|post|NN|_ stationary|stationary|JJ|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_ post|post|NN|_ stationary|stationary|JJ|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ Late|late|JJ|_ log|log|NN|_ phase|phase|NN|_ OD|od|NN|_ 1.6|1.6|CD|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 0.1|0.1|CD|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 0.2|0.2|CD|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 0.3|0.3|CD|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 0.4|0.4|CD|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 0.8|0.8|CD|_
phase|phase|NN|_ of|of|IN|_ growth|growth|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 1.4|1.4|CD|_
Prior|prior|RB|_ to|to|TO|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ harvested|harvest|VBN|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80.0|-80.0|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ RNAlater|rnalater|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
rna|rna|NN|GEN treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ RNA|rna|NN|_ treatment|treatment|NN|_
rna|rna|NN|GEN treatment|treatment|NN|_ :|:|:|_ rRNA|rrna|NN|_ depleted|deplete|VBD|_
rna|rna|NN|GEN treatment|treatment|NN|_ :|:|:|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ ;|;|:|_ Terminal|terminal|JJ|_ Exonuclease|exonuclease|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ 04|04|CD|_ _|_|NN|_ rep1|rep1|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ 04|04|CD|_ _|_|NN|_ rep2|rep2|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ 04|04|CD|_ _|_|SYM|_ TEX|TEX|NNP|_
rpoS|rpos|NN|GEN _|_|CD|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ 16|16|CD|_ _|_|NN|_ rep1|rep1|NN|_
rpoS|rpos|NN|GEN _|_|NN|_ 180|180|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ TEX|TEX|NNP|_
Sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ by|by|IN|_ conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ sample|sample|NN|_ alignment|alignment|NN|_ -LRB-|-lrb-|-LRB-|_ BAM|bam|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|VBZ|_ to|to|TO|_ strand-specific|strand-specific|JJ|_ base|base|NN|_ count|count|NN|_ -LRB-|-lrb-|-LRB-|_ WIG|wig|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ To|to|TO|_ accomplish|accomplish|VB|_ this|this|DT|_ an|a|DT|_ in-house|in-house|JJ|_ script|script|NN|_ was|be|VBD|_ created|create|VBN|_ to|to|TO|_ extract|extract|VB|_ strand-specific|strand-specific|JJ|_ base|base|NN|_ count|count|NN|_ data|datum|NNS|_ from|from|IN|_ BAM|BAM|NNP|_ files|file|NNS|_ -LRB-|-lrb-|-LRB-|_ outputs|output|NNS|_ are|be|VBP|_ positive|positive|JJ|_ and|and|CC|_ negative|negative|JJ|_ strand|strand|NN|_ WIG|wig|NN|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ First|first|RB|_ ,|,|,|_ the|the|DT|_ script|script|NN|_ reads|read|VBZ|_ in|in|IN|_ the|the|DT|_ paired-end|paired-end|JJ|_ BAM|bam|NN|_ file|file|NN|_ and|and|CC|_ counts|count|VBZ|_ the|the|DT|_ nucleotides|nucleotide|NNS|_ spanning|span|VBG|_ inserts|insert|NNS|_ between|between|IN|_ the|the|DT|_ mated|mate|VBN|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ reads|read|VBZ|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ the|the|DT|_ script|script|NN|_ pulls|pull|VBZ|_ in|in|IN|_ the|the|DT|_ orphan|orphan|JJ|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ reads|read|VBZ|_ from|from|IN|_ the|the|DT|_ respective|respective|JJ|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ increments|increment|NNS|_ the|the|DT|_ base|base|NN|_ counts|count|VBZ|_ at|at|IN|_ each|each|DT|_ base|base|NN|_ location|location|NN|_ without|without|IN|_ duplicating|duplicate|VBG|_ the|the|DT|_ reads|read|VBZ|_ already|already|RB|_ incremented|increment|VBN|_ from|from|IN|_ the|the|DT|_ paired|paired|JJ|_ ends|end|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
sub|sub|NN|_ strain|strain|NN|_ :|:|:|_ BW38028|bw38028|NN|_
sub|sub|NN|_ strain|strain|NN|_ :|:|:|_ BW39452|bw39452|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ WIG|wig|NN|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ showing|show|VBG|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ sequence|sequence|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ normalized|normalize|VBN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ XSEQ|xseq|NN|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ the|the|DT|_ SOLiD|solid|NN|_ 4|4|CD|_ Genetic|genetic|JJ|_ Analyzer|Analyzer|NNP|_ System|System|NNP|_ are|be|VBP|_ passed|pass|VBN|_ through|through|IN|_ the|the|DT|_ ABI|ABI|NNP|_ Sequence|sequence|NN|_ Accuracy|Accuracy|NNP|_ Enhancement|enhancement|NN|_ Tool|Tool|NNP|_ -LRB-|-lrb-|-LRB-|_ SAET|SAET|NNP|_ -RRB-|-rrb-|-RRB-|_
Used|use|VBD|_ SAMTOOLS|samtools|NN|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ PMID|pmid|NN|_ 1950593|1950593|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ sort|sort|VB|_ and|and|CC|_ index|index|NN|_ the|the|DT|_ SAM|SAM|NNP|_ files|file|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ Bowtie|Bowtie|NNP|_ and|and|CC|_ convert|convert|VB|_ them|they|PRP|_ to|to|TO|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_
WIG|wig|NN|_ files|file|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ in-house|in-house|JJ|_ script|script|NN|_ that|that|WDT|_ reads|read|VBZ|_ in|in|IN|_ the|the|DT|_ raw|raw|JJ|_ WIG|wig|NN|_ files|file|NNS|_ while|while|IN|_ excluding|exclude|VBG|_ counts|count|NNS|_ from|from|IN|_ all|all|DT|_ 22|22|CD|_ rRNA|rrna|NN|_ genes|gene|NNS|_ .|.|.|_ A|a|DT|_ simple|simple|JJ|_ global|global|JJ|_ normalization|normalization|NN|_ approach|approach|NN|_ was|be|VBD|_ utilized|utilize|VBN|_ that|that|IN|_ multiplied|multiply|VBD|_ the|the|DT|_ count|count|NN|_ at|at|IN|_ each|each|DT|_ base|base|NN|_ location|location|NN|_ by|by|IN|_ 1|1|CD|_ billion|billion|CD|_ and|and|CC|_ divides|divide|VBZ|_ that|that|IN|_ value|value|NN|_ by|by|IN|_ the|the|DT|_ sum|sum|NN|_ of|of|IN|_ base|base|NN|_ counts|count|VBZ|_ at|at|IN|_ all|all|DT|_ base|base|NN|_ locations|location|NNS|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ .|.|.|_ This|this|DT|_ normalization|normalization|NN|_ strategy|strategy|NN|_ is|be|VBZ|_ anlogous|anlogous|JJ|_ to|to|TO|_ the|the|DT|_ Total|total|JJ|_ Count|count|NN|_ approach|approach|NN|_ used|use|VBD|_ for|for|IN|_ normalizing|normalize|VBG|_ gene-specific|gene-specific|JJ|_ read|read|NN|_ alignments|alignment|NNS|_ .|.|.|_ In|in|IN|_ this|this|DT|_ way|way|NN|_ ,|,|,|_ the|the|DT|_ base|base|NN|_ counts|count|NNS|_ are|be|VBP|_ expressed|express|VBN|_ as|as|IN|_ parts|part|NNS|_ per|per|IN|_ billion|billion|CD|_ .|.|.|_
WIG|wig|NN|_ files|file|NNS|_ were|be|VBD|_ viewed|view|VBN|_ and|and|CC|_ annotated|annotated|JJ|_ using|use|VBG|_ Jbrowse|Jbrowse|NNP|_ and|and|CC|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ .|.|.|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ BW38038|bw38038|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ BW39452|bw39452|NN|_ -LRB-|-lrb-|-LRB-|_ ΔrpoS|δrpos|NN|_ -RRB-|-rrb-|-RRB-|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP as|as|IN|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ in|in|IN|_ a|a|DT|_ 2L|2L|NNP|_ B.|B.|NNP|_ Braun|Braun|NNP|_ Biostat|Biostat|NNP|_ ®|®|NN|_ B|b|NN|_ fermenter|fermenter|NN|_ with|with|IN|_ working|work|VBG|_ volume|volume|NN|_ of|of|IN|_ 1|1|CD|_ L|l|NN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ pH|ph|NN|_ was|be|VBD|_ kept|keep|VBN|_ constant|constant|JJ|_ at|at|IN|_ 7.4|7.4|CD|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ dissolved|dissolve|VBD|_ oxygen|oxygen|NN|_ was|be|VBD|_ maintained|maintain|VBN|_ above|above|IN|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ saturation|saturation|NN|_ by|by|IN|_ adjusting|adjust|VBG|_ the|the|DT|_ agitation|agitation|NN|_ speeds|speed|NNS|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ of|of|IN|_ 270|270|CD|_ --|--|:|_ 500|500|CD|_ rpm|rpm|NN|_ with|with|IN|_ fixed|fix|VBN|_ 1.5|1.5|CD|_ liter|liter|NN|_
WT|WT|NNP|_ _|_|SYM|_ 01|01|CD|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 02|02|CD|_ _|_|NN|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 03|03|CD|_ _|_|NN|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 04|04|CD|_ _|_|NN|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 04|04|CD|_ _|_|NN|_ rep2|rep2|NN|_
WT|wt|JJ|_ _|_|NN|_ 04-R|04-r|NN|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 04|04|CD|_ _|_|SYM|_ TEX|TEX|NNP|_
WT|WT|NNP|_ _|_|SYM|_ 08|08|CD|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 14|14|CD|_ _|_|NN|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 16|16|CD|_ _|_|NN|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 16-R|16-r|NN|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 180|180|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
WT|wt|JJ|_ _|_|NN|_ 30min-R|30min-r|NN|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ TEX|TEX|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genomic|genomic|JJ|_ dna|dna|NN|_
genomic|genomic|JJ|_ DNA|dna|NN|_
MG1655|mg1655|NN|_ ,|,|,|_ SD197|sd197|NN|_ ,|,|,|_ SB227|sb227|NN|_ ,|,|,|_ SF301|sf301|NN|_ and|and|CC|_ SS046|ss046|NN|_
MG1655|mg1655|NN|_ ,|,|,|_ SD197|sd197|NN|_ ,|,|,|_ SB227|sb227|NN|_ ,|,|,|_ SF301|sf301|NN|_ and|and|CC|_ SS046|ss046|NN|_
ration|ration|NN|_ of|of|IN|_ median|median|NN|_ -LRB-|-lrb-|-LRB-|_ 635|635|CD|_
Ratio|ratio|NN|_ of|of|IN|_ median|median|JJ|_
reference|reference|NN|_ DNA|dna|NN|_
SB10|sb10|NN|_ _|_|NN|_ 1|1|CD|_
SB10|sb10|NN|_ _|_|NN|_ 2|2|CD|_
SB10|sb10|NN|_ _|_|CD|_ 3|3|CD|_
SB1|sb1|NN|_ _|_|NN|_ 1|1|CD|_
SB11|sb11|NN|_ _|_|NN|_ 1|1|CD|_
SB11|sb11|NN|_ _|_|NN|_ 2|2|CD|_
SB11|sb11|NN|_ _|_|CD|_ 3|3|CD|_
SB1|sb1|NN|_ _|_|NN|_ 2|2|CD|_
SB12|sb12|NN|_ _|_|NN|_ 1|1|CD|_
SB12|sb12|NN|_ _|_|NN|_ 2|2|CD|_
SB12|sb12|NN|_ _|_|CD|_ 3|3|CD|_
SB1|sb1|NN|_ _|_|CD|_ 3|3|CD|_
SB13|sb13|NN|_ _|_|NN|_ 1|1|CD|_
SB13|sb13|NN|_ _|_|NN|_ 2|2|CD|_
SB13|sb13|NN|_ _|_|CD|_ 3|3|CD|_
SB14|sb14|NN|_ _|_|NN|_ 1|1|CD|_
SB14|sb14|NN|_ _|_|NN|_ 2|2|CD|_
SB14|sb14|NN|_ _|_|CD|_ 3|3|CD|_
SB15|sb15|NN|_ _|_|NN|_ 1|1|CD|_
SB15|sb15|NN|_ _|_|NN|_ 2|2|CD|_
SB15|sb15|NN|_ _|_|CD|_ 3|3|CD|_
SB16|sb16|NN|_ _|_|NN|_ 1|1|CD|_
SB16|sb16|NN|_ _|_|NN|_ 2|2|CD|_
SB16|sb16|NN|_ _|_|CD|_ 3|3|CD|_
SB17|sb17|NN|_ _|_|NN|_ 1|1|CD|_
SB17|sb17|NN|_ _|_|NN|_ 2|2|CD|_
SB17|sb17|NN|_ _|_|CD|_ 3|3|CD|_
SB18|sb18|NN|_ _|_|NN|_ 1|1|CD|_
SB18|sb18|NN|_ _|_|NN|_ 2|2|CD|_
SB18|sb18|NN|_ _|_|CD|_ 3|3|CD|_
SB1|sb1|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
SB2|sb2|NN|_ _|_|NN|_ 1|1|CD|_
SB2|sb2|NN|_ _|_|NN|_ 2|2|CD|_
SB2|sb2|NN|_ _|_|CD|_ 3|3|CD|_
SB3|sb3|NN|_ _|_|NN|_ 1|1|CD|_
SB3|sb3|NN|_ _|_|NN|_ 2|2|CD|_
SB3|sb3|NN|_ _|_|CD|_ 3|3|CD|_
SB5|sb5|NN|_ _|_|NN|_ 1|1|CD|_
SB5|sb5|NN|_ _|_|NN|_ 2|2|CD|_
SB5|sb5|NN|_ _|_|CD|_ 3|3|CD|_
SB6|sb6|NN|_ _|_|NN|_ 1|1|CD|_
SB6|sb6|NN|_ _|_|NN|_ 2|2|CD|_
SB6|sb6|NN|_ _|_|CD|_ 3|3|CD|_
SB7|sb7|NN|_ _|_|NN|_ 1|1|CD|_
SB7|sb7|NN|_ _|_|NN|_ 2|2|CD|_
SB7|sb7|NN|_ _|_|CD|_ 3|3|CD|_
SB8|sb8|NN|_ _|_|NN|_ 1|1|CD|_
SB8|sb8|NN|_ _|_|NN|_ 2|2|CD|_
SB8|sb8|NN|_ _|_|CD|_ 3|3|CD|_
SB9|sb9|NN|_ _|_|CD|_ 1|1|CD|_
SB9|sb9|NN|_ _|_|NN|_ 2|2|CD|_
SB9|sb9|NN|_ _|_|SYM|_ 3|3|CD|_
SD10|sd10|NN|_ _|_|NN|_ 1|1|CD|_
SD10|sd10|NN|_ _|_|NN|_ 2|2|CD|_
SD10|sd10|NN|_ _|_|CD|_ 3|3|CD|_
SD11|sd11|NN|_ _|_|NN|_ 1|1|CD|_
SD11|sd11|NN|_ _|_|NN|_ 2|2|CD|_
SD11|sd11|NN|_ _|_|CD|_ 3|3|CD|_
SD12|sd12|NN|_ _|_|NN|_ 1|1|CD|_
SD12|sd12|NN|_ _|_|NN|_ 2|2|CD|_
SD12|sd12|NN|_ _|_|CD|_ 3|3|CD|_
SD13|sd13|NN|_ _|_|NN|_ 1|1|CD|_
SD13|sd13|NN|_ _|_|NN|_ 2|2|CD|_
SD13|sd13|NN|_ _|_|CD|_ 3|3|CD|_
SD2|sd2|NN|_ _|_|NN|_ 1|1|CD|_
SD2|sd2|NN|_ _|_|NN|_ 2|2|CD|_
SD2|sd2|NN|_ _|_|CD|_ 3|3|CD|_
SD3|sd3|NN|_ _|_|NN|_ 1|1|CD|_
SD3|sd3|NN|_ _|_|NN|_ 2|2|CD|_
SD3|sd3|NN|_ _|_|CD|_ 3|3|CD|_
SD4|sd4|NN|_ _|_|NN|_ 1|1|CD|_
SD4|sd4|NN|_ _|_|NN|_ 2|2|CD|_
SD4|sd4|NN|_ _|_|CD|_ 3|3|CD|_
SD5|sd5|NN|_ _|_|NN|_ 1|1|CD|_
SD5|sd5|NN|_ _|_|NN|_ 2|2|CD|_
SD5|sd5|NN|_ _|_|CD|_ 3|3|CD|_
SD6|sd6|NN|_ _|_|NN|_ 1|1|CD|_
SD6|sd6|NN|_ _|_|NN|_ 2|2|CD|_
SD6|sd6|NN|_ _|_|CD|_ 3|3|CD|_
SD7|sd7|NN|_ _|_|NN|_ 1|1|CD|_
SD7|sd7|NN|_ _|_|NN|_ 2|2|CD|_
SD7|sd7|NN|_ _|_|CD|_ 3|3|CD|_
SD8|sd8|NN|_ _|_|NN|_ 1|1|CD|_
SD8|sd8|NN|_ _|_|NN|_ 2|2|CD|_
SD8|sd8|NN|_ _|_|CD|_ 3|3|CD|_
SD9|sd9|NN|_ _|_|NN|_ 1|1|CD|_
SD9|sd9|NN|_ _|_|NN|_ 2|2|CD|_
SD9|sd9|NN|_ _|_|CD|_ 3|3|CD|_
SF1a|sf1a|NN|_ _|_|NN|_ 1|1|CD|_
SF1a|sf1a|NN|_ _|_|NN|_ 2|2|CD|_
SF1a|sf1a|NN|_ _|_|CD|_ 3|3|CD|_
SF1b|sf1b|NN|_ _|_|NN|_ 1|1|CD|_
SF1b|sf1b|NN|_ _|_|NN|_ 2|2|CD|_
SF1b|sf1b|NN|_ _|_|CD|_ 3|3|CD|_
SF2b|sf2b|NN|_ _|_|NN|_ 1|1|CD|_
SF2b|sf2b|NN|_ _|_|NN|_ 2|2|CD|_
SF2b|sf2b|NN|_ _|_|CD|_ 3|3|CD|_
SF3|sf3|NN|_ _|_|NN|_ 1|1|CD|_
SF3|sf3|NN|_ _|_|NN|_ 2|2|CD|_
SF3|sf3|NN|_ _|_|CD|_ 3|3|CD|_
SF4a|sf4a|NN|_ _|_|NN|_ 1|1|CD|_
SF4a|sf4a|NN|_ _|_|NN|_ 2|2|CD|_
SF4a|sf4a|NN|_ _|_|CD|_ 3|3|CD|_
SF4b|sf4b|NN|_ _|_|NN|_ 1|1|CD|_
SF4b|sf4b|NN|_ _|_|NN|_ 2|2|CD|_
SF4b|sf4b|NN|_ _|_|CD|_ 3|3|CD|_
SF5|sf5|NN|_ _|_|NN|_ 2|2|CD|_
SF5|sf5|NN|_ _|_|CD|_ 3|3|CD|_
SF6|sf6|NN|_ _|_|NN|_ 1|1|CD|_
SF6|sf6|NN|_ _|_|NN|_ 2|2|CD|_
SF6|sf6|NN|_ _|_|CD|_ 3|3|CD|_
SFx|sfx|NN|_ _|_|NN|_ 2|2|CD|_
SFx|SFx|NNP|_ _|_|SYM|_ 3|3|CD|_
SFy|sfy|NN|_ _|_|NN|_ 1|1|CD|_
SFy|sfy|NN|_ _|_|NN|_ 2|2|CD|_
SFy|sfy|NN|_ _|_|CD|_ 3|3|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ 13|13|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ 14|14|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ 15|15|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ 15|15|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ 16|16|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ 17|17|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ 18|18|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serogroup|serogroup|NN|_ 1|1|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serogroup|serogroup|NN|_ 2|2|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 1|1|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 10|10|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 11|11|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 12|12|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 13|13|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype2|serotype2|NN|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 2|2|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype3|serotype3|NN|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 3|3|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 5|5|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 6|6|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 7|7|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 7|7|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 8|8|CD|_
Shigella|shigella|NN|_ boydii|boydii|NN|_ serotype|serotype|NN|_ 9|9|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 10|10|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 11|11|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 12|12|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 13|13|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 2|2|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 3|3|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 4|4|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 5|5|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 6|6|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 7|7|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteriae|NN|_ 8|8|CD|_
Shigella|shigella|NN|_ dysenteriae|dysenteria|NNS|_ 9|9|CD|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 1a|1a|NN|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 1b|1b|NN|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 2b|2b|JJ|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 3|3|CD|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 4a|4a|NN|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 4b|4b|NN|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 5|5|CD|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ 6|6|CD|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ variant|variant|JJ|_ x|x|NN|_
Shigella|shigella|NN|_ flexneri|flexneri|NN|_ variant|variant|JJ|_ y|y|NN|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ 5|5|CD|_ l|l|NN|_ fermentor|fermentor|JJ|_ BIOSTAT|biostat|NN|_ B-DCU|b-dcu|NN|_ -LRB-|-lrb-|-LRB-|_ Sartorius|Sartorius|NNP|_ BBI|BBI|NNP|_ Systems|Systems|NNPS|_ Inc.|Inc.|NNP|_ .|.|.|_ Melsungen|melsungen|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ controlled|control|VBN|_ temperature|temperature|NN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ pH|ph|NN|_ 7.0|7.0|CD|_ ,|,|,|_ and|and|CC|_ dissolved|dissolve|VBD|_ oxygen|oxygen|NN|_ tension|tension|NN|_ 30|30|CD|_ %|%|NN|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ volume|volume|NN|_ was|be|VBD|_ 2|2|CD|_ l.|l.|NN|_ All|all|DT|_ reagents|reagent|NNS|_ were|be|VBD|_ purchased|purchase|VBN|_ from|from|IN|_ Sigma-Aldrich|Sigma-Aldrich|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ .|.|.|_ The|the|DT|_ synthetic|synthetic|JJ|_ culture|culture|NN|_ medium|medium|NN|_ had|have|VBD|_ the|the|DT|_ following|follow|VBG|_ composition|composition|NN|_ -LRB-|-lrb-|-LRB-|_ g|g|NN|_ l-1|l-1|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 8|8|CD|_ ,|,|,|_ glucose|glucose|NN|SUPP ;|;|:|_ 14.6|14.6|CD|_ ,|,|,|_ K2HPO4|k2hpo4|NN|_ ;|;|:|_ 3.6|3.6|CD|_ ,|,|,|_ NaH2PO4|nah2po4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ;|;|:|_ 2.68|2.68|CD|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ;|;|:|_ 2|2|CD|_ ,|,|,|_ Na2SO4|na2so4|NN|_ ;|;|:|_ 1|1|CD|_ ,|,|,|_ MgSO4|mgso4|NN|_ ;|;|:|_ 1|1|CD|_ ,|,|,|_ Na-citrate|na-citrate|NN|_ ;|;|:|_ 0.5|0.5|CD|_ ,|,|,|_ NH4Cl|nh4cl|NN|_ ;|;|:|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ 10|10|CD|_ mg|mg|NN|_ l-1|l-1|NN|_ of|of|IN|_ thiamine|thiamine|NN|SUPP ;|;|:|_ 3|3|CD|_ ml|ml|NN|_ of|of|IN|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ g|g|NN|_ l-1|l-1|NN|_ 20.0|20.0|CD|_ ,|,|,|_ Na-EDTA|na-edta|NN|_ ;|;|:|_ 15.0|15.0|CD|_ ,|,|,|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6H2O|6h2o|NN|_ ;|;|:|_ 0.5|0.5|CD|_ ,|,|,|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2H2O|2h2o|NN|_ ;|;|:|_ 0.2|0.2|CD|_ ,|,|,|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7H2O|7h2o|NN|_ ;|;|:|_ 0.2|0.2|CD|_ ,|,|,|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6H2O|6h2o|NN|_ ;|;|:|_ 0.2|0.2|CD|_ ,|,|,|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5H2O|5h2o|NN|_ ;|;|:|_ 0.2|0.2|CD|_ ,|,|,|_ MnSO4|mnso4|NN|_ ·|·|NN|_ 4H2O|4h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ chemostat|chemostat|NN|_ culture|culture|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ adding|add|VBG|_ feed|feed|NN|_ medium|medium|NN|_
BL21|bl21|NN|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.20|0.20|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.20|0.20|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.20|0.20|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.20|0.20|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 4|4|LS|_ -RRB-|-rrb-|-RRB-|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.46|0.46|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 1|1|LS|_ -RRB-|-rrb-|-RRB-|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.46|0.46|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.46|0.46|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 3|3|LS|_ -RRB-|-rrb-|-RRB-|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.46|0.46|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 4|4|LS|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ samples|sample|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ taken|take|VBN|_ during|during|IN|_ fermentation|fermentation|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ the|the|DT|_ cultivation|cultivation|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 10,000|10,000|CD|_ g|g|NN|_ ,|,|,|_ 1|1|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ separated|separate|VBN|_ from|from|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ ,|,|,|_ and|and|CC|_ rapidly|rapidly|RB|_ frozen|freeze|VBN|_ in|in|IN|_ dry|dry|JJ|_ ice|ice|NN|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ until|until|IN|_ analysis|analysis|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.20|0.20|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ mu|mu|NN|_ =|=|JJ|_ 0.46|0.46|CD|_ -RRB-|-rrb-|-RRB-|_
Expression|expression|NN|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ the|the|DT|_ Microarray|Microarray|NNP|_ Analysis|analysis|NN|_ Suite|suite|NN|_ ,|,|,|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ Affymetrix|Affymetrix|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Global|global|JJ|_ scaling|scaling|NN|_ was|be|VBD|_ performed|perform|VBN|_ to|to|TO|_ compare|compare|VB|_ genes|gene|NNS|_ between|between|IN|_ chips|chip|NNS|_ .|.|.|_ Each|each|DT|_ chip|chip|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ a|a|DT|_ target|target|NN|_ intensity|intensity|NN|_ value|value|NN|_ of|of|IN|_ 2,500|2,500|CD|_ .|.|.|_ Expression|expression|NN|_ analysis|analysis|NN|_ files|file|NNS|_ created|create|VBN|_ by|by|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ ,|,|,|_ version|version|NN|_ 5.0|5.0|CD|_ ,|,|,|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ for|for|IN|_ data|datum|NNS|_ formatting|formatting|NN|_ .|.|.|_
Genotype|Genotype|NNP|_ :|:|:|_ F|f|NN|_ -|-|:|_ ompT|ompt|NN|GEN hsdSB|hsdsb|NN|_ -LRB-|-lrb-|-LRB-|_ rB-mB|rb-mb|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ gal|gal|NN|_ dcm|dcm|NN|GEN -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
Trizol|trizol|NN|_ extraction|extraction|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ M63|m63|NN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ cell|cell|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ controlled|control|VBN|_ ~|~|SYM|_ 10|10|CD|_ ^|^|SYM|_ 8|8|CD|_ cells|cell|NNS|_
condition|condition|NN|_ :|:|:|_ 37ºC|37ºc|NN|_
condition|condition|NN|_ :|:|:|_ 45ºC|45ºc|NN|_
E.|e.|FW|_ coli|coli|FW|_ Type|type|NN|_ _|_|CD|_ II|ii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ II|ii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ II|ii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ Type|type|NN|_ _|_|CD|_ II|ii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ II|ii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ II|ii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ Type|type|NN|_ _|_|CD|_ III|iii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ III|iii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ III|iii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ Type|type|NN|_ _|_|CD|_ III|iii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ III|iii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ Type|type|NN|_ _|_|CD|_ III|iii|CD|_ genotype|genotype|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ written|write|VBN|_ in|in|IN|_ R|r|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ finite|finite|JJ|_ hybridisation|hybridisation|NN|_ -LRB-|-lrb-|-LRB-|_ FH|fh|NN|_ -RRB-|-rrb-|-RRB-|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Ono|Ono|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ thermodynamic|thermodynamic|JJ|_ model|model|NN|_ of|of|IN|_ non-specific|non-specific|JJ|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ NSB|nsb|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ short|short|JJ|_ nucleotide|nucleotide|NN|_ microarrays|microarray|NNS|_ -LRB-|-lrb-|-LRB-|_ Furusawa|Furusawa|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ DH1ΔleuB|dh1δleub|NN|_ :|:|:|_ :|:|:|_ gfpuv5-kmr|gfpuv5-kmr|JJ|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ cold|cold|JJ|_ phenol-ethanol|phenol-ethanol|JJ|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ of|of|IN|_ phenol|phenol|NN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ prepared|prepare|VBN|_ in|in|IN|_ advance|advance|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 7,000|7,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ in|in|IN|_ RNA|rna|NN|_ Later|later|RB|_ solution|solution|NN|_ at|at|IN|_ -80|-80|CD|_ ºC|ºc|NN|_ .|.|.|_ The|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Venlo|Venlo|NNP|_ ,|,|,|_ Netherlands|Netherlands|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ isolate|isolate|VB|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ with|with|IN|_ RNaseOut|rnaseout|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacture|manufacture|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ saturated|saturated|JJ|_ phenol|phenol|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655-C8-1|mg1655-c8-1|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655-C8-3|mg1655-c8-3|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655-control-1|mg1655-control-1|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655-control-2|mg1655-control-2|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655-control-3|mg1655-control-3|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655-MOPS|mg1655-mops|NN|_ +2|+2|CD|_ %|%|NN|_ Dextrose|dextrose|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655-MOPS|mg1655-mops|NN|_ +2|+2|CD|_ %|%|NN|_ Dextrose|dextrose|NN|_ +10|+10|CD|_ mM|mm|NN|KWSUPP C8|c8|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED +|+|CC|_ 2|2|CD|_ %|%|NN|_ Dextrose|dextrose|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ +|+|CC|_ -|-|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP octanoic|octanoic|JJ|_ acid|acid|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ =|=|JJ|_ 7.0|7.0|CD|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ OD550|od550|NN|_ 0.05|0.05|CD|_ to|to|TO|_ ~|~|CD|_ 0.8|0.8|CD|_ and|and|CC|_ harvested|harvest|VBN|_ at|at|IN|_ Midlog|Midlog|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
MATLAB|MATLAB|NNP|_ v.|v.|CC|_ R2012b|r2012b|NN|_ program|program|NN|_ using|use|VBG|_ GCRMA|GCRMA|NNP|_ algorithm|algorithm|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ treatment|treatment|NN|_ condition|condition|NN|_ includes|include|VBZ|_ adding|add|VBG|_ 10|10|CD|_ mM|mm|NN|KWSUPP octanoic|octanoic|JJ|_ acid|acid|NN|_ during|during|IN|_ logarithmic|logarithmic|JJ|_ growth|growth|NN|_ .|.|.|_
As|as|IN|_ described|describe|VBN|_ in|in|IN|_ description|description|NN|_
As|as|IN|_ described|describe|VBN|_ in|in|IN|_ the|the|DT|_ description|description|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ grown|grow|VBN|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ added|add|VBN|_ 5|5|CD|_ μM|μm|NN|_ TPEN|tpen|NN|_
E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ grown|grow|VBN|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ without|without|IN|_ added|add|VBN|_ TPEN|tpen|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
mRNA|mrna|NN|_
Transcriptional|transcriptional|JJ|_ response|response|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ to|to|TO|_ TPEN|tpen|NN|_ -LRB-|-lrb-|-LRB-|_ m1|m1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ response|response|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ to|to|TO|_ TPEN|tpen|NN|_ -LRB-|-lrb-|-LRB-|_ m2|m2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ response|response|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ to|to|TO|_ TPEN|tpen|NN|_ -LRB-|-lrb-|-LRB-|_ m3|m3|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ response|response|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ to|to|TO|_ TPEN|tpen|NN|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ response|response|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ to|to|TO|_ TPEN|tpen|NN|_ -LRB-|-lrb-|-LRB-|_ t2|t2|NN|_ -RRB-|-rrb-|-RRB-|_
Transcriptional|transcriptional|JJ|_ response|response|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ to|to|TO|_ TPEN|tpen|NN|_ -LRB-|-lrb-|-LRB-|_ t3|t3|NN|_ -RRB-|-rrb-|-RRB-|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ either|either|CC|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 2.8-liter|2.8-liter|JJ|_ flask|flask|NN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ aeration|aeration|NN|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ reached|reach|VBD|_ 0.3|0.3|CD|_ .|.|.|_
bacteria|bacterium|NNS|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E|e|NN|_ coli|coli|NN|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ the|the|DT|_ footprint|footprint|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ footprint|footprint|NN|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ at|at|IN|_ 37C|37c|NN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4C|4c|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
media|media|NNS|_ :|:|:|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_
mRNA-seq|mrna-seq|NN|_ in|in|IN|_ rich|rich|JJ|_ defined|define|VBN|_ media|media|NNS|_
Ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ '|'|''|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ More|more|RBR|_ at|at|IN|_ G.W.|G.W.|NNP|_ Li|Li|NNP|_ ,|,|,|_ D.|D.|NNP|_ Burkhardt|Burkhardt|NNP|_ ,|,|,|_ C.A.|C.A.|NNP|_ Gross|Gross|NNP|_ ,|,|,|_ J.|J.|NNP|_ S.|S.|NNP|_ Weissman|Weissman|NNP|_ -LRB-|-lrb-|-LRB-|_ Cell|cell|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_ files|file|NNS|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E|E|NNP|_ coli|coli|NN|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
EC|EC|NNP|_ _|_|VBD|_ Cont1|cont1|NN|_ _|_|NN|_ DNA|dna|NN|_
EC|ec|NN|_ _|_|CD|_ Cont1|cont1|NN|_ _|_|NN|_ RNA|rna|NN|_
EC|ec|NN|_ _|_|CD|_ Cont2|cont2|NN|_ _|_|NN|_ DNA|dna|NN|_
EC|ec|NN|_ _|_|CD|_ Cont2|cont2|NN|_ _|_|NN|_ RNA|rna|NN|_
EC|ec|NN|_ _|_|CD|_ Trim1|trim1|NN|_ _|_|NN|_ DNA|dna|NN|_
EC|ec|NN|_ _|_|CD|_ Trim1|trim1|NN|_ _|_|NN|_ RNA|rna|NN|_
EC|ec|NN|_ _|_|CD|_ Trim2|trim2|NN|_ _|_|NN|_ DNA|dna|NN|_
EC|ec|NN|_ _|_|CD|_ Trim2|trim2|NN|_ _|_|NN|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ all|all|PDT|_ the|the|DT|_ samples|sample|NNS|_ ;|;|:|_ when|when|WRB|_ 1|1|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Streptococcus|streptococcus|NN|_ pneumoniae|pneumoniae|FW|_ D39|d39|NN|_ -LRB-|-lrb-|-LRB-|_ assembly|assembly|NN|_ ASM1436v1|asm1436v1|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ 1.8|1.8|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ following|follow|VBG|_ protocol|protocol|NN|_ :|:|:|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ first|first|JJ|_ treated|treat|VBN|_ with|with|IN|_ rDNase|rdnase|NN|_ .|.|.|_ From|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ molecules|molecule|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ fragmented|fragmented|JJ|_ with|with|IN|_ ultrasound|ultrasound|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ pulses|pulse|NNS|_ of|of|IN|_ 30|30|CD|_ sec|sec|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Firststrand|Firststrand|NNP|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ primed|prime|VBN|_ with|with|IN|_ a|a|DT|_ N6|n6|NN|_ randomized|randomize|VBD|_ primer|primer|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ was|be|VBD|_ finally|finally|RB|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ 16-18|16-18|CD|_ cycles|cycle|NNS|_ ,|,|,|_ depending|depend|VBG|_ on|on|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ a|a|DT|_ proof|proof|NN|_ reading|reading|NN|_ enzyme|enzyme|NN|_ .|.|.|_ Aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ were|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ .|.|.|_
Library|Library|NNP|_ preparation|preparation|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ following|follow|VBG|_ protocol|protocol|NN|_ :|:|:|_ the|the|DT|_ DNA|dna|NN|_ samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ultrasound|ultrasound|NN|_ -LRB-|-lrb-|-LRB-|_ 3-5|3-5|CD|_ pulses|pulse|NNS|_ of|of|IN|_ 30|30|CD|_ sec|sec|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ end-repair|end-repair|NN|_ ,|,|,|_ TruSeq|truseq|NN|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ DNA|dna|NN|_ fragments|fragment|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ the|the|DT|_ DNA|dna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ about|about|RB|_ 20-30|20-30|CD|_ ng|ng|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depleted|deplete|VBD|_
OTHER|OTHER|NNP|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ strain|strain|NN|_ JM83|jm83|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ 1|1|CD|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_ In|in|IN|_ short|short|RB|_ ,|,|,|_ exons|exon|NNS|_ from|from|IN|_ all|all|DT|_ isoforms|isoform|NNS|_ of|of|IN|_ a|a|DT|_ gene|gene|NN|_ were|be|VBD|_ merged|merge|VBN|_ to|to|TO|_ create|create|VB|_ one|one|CD|_ meta-transcript|meta-transcript|JJ|_ .|.|.|_ The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ falling|fall|VBG|_ in|in|IN|_ the|the|DT|_ exons|exon|NNS|_ of|of|IN|_ this|this|DT|_ meta-transcript|meta-transcript|JJ|_ were|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ meta-transcript|meta-transcript|JJ|_ and|and|CC|_ by|by|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ the|the|DT|_ library|library|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ samples|sample|NNS|_ this|this|DT|_ was|be|VBD|_ done|do|VBN|_ internally|internally|RB|_ by|by|IN|_ Rockhopper|Rockhopper|NNP|_ version|version|NN|_ 1.21|1.21|CD|_ after|after|IN|_ aligning|align|VBG|_ reads|read|VBZ|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
S.|S.|NNP|_ pneumoniae|pneumoniae|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ D39|d39|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Rockhopper|rockhopper|JJ|_ version|version|NN|_ 1.21|1.21|CD|_ ,|,|,|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_ E.|e.|FW|_ coli|coli|FW|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ K-12|k-12|NN|_ ,|,|,|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ whole|whole|JJ|_ genome|genome|NN|_ with|with|IN|_ Bowtie|bowtie|NN|_ 2|2|CD|_ ,|,|,|_ using|use|VBG|_ parameters|parameter|NNS|_ --|--|:|_ mixed|mixed|JJ|_ --|--|:|_ discordant|discordant|JJ|_ -|-|:|_ D|d|NN|_ 10|10|CD|_ -|-|:|_ R|r|NN|_ 2|2|CD|_ -|-|:|_ N|n|NN|_ 0|0|CD|_ -|-|:|_ L|l|NN|_ 22|22|CD|_ -|-|:|_ i|i|FW|_ S|s|NN|_ ,0,2.50|,0,2.50|CD|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ JM83|jm83|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 0.5|0.5|CD|_ μg|μg|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ none|none|NN|_ -LRB-|-lrb-|-LRB-|_ untreated|untreated|JJ|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
Trimethoprim-treated|trimethoprim-treated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
Untreated|untreated|JJ|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_
BW25113-pCA24N|bw25113-pca24n|NN|_ _|_|CD|_ arT|art|NN|_ LB|lb|NN|_ 90|90|CD|_ min|min|NN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
BW25113-pCA24N|bw25113-pca24n|NN|_ LB|lb|NN|_ 90|90|CD|_ min|min|NN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ -LRB-|-lrb-|-LRB-|_ Biospec|biospec|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ mRNA|mrna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RNALater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ ethanol-dry|ethanol-dry|JJ|_ ice|ice|NN|_ .|.|.|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ GenomeChipOperating|GenomeChipOperating|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ GCOS|GCOS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
genotype|genotype|NN|_
overexpression|overexpression|NN|_ of|of|IN|_ arT|art|NN|_ -LRB-|-lrb-|-LRB-|_ pCA24N|pca24n|NN|_ _|_|CD|_ arT|art|NN|_ -RRB-|-rrb-|-RRB-|_
overexpression|overexpression|NN|_ of|of|IN|_ empty|empty|JJ|_ vector|vector|NN|_ -LRB-|-lrb-|-LRB-|_ pCA24N|pca24n|NN|_ -RRB-|-rrb-|-RRB-|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LBCm30|lbcm30|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ fresh|fresh|JJ|_ LBCm30|lbcm30|NN|_ ,|,|,|_ grown|grow|VBN|_ for|for|IN|_ 2.5|2.5|CD|_ h|h|NN|_ ,|,|,|_ and|and|CC|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ for|for|IN|_ 90|90|CD|_ min|min|NN|_ -LRB-|-lrb-|-LRB-|_ final|final|JJ|_ OD600|od600|NN|_ =|=|JJ|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ 2|2|CD|_ %|%|NN|_ NaCl|nacl|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 3.5|3.5|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 3.5|3.5|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 4.5|4.5|CD|_ %|%|NN|_ NaCl|nacl|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 5.5|5.5|CD|_ %|%|NN|_ NaCl|nacl|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 5|5|CD|_ %|%|NN|_ NaCl|nacl|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ,|,|,|_ stressed|stress|VBN|_ by|by|IN|_ NaCl|nacl|NN|_ ,|,|,|_ in|in|IN|_ presence|presence|NN|_ of|of|IN|_ glycine|glycine|NN|_ betaine|betaine|NN|_
E.|e.|FW|_ coli|coli|FW|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ glucose|glucose|NN|SUPP minimal|minimal|JJ|_ medium|medium|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ the|the|DT|_ osmoprotectant|osmoprotectant|JJ|_ glycine|glycine|NN|_ beatine|beatine|NN|_ with|with|IN|_ a|a|DT|_ range|range|NN|_ of|of|IN|_ salt|salt|NN|_ concentrations|concentration|NNS|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 3.5|3.5|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ repeats|repeat|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 4.5|4.5|CD|_ ,|,|,|_ 5|5|CD|_ and|and|CC|_ 5.5|5.5|CD|_ %|%|NN|_ NaCl|nacl|NN|_ .|.|.|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ inoculated|inoculate|VBN|_ at|at|IN|_ 104|104|CD|_ cfu|cfu|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ by|by|IN|_ lysis|lysis|NN|_ in|in|IN|_ lysozyme|lysozyme|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|exponential|JJ|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
The|the|DT|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ is|be|VBZ|_ based|base|VBN|_ on|on|IN|_ cross|cross|NN|_ validation|validation|NN|_ with|with|IN|_ datasets|dataset|NNS|_ generated|generate|VBN|_ by|by|IN|_ Monte-Carlo|Monte-Carlo|NNP|_ simulation|simulation|NN|_ .|.|.|_ The|the|DT|_ null|null|JJ|_ hypothesis|hypothesis|NN|_ was|be|VBD|_ that|that|IN|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ changes|change|NNS|_ monotonously|monotonously|RB|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ NaCl|nacl|NN|_ concentration|concentration|NN|_ .|.|.|_ The|the|DT|_ existence|existence|NN|_ of|of|IN|_ a|a|DT|_ deviation|deviation|NN|_ from|from|IN|_ monotony|monotony|NN|_ was|be|VBD|_ tested|test|VBN|_ by|by|IN|_ F-tests|f-test|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ probe|probe|NN|_ .|.|.|_ By|by|IN|_ comparing|compare|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ probes|probe|NNS|_ with|with|IN|_ the|the|DT|_ lowest|lowest|JJS|_ p|p|NN|_ -LRB-|-lrb-|-LRB-|_ F|f|NN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ NaCl|nacl|NN|_ concentrations|concentration|NNS|_ with|with|IN|_ analogous|analogous|JJ|_ results|result|NNS|_ generated|generate|VBN|_ from|from|IN|_ Monte-Carlo|Monte-Carlo|NNP|_ sampling|sampling|NN|_ of|of|IN|_ the|the|DT|_ null|null|JJ|_ hypothesis|hypothesis|NN|_ ,|,|,|_ we|we|PRP|_ show|show|VBP|_ that|that|IN|_ it|it|PRP|_ is|be|VBZ|_ very|very|RB|_ unlikely|unlikely|JJ|_ that|that|IN|_ a|a|DT|_ switch|switch|NN|_ between|between|IN|_ 4.5|4.5|CD|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ NaCl|nacl|NN|_ could|could|MD|_ have|have|VB|_ happened|happen|VBN|_ by|by|IN|_ chance|chance|NN|_ -LRB-|-lrb-|-LRB-|_ in|in|IN|_ fact|fact|NN|_ p|p|NN|_ <<|<<|CD|_ 0.01|0.01|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ normalised|normalised|JJ|_ manually|manually|RB|_ in|in|IN|_ Excel|Excel|NNP|_ .|.|.|_ For|for|IN|_ each|each|DT|_ spot|spot|NN|_ ,|,|,|_ the|the|DT|_ median|median|NN|_ of|of|IN|_ the|the|DT|_ spot|spot|NN|_ intensity|intensity|NN|_ minus|minus|CC|_ the|the|DT|_ background|background|NN|_ were|be|VBD|_ considered|consider|VBN|_ .|.|.|_ Because|because|IN|_ we|we|PRP|_ wanted|want|VBD|_ to|to|TO|_ compare|compare|VB|_ different|different|JJ|_ environmental|environmental|JJ|_ conditions|condition|NNS|_ ,|,|,|_ the|the|DT|_ cDNA|cdna|NN|_ signal|signal|NN|_ in|in|IN|_ each|each|DT|_ condition|condition|NN|_ was|be|VBD|_ normalised|normalised|JJ|_ to|to|TO|_ that|that|DT|_ of|of|IN|_ gDNA|gdna|NN|_ with|with|IN|_ M|m|NN|_ =|=|JJ|_ ln|ln|NN|_ -LRB-|-lrb-|-LRB-|_ cDNA|cdna|NN|_
0.5|0.5|CD|_ mg|mg|NN|_
antibody|antibody|NN|_ :|:|:|_ anti-DksA|anti-dksa|JJ|_ rabbit|rabbit|NN|_ polyclonal|polyclonal|JJ|_ antisera|antisera|NNS|_
antibody|antibody|NN|_ :|:|:|_ anti-RNAP|anti-rnap|JJ|_ b|b|NN|_ subunit|subunit|NN|_ NT63|nt63|NN|_ monoclonal|monoclonal|JJ|_ antibodies|antibody|NNS|_
antibody|antibody|NN|_ :|:|:|_ anti-s70|anti-s70|JJ|_ monoclonal|monoclonal|JJ|_ antibodies|antibody|NNS|_
antibody|antibody|NN|_ :|:|:|_ None|none|NN|_ ,|,|,|_ input|input|NN|_ DNA|dna|NN|_
Cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ before|before|IN|_ quenching|quench|VBG|_ with|with|IN|_ ice-cold|ice-cold|JJ|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ 100mM|100mm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ ,|,|,|_ washed|wash|VBN|_ with|with|IN|_ ice-cold|ice-cold|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ ml|ml|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300mM|300mM|NNP|_ NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ Misonix|Misonix|NNP|_ sonicator|sonicator|NN|_ -LRB-|-lrb-|-LRB-|_ S-4000|s-4000|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ cup|cup|NN|_ horn|horn|NN|_ -LRB-|-lrb-|-LRB-|_ 431C|431c|NN|_ -RRB-|-rrb-|-RRB-|_ set|set|NN|_ at|at|IN|_ 60|60|CD|_ %|%|NN|_ output|output|NN|_ ,|,|,|_ 10|10|CD|_ sec|sec|NN|_ ON|ON|NNP|_ and|and|CC|_ 10|10|CD|_ sec|sec|NN|_ OFF|off|NN|_ ,|,|,|_ for|for|IN|_ a|a|DT|_ total|total|JJ|_ sonication|sonication|NN|_ time|time|NN|_ of|of|IN|_ 16|16|CD|_ min|min|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
DdksA|ddksa|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ leucine|leucine|NN|SUPP ,|,|,|_ isoleucine|isoleucine|NN|_ ,|,|,|_ valine|valine|NN|_ ,|,|,|_ glycine|glycine|NN|_ ,|,|,|_ phenylalanine|phenylalanine|NN|SUPP ,|,|,|_ threonine|threonine|NN|_ -LRB-|-lrb-|-LRB-|_ 40|40|CD|_ mg|mg|NN|_
DksA|dksa|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ DdksA|ddksa|NN|_ cells|cell|NNS|_
DksA|dksa|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ wt|wt|JJ|_ cells|cell|NNS|_
DksA|dksa|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|NN|_ untreated|untreated|JJ|_
DksA|dksa|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep1|rep1|NN|_
DksA|dksa|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep2|rep2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_ DdksA|ddksa|NN|_
Input|input|NN|_ DNA|dna|NN|_ from|from|IN|_ DdksA|ddksa|NN|_ cells|cell|NNS|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ starved|starve|VBN|_ DdksA|ddksa|NN|_ cells|cell|NNS|_
Input|Input|NNP|_ DNA|dna|NN|_ from|from|IN|_ starved|starve|VBN|_ wt|wt|JJ|_ cells|cell|NNS|_
Input|input|NN|_ DNA|dna|NN|_ from|from|IN|_ wt|wt|JJ|_ cells|cell|NNS|_
None|none|NN|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ DdksA|ddksa|NN|_ cells|cell|NNS|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ starved|starve|VBN|_ DdksA|ddksa|NN|_ cells|cell|NNS|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ starved|starve|VBN|_ wt|wt|JJ|_ cells|cell|NNS|_
RNAP|rnap|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ wt|wt|JJ|_ cells|cell|NNS|_
RNAP|rnap|NN|_ _|_|NN|_ DdksA|ddksa|NN|_ _|_|CD|_ SHX|SHX|NNP|_ _|_|CD|_ rep1|rep1|NN|_
RNAP|rnap|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|CD|_ SHX|SHX|NNP|_ _|_|CD|_ rep2|rep2|NN|_
RNAP|rnap|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep1|rep1|NN|_
RNAP|rnap|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep2|rep2|NN|_
RNAP|rnap|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ SHX|shx|NN|_ _|_|CD|_ rep1|rep1|NN|_
RNAP|rnap|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ SHX|shx|NN|_ _|_|CD|_ rep2|rep2|NN|_
RNAP|rnap|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep1|rep1|NN|_
RNAP|rnap|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep2|rep2|NN|_
s70|s70|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ DdksA|ddksa|NN|_ cells|cell|NNS|_
s70|s70|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ starved|starve|VBN|_ DdksA|ddksa|NN|_ cells|cell|NNS|_
s70|s70|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ starved|starve|VBN|_ wt|wt|JJ|_ cells|cell|NNS|_
s70|s70|NN|_ ChIP|chip|NN|_ DNA|dna|NN|_ from|from|IN|_ wt|wt|JJ|_ cells|cell|NNS|_
s70|s70|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|CD|_ SHX|SHX|NNP|_ _|_|CD|_ rep1|rep1|NN|_
s70|s70|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|CD|_ SHX|SHX|NNP|_ _|_|CD|_ rep2|rep2|NN|_
s70|s70|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep1|rep1|NN|_
s70|s70|NN|_ _|_|CD|_ DdksA|ddksa|NN|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep2|rep2|NN|_
s70|s70|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ SHX|shx|NN|_ _|_|CD|_ rep1|rep1|NN|_
s70|s70|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ SHX|shx|NN|_ _|_|CD|_ rep2|rep2|NN|_
s70|s70|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep1|rep1|NN|_
s70|s70|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ untreated|untreated|JJ|_ _|_|NN|_ rep2|rep2|NN|_
The|the|DT|_ log2-ratio|log2-ratio|NN|_ is|be|VBZ|_ computed|compute|VBN|_ and|and|CC|_ scaled|scale|VBN|_ to|to|TO|_ center|center|VB|_ the|the|DT|_ ratio|ratio|NN|_ data|datum|NNS|_ around|around|IN|_ zero|zero|CD|_ .|.|.|_ Scaling|scaling|NN|_ is|be|VBZ|_ performed|perform|VBN|_ by|by|IN|_ subtracting|subtract|VBG|_ the|the|DT|_ bi-weight|bi-weight|JJ|_ mean|mean|NN|_ for|for|IN|_ the|the|DT|_ log2-ratio|log2-ratio|JJ|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ features|feature|NNS|_ on|on|IN|_ the|the|DT|_ array|array|NN|_ from|from|IN|_ each|each|DT|_ log2-ratio|log2-ratio|JJ|_ value|value|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ mg|mg|NN|_
treatment|treatment|NN|_ :|:|:|_ None|none|NN|_
Wild-types|wild-types|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ leucine|leucine|NN|SUPP ,|,|,|_ isoleucine|isoleucine|NN|_ ,|,|,|_ valine|valine|NN|_ ,|,|,|_ glycine|glycine|NN|_ ,|,|,|_ phenylalanine|phenylalanine|NN|SUPP ,|,|,|_ threonine|threonine|NN|_ -LRB-|-lrb-|-LRB-|_ 40|40|CD|_ mg|mg|NN|_
agent|agent|NN|_ :|:|:|_ DPD|dpd|NN|_
agent|agent|NN|_ :|:|:|_ DPD|dpd|NN|_ and|and|CC|_ rifampicin|rifampicin|NN|SUPP
agent|agent|NN|_ :|:|:|_ Fe|Fe|NNP|_
agent|agent|NN|_ :|:|:|_ Fe|Fe|NNP|_ and|and|CC|_ rifampicin|rifampicin|NN|SUPP
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-myc|anti-myc|JJ|_ -LRB-|-lrb-|-LRB-|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotech|Biotech|NNP|_ ,|,|,|_ sc-28207|sc-28207|NN|_ -RRB-|-rrb-|-RRB-|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RpoB|anti-rpob|NN|_ -LRB-|-lrb-|-LRB-|_ Neoclone|Neoclone|NNP|_ ,|,|,|_ WP002|wp002|NN|_ -RRB-|-rrb-|-RRB-|_
ChIP-exo|chip-exo|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ genome|genome|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ using|use|VBG|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ S|s|NN|_
ChIP-Seq|chip-seq|JJ|_
ChIP-seq|chip-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Fur-8-myc|fur-8-myc|NN|_ tagged|tag|VBD|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_ For|for|IN|_ the|the|DT|_ rifampicin-treated|rifampicin-treated|JJ|_ cultures|culture|NNS|_ ,|,|,|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP dissolved|dissolve|VBN|_ in|in|IN|_ methanol|methanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 150|150|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Fur|Fur|NNP|TF with|with|IN|_ DPD|dpd|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
Fur|Fur|NNP|TF with|with|IN|_ DPD|dpd|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
Fur|Fur|NNP|TF with|with|IN|_ Fe|Fe|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
Fur|Fur|NNP|TF with|with|IN|_ Fe|Fe|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
genotype|genotype|NN|_
Immunoprecipitated|immunoprecipitate|VBN|_ DNA|dna|NN|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ ChIP-exo|ChIP-exo|NNP|_
RpoB|rpob|NN|_ with|with|IN|_ DPD|dpd|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
RpoB|rpob|NN|_ with|with|IN|_ DPD|dpd|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
RpoB|rpob|NN|_ with|with|IN|_ DPD|dpd|NN|_ and|and|CC|_ rifampicin|rifampicin|NN|SUPP 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
RpoB|rpob|NN|_ with|with|IN|_ DPD|dpd|NN|_ and|and|CC|_ rifampicin|rifampicin|NN|SUPP 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
RpoB|rpob|NN|_ with|with|IN|_ Fe|Fe|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
RpoB|rpob|NN|_ with|with|IN|_ Fe|Fe|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
RpoB|rpob|NN|_ with|with|IN|_ Fe|Fe|NNP|_ and|and|CC|_ rifampicin|rifampicin|NN|SUPP 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
RpoB|rpob|NN|_ with|with|IN|_ Fe|Fe|NNP|_ and|and|CC|_ rifampicin|rifampicin|NN|SUPP 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|chip-exo|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ in|in|IN|_ gff|gff|NN|_ format|format|NN|_ which|which|WDT|_ has|have|VBZ|_ 8|8|CD|_ columns|column|NNS|_ :|:|:|_ sequence|sequence|NN|_ id|id|NN|_ ,|,|,|_ source|source|NN|_ -LRB-|-lrb-|-LRB-|_ empty|empty|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ feature|feature|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_
agent|agent|NN|_ :|:|:|_ DPD|dpd|NN|_
agent|agent|NN|_ :|:|:|_ Fe|Fe|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ Δfur|δfur|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ For|for|IN|_ iron|iron|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ FeCl2|fecl2|NN|_ were|be|VBD|_ treated|treat|VBN|_ from|from|IN|_ the|the|DT|_ beginning|beginning|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ and|and|CC|_ for|for|IN|_ DPD|dpd|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 0.2|0.2|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ DPD|dpd|NN|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ early-log|early-log|JJ|_ phase|phase|NN|_ and|and|CC|_ continued|continue|VBD|_ to|to|TO|_ culture|culture|NN|_ for|for|IN|_ additional|additional|JJ|_ 2h|2h|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
genotype|genotype|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma-delimited|comma-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WT|wt|NN|_ with|with|IN|_ DPD|dpd|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
WT|wt|NN|_ with|with|IN|_ DPD|dpd|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
WT|wt|NN|_ with|with|IN|_ Fe|Fe|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
WT|wt|NN|_ with|with|IN|_ Fe|Fe|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
Δfur|δfur|NN|_ with|with|IN|_ DPD|dpd|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
Δfur|δfur|NN|_ with|with|IN|_ DPD|dpd|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
Δfur|δfur|NN|_ with|with|IN|_ Fe|Fe|NNP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
Δfur|δfur|NN|_ with|with|IN|_ Fe|Fe|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ RNA-seq|rna-seq|NN|_ -RRB-|-rrb-|-RRB-|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_ 10.10.1.1|10.10.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 120|120|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 120|120|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ prior|prior|RB|_ to|to|TO|_ CORM-3|corm-3|NN|_ addition|addition|NN|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ prior|prior|RB|_ to|to|TO|_ CORM-3|corm-3|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ -RRB-|-rrb-|-RRB-|_
Batch|batch|NN|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ hemA|hema|NN|GEN defined|define|VBN|_ medium|medium|NN|_ ,|,|,|_ prior|prior|RB|_ to|to|TO|_ iCORM-3|icorm-3|NN|_ addition|addition|NN|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ directly|directly|RB|_ into|into|IN|_ phenol|phenol|NN|_ :|:|:|_ ethanol|ethanol|NN|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Slide|slide|NN|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 120|120|CD|_
Slide|Slide|NNP|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 120|120|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 60|60|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 13|13|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 120|120|CD|_
Slide|Slide|NNP|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 60|60|CD|_
Slide|Slide|NNP|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|SYM|_ Cy3|cy3|NN|_ 120|120|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 14|14|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 60|60|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 15|15|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|SYM|_ Cy3|cy3|NN|_ 120|120|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 15|15|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 15|15|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 15|15|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 60|60|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 15|15|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 15|15|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|Slide|NNP|_ 15|15|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 15|15|CD|_ _|_|CD|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 60|60|CD|_
Slide|slide|NN|_ 16|16|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 120|120|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 16|16|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 60|60|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 16|16|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 16|16|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 120|120|CD|_
Slide|slide|NN|_ 16|16|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 16|16|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 16|16|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 60|60|CD|_
Slide|slide|NN|_ 16|16|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 17|17|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 17|17|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 120|120|CD|_
Slide|slide|NN|_ 17|17|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 17|17|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 17|17|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 60|60|CD|_
Slide|slide|NN|_ 17|17|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 17|17|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 17|17|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ CORM-3|corm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 34|34|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 34|34|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 120|120|CD|_
Slide|slide|NN|_ 34|34|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 34|34|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 34|34|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 60|60|CD|_
Slide|slide|NN|_ 34|34|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 34|34|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 34|34|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 35|35|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 120|120|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 35|35|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 60|60|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 35|35|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 35|35|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 120|120|CD|_
Slide|slide|NN|_ 35|35|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 35|35|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 35|35|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 60|60|CD|_
Slide|slide|NN|_ 35|35|CD|_ _|_|NN|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 36|36|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|SYM|_ Cy3|cy3|NN|_ 120|120|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 36|36|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 36|36|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 36|36|CD|_ _|_|SYM|_ hemA|hema|NN|GEN _|_|CD|_ iCORM-3|icorm-3|NN|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 60|60|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 36|36|CD|_ _|_|SYM|_ hemA|hema|NN|GEN vs.|vs.|FW|_ WT|wt|FW|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ hemA|hema|NN|GEN Cy5|cy5|NN|_ WT|WT|NNP|_
Slide|Slide|NNP|_ 36|36|CD|_ _|_|SYM|_ hemA|hema|NN|GEN vs.|vs.|FW|_ WT|wt|FW|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ hemA|hema|NN|GEN Cy5|cy5|NN|_ WT|wt|JJ|_
Slide|slide|NN|_ 36|36|CD|_ _|_|CD|_ WT|WT|NNP|_ vs.|vs.|CC|_ hemA|hemA|NNP|GEN t|t|NN|_ =|=|JJ|_ 0|0|CD|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ WT|WT|NNP|_ Cy5|Cy5|NNP|_ hemA|hemA|NNP|GEN
Slide|Slide|NNP|_ 36|36|CD|_ _|_|CD|_ WT|WT|NNP|_ vs.|vs.|CC|_ hemA|hemA|NNP|GEN t|t|NN|_ =|=|JJ|_ 0|0|CD|_ _|_|NN|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ WT|wt|JJ|_ Cy5|cy5|NN|_ hemA|hema|NN|GEN
strain|strain|NN|_ :|:|:|_ hemA|hema|NN|GEN strain|strain|NN|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ Wild|Wild|NNP|_ type|type|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 120|120|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ CORM-3|corm-3|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 120|120|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ exposed|expose|VBN|_ to|to|TO|_ 100uM|100um|VB|_ iCORM-3|icorm-3|NN|_ for|for|IN|_ 60|60|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ prior|prior|RB|_ to|to|TO|_ CORM-3|corm-3|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ prior|prior|RB|_ to|to|TO|_ iCORM-3|icorm-3|NN|_ addition|addition|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ -RRB-|-rrb-|-RRB-|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
Demultiplexing|demultiplexing|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Fastq|fastq|JJ|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
Hot|hot|JJ|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ Sharma|sharma|FW|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ ,|,|,|_ Bloomberg|Bloomberg|NNP|_ 1990|1990|CD|_ ,|,|,|_ EMBO|EMBO|NNP|_ J|J|NNP|_ -RRB-|-rrb-|-RRB-|_
LB|lb|NN|_ 0.4|0.4|CD|_ B1|b1|NN|_ TEX|tex|NN|_ neg|neg|NN|_ L1|l1|NN|_ GA|ga|NN|_
LB|lb|NN|_ 0.4|0.4|CD|_ B1|b1|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ GA|ga|NN|_
LB|lb|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L1|l1|NN|_ HS1|hs1|NN|_
LB|lb|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L1|l1|NN|_ HS2|hs2|NN|_
LB|lb|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ HS1|hs1|NN|_
LB|lb|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ HS2|hs2|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B1|b1|NN|_ TEX|tex|NN|_ neg|neg|NN|_ L1|l1|NN|_ GA|ga|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B1|b1|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L2|l2|NN|_ HS2|hs2|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B1|b1|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ GA|ga|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B1|b1|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L2|l2|NN|_ HS2|hs2|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L1|l1|NN|_ HS1|hs1|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L1|l1|NN|_ HS2|hs2|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L2|l2|NN|_ HS2|hs2|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ HS1|hs1|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ HS2|hs2|NN|_
LB|lb|NN|_ 2.0|2.0|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L2|l2|NN|_ HS2|hs2|NN|_
M63|m63|NN|_ 0.4|0.4|CD|_ B1|b1|NN|_ TEX|tex|NN|_ neg|neg|NN|_ L1|l1|NN|_ GA|ga|NN|_
M63|m63|NN|_ 0.4|0.4|CD|_ B1|b1|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ GA|ga|NN|_
M63|m63|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L1|l1|NN|_ HS1|hs1|NN|_
M63|m63|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ neg|neg|NNP|_ L1|l1|NN|_ HS2|hs2|NN|_
M63|m63|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ HS1|hs1|NN|_
M63|m63|NN|_ 0.4|0.4|CD|_ B2|b2|NN|_ TEX|TEX|NNP|_ pos|po|VBZ|_ L1|l1|NN|_ HS2|hs2|NN|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
medium|medium|NN|_ :|:|:|_ M63|m63|NN|_
Read|read|VBP|_ mapping|map|VBG|_ using|use|VBG|_ segemehl|segemehl|NN|_ version|version|NN|_ 0.13|0.13|CD|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
RNA-Seq|rna-seq|NN|_
Samples|sample|NNS|_ were|be|VBD|_ mixed|mixed|JJ|_ ,|,|,|_ incubated|incubate|VBN|_ on|on|IN|_ ice|ice|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ after|after|IN|_ which|which|WDT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4150|4150|CD|_ rpm|rpm|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ snap|snap|JJ|_ frozen|freeze|VBN|_ in|in|IN|_ an|a|DT|_ ethanol|ethanol|NN|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ TRAPL|trapl|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Munich|Munich|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ tailed|tail|VBN|_ by|by|IN|_ using|use|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ .|.|.|_ The|the|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ PPP|ppp|NN|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ monophosphate|monophosphate|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ concentration|concentration|NN|_ of|of|IN|_ 20-30|20-30|CD|_ ng|ng|NN|_
To|to|TO|_ harvest|harvest|VB|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ ,|,|,|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ wild|wild|JJ|_ type|type|NN|_ MG1655|mg1655|NN|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ ˚C|˚c|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ back|back|RB|_ 1:500|1:500|CD|_ in|in|IN|_ either|either|CC|_ fresh|fresh|JJ|_ LB|lb|NN|_ or|or|CC|_ M63|m63|NN|_ minimal|minimal|JJ|_ glucose|glucose|NN|SUPP medium|medium|NN|_ and|and|CC|_ allowed|allow|VBN|_ to|to|TO|_ grow|grow|VB|_ until|until|IN|_ the|the|DT|_ cultures|culture|NNS|_ reached|reach|VBD|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ and|and|CC|_ 2.0|2.0|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ for|for|IN|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ M63|m63|NN|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.4|0.4|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ Ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ acid|acid|NN|_ phenol|phenol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ samples|sample|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 2.0|2.0|CD|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ stop|stop|NN|_ solution|solution|NN|_ .|.|.|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ CEL|CEL|NNP|_
affyexp|affyexp|JJ|_ _|_|NN|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ CEL|CEL|NNP|_
affyexp|affyexp|JJ|_ _|_|NN|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 3|3|CD|_ .|.|.|_ CEL|CEL|NNP|_
affyexp|affyexp|JJ|_ _|_|NN|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_
affyexp|affyexp|JJ|_ _|_|NN|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ CEL|CEL|NNP|_
affyexp|affyexp|JJ|_ _|_|NN|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ CEL|CEL|NNP|_
affyexp|affyexp|JJ|_ _|_|NN|_ delta-arcA|delta-arca|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 3|3|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 3|3|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ delta-fnr|delta-fnr|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 3|3|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 3|3|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ CEL|cel|NN|_
affyexp|affyexp|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 3|3|CD|_ .|.|.|_ CEL|CEL|NNP|_
All|All|NNP|_ strains|strain|NNS|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ were|be|VBD|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ and|and|CC|_ its|its|PRP$|_ derivatives|derivative|NNS|_ .|.|.|_ The|the|DT|_ deletion|deletion|NN|_ mutants|mutant|NNS|_ -LRB-|-lrb-|-LRB-|_ Δfnr|δfnr|NN|_ and|and|CC|_ ΔarcA|δarca|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ a|a|DT|_ λ|λ|NN|_ red|red|JJ|_ and|and|CC|_ FLP-mediated|flp-mediated|JJ|_ site-specific|site-specific|JJ|_ recombination|recombination|NN|_ method|method|NN|_ .|.|.|_ Glycerol|glycerol|NN|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED containing|contain|VBG|_ 0.2|0.2|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ w|w|NN|_
culture|culture|NN|_ condition|condition|NN|_ :|:|:|_ anaerobic|anaerobic|JJ|_ fermentive|fermentive|JJ|_ condition|condition|NN|_
culture|culture|NN|_ condition|condition|NN|_ :|:|:|_ nitrate|nitrate|VB|SUPP respiratory|respiratory|JJ|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_
Raw|raw|NN|_ CEL|cel|NN|_ files|file|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ robust|robust|JJ|_ multi-array|multi-array|JJ|_ average|average|NN|_ for|for|IN|_ normalization|normalization|NN|_ and|and|CC|_ calculation|calculation|NN|_ of|of|IN|_ probe|probe|NN|_ intensities|intensity|NNS|_ .|.|.|_ The|the|DT|_ processed|process|VBN|_ probe|probe|NN|_ signals|signal|NNS|_ derived|derive|VBN|_ from|from|IN|_ each|each|DT|_ microarray|microarray|NN|_ were|be|VBD|_ averaged|average|VBN|_ for|for|IN|_ both|both|CC|_ the|the|DT|_ wild|wild|JJ|_ type|type|NN|_ and|and|CC|_ deletion|deletion|NN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ GCRMA|GCRMA|NNP|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.13|2.13|CD|_ -RRB-|-rrb-|-RRB-|_ from|from|IN|_ Bioconductor|Bioconductor|NNP|_ in|in|IN|_ R.|R.|NNP|_
Samples|sample|NNS|_ for|for|IN|_ transcriptome|transcriptome|NN|_ analysis|analysis|NN|_ were|be|VBD|_ taken|take|VBN|_ from|from|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_ .|.|.|_ From|from|IN|_ the|the|DT|_ cells|cell|NNS|_ treated|treat|VBN|_ by|by|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ RNeasy|rneasy|JJ|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ .|.|.|_
Cells|cell|NNS|_ at|at|IN|_ appropriate|appropriate|JJ|_ cell|cell|NN|_ density|density|NN|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ by|by|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 25|25|CD|_ min|min|NN|_ .|.|.|_ Following|follow|VBG|_ quenching|quench|VBG|_ the|the|DT|_ unused|unused|JJ|_ formaldehyde|formaldehyde|NN|_ with|with|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 125|125|CD|_ mM|mm|NN|KWSUPP glycine|glycine|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ Buffered|buffer|VBN|_ Saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ washed|wash|VBN|_ cells|cell|NNS|_ were|be|VBD|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ composed|compose|VBN|_ of|of|IN|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ ug|ug|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ biotin|biotin|NN|SUPP conjugated|conjugate|VBN|_ anti-c-myc|anti-c-myc|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ HRP-conjugated|hrp-conjugated|JJ|_ sheep|sheep|NN|_ anti-mouse|anti-mouse|JJ|_ IgG|igg|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ vendor|vendor|NN|_ :|:|:|_ Amersham|Amersham|NNP|_ Biosciences|Biosciences|NNP|_
chip|chip|NN|_ antibody|antibody|NN|_ vendor|vendor|NN|_ :|:|:|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotechnology|Biotechnology|NNP|_
chip-ArcA|chip-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 1|1|CD|_
chip-ArcA|chip-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 2|2|CD|_
chip-ArcA|chip-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 3|3|CD|_
chip-ArcA|chip-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 1|1|CD|_
chip-ArcA|chip-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 2|2|CD|_
chip-ArcA|chip-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 3|3|CD|_
chip-Fnr|chip-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 1|1|CD|_
chip-Fnr|chip-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 2|2|CD|_
chip-Fnr|chip-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 3|3|CD|_
chip-Fnr|chip-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 1|1|CD|_
chip-Fnr|chip-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 2|2|CD|_
chip-Fnr|chip-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4CL|nh4cl|NN|_ _|_|CD|_ NO3|no3|NN|_ _|_|NN|_ 3|3|CD|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ ArcA-8myc|arca-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ rabbit|rabbit|NN|_ serum|serum|NN|_ containing|contain|VBG|_ myc|myc|NN|_ antibody|antibody|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ ArgR-8myc|argr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ rabbit|rabbit|NN|_ serum|serum|NN|_ containing|contain|VBG|_ myc|myc|NN|_ antibody|antibody|NN|_ .|.|.|_
Cross-linked|cross-linked|JJ|_ and|and|CC|_ sonicated|sonicated|JJ|_ chromatin|chromatin|NN|_ complex|complex|NN|_ of|of|IN|_ Fnr-8myc|fnr-8myc|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ rabbit|rabbit|NN|_ serum|serum|NN|_ containing|contain|VBG|_ myc|myc|NN|_ antibody|antibody|NN|_ .|.|.|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArcA-8myc|ArcA-8myc|NNP|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ antibody|antibody|NN|_ anaerobic|anaerobic|JJ|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArcA-8myc|ArcA-8myc|NNP|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ antibody|antibody|NN|_ NO3|no3|NN|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArcA|ArcA|NNP|TF ChIP|chip|NN|_ DNA|dna|NN|_ anaerobic|anaerobic|JJ|_
E.|E.|NNP|_ Coli|Coli|NNP|_ ArcA|ArcA|NNP|TF ChIP|chip|NN|_ DNA|dna|NN|_ NO3|no3|NN|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Fnr-8myc|fnr-8myc|JJ|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ antibody|antibody|NN|_ anaerobic|anaerobic|JJ|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Fnr-8myc|fnr-8myc|JJ|_ ChIP|chip|NN|_ DNA|dna|NN|_ Mock|mock|NN|_ antibody|antibody|NN|_ NO3|no3|NN|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Fnr|Fnr|NNP|_ ChIP|ChIP|NNP|_ DNA|DNA|NNP|_ anaerobic|anaerobic|JJ|_
E.|E.|NNP|_ Coli|Coli|NNP|_ Fnr|Fnr|NNP|_ ChIP|ChIP|NNP|_ DNA|DNA|NNP|_ NO3|no3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_
The|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ per|per|IN|_ channel|channel|NN|_ quantile|quantile|NN|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 19|19|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 185|185|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ IP|IP|NNP|_
background|background|NN|_ strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
CHP|chp|NN|_ files|file|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ Expression|expression|NN|_ Control|control|NN|_ .|.|.|_ Downstream|downstream|JJ|_ data|data|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ 12|12|CD|_ ,|,|,|_ CEL|CEL|NNP|_ files|file|NNS|_ were|be|VBD|_ imported|import|VBN|_ using|use|VBG|_ RMA|RMA|NNP|_ algorithm|algorithm|NN|_ and|and|CC|_ median|median|JJ|_ normalization|normalization|NN|_ was|be|VBD|_ performed|perform|VBN|_ .|.|.|_
Cirpofloxacin|cirpofloxacin|NN|_ treated|treat|VBN|_ fur|fur|NN|GEN mutant|mutant|JJ|_ sample|sample|NN|_ at|at|IN|_ T1h|t1h|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Cirpofloxacin|cirpofloxacin|NN|_ treated|treat|VBN|_ fur|fur|NN|GEN mutant|mutant|JJ|_ sample|sample|NN|_ at|at|IN|_ T1h|t1h|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Cirpofloxacin|cirpofloxacin|NN|_ treated|treat|VBN|_ WT|wt|JJ|_ sample|sample|NN|_ at|at|IN|_ T1h|t1h|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Cirpofloxacin|cirpofloxacin|NN|_ treated|treat|VBN|_ WT|wt|JJ|_ sample|sample|NN|_ at|at|IN|_ T1h|t1h|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_ and|and|CC|_ fur|fur|NN|GEN mutant|mutant|JJ|_ strains|strain|NNS|_ were|be|VBD|_ cultivated|cultivate|VBN|_ at|at|IN|_ 37Co|37co|NN|_ in|in|IN|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED medium|medium|NN|MED using|use|VBG|_ Erlenmeyer|Erlenmeyer|NNP|_ flasks|flask|NNS|_ .|.|.|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ OVN|ovn|NN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ng|ng|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
FUR|fur|NN|_ _|_|CD|_ CPR|CPR|NNP|_ _|_|SYM|_ 1|1|CD|_
FUR|fur|NN|_ _|_|CD|_ CPR|CPR|NNP|_ _|_|SYM|_ 2|2|CD|_
FUR|fur|NN|_ _|_|CD|_ noCPR|nocpr|NN|_ _|_|NN|_ 1|1|CD|_
FUR|fur|NN|_ _|_|CD|_ noCPR|nocpr|NN|_ _|_|NN|_ 2|2|CD|_
genotype|genotype|NN|_
Non-treated|non-treated|JJ|_ ,|,|,|_ fur|fur|NN|GEN mutant|mutant|JJ|_ sample|sample|NN|_ at|at|IN|_ T0|t0|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Non-treated|non-treated|JJ|_ ,|,|,|_ fur|fur|NN|GEN mutant|mutant|JJ|_ sample|sample|NN|_ at|at|IN|_ T0|t0|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Non-treated|non-treated|JJ|_ ,|,|,|_ WT|wt|JJ|_ control|control|NN|_ at|at|IN|_ T0|t0|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 1|1|CD|_
Non-treated|non-treated|JJ|_ ,|,|,|_ WT|wt|JJ|_ control|control|NN|_ at|at|IN|_ T0|t0|NN|_ ,|,|,|_ biological|biological|JJ|_ rep|rep|NN|GEN 2|2|CD|_
Samples|sample|NNS|_ for|for|IN|_ microarray|microarray|NN|_ analyses|analysis|NNS|_ were|be|VBD|_ taken|take|VBN|_ before|before|IN|_ ciprofloxacin|ciprofloxacin|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ t0|t0|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ at|at|IN|_ 1|1|CD|_ hour|hour|NN|_ post-treatment|post-treatment|JJ|_ -LRB-|-lrb-|-LRB-|_ t1|t1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cell|cell|NN|_ concentration|concentration|NN|_ was|be|VBD|_ adjusted|adjust|VBN|_ to|to|TO|_ 109|109|CD|_ cells|cell|NNS|_
We|we|PRP|_ compared|compare|VBD|_ the|the|DT|_ microarray-determined|microarray-determined|JJ|_ mRNA|mrna|NN|_ profiles|profile|NNS|_ -LRB-|-lrb-|-LRB-|_ Affymetrix|Affymetrix|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Genome|Genome|NNP|_ 2.0|2.0|CD|_ Array|array|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ Δfur|δfur|NN|_ and|and|CC|_ WT|wt|JJ|_ genotypes|genotype|NNS|_ in|in|IN|_ response|response|NN|_ to|to|TO|_ ciprofloxacin|ciprofloxacin|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ng|ng|NN|_
WT|WT|NNP|_ _|_|NNP|_ CPR|CPR|NNP|_ _|_|SYM|_ 1|1|CD|_
WT|wt|JJ|_ _|_|NN|_ CPR|CPR|NNP|_ _|_|SYM|_ 2|2|CD|_
WT|wt|JJ|_ _|_|NN|_ noCPR|nocpr|NN|_ _|_|NN|_ 1|1|CD|_
WT|wt|JJ|_ _|_|NN|_ noCPR|nocpr|NN|_ _|_|NN|_ 2|2|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ modified|modify|VBN|_ M63|m63|NN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ cell|cell|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ controlled|control|VBN|_ ~|~|SYM|_ 10|10|CD|_ ^|^|SYM|_ 8|8|CD|_ cells|cell|NNS|_
condition|condition|NN|_ :|:|:|_ histidine|histidine|NN|_ depleted|deplete|VBD|_
condition|condition|NN|_ :|:|:|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ written|write|VBN|_ in|in|IN|_ R|r|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ finite|finite|JJ|_ hybridisation|hybridisation|NN|_ -LRB-|-lrb-|-LRB-|_ FH|fh|NN|_ -RRB-|-rrb-|-RRB-|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Ono|Ono|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ thermodynamic|thermodynamic|JJ|_ model|model|NN|_ of|of|IN|_ non-specific|non-specific|JJ|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ NSB|nsb|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ short|short|JJ|_ nucleotide|nucleotide|NN|_ microarrays|microarray|NNS|_ -LRB-|-lrb-|-LRB-|_ Furusawa|Furusawa|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ log10|log10|NN|_ mRNA|mrna|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ pM|pm|NN|_ -RRB-|-rrb-|-RRB-|_ data|datum|NNS|_ are|be|VBP|_ provided|provide|VBN|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ SERIES|series|NN|_ record|record|NN|_ .|.|.|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU11|osu11|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisA|osu12-hisa|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisB|osu12-hisb|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisC|osu12-hisc|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisD|osu12-hisd|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisF|osu12-hisf|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisG|osu12-hisg|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ >|>|JJR|_ 10|10|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ depleted|deplete|VBN|_ ,|,|,|_ 2|2|CD|_ hrs|hr|NNS|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
OSU12-hisI|osu12-hisi|NN|_ ,|,|,|_ histidine|histidine|NN|_ supplied|supply|VBD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisA|δhisa|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisB|δhisb|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisC|δhisc|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisD|δhisd|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisF|δhisf|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisG|δhisg|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔhisI|δhisi|NN|_ :|:|:|_ :|:|:|_ cat|cat|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
strain|strain|NN|_ :|:|:|_ DH1|dh1|NN|_ ΔintC|δintc|NN|_ :|:|:|_ :|:|:|_ Ptrc-dsred|ptrc-dsred|JJ|_ .|.|.|_ t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN|_ ΔgalK|δgalk|NN|_ :|:|:|_ :|:|:|_ PtetA-gfpuv5|pteta-gfpuv5|NN|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ cold|cold|JJ|_ phenol-ethanol|phenol-ethanol|JJ|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ of|of|IN|_ phenol|phenol|NN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ prepared|prepare|VBN|_ in|in|IN|_ advance|advance|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 16,000|16,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
After|after|IN|_ 5|5|CD|_ h|h|NN|_ of|of|IN|_ NP-TiO2|np-tio2|NN|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ mQ|mq|NN|_ water|water|NN|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ exposure|exposure|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ with|with|IN|_ two|two|CD|_ volumes|volume|NNS|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ SAS|SAS|NNP|_ ,|,|,|_ France|France|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 7,000|7,000|CD|_ g|g|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Cell|cell|NN|_ exposure|exposure|NN|_ to|to|TO|_ NP-TiO2|np-tio2|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ Milli-Q|milli-q|JJ|_ water|water|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 500|500|CD|_ µl|µl|NN|_ of|of|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ and|and|CC|_ 500|500|CD|_ µl|µl|NN|_ of|of|IN|_ the|the|DT|_ NP-TiO2|np-tio2|NN|_ stock|stock|NN|_ suspension|suspension|NN|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ mQ|mq|NN|_ water|water|NN|_ for|for|IN|_ the|the|DT|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ prepared|prepare|VBN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ and|and|CC|_ then|then|RB|_ added|add|VBD|_ to|to|TO|_ the|the|DT|_ NaCl|nacl|NN|_ solution|solution|NN|_ to|to|TO|_ obtain|obtain|VB|_ final|final|JJ|_ concentrations|concentration|NNS|_ of|of|IN|_ 10E7|10e7|NN|_ cells|cell|NNS|_
Ecoli|ecoli|JJ|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 5h|5h|NN|_ _|_|CD|_ rep1|rep1|NN|_
Ecoli|ecoli|JJ|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 5h|5h|NN|_ _|_|CD|_ rep2|rep2|NN|_
Ecoli|ecoli|JJ|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 5h|5h|NN|_ _|_|CD|_ rep3|rep3|NN|_
Ecoli|ecoli|JJ|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ 5h|5h|JJ|_ _|_|NN|_ rep4|rep4|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 5h|5h|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 5h|5h|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 5h|5h|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
E.coli|e.coli|NNS|_ ,|,|,|_ control|control|JJ|_ culture|culture|NN|_ ,|,|,|_ 5h|5h|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ replicate|replicate|VB|_ 4|4|CD|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ NP-TiO2|np-tio2|NN|_ _|_|CD|_ 5h|5h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ NP-TiO2|np-tio2|NN|_ _|_|CD|_ 5h|5h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ NP-TiO2|np-tio2|NN|_ _|_|CD|_ 5h|5h|JJ|_ _|_|NN|_ rep3|rep3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ NP-TiO2|np-tio2|NN|_ _|_|CD|_ 5h|5h|JJ|_ _|_|NN|_ rep4|rep4|NN|_
E.coli|e.coli|NNS|_ ,|,|,|_ NP-TiO2|np-tio2|NN|_ exposed|expose|VBN|_ culture|culture|NN|_ ,|,|,|_ 5h|5h|NN|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ 100|100|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Image|image|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 7|7|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Device|device|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ background|background|NN|_ was|be|VBD|_ defined|define|VBN|_ with|with|IN|_ the|the|DT|_ ``|``|``|_ Local|local|JJ|_ features|feature|NNS|_ background|background|NN|_ median|median|NN|_ ''|''|''|_ method|method|NN|_ .|.|.|_ Quantile|quantile|JJ|_ normalization|normalization|NN|_ was|be|VBD|_ applied|apply|VBN|_ on|on|IN|_ the|the|DT|_ total|total|JJ|_ number|number|NN|_ of|of|IN|_ spots|spot|NNS|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.11.1|2.11.1|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ the|the|DT|_ LIMMA|LIMMA|NNP|_ software|software|NN|_ package|package|NN|_ .|.|.|_ Spots|spot|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ K12|k12|NN|_ species|species|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ .|.|.|_
incubation|incubation|NN|_ condition|condition|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ dark|dark|NN|_ ,|,|,|_ 5h|5h|NN|_ ,|,|,|_ 20|20|CD|_ °C|°c|NN|_ ,|,|,|_ 150|150|CD|_ rpm|rpm|NN|_
incubation|incubation|NN|_ medium|medium|NN|_ :|:|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_
incubation|incubation|NN|_ medium|medium|NN|_ :|:|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ +|+|CC|_ 100|100|CD|_ mg|mg|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cells|cell|NNS|_ with|with|IN|_ the|the|DT|_ UltraClean|UltraClean|NNP|_ Microbial|Microbial|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ MO|MO|NNP|_ BIO|BIO|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ extraction|extraction|NN|_ ,|,|,|_ contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ DNAse|dnase|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ phenol|phenol|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 100|100|CD|_ μg|μg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 10|10|CD|_ μg|μg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ without|without|IN|_ treatment|treatment|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEF|mazef|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 100|100|CD|_ μg|μg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEF|mazef|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 10|10|CD|_ μg|μg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEF|mazef|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ without|without|IN|_ treatment|treatment|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEFlexA3|mazeflexa3|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 100|100|CD|_ μg|μg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEFlexA3|mazeflexa3|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 10|10|CD|_ μg|μg|NN|_
E.|E.|NNP|_ coli|coli|NN|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEFlexA3|mazeflexa3|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ without|without|IN|_ treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Gene|gene|NN|_ selection|selection|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ the|the|DT|_ False|False|NNP|_ Discovery|Discovery|NNP|_ Rate|Rate|NNP|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ correction|correction|NN|_ procedure|procedure|NN|_ for|for|IN|_ adjusting|adjust|VBG|_ genes|gene|NNS|_ with|with|IN|_ p-value|p-value|JJ|_ smaller|smaller|JJR|_ than|than|IN|_ 0.05|0.05|CD|_ and|and|CC|_ Fold|Fold|NNP|_ Change|Change|NNP|_ greater|greater|JJR|_ than|than|IN|_ 2|2|CD|_ .|.|.|_
genotype|genotype|NN|_ :|:|:|_ ∆|∆|CD|_ mazEF|mazef|NN|_
genotype|genotype|NN|_ :|:|:|_ ∆|∆|SYM|_ mazEFlexA3|mazeflexa3|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
∆|∆|SYM|_ mazEF|mazef|NN|_ 0|0|CD|_ μg|μg|NN|_
∆|∆|CD|_ mazEF|mazef|NN|_ 100|100|CD|_ μg|μg|NN|_
∆|∆|CD|_ mazEF|mazef|NN|_ 10|10|CD|_ μg|μg|NN|_
∆|∆|CD|_ mazEFlexA3|mazeflexa3|NN|_ 0|0|CD|_ μg|μg|NN|_
∆|∆|CD|_ mazEFlexA3|mazeflexa3|NN|_ 100|100|CD|_ μg|μg|NN|_
∆|∆|CD|_ mazEFlexA3|mazeflexa3|NN|_ 10|10|CD|_ μg|μg|NN|_
RMA|rma|NN|_ normalization|normalization|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ CELL|cell|NN|_ files|files|NNS|_ using|use|VBG|_ the|the|DT|_ Partek|Partek|NNP|_ Genomic|genomic|JJ|_ Suite|suite|NN|_ 6.5|6.5|CD|_ .|.|.|_ Additional|additional|JJ|_ statistical|statistical|JJ|_ analysis|analysis|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ Spotfire|Spotfire|NNP|_ software|software|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ Somerville|Somerville|NNP|_ ,|,|,|_ MA|MA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ custom|custom|NN|_ Matlab|Matlab|NNP|_ -LRB-|-lrb-|-LRB-|_ R2010B|r2010b|NN|_ -RRB-|-rrb-|-RRB-|_ routines|routine|NNS|_ .|.|.|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 100|100|CD|_ μg|μg|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 10|10|CD|_ μg|μg|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ without|without|IN|_ treatment|treatment|NN|_ .|.|.|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEF|mazef|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 100|100|CD|_ μg|μg|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEF|mazef|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 10|10|CD|_ μg|μg|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEF|mazef|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ without|without|IN|_ treatment|treatment|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEFlexA3|mazeflexa3|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 100|100|CD|_ μg|μg|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEFlexA3|mazeflexa3|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ 10|10|CD|_ μg|μg|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ MC4100relA|mc4100rela|NN|_ +|+|CC|_ ∆|∆|SYM|_ mazEFlexA3|mazeflexa3|NN|_ in|in|IN|_ mid|mid|JJ|_ log|log|NN|_ phase|phase|NN|_ incubated|incubate|VBN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ without|without|IN|_ treatment|treatment|NN|_
treatment|treatment|NN|_ :|:|:|_ 0|0|CD|_ μg|μg|NN|_
treatment|treatment|NN|_ :|:|:|_ 100|100|CD|_ μg|μg|NN|_
treatment|treatment|NN|_ :|:|:|_ 10|10|CD|_ μg|μg|NN|_
We|we|PRP|_ extracted|extract|VBD|_ RNA|rna|NN|_ using|use|VBG|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ combined|combine|VBN|_ with|with|IN|_ RNase-Free|rnase-free|JJ|_ DNase|dnase|NN|_ Set|set|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
We|we|PRP|_ grew|grow|VBD|_ cells|cell|NNS|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.5-0.6|0.5-0.6|CD|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ we|we|PRP|_ divided|divide|VBD|_ each|each|DT|_ culture|culture|NN|_ into|into|IN|_ 500µl|500µl|JJ|_ aliquots|aliquot|NNS|_ to|to|TO|_ which|which|WDT|_ we|we|PRP|_ added|add|VBD|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ NA|NA|NNP|_ .|.|.|_
We|we|PRP|_ incubated|incubate|VBD|_ each|each|DT|_ aliquot|aliquot|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ with|with|IN|_ NA|na|NN|_
WT|wt|NN|_ 0|0|CD|_ μg|μg|NN|_
WT|wt|NN|_ 100|100|CD|_ μg|μg|NN|_
WT|wt|VBD|_ 10|10|CD|_ μg|μg|NN|_
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_ .|.|.|_
Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 1|1|CD|_ L|l|NN|_ volumes|volume|NNS|_ of|of|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED ,|,|,|_ supplemented|supplement|VBN|_ with|with|IN|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g|g|NN|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ 40|40|CD|_ g|g|NN|_ EtOH|etoh|NN|_
ethanol|ethanol|NN|_ treatment|treatment|NN|_ :|:|:|_ no|no|DT|_ ethanol|ethanol|NN|_ exposure|exposure|NN|_
Ethanol|ethanol|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ g|g|NN|_
For|for|IN|_ metagene|metagene|NN|_ analyses|analysis|NNS|_ -LRB-|-lrb-|-LRB-|_ gene-segment|gene-segment|NN|_ analyses|analysis|NNS|_ and|and|CC|_ codon-type|codon-type|JJ|_ analyses|analysis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pseudogenes|pseudogene|NNS|_ and|and|CC|_ genes|gene|NNS|_ not|not|RB|_ represented|represent|VBN|_ in|in|IN|_ one|one|CD|_ or|or|CC|_ more|more|JJR|_ datasets|dataset|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ ,|,|,|_ leaving|leave|VBG|_ 3048|3048|CD|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ ll|ll|NN|_ genes|gene|NNS|_ \|\|VBP|_ dataset|dataset|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ for|for|IN|_ list|list|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ ll|ll|NN|_ genes|gene|NNS|_ \|\|VBP|_ ,|,|,|_ \|\|VBP|_ low|low|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ \|\|NN|_ ,|,|,|_ and|and|CC|_ \|\|RB|_ high|high|JJ|_ ribosome|ribosome|NN|_ occupancy|occupancy|NN|_ \|\|NN|_ gene|gene|NN|_ sets|set|NNS|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ 2011|2011|CD|_ ,|,|,|_ Cell|cell|NN|_ 147|147|CD|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 1295-1308|1295-1308|CD|_ -LRB-|-lrb-|-LRB-|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3277850|pmc3277850|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ fragments|fragment|NNS|_ of|of|IN|_ total|total|NN|_ mRNA|mrna|NN|_ or|or|CC|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ '|'|''|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ and|and|CC|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ .|.|.|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T0|t0|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 1|1|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T0|t0|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 2|2|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T0|t0|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 1|1|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T0|t0|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 2|2|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 1|1|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 2|2|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 1|1|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 2|2|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 1|1|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 2|2|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 1|1|CD|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ EP61|ep61|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 2|2|CD|_
Raw|raw|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ by|by|IN|_ two|two|CD|_ nt|nt|NNS|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ -LRB-|-lrb-|-LRB-|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ non-templated|non-templated|JJ|_ nts|nt|NNS|_ added|add|VBN|_ by|by|IN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ then|then|RB|_ mapped|map|VBN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ Aligner|Aligner|NNP|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ No|no|DT|_
ribosome-protected|ribosome-protected|JJ|_ :|:|:|_ Yes|yes|UH|_
RNA-Seq|rna-seq|JJ|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
Signals|signal|NNS|_ mapping|map|VBG|_ to|to|TO|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ regions|region|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ datasets|dataset|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ supplementary|supplementary|JJ|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ EP61|ep61|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Gene|Gene|NNP|_ _|_|NNP|_ lists|list|VBZ|_ _|_|SYM|_ GEO.xls|geo.xls|NNS|_ ;|;|:|_ The|the|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ contains|contain|VBZ|_ gene|gene|NN|_ lists|list|NNS|_ used|use|VBN|_ in|in|IN|_ data|data|NN|_ analysis|analysis|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ with|with|IN|_ non-coding|non-coding|JJ|_ RNAs|rna|NNS|_ removed|remove|VBD|_ ,|,|,|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ with|with|IN|_ a|a|DT|_ \|\|SYM|_ -|-|:|_ \|\|SYM|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ a|a|DT|_ \|\|NN|_ +|+|CC|_ \|\|NN|_ as|as|IN|_ the|the|DT|_ final|final|JJ|_ character|character|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ name|name|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T0|t0|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 2|2|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T0|t0|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 1|1|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T0|t0|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 2|2|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 1|1|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 2|2|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 1|1|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T1|t1|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 2|2|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 1|1|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RNA|rna|NN|_ rep|rep|NN|GEN 2|2|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 1|1|CD|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ T2|t2|NN|_ RP|rp|NN|_ rep|rep|NN|GEN 2|2|CD|_
Aerobic|aerobic|JJ|_ culture|culture|NN|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.7|1.7|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ C|c|NN|_ in|in|IN|_ gas-sparged|gas-sparged|JJ|_ Roux|Roux|NNP|_ bottles|bottle|NNS|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ .|.|.|_
Culture|culture|NN|_ samples|sample|NNS|_ were|be|VBD|_ transferred|transfer|VBN|_ directly|directly|RB|_ into|into|IN|_ an|a|DT|_ ice-cold|ice-cold|JJ|_ ethanol|ethanol|NN|_
Each|each|DT|_ dataset|dataset|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ prior|prior|RB|_ to|to|TO|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v1|asm584v1|NN|_ ,|,|,|_ U00096|u00096|NN|_ .2|.2|NN|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Parkhomchuk|Parkhomchuk|NNP|_ et|et|FW|_ al.|al.|FW|_ 2009|2009|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ 37|37|CD|_ :|:|:|_ e123|e123|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ ribosome-depleted|ribosome-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ used|use|VBN|_ as|as|IN|_ template|template|NN|_ for|for|IN|_ cDNA|cdna|NN|_ synhtesis|synhtesis|NN|_ .|.|.|_ dUTP|dutp|NN|_ was|be|VBD|_ included|include|VBN|_ in|in|IN|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ reaction|reaction|NN|_ in|in|IN|_ addition|addition|NN|_ to|to|TO|_ dTTP|dttp|NN|_ to|to|TO|_ chemically|chemically|RB|_ mark|mark|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ .|.|.|_ cDNAs|cdna|NNS|_ were|be|VBD|_ size-selected|size-selected|JJ|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ sequencing|sequencing|NN|_ adapters|adapter|NNS|_ followed|follow|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ cleavage|cleavage|NN|_ to|to|TO|_ generate|generate|VB|_ adapter-ligated|adapter-ligated|JJ|_ single-stranded|single-stranded|JJ|_ cDNAs|cdna|NNS|_ .|.|.|_
Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ RL2325|rl2325|NN|_ -RRB-|-rrb-|-RRB-|_ RNA-seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ ID|id|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ short|short|JJ|_ oligonucleotide|oligonucleotide|NN|_ alignment|alignment|NN|_ program|program|NN|_ -LRB-|-lrb-|-LRB-|_ SOAP|soap|NN|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ samples|sample|NNS|_ using|use|VBG|_ hot|hot|JJ|_ phenol|phenol|NN|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ determined|determine|VBN|_ from|from|IN|_ agarose|agarose|NN|_ gels|gel|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ RL2325|rl2325|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ are|be|VBP|_ WIG|WIG|NNP|_ files|file|NNS|_ normalized|normalize|VBD|_ to|to|TO|_ reads|read|VBZ|_ per|per|IN|_ million|million|CD|_ per|per|IN|_ position|position|NN|_ .|.|.|_ Those|those|DT|_ designated|designate|VBN|_ \|\|NN|_ minus|minus|CC|_ \|\|NN|_ cover|cover|VBP|_ the|the|DT|_ minus|minus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ ;|;|:|_ those|those|DT|_ with|with|IN|_ designated|designate|VBN|_ \|\|NN|_ plus|plus|CC|_ \|\|NN|_ cover|cover|VBP|_ the|the|DT|_ plus|plus|CC|_ strand|strand|NN|_ of|of|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_
Wild-type|wild-type|JJ|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ RNA-seq|rna-seq|NN|_
Bacteria|bacterium|NNS|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ nascent|nascent|JJ|_ transcript|transcript|NN|_ .|.|.|_
Cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ in|in|IN|_ 250|250|CD|_ mL|ml|NN|_ increments|increment|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ over|over|IN|_ 0.22|0.22|CD|_ μm|μm|NN|_ nitrocellulose|nitrocellulose|NN|_ filters|filters|NNS|_ -LRB-|-lrb-|-LRB-|_ GE|GE|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ to|to|TO|_ simultaneously|simultaneously|RB|_ halt|halt|VB|_ all|all|DT|_ transcriptional|transcriptional|JJ|_ progress|progress|NN|_ .|.|.|_ Frozen|frozen|JJ|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ μg|μg|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ pulverized|pulverize|VBN|_ on|on|IN|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ mixer|mixer|NN|_ mill|mill|NN|_ 6|6|CD|_ times|time|NNS|_ at|at|IN|_ 15|15|CD|_ Hz|hz|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 500|500|CD|_ μL|μl|NN|_ frozen|frozen|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ NP-40|np-40|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NH4Cl|nh4cl|NN|_ ,|,|,|_ 50|50|CD|_ U|U|NNP|_
Ecoli|Ecoli|NNP|_ _|_|NNP|_ WT|WT|NNP|_ _|_|NNP|_ RNAseq|RNAseq|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ 500|500|CD|_ mL|ml|NN|_ liquid|liquid|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 2.8|2.8|CD|_ L|l|NN|_ flasks|flask|NNS|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 180|180|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ from|from|IN|_ an|a|DT|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 600|600|CD|_ nm|nm|NN|_ -RRB-|-rrb-|-RRB-|_ 0.05|0.05|CD|_ to|to|TO|_ OD|od|CD|_ 0.45|0.45|CD|_ ±|±|SYM|_ 0.05|0.05|CD|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ rich|rich|JJ|_ defined|define|VBN|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ :|:|:|_ NC|nc|NN|_ _|_|SYM|_ 000913|000913|CD|_
genotype|genotype|NN|_
media|media|NNS|_ :|:|:|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Media|Media|NNP|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_ files|file|NNS|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ full|full|JJ|_ library|library|NN|_ construction|construction|NN|_ protocol|protocol|NN|_ was|be|VBD|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Churchman|Churchman|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nature|Nature|NNP|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Purified|purify|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ dephosphorylated|dephosphorylate|VBN|_ with|with|IN|_ T4|t4|NN|_ PNK|pnk|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ ligated|ligate|VBD|_ to|to|TO|_ a|a|DT|_ 5|5|CD|_ '|'|''|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ to|to|TO|_ generate|generate|VB|_ RNA|rna|NN|_ ranging|range|VBG|_ from|from|IN|_ 30-100|30-100|CD|_ nt|nt|NNS|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ single-stranded|single-stranded|JJ|_ DNA|dna|NN|_ circularized|circularize|VBN|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ a|a|SYM|_ -|-|:|_ v|v|LS|_ 3|3|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
EvgSc|evgsc|NN|_ _|_|NN|_ 1|1|CD|_
EvgSc|evgsc|NN|_ _|_|NN|_ 2|2|CD|_
EvgSc|evgsc|NN|_ mutant|mutant|JJ|_ rep|rep|NN|GEN 1|1|CD|_
EvgSc|evgsc|NN|_ mutant|mutant|JJ|_ rep|rep|NN|GEN 2|2|CD|_
EvgSc|evgsc|NN|_ _|_|CD|_ ompR|ompr|NN|GEN _|_|NN|_ 1|1|CD|_
EvgSc|evgsc|NN|_ _|_|CD|_ ompR|ompr|NN|GEN _|_|NN|_ 2|2|CD|_
EvgSc|evgsc|NN|_ ompR|ompr|NN|GEN double|double|JJ|_ mutant|mutant|JJ|_ rep|rep|NN|GEN 1|1|CD|_
EvgSc|evgsc|NN|_ ompR|ompr|NN|GEN double|double|JJ|_ mutant|mutant|JJ|_ rep|rep|NN|GEN 2|2|CD|_
genotype|genotype|NN|_ :|:|:|_ EvgSc|evgsc|NN|_ KO|ko|NN|_
genotype|genotype|NN|_ :|:|:|_ EvgSc|evgsc|NN|_ ompR|ompr|NN|GEN KO|ko|NN|_
genotype|genotype|NN|_ :|:|:|_ ompR|ompr|NN|GEN KO|ko|NN|_
genotype|genotype|NN|_ :|:|:|_ Wild|Wild|NNP|_ Type|type|NN|_
LB|lb|NN|MED media|media|NNS|MED
ompR|ompr|NN|GEN _|_|NN|_ 1|1|CD|_
ompR|ompr|NN|GEN _|_|NN|_ 2|2|CD|_
ompR|ompr|NN|GEN mutant|mutant|JJ|_ rep|rep|NN|GEN 1|1|CD|_
ompR|ompr|NN|GEN mutant|mutant|JJ|_ rep|rep|NN|GEN 2|2|CD|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAeasy|rnaeasy|NN|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ NanoDrop-1000|nanodrop-1000|NN|_ spectrophotometer|spectrophotometer|NN|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ with|with|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ scanned|scan|VBN|_ images|image|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ 10.5|10.5|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ -LRB-|-lrb-|-LRB-|_ protocol|protocol|NN|_ GE1|ge1|NN|_ _|_|NN|_ 105|105|CD|_ _|_|SYM|_ Dec08|dec08|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
wild|wild|JJ|_ type|type|NN|_ rep|rep|NN|GEN 1|1|CD|_
wild|wild|JJ|_ type|type|NN|_ rep|rep|NN|GEN 2|2|CD|_
WT|wt|JJ|_ _|_|NN|_ 1|1|CD|_
WT|wt|JJ|_ _|_|NN|_ 2|2|CD|_
Automatic|Automatic|NNP|_ extractor|extractor|NN|_ in|in|IN|_ Verigene|verigene|JJ|_ system|system|NN|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
Blood|blood|NN|_ culture|culture|NN|_
Blood|blood|NN|_ culture|culture|NN|_ bottle|bottle|NN|_
culture|culture|NN|_ system|system|NN|_ :|:|:|_ BACTEC|BACTEC|NNP|_
Direct|Direct|NNP|_ testing|testing|NN|_ of|of|IN|_ culture|culture|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Standard|standard|JJ|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ after|after|IN|_ centrifugation|centrifugation|NN|_ of|of|IN|_ culture|culture|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Supernatant|supernatant|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
gram|gram|NN|_ status|status|NN|_ :|:|:|_ Gram-negative|gram-negative|JJ|_
Sample|sample|VBP|_ 79|79|CD|_
Scatter|scatter|JJ|_ signal|signal|NN|_ intensity|intensity|NN|_ after|after|IN|_ illumination|illumination|NN|_ at|at|IN|_ 150|150|CD|_ ms|m|NNS|_ exposure|exposure|NN|_ without|without|IN|_ normalization|normalization|NN|_ ,|,|,|_ without|without|IN|_ transformation|transformation|NN|_ .|.|.|_ The|the|DT|_ non-normalized|non-normalized|JJ|_ signals|signal|NNS|_ form|form|VBP|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ conclusions|conclusion|NNS|_ in|in|IN|_ the|the|DT|_ accompanying|accompany|VBG|_ manuscript|manuscript|NN|_ .|.|.|_
source|source|NN|_ :|:|:|_ Peripheral|peripheral|JJ|_ blood|blood|NN|_
treatment|treatment|NN|_ :|:|:|_ Supernatant|supernatant|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ LB|lb|NN|MED medium|medium|NN|MED to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.55-0.6|0.55-0.6|CD|_
culture|culture|NN|_ denity|denity|NN|_ :|:|:|_ OD600|od600|NN|_ =|=|JJ|_ 0.55-0.6|0.55-0.6|CD|_ culture|culture|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
LOWESS|lowess|NN|_ normalized|normalize|VBD|_ ,|,|,|_ background|background|NN|_ subtracted|subtract|VBD|_ data|datum|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ signals|signal|NNS|_ .|.|.|_ Agilent|Agilent|NNP|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ 7.3|7.3|CD|_ was|be|VBD|_ used|use|VBN|_ .|.|.|_
pFlag-only|pflag-only|NN|_ control|control|NN|_
RhIB|rhib|NN|_ wild|wild|JJ|_ type|type|NN|_
RhlBP238L|rhlbp238l|NN|_ mutant|mutant|JJ|_
RhlBP238L|rhlbp238l|NN|_ vs|vs|CC|_ flag|flag|NN|_ only|only|RB|_ 1|1|CD|_
RhlBP238L|rhlbp238l|NN|_ vs|vs|CC|_ flag|flag|NN|_ only|only|RB|_ 2|2|CD|_
RhlBP238L|rhlbp238l|NN|_ vs|vs|CC|_ flag|flag|NN|_ only|only|RB|_ 3|3|CD|_
RhlBwt|rhlbwt|NN|_ vs|vs|CC|_ flag|flag|NN|_ only|only|RB|_ 1|1|CD|_
RhlBwt|rhlbwt|NN|_ vs|vs|CC|_ flag|flag|NN|_ only|only|RB|_ 2|2|CD|_
RhlBwt|rhlbwt|NN|_ vs|vs|CC|_ flag|flag|NN|_ only|only|RB|_ 3|3|CD|_
strain|strain|NN|_ :|:|:|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ rne131|rne131|NN|_ DrhlB|drhlb|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
All|All|NNP|_ cultures|culture|NNS|_ grown|grow|VBN|_ up|up|RB|_ to|to|TO|_ 0.6|0.6|CD|_ OD600|od600|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Samples|sample|NNS|_ 1,2,5|1,2,5|CD|_ and|and|CC|_ 6|6|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ whereas|whereas|IN|_ samples|sample|NNS|_ 3|3|CD|_ and|and|CC|_ 4|4|CD|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
analysis|analysis|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_
analysis|analysis|NN|_ :|:|:|_ in|in|FW|_ vivo|vivo|FW|_
Basecalls|basecall|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ .1.8|.1.8|CD|_
Cultures|culture|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ and|and|CC|_ 2|2|CD|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 44|44|CD|_ °C|°c|NN|_ for|for|IN|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ growth|growth|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cell|cell|NN|_ cultures|culture|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
genotype|genotype|NN|_ :|:|:|_ n|n|NN|_
genotype|genotype|NN|_ :|:|:|_ rne-3071|rne-3071|NN|_ -LRB-|-lrb-|-LRB-|_ ts|t|NNS|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ rne|rne|NN|GEN wild-type|wild-type|JJ|_
genotype|genotype|NN|_ :|:|:|_ rng|rng|NN|GEN mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ rng|rng|NN|GEN wild-type|wild-type|JJ|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
incubation|incubation|NN|_ time|time|NN|_ :|:|:|_ n|n|NN|_
Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
rne-3071|rne-3071|NN|_ ts|t|NNS|_
rne|rne|NN|GEN wild-type|wild-type|JJ|_
rng|rng|NN|GEN mutant|mutant|JJ|_
rng|rng|NN|GEN wild-type|wild-type|JJ|_
Sequence|sequence|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ reads|read|VBZ|_ and|and|CC|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|workbench|JJ|_ 6.0.1|6.0.1|CD|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
strain|strain|NN|_ :|:|:|_ GM11|gm11|NN|_
strain|strain|NN|_ :|:|:|_ MC1061|mc1061|NN|_
strain|strain|NN|_ :|:|:|_ N3431|n3431|NN|_
strain|strain|NN|_ :|:|:|_ N3433|n3433|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ in|in|IN|_ tab|tab|NN|_ delimited|delimit|VBD|_ format|format|NN|_ .|.|.|_ Separate|separate|JJ|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ and|and|CC|_ reverse|reverse|JJ|_ strands|strand|NNS|_ .|.|.|_ The|the|DT|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ coordinates|coordinate|VBZ|_ should|should|MD|_ be|be|VB|_ the|the|DT|_ same|same|JJ|_ .|.|.|_ Each|each|DT|_ line|line|NN|_ in|in|IN|_ the|the|DT|_ data|data|NN|_ set|set|NN|_ represents|represent|VBZ|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ a|a|DT|_ sequence|sequence|NN|_ that|that|WDT|_ could|could|MD|_ be|be|VB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ .|.|.|_
T170V|t170v|NN|_ 0|0|CD|_ min|min|NN|_
T170V|t170v|NN|_ 10|10|CD|_ min|min|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ as|as|IN|_ desribed|desribe|VBN|_ in|in|IN|_ Kime|Kime|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2008|2008|CD|_
All|All|NNP|_ samples|sample|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ extraction|extraction|NN|_ with|with|IN|_ DNA|dna|NN|_ digestion|digestion|NN|_ ,|,|,|_ following|follow|VBG|_ standard|standard|JJ|_ protocol|protocol|NN|_
BigWIG|bigwig|NN|_ files|file|NNS|_ were|be|VBD|_ viewed|view|VBN|_ and|and|CC|_ annotated|annotated|JJ|_ using|use|VBG|_ Jbrowse|Jbrowse|NNP|_ and|and|CC|_ Integrated|Integrated|NNP|_ Genome|Genome|NNP|_ Viewer|Viewer|NNP|_ .|.|.|_
cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ at|at|IN|_ Vertis|Vertis|NNP|_ in|in|IN|_ Germany|Germany|NNP|_ using|use|VBG|_ a|a|DT|_ ligation|ligation|NN|_ based|base|VBN|_ stratagey|stratagey|NN|_ for|for|IN|_ Illumina|Illumina|NNP|_ whole|whole|JJ|_ transcriptome|transcriptome|NN|_ sequencing|sequencing|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ DNase|dnase|NN|_ I|i|CD|_ digested|digest|VBN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ RNase|rnase|NN|_ III|iii|CD|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ labeled|label|VBN|_ as|as|IN|_ TEX|TEX|NNP|_ were|be|VBD|_ also|also|RB|_ subsequently|subsequently|RB|_ digested|digest|VBN|_ with|with|IN|_ Terminator|Terminator|NNP|_ Exonuclease|Exonuclease|NNP|_ -LRB-|-lrb-|-LRB-|_ TEX|TEX|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Pyrophosphate|pyrophosphate|NN|_ groups|group|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ ′|′|NN|_ terminus|terminus|NN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ an|a|DT|_ RNA|rna|NN|_ adapter|adapter|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 5|5|CD|_ ′|′|NN|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Cell|cell|NN|_ culture|culture|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW38028|bw38028|NN|_
For|for|IN|_ alignment|alignment|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ contained|contain|VBN|_ within|within|IN|_ the|the|DT|_ fastq|fastq|NN|_ files|file|VBZ|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ RefSeq|refseq|NN|_ NC|nc|NN|_ _|_|CD|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ short|short|JJ|_ read|read|NN|_ alignment|alignment|NN|_ tool|tool|NN|_ Bowtie2|bowtie2|NN|_ was|be|VBD|_ utilized|utilize|VBN|_ under|under|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_ Bowtie|Bowtie|NNP|_ parameters|parameter|NNS|_ were|be|VBD|_ set|set|VBN|_ to|to|TO|_ include|include|VB|_ only|only|RB|_ perfect|perfect|JJ|_ matches|match|NNS|_ and|and|CC|_ map|map|NN|GEN once|once|RB|_ reads|read|VBZ|_ that|that|IN|_ map|map|NN|GEN to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ genome|genome|NN|_ location|location|NN|_ ,|,|,|_ i.e.|i.e.|FW|_ ,|,|,|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ are|be|VBP|_ retained|retain|VBN|_ .|.|.|_ The|the|DT|_ output|output|NN|_ Bowtie2|bowtie2|NN|_ was|be|VBD|_ a|a|DT|_ SAM|SAM|NNP|_ files|file|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Reference|Reference|NNP|_ genome|genome|NN|_ for|for|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ RefSeq|refseq|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
genotype|genotype|NN|_ :|:|:|_ rpoS|rpos|NN|GEN
genotype|genotype|NN|_ :|:|:|_ wt|wt|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_ post|post|NN|_ stationary|stationary|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Log|log|VB|_ phase|phase|NN|_ OD|od|NN|_ 0.4|0.4|CD|_
Prior|prior|RB|_ to|to|TO|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ harvested|harvest|VBN|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80.0|-80.0|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ RNAlater|rnalater|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ N|n|NN|_ _|_|CD|_ strv|strv|NN|_
rpoS|rpos|NN|GEN _|_|CD|_ N|n|NN|_ _|_|SYM|_ strv|strv|FW|_ _|_|FW|_ TEX|tex|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ no|no|DT|_ RNA|rna|NN|_ treatment|treatment|NN|_
Sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ by|by|IN|_ conversion|conversion|NN|_ of|of|IN|_ the|the|DT|_ sample|sample|NN|_ alignment|alignment|NN|_ -LRB-|-lrb-|-LRB-|_ BAM|bam|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|VBZ|_ to|to|TO|_ strand-specific|strand-specific|JJ|_ base|base|NN|_ count|count|NN|_ -LRB-|-lrb-|-LRB-|_ BigWIG|bigwig|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ To|to|TO|_ accomplish|accomplish|VB|_ this|this|DT|_ an|a|DT|_ in-house|in-house|JJ|_ script|script|NN|_ was|be|VBD|_ created|create|VBN|_ to|to|TO|_ extract|extract|VB|_ strand-specific|strand-specific|JJ|_ base|base|NN|_ count|count|NN|_ data|datum|NNS|_ from|from|IN|_ BAM|BAM|NNP|_ files|file|NNS|_ -LRB-|-lrb-|-LRB-|_ outputs|output|NNS|_ are|be|VBP|_ positive|positive|JJ|_ and|and|CC|_ negative|negative|JJ|_ strand|strand|NN|_ BigWIG|bigwig|NN|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ BW38028|bw38028|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BigWIG|bigwig|NN|_ files|file|NNS|_ are|be|VBP|_ provided|provide|VBN|_ showing|show|VBG|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ sequence|sequence|NN|_ reads|read|VBZ|_ .|.|.|_
The|the|DT|_ data|datum|NNS|_ output|output|NN|_ from|from|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Hiseq|Hiseq|NNP|_ System|System|NNP|_ was|be|VBD|_ obtained|obtain|VBN|_ directly|directly|RB|_ from|from|IN|_ Vertis|Vertis|NNP|_
treatment|treatment|NN|_ :|:|:|_ Carbon|Carbon|NNP|_ starvation|starvation|NN|_
treatment|treatment|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_ sample|sample|NN|_
treatment|treatment|NN|_ :|:|:|_ Nitrogen|nitrogen|NN|_ starvation|starvation|NN|_
Used|use|VBD|_ SAMTOOLS|samtools|NN|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ PMID|pmid|NN|_ 1950593|1950593|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ sort|sort|VB|_ and|and|CC|_ index|index|NN|_ the|the|DT|_ SAM|SAM|NNP|_ files|file|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ Bowtie2|bowtie2|NN|_ and|and|CC|_ convert|convert|VB|_ them|they|PRP|_ to|to|TO|_ BAM|BAM|NNP|_ format|format|NN|_ .|.|.|_
Wild|Wild|NNP|_ type|type|NN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ BW38038|bw38038|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ BW39452|bw39452|NN|_ -LRB-|-lrb-|-LRB-|_ ΔrpoS|δrpos|NN|_ -RRB-|-rrb-|-RRB-|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP minimal|minimal|JJ|_ medium|medium|NN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP as|as|IN|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ pH|ph|NN|_ was|be|VBD|_ initially|initially|RB|_ 7.4|7.4|CD|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ agitation|agitation|NN|_ speed|speed|NN|_ was|be|VBD|_ 500|500|CD|_ rpm|rpm|NN|_ .|.|.|_ Culture|culture|NN|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ during|during|IN|_ logarithmic|logarithmic|JJ|_ growth|growth|NN|_ and|and|CC|_ following|follow|VBG|_ entry|entry|NN|_ into|into|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase for|for|IN|_ the|the|DT|_ WT|WT|NNP|_ and|and|CC|_ rpoS|rpos|NN|GEN mutant|mutant|NN|_ .|.|.|_ OD600|od600|CD|_ measurements|measurement|NNS|_ were|be|VBD|_ made|make|VBN|_ on|on|IN|_ a|a|DT|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ DU|DU|NNP|_ 800|800|CD|_ spectrophotometer|spectrophotometer|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ directly|directly|RB|_ into|into|IN|_ ice-cold|ice-cold|JJ|_ RNAlater|rnalater|NN|_ at|at|IN|_ a|a|DT|_ 1:1|1:1|CD|_ dilution|dilution|NN|_ to|to|TO|_ protect|protect|VB|_ RNA|rna|NN|_ from|from|IN|_ degradation|degradation|NN|_ and|and|CC|_ cells|cell|NNS|_ then|then|RB|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8000rpm|8000rpm|CD|_ for|for|IN|_ 10|10|CD|_ minutes|minute|NNS|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ in|in|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ RNAlater|rnalater|NN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ log|log|NN|_
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ log|log|NN|_ _|_|CD|_ TEX|TEX|NNP|_
WT|WT|NNP|_ _|_|VBD|_ glucose|glucose|NN|SUPP _|_|CD|_ stat|stat|NN|_
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ stat|stat|NN|_ _|_|CD|_ TEX|TEX|NNP|_
WT|WT|NNP|_ _|_|VBD|_ N|n|NN|_ _|_|CD|_ strv|strv|NN|_
WT|wt|JJ|_ _|_|NN|_ N|n|NN|_ _|_|CD|_ strv|strv|NN|_ _|_|CD|_ TEX|TEX|NNP|_
10|10|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ sodium|sodium|NN|_ phosphate|phosphate|NN|_ and|and|CC|_ formaldehyde|formaldehyde|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ %|%|NN|_ were|be|VBD|_ then|then|RB|_ added|add|VBN|_ .|.|.|_ After|after|IN|_ 10|10|CD|_ min|min|NN|_ of|of|IN|_ incubation|incubation|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ 30|30|CD|_ min|min|NN|_ in|in|IN|_ ice|ice|NN|_
bacterial|bacterial|JJ|_ cell|cell|NN|_ culture|culture|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-Flag|anti-flag|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_
ChIP-Seq|chip-seq|NN|_
Cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ and|and|CC|_ washed|wash|VBN|_ two|two|CD|_ times|time|NNS|_ with|with|IN|_ ice-cold|ice-cold|JJ|_ PBS|PBS|NNP|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 450μl|450μl|NN|_ of|of|IN|_ TES|tes|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 50mM|50mm|NN|_ Tris-HCl|tris-hcl|NN|_ pH|ph|NN|_ 7.5|7.5|CD|_ ,|,|,|_ 150mM|150mm|NN|_ NaCl|nacl|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 20μl|20μl|NN|_ of|of|IN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 13.6|13.6|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Reference|Reference|NNP|_ genome|genome|NN|_ used|use|VBN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ :|:|:|_ iGenome|iGenome|NNP|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
genotype|genotype|NN|_ :|:|:|_ ΔbolA|δbola|NN|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ processing|processing|NN|_ in|in|FW|_ vitro|vitro|FW|_ samples|sample|NNS|_ to|to|TO|_ generate|generate|VB|_ a|a|DT|_ library|library|NN|_ of|of|IN|_ short|short|JJ|_ inserts|insert|NNS|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ DNA|dna|NN|_ Colonies|colony|NNS|_ Template|Template|NNP|_ Library|Library|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ Fasteris|Fasteris|NNP|_ SA|SA|NNP|_ ,|,|,|_ Switzerland|Switzerland|NNP|_
Mapping|mapping|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ tool|tool|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.5.9|0.5.9|CD|_ -RRB-|-rrb-|-RRB-|_ against|against|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_
Peak|peak|JJ|_ detection|detection|NN|_ and|and|CC|_ count|count|NN|_ of|of|IN|_ coverage|coverage|NN|_ were|be|VBD|_ done|do|VBN|_ using|use|VBG|_ SEQMONK|SEQMONK|NNP|_ version|version|NN|_ 0.21.0|0.21.0|CD|_ by|by|IN|_ Fasteris|Fasteris|NNP|_ SA|SA|NNP|_
Reference|Reference|NNP|_ genome|genome|NN|_ used|use|VBN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ :|:|:|_ iGenome|igenome|NN|_
strain|strain|NN|_ :|:|:|_ no|no|DT|_ tag|tag|NN|GEN
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_ 3xflag|3xflag|NN|_ strain|strain|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ file|file|NN|_ file|file|NN|_ with|with|IN|_ raw|raw|JJ|_ and|and|CC|_ normalized|normalize|VBD|_ counts|count|NNS|_ of|of|IN|_ coverage|coverage|NN|_
The|the|DT|_ ΔbolA|δbola|NN|_ and|and|CC|_ wt|wt|JJ|_ 3xflag|3xflag|NN|_ strains|strain|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ perform|perform|VB|_ ChIP-seq|chip-seq|JJ|_ experiments|experiment|NNS|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1|1|CD|_
wild|wild|JJ|_ type|type|NN|_
ΔbolA|δbola|NN|_
At|at|IN|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ length|length|NN|_ of|of|IN|_ time|time|NN|_ .|.|.|_
bacteria|bacterium|NNS|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30C|30c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD420|od420|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ 4|4|CD|_ subcultures|subculture|NNS|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ OD|od|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E|e|NN|_ coli|coli|NN|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ the|the|DT|_ footprint|footprint|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ footprint|footprint|NN|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ detail|detail|NN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ rapidly|rapidly|RB|_ filtered|filter|VBN|_ at|at|IN|_ 37C|37c|NN|_ by|by|IN|_ passing|pass|VBG|_ through|through|IN|_ a|a|DT|_ nitrocellulose|nitrocellulose|NN|_ filter|filter|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ was|be|VBD|_ were|be|VBD|_ rapidly|rapidly|RB|_ collected|collect|VBN|_ using|use|VBG|_ a|a|DT|_ pre-warmed|pre-warmed|JJ|_ metal|metal|NN|_ table|table|NN|_ crumber|crumber|NN|_ ,|,|,|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ frozen|frozen|JJ|_ droplets|droplet|NNS|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ .|.|.|_ Cells|cell|NNS|_ and|and|CC|_ lysis|lysis|NN|_ buffer|buffer|NN|_ were|be|VBD|_ pulverized|pulverize|VBN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ canisters|canister|NNS|_ -LRB-|-lrb-|-LRB-|_ Retsch|retsch|NN|_ -RRB-|-rrb-|-RRB-|_ pre-chilled|pre-chilled|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ TissueLyser|TissueLyser|NNP|_ II|II|NNP|_ .|.|.|_ Pulverized|pulverize|VBN|_ lysate|lysate|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ and|and|CC|_ clarified|clarify|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 4C|4c|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
media|media|NNS|_ :|:|:|_ fully|fully|RB|_ supplemented|supplement|VBN|_ MOPS|mop|NNS|MED glucose|glucose|NN|SUPP media|media|NNS|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ mRNA|mrna|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ ribosome|ribosome|NN|_ protected|protect|VBD|_ mRNA|mrna|NN|_
mRNA-seq|mrna-seq|NN|_ in|in|IN|_ rich|rich|JJ|_ defined|define|VBN|_ media|media|NNS|_
mRNA-seq|mrna-seq|NN|_ MicL-S|micl-s|NN|_ t0|t0|NN|_
mRNA-seq|mrna-seq|NN|_ MicL-S|micl-s|NN|_ t10|t10|NN|_
mRNA-seq|mrna-seq|NN|_ MicL-S|micl-s|NN|_ t20|t20|NN|_
mRNA-seq|mrna-seq|NN|_ MicL-S|micl-s|NN|_ t4|t4|NN|_
mRNA-seq|mrna-seq|NN|_ MicL|micl|NN|_ t0|t0|NN|_
mRNA-seq|mrna-seq|NN|_ MicL|micl|NN|_ t10|t10|NN|_
mRNA-seq|mrna-seq|NN|_ MicL|micl|NN|_ t20|t20|NN|_
mRNA-seq|mrna-seq|NN|_ MicL|micl|NN|_ t4|t4|NN|_
mRNA-seq|mrna-seq|NN|_ Vector|Vector|NNP|_ t0|t0|NN|_
mRNA-seq|mrna-seq|NN|_ Vector|Vector|NNP|_ t20|t20|NN|_
mRNA-seq|mrna-seq|NN|_ WT|wt|JJ|_ t10|t10|NN|_
mRNA-seq|mrna-seq|NN|_ WT|wt|JJ|_ t4|t4|NN|_
plasmid|plasmid|NN|_ :|:|:|_ empty|empty|JJ|_ vector|vector|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pMicL|pmicl|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pMicL-S|pmicl-s|NN|_
ribosome|ribosome|NN|_ profiling|profiling|NN|_ in|in|IN|_ rich|rich|JJ|_ defined|define|VBN|_ media|media|NNS|_
ribosome|ribosome|NN|_ profiling|profile|VBG|_ MicL|micl|NN|_ t0|t0|NN|_
ribosome|ribosome|NN|_ profiling|profile|VBG|_ MicL|micl|NN|_ t20|t20|NN|_
Ribosome|ribosome|NN|_ protected|protect|VBD|_ and|and|CC|_ total|total|JJ|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ via|via|IN|_ gel|gel|NN|_ purification|purification|NN|_ .|.|.|_ Fragments|fragment|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 5|5|CD|_ '|'|''|_ adenylated|adenylate|VBN|_ DNA|dna|NN|_ oligo|oligo|JJ|_ .|.|.|_ After|after|IN|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ the|the|DT|_ single|single|JJ|_ stranded|stranded|JJ|_ DNA|dna|NN|_ was|be|VBD|_ circularized|circularize|VBN|_ ,|,|,|_ and|and|CC|_ PCR|pcr|NN|_ amplified|amplify|VBD|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ More|more|JJR|_ details|detail|NNS|_ at|at|IN|_ MS|ms|NN|_ Guo|Guo|NNP|_ ,|,|,|_ TB|tb|NN|_ Updegrove|Updegrove|NNP|_ ,|,|,|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ Genes|gene|NNS|_ Dev|dev|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_ files|file|NNS|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E|E|NNP|_ coli|coli|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ 1|1|LS|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ --|--|:|_ best|best|JJS|_ .|.|.|_ This|this|DT|_ allows|allow|VBZ|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reports|report|NNS|_ only|only|RB|_ reads|read|VBZ|_ that|that|IN|_ align|align|NN|_ 1|1|CD|_ or|or|CC|_ fewer|fewer|JJR|_ times|time|NNS|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 318|318|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 320|320|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ 327|327|CD|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol|vol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ ACSH|ACSH|NNP|_ ,|,|,|_ Exp|Exp|NNP|_
GLBRCE1|GLBRCE1|NNP|_ _|_|NNP|_ ACSH|ACSH|NNP|_ _|_|VBD|_ Exp|Exp|NNP|_ _|_|SYM|_ rep318|rep318|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|NNP|_ Exp|Exp|NNP|_ _|_|SYM|_ rep320|rep320|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|NNP|_ Exp|Exp|NNP|_ _|_|SYM|_ rep327|rep327|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ ACSH|ACSH|NNP|_ ,|,|,|_ Stat1|stat1|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|SYM|_ Stat1|stat1|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|SYM|_ Stat1|stat1|NN|_ _|_|CD|_ rep320|rep320|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|SYM|_ Stat1|stat1|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ ACSH|ACSH|NNP|_ ,|,|,|_ Stat2|stat2|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|SYM|_ Stat2|stat2|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|SYM|_ Stat2|stat2|NN|_ _|_|CD|_ rep320|rep320|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|SYM|_ Stat2|stat2|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ ACSH|ACSH|NNP|_ ,|,|,|_ Trans|Trans|NNP|_
GLBRCE1|GLBRCE1|NNP|_ _|_|NNP|_ ACSH|ACSH|NNP|_ _|_|VBD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep318|rep318|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep318|rep318|CD|_ _|_|NN|_ 2|2|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep320|rep320|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep327|rep327|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ ,|,|,|_ Exp|exp|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 2|2|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ rep320|rep320|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ ,|,|,|_ Exp|exp|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ rep320|rep320|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ ,|,|,|_ Stat1|stat1|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ rep320|rep320|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ ,|,|,|_ Stat2|stat2|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|SYM|_ Stat2|stat2|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|SYM|_ Stat2|stat2|NN|_ _|_|CD|_ rep320|rep320|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|SYM|_ Stat2|stat2|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ ,|,|,|_ Trans|Trans|NNP|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep318|rep318|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep320|rep320|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep327|rep327|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ ,|,|,|_ Stat1|stat1|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ rep318|rep318|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ rep320|rep320|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ ,|,|,|_ Stat2|stat2|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Stat2|stat2|NN|_ _|_|CD|_ rep327|rep327|NN|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ ,|,|,|_ SynH|synh|NN|_ ,|,|,|_ Trans|Trans|NNP|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep318|rep318|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep320|rep320|CD|_ _|_|NN|_ 1|1|CD|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ SynH|synh|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|SYM|_ rep327|rep327|CD|_ _|_|NN|_ 1|1|CD|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat2|stat2|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
medium|medium|NN|_ :|:|:|_ ACSH|ACSH|NNP|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
Probe|probe|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ preprocessed|preprocess|VBN|_ using|use|VBG|_ robust|robust|JJ|_ multichip|multichip|NN|_ averaging|averaging|NN|_ -LRB-|-lrb-|-LRB-|_ RMA|rma|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ program|program|NN|_ ArrayStar|arraystar|NN|_ -LRB-|-lrb-|-LRB-|_ DNASTAR|dnastar|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ gene|gene|NN|_ expression|expression|NN|_ signals|signal|NNS|_ were|be|VBD|_ quantile-normalized|quantile-normalize|VBN|_ across|across|IN|_ all|all|DT|_ samples|sample|NNS|_ using|use|VBG|_ the|the|DT|_ normalize.quantiles|normalize.quantiles|JJ|_ function|function|NN|_ in|in|IN|_ the|the|DT|_ Bioconductor|Bioconductor|NNP|_ package|package|NN|_ for|for|IN|_ R.|R.|NNP|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
technical|technical|JJ|_ replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
technical|technical|JJ|_ replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol|vol|NN|_
E.coli|e.coli|NN|_ ethanologen|ethanologen|NN|_ strain|strain|NN|_ GLBRCE1|glbrce1|NN|_ or|or|CC|_ GLBRCE1|glbrce1|NN|_ lacking|lack|VBG|_ the|the|DT|_ plasmid-borne|plasmid-borne|JJ|_ PET|pet|NN|_ cassette|cassette|NN|_ -LRB-|-lrb-|-LRB-|_ GLBRCE1|glbrce1|NN|_ _|_|CD|_ pBBR|pbbr|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ AFEX|AFEX|NNP|_ corn|corn|NN|_ stover|stover|NN|_ hydrolysate|hydrolysate|NN|_ -LRB-|-lrb-|-LRB-|_ ACSH|acsh|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_ .|.|.|_ One|one|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ each|each|DT|_ medium|medium|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ at|at|IN|_ 3|3|CD|_ time|time|NN|_ points|point|NNS|_ ,|,|,|_ corresponding|correspond|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ -LRB-|-lrb-|-LRB-|_ Exp|exp|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transitional|transitional|JJ|_ -LRB-|-lrb-|-LRB-|_ Trans|Trans|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ Stat|stat|NN|_ -RRB-|-rrb-|-RRB-|_ growth|growth|NN|_ phases|phase|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_ _|_|CD|_ pBBR|pbbr|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|NNP|_ Exp|Exp|NNP|_
GLBRCE1|GLBRCE1|NNP|_ _|_|NNP|_ ACSH|ACSH|NNP|_ _|_|VBD|_ Stat|stat|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|NNP|_ Trans|Trans|NNP|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ pBBR|pbbr|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|NNP|_ Exp|Exp|NNP|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ pBBR|pbbr|NN|_ _|_|SYM|_ ACSH|ACSH|NNP|_ _|_|VBD|_ Stat|stat|NN|_
GLBRCE1|glbrce1|NN|_ _|_|CD|_ pBBR|pbbr|NN|_ _|_|CD|_ ACSH|ACSH|NNP|_ _|_|NNP|_ Trans|Trans|NNP|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat|stat|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
medium|medium|NN|_ :|:|:|_ ACSH|ACSH|NNP|_
Probe|Probe|NNP|_ signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ preprocessed|preprocess|VBN|_ using|use|VBG|_ robust|robust|JJ|_ multichip|multichip|NN|_ averaging|averaging|NN|_ -LRB-|-lrb-|-LRB-|_ RMA|rma|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ program|program|NN|_ ArrayStar|arraystar|NN|_ -LRB-|-lrb-|-LRB-|_ DNASTAR|dnastar|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ gene|gene|NN|_ expression|expression|NN|_ signals|signal|NNS|_ were|be|VBD|_ quantile-normalized|quantile-normalize|VBN|_ across|across|IN|_ all|all|DT|_ samples|sample|NNS|_ using|use|VBG|_ the|the|DT|_ normalize.quantiles|normalize.quantiles|JJ|_ function|function|NN|_ in|in|IN|_ the|the|DT|_ Bioconductor|Bioconductor|NNP|_ package|package|NN|_ for|for|IN|_ R.|R.|NNP|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_ _|_|CD|_ pBBR|pbbr|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol|vol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stat|stat|NN|_ 1|1|CD|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stat|stat|NN|_ 2|2|CD|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ transition|transition|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S1|s1|NN|_ _|_|CD|_ T10|t10|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S1|s1|NN|_ _|_|CD|_ T3|t3|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S1|s1|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S2|s2|NN|_ _|_|CD|_ T4|t4|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S2|s2|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S2|s2|NN|_ _|_|CD|_ T8|t8|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S3|s3|NN|_ _|_|CD|_ T11|t11|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S3|s3|NN|_ _|_|CD|_ T3|t3|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S3|s3|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S5|s5|NN|_ _|_|CD|_ T4|t4|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S5|s5|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS477|lims477|NN|_ _|_|CD|_ S5|s5|NN|_ _|_|CD|_ T8|t8|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S1|s1|NN|_ _|_|CD|_ T3|t3|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S1|s1|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S1|s1|NN|_ _|_|CD|_ T8|t8|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S2|s2|NN|_ _|_|CD|_ T2|t2|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S2|s2|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S2|s2|NN|_ _|_|CD|_ T8|t8|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S5|s5|NN|_ _|_|CD|_ T2|t2|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S5|s5|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S5|s5|NN|_ _|_|CD|_ T8|t8|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S6|s6|NN|_ _|_|CD|_ T4|t4|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S6|s6|NN|_ _|_|CD|_ T6|t6|NN|_
LIMS484|lims484|NN|_ _|_|CD|_ S6|s6|NN|_ _|_|CD|_ T8|t8|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ +|+|CC|_ LTs|lts|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ w|w|NN|_
Probe|Probe|NNP|_ signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ preprocessed|preprocess|VBN|_ using|use|VBG|_ robust|robust|JJ|_ multichip|multichip|NN|_ averaging|averaging|NN|_ -LRB-|-lrb-|-LRB-|_ RMA|rma|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ program|program|NN|_ ArrayStar|arraystar|NN|_ -LRB-|-lrb-|-LRB-|_ DNASTAR|dnastar|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ gene|gene|NN|_ expression|expression|NN|_ signals|signal|NNS|_ were|be|VBD|_ quantile-normalized|quantile-normalize|VBN|_ across|across|IN|_ all|all|DT|_ samples|sample|NNS|_ using|use|VBG|_ the|the|DT|_ normalize.quantiles|normalize.quantiles|JJ|_ function|function|NN|_ in|in|IN|_ the|the|DT|_ Bioconductor|Bioconductor|NNP|_ package|package|NN|_ for|for|IN|_ R.|R.|NNP|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol|vol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
Fermentations|fermentation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3L|3l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|ACSH|NNP|_ ,|,|,|_ SynH|synh|NN|_ ,|,|,|_ SynH|synh|NN|_ +|+|CC|_ LT|lt|NN|_ ,|,|,|_ or|or|CC|_ SynH|synh|NN|_ +|+|CC|_ Acid|acid|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp1|exp1|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp2|exp2|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp3|exp3|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat|stat|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat2|stat2|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
medium|medium|NN|_ :|:|:|_ ACSH|ACSH|NNP|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|NN|_ Acids|acid|NNS|_ _|_|VBP|_ Amides|amide|NNS|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
Probe|probe|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ preprocessed|preprocess|VBN|_ using|use|VBG|_ robust|robust|JJ|_ multichip|multichip|NN|_ averaging|averaging|NN|_ -LRB-|-lrb-|-LRB-|_ RMA|rma|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ program|program|NN|_ ArrayStar|arraystar|NN|_ -LRB-|-lrb-|-LRB-|_ DNASTAR|dnastar|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ gene|gene|NN|_ expression|expression|NN|_ signals|signal|NNS|_ were|be|VBD|_ quantile-normalized|quantile-normalize|VBN|_ across|across|IN|_ all|all|DT|_ samples|sample|NNS|_ using|use|VBG|_ the|the|DT|_ normalize.quantiles|normalize.quantiles|JJ|_ function|function|NN|_ in|in|IN|_ the|the|DT|_ Bioconductor|Bioconductor|NNP|_ package|package|NN|_ for|for|IN|_ R.|R.|NNP|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
X515|x515|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 424287A03|424287a03|NN|_
X515|x515|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475655A02|475655a02|NN|_
X515|x515|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 475649A04s|475649a04|NNS|_
X515|x515|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 475654A02|475654a02|NN|_
X515|x515|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 475585A04|475585a04|NN|_
X515|x515|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 424219A04|424219a04|NN|_
X515|x515|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475655A03|475655a03|NN|_
X515|x515|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 475644A04|475644a04|NN|_
X515|x515|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 475649A01|475649a01|NN|_
X515|x515|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 424219A01s|424219a01|NNS|_
X515|x515|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475585A02s|475585a02|NNS|_
X515|x515|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 424221A04|424221a04|NN|_
X515|x515|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 475649A02|475649a02|NN|_
X515|x515|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 475641A04|475641a04|NN|_
X515|x515|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475585A03|475585a03|NN|_
X515|x515|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475644A01|475644a01|NN|_
X515|x515|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 424221A03|424221a03|NN|_
X515|x515|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 424287A04|424287a04|NN|_
X515|x515|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 475655A04|475655a04|NN|_
X520|x520|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 424221A01|424221a01|NN|_
X520|x520|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 475649A03|475649a03|NN|_
X520|x520|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 475655A01|475655a01|NN|_
X520|x520|NN|_ _|_|CD|_ V1|v1|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 475641A01|475641a01|NN|_
X520|x520|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T3|t3|NN|_ _|_|CD|_ 424221A02|424221a02|NN|_
X520|x520|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475641A03|475641a03|NN|_
X520|x520|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 424287A02|424287a02|NN|_
X520|x520|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 475654A01|475654a01|NN|_
X520|x520|NN|_ _|_|CD|_ V2|v2|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 424219A02|424219a02|NN|_
X520|x520|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475654A04|475654a04|NN|_
X520|x520|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 475641A02|475641a02|NN|_
X520|x520|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 475644A02s|475644a02|NNS|_
X520|x520|NN|_ _|_|CD|_ V3|v3|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 424219A03|424219a03|NN|_
X520|x520|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ 475654A03|475654a03|NN|_
X520|x520|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ 424287A01|424287a01|NN|_
X520|x520|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T7|t7|NN|_ _|_|CD|_ 475644A03|475644a03|NN|_
X520|x520|NN|_ _|_|CD|_ V4|v4|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ 475585A01|475585a01|NN|_
Each|each|DT|_ strain|strain|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ the|the|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ into|into|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ M9|m9|NN|_ medium|medium|NN|_ for|for|IN|_ preculture|preculture|NN|_ .|.|.|_ Five-microliter|five-microliter|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ preculture|preculture|JJ|_ medium|medium|NN|_ cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ the|the|DT|_ fresh|fresh|JJ|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ M9|m9|NN|_ with|with|IN|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Evolved|evolve|VBD|_ strain|strain|NN|_ A|a|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 1|1|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ A|a|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 2|2|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ A|a|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 3|3|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ A|a|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 4|4|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ A|a|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 5|5|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ B|b|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 1|1|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ B|b|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 2|2|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ B|b|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 3|3|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ B|b|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 4|4|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ B|b|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 5|5|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ C|c|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 1|1|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ C|c|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 2|2|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ C|c|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 3|3|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ C|c|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 4|4|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ C|c|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 5|5|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ D|d|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 1|1|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ D|d|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 2|2|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ D|d|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 3|3|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ D|d|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 4|4|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ D|d|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 5|5|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ E|e|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 1|1|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ E|e|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 2|2|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ E|e|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 3|3|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ E|e|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 4|4|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ E|e|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 5|5|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ F|f|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 1|1|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ F|f|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 2|2|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ F|f|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 3|3|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ F|f|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 4|4|CD|_
Evolved|evolve|VBN|_ strain|strain|NN|_ F|f|NN|_ ,|,|,|_ time|time|NN|_ point|point|NN|_ 5|5|CD|_
Log10|log10|NN|_ mRNA|mrna|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ pM|pm|NN|_ -RRB-|-rrb-|-RRB-|_ data|datum|NNS|_ are|be|VBP|_ provided|provide|VBN|_ as|as|IN|_ a|a|DT|_ supplementary|supplementary|JJ|_ file|file|NN|_ .|.|.|_ Expression|expression|NN|_ levels|level|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2003|2003|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Parent|Parent|NNP|_ strain|strain|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_
Parent|Parent|NNP|_ strain|strain|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ as|as|IN|_ adaptive|adaptive|JJ|_ evolved|evolve|VBD|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ strain|strain|NN|_ to|to|TO|_ M9|m9|NN|_ synthetic|synthetic|JJ|_ medium|medium|NN|_ without|without|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_
platform|platform|NN|_ _|_|CD|_ id|id|NN|_ _|_|CD|_ id|id|NN|_ design|design|NN|_ :|:|:|_ EcFS|ecfs|NN|_ _|_|NN|_ 1|1|CD|_
platform|platform|NN|_ _|_|CD|_ id|id|NN|_ _|_|CD|_ id|id|NN|_ design|design|NN|_ :|:|:|_ EcFS|ecfs|NN|_ _|_|NN|_ 2|2|CD|_
platform|platform|NN|_ _|_|CD|_ id|id|NN|_ _|_|CD|_ id|id|NN|_ design|design|NN|_ :|:|:|_ EcFS|ecfs|NN|_ _|_|NN|_ 3|3|CD|_
Strain|strain|NN|_ A|a|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1224|1224|CD|_ hours|hour|NNS|_ .|.|.|_
Strain|strain|NN|_ A|a|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1824|1824|CD|_ hours|hour|NNS|_ .|.|.|_
Strain|strain|NN|_ A|a|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 2496|2496|CD|_ hours|hour|NNS|_ .|.|.|_
Strain|strain|NN|_ A|a|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 384|384|CD|_ hours|hour|NNS|_ .|.|.|_
Strain|strain|NN|_ A|a|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 744|744|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ B|b|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1224|1224|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ B|b|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1824|1824|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ B|b|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 2496|2496|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ B|b|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 384|384|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ B|b|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 744|744|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ C|c|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1224|1224|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ C|c|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1824|1824|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ C|c|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 2496|2496|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ C|c|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 384|384|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ C|c|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 744|744|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ D|d|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1224|1224|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ D|d|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1824|1824|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ D|d|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 2496|2496|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ D|d|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 384|384|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ D|d|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 744|744|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ E|e|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1224|1224|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ E|e|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1824|1824|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ E|e|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 2496|2496|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ E|e|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 384|384|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ E|e|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 744|744|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ F|f|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1224|1224|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ F|f|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 1824|1824|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ F|f|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 2496|2496|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ F|f|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 384|384|CD|_ hours|hour|NNS|_ .|.|.|_
strain|strain|NN|_ F|f|NN|_ of|of|IN|_ experimental|experimental|JJ|_ evolution|evolution|NN|_ under|under|IN|_ ethanol|ethanol|NN|_ stress|stress|NN|_ in|in|IN|_ 744|744|CD|_ hours|hour|NNS|_ .|.|.|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 8,000|8,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
To|to|TO|_ obtain|obtain|VB|_ the|the|DT|_ absolute|absolute|JJ|_ expression|expression|NN|_ levels|level|NNS|_ of|of|IN|_ genes|gene|NNS|_ from|from|IN|_ microarray|microarray|NN|_ raw|raw|JJ|_ data|datum|NNS|_ ,|,|,|_ we|we|PRP|_ used|use|VBD|_ the|the|DT|_ Finite|Finite|NNP|_ Hybridization|hybridization|NN|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Furusawa|furusawa|NN|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ ;|;|:|_ Ono|Ono|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ from|from|IN|_ cells|cell|NNS|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNA|dna|NN|_ digestion|digestion|NN|_ .|.|.|_
ACSH|ACSH|NNP|_ _|_|VBD|_ Exp|Exp|NNP|_ _|_|NNP|_ CIYS|CIYS|NNP|_
ACSH|ACSH|NNP|_ _|_|VBD|_ Exp|Exp|NNP|_ _|_|NNP|_ CNFT|CNFT|NNP|_
ACSH|ACSH|NNP|_ _|_|VBD|_ Stat1|stat1|NN|_ _|_|CD|_ CNFW|CNFW|NNP|_
ACSH|ACSH|NNP|_ _|_|VBD|_ Stat1|stat1|NN|_ _|_|CD|_ CNGG|CNGG|NNP|_
ACSH|ACSH|NNP|_ _|_|VBD|_ Trans|Trans|NNP|_ _|_|NNP|_ CIYT|CIYT|NNP|_
ACSH|ACSH|NNP|_ _|_|VBD|_ Trans|Trans|NNP|_ _|_|NNP|_ CNFU|CNFU|NNP|_
Basecalling|Basecalling|NNP|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ sequencers|sequencer|NNS|_ using|use|VBG|_ the|the|DT|_ sequencer|sequencer|NN|_ 's|'s|POS|_ Real-Time|Real-Time|NNP|_ Analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ RTA|rta|NN|_ -RRB-|-rrb-|-RRB-|_ software|software|NN|_ .|.|.|_ CASAVA|CASAVA|NNP|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ process|process|VB|_ the|the|DT|_ basecalled|basecalled|JJ|_ data|datum|NNS|_ into|into|IN|_ FASTQ|fastq|NN|_ format|format|NN|_ .|.|.|_
Cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ transcriptomic|transcriptomic|JJ|_ analysis|analysis|NN|_ were|be|VBD|_ collected|collect|VBN|_ into|into|IN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 1.25|1.25|CD|_ ml|ml|NN|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ -LRB-|-lrb-|-LRB-|_ vol|vol|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism GLBRCE1|glbrce1|NN|_
FASTQ|fastq|NN|_ formatted|format|VBD|_ sequence|sequence|NN|_ files|file|NNS|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ Illumina|Illumina|NNP|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ GLBRCE1|glbrce1|NN|_ reference|reference|NN|_ genome|genome|NN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ version|version|NN|_ 0.12.7|0.12.7|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ '|'|''|_ --|--|:|_ nofw|nofw|NN|_ '|'|''|_ strand-specific|strand-specific|JJ|_ parameter|parameter|NN|_ and|and|CC|_ maximal|maximal|JJ|_ distance|distance|NN|_ between|between|IN|_ the|the|DT|_ paired|paired|JJ|_ reads|read|VBZ|_ of|of|IN|_ 1000|1000|CD|_ bp|bp|NN|_ .|.|.|_ NOTE|note|VB|_ :|:|:|_ Genome|Genome|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_ -LRB-|-lrb-|-LRB-|_ ASM584v2|asm584v2|NN|_ -RRB-|-rrb-|-RRB-|_ represents|represent|VBZ|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ strain|strain|NN|_ used|use|VBN|_ in|in|IN|_ our|we|PRP$|_ study|study|NN|_ was|be|VBD|_ modified|modify|VBN|_ from|from|IN|_ the|the|DT|_ parental|parental|JJ|_ strain|strain|NN|_ by|by|IN|_ replacing|replace|VBG|_ gene|gene|NN|_ pflB|pflb|NN|GEN with|with|IN|_ an|a|DT|_ insertion|insertion|NN|_ that|that|WDT|_ contained|contain|VBD|_ 3|3|CD|_ different|different|JJ|_ genes|gene|NNS|_ .|.|.|_
Fermentations|Fermentations|NNPS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ 3|3|CD|_ L|l|NN|_ bioreactors|bioreactor|NNS|_ -LRB-|-lrb-|-LRB-|_ Applikon|Applikon|NNP|_ Biotechnology|Biotechnology|NNP|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ 2.45|2.45|CD|_ L|l|NN|_ of|of|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ media|media|NNS|_ ,|,|,|_ and|and|CC|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ ACSH|acsh|NN|_ or|or|CC|_ SynH|synh|NN|_ with|with|IN|_ initial|initial|JJ|_ OD|od|NN|_ at|at|IN|_ 0.2|0.2|CD|_ ,|,|,|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ overnight|overnight|RB|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ inoculated|inoculate|VBN|_ into|into|IN|_ bioreactors|bioreactor|NNS|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.2|0.2|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exp|exp|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stat1|stat1|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Trans|Trans|NNP|_
medium|medium|NN|_ :|:|:|_ ACSH|ACSH|NNP|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_
medium|medium|NN|_ :|:|:|_ SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_
Probabilistic|probabilistic|JJ|_ expression|expression|NN|_ counting|counting|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ by|by|IN|_ Expectation-Maximization|expectation-maximization|NN|_ -LRB-|-lrb-|-LRB-|_ RSEM|rsem|NN|_ -RRB-|-rrb-|-RRB-|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ and|and|CC|_ Dewey|Dewey|NNP|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ cells|cell|NNS|_ pellets|pellet|NNS|_ by|by|IN|_ lysozyme|lysozyme|NN|_ treatment|treatment|NN|_ and|and|CC|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ ,|,|,|_ analyzed|analyze|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ to|to|TO|_ confirm|confirm|VB|_ integrity|integrity|NN|_ ,|,|,|_ quantified|quantify|VBN|_ using|use|VBG|_ a|a|DT|_ Nanodrop|Nanodrop|NNP|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_
strain|strain|NN|_ :|:|:|_ GLBRCE1|glbrce1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ file|file|NN|_ contains|contain|VBZ|_ counts|count|NNS|_ generated|generate|VBN|_ using|use|VBG|_ RSEM|rsem|NN|_ software|software|NN|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ transcripts|transcript|NNS|_ excluded|exclude|VBN|_ .|.|.|_
SynH|synh|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ BXHU|bxhu|NN|_
SynH|synh|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ CBYS|cbys|NN|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ BXNX|bxnx|NN|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ CBYU|cbyu|NN|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Exp|exp|NN|_ _|_|CD|_ CCOG|ccog|NN|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ BXNB|bxnb|NN|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ BXNZ|bxnz|NN|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ CHBW|chbw|NN|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|CD|_ BXNC|BXNC|NNP|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|CD|_ BXXC|BXXC|NNP|_
SynH|synh|NN|_ _|_|CD|_ LT|lt|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|CD|_ CBYW|CBYW|NNP|_
SynH|synh|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ CBYN|cbyn|NN|_
SynH|synh|NN|_ _|_|CD|_ Stat1|stat1|NN|_ _|_|CD|_ CUOC|cuoc|NN|_
SynH|synh|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|CD|_ CUNZ|CUNZ|NNP|_
SynH|synh|NN|_ _|_|CD|_ Trans|Trans|NNP|_ _|_|NNP|_ CUOB|CUOB|NNP|_
Total|Total|NNP|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 2ug|2ug|JJ|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ --|--|:|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ illumina|illumina|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ using|use|VBG|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 2|2|CD|_ mins|min|NNS|_ ,|,|,|_ targeting|target|VBG|_ fragments|fragment|NNS|_ ranging|range|VBG|_ from|from|IN|_ 200-300bp|200-300bp|JJ|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Agencourt|agencourt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Reverse|reverse|JJ|_ Transcription|transcription|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ an|a|DT|_ initial|initial|JJ|_ annealing|annealing|NN|_ of|of|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermenta|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|NN|_ for|for|IN|_ 5|5|CD|_ mins|min|NNS|_ ,|,|,|_ follow|follow|VBP|_ by|by|IN|_ an|a|DT|_ incubation|incubation|NN|_ of|of|IN|_ 42C|42c|NN|_ for|for|IN|_ 50|50|CD|_ mins|min|NNS|_ and|and|CC|_ an|a|DT|_ inactivation|inactivation|NN|_ step|step|NN|_ at|at|IN|_ 70C|70C|NNP|_ for|for|IN|_ 10|10|CD|_ mins|min|NNS|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ dNTP|dntp|NN|_ mix|mix|NN|_ where|where|WRB|_ dTTP|dttp|NN|_ is|be|VBZ|_ replaced|replace|VBN|_ by|by|IN|_ dUTP|dutp|NN|_ .|.|.|_ Reaction|reaction|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 16C|16c|NN|_ for|for|IN|_ 1h|1h|NN|_ .|.|.|_ Double|double|JJ|_ stranded|strand|VBN|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ and|and|CC|_ selected|select|VBN|_ for|for|IN|_ targeted|target|VBN|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 200-300bp|200-300bp|JJ|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ The|the|DT|_ dscDNA|dscdna|NN|_ were|be|VBD|_ then|then|RB|_ blunt-ended|blunt-ended|JJ|_ ,|,|,|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ were|be|VBD|_ adenylated|adenylate|VBN|_ with|with|IN|_ a|a|DT|_ single|single|JJ|_ A|a|NN|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ with|with|IN|_ library|library|NN|_ adapters|adapter|NNS|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Ampure|Ampure|NNP|_ XP|xp|NN|_ beads|bead|NNS|_ .|.|.|_ Digestion|digestion|NN|_ of|of|IN|_ dUTP|dutp|NN|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ using|use|VBG|_ AmpErase|AmpErase|NNP|_ UNG|UNG|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ .|.|.|_ Digested|digest|VBN|_ cDNA|cdna|NN|_ was|be|VBD|_ again|again|RB|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ This|this|DT|_ was|be|VBD|_ followed|follow|VBN|_ by|by|IN|_ amplification|amplification|NN|_ by|by|IN|_ 10|10|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ using|use|VBG|_ Kapa|Kapa|NNP|_ Library|Library|NNP|_ Amplification|Amplification|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ library|library|NN|_ was|be|VBD|_ cleaned|clean|VBN|_ up|up|RP|_ with|with|IN|_ Ampure|Ampure|NNP|_ SPRI|SPRI|NNP|_ beads|bead|NNS|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ done|do|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ generating|generate|VBG|_ paired|paired|JJ|_ end|end|NN|_ reads|read|VBZ|_ of|of|IN|_ 100bp|100bp|JJ|_ each|each|DT|_ .|.|.|_ Note|note|VB|_ :|:|:|_ Target|target|NN|_ fragments|fragment|NNS|_ here|here|RB|_ refers|refer|VBZ|_ to|to|TO|_ the|the|DT|_ insert|insert|NN|_ only|only|RB|_ ,|,|,|_ that|that|DT|_ is|be|VBZ|_ the|the|DT|_ cDNA|cdna|NN|_ .|.|.|_ The|the|DT|_ actual|actual|JJ|_ size|size|NN|_ we|we|PRP|_ use|use|VBP|_ in|in|IN|_ selection|selection|NN|_ will|will|MD|_ be|be|VB|_ larger|larger|JJR|_ ,|,|,|_ typically|typically|RB|_ the|the|DT|_ target|target|NN|_ fragment|fragment|NN|_ size|size|NN|_ +|+|CC|_ 125bp|125bp|NN|_ adaptors|adaptor|NNS|_ -LRB-|-lrb-|-LRB-|_ ~|~|CD|_ 300-450bp|300-450bp|JJ|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
BW25113|bw25113|NN|_ HEPES-glu|hepes-glu|NN|_ 30|30|CD|_ min|min|NN|_ 4.5|4.5|CD|_ %|%|NN|_ deoxycholate|deoxycholate|NN|SUPP
BW25113|bw25113|NN|_ with|with|IN|_ deoxycholate|deoxycholate|NN|SUPP stress|stress|NN|_
BW25113|bw25113|NN|_ ΔmqsRA|δmqsra|NN|_ HEPES-glu|hepes-glu|NN|_ 30|30|CD|_ min|min|NN|_ 4.5|4.5|CD|_ %|%|NN|_ deoxycholate|deoxycholate|NN|SUPP
BW25113|bw25113|NN|_ ΔmqsRA|δmqsra|NN|_ with|with|IN|_ deoxycholate|deoxycholate|NN|SUPP stress|stress|NN|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ using|use|VBG|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ -LRB-|-lrb-|-LRB-|_ Biospec|biospec|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ mRNA|mrna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ RNALater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ ethanol-dry|ethanol-dry|JJ|_ ice|ice|NN|_ .|.|.|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ Affymetrix|Affymetrix|NNP|_ GenomeChipOperating|GenomeChipOperating|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ GCOS|GCOS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
genotype|genotype|NN|_
Strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_ 16|16|CD|_ h|h|NN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.05|0.05|CD|_ in|in|IN|_ HEPES-glucose|hepes-glucose|NN|_ -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ ,|,|,|_ and|and|CC|_ exposed|expose|VBN|_ to|to|TO|_ 4.5|4.5|CD|_ %|%|NN|_ deoxycholate|deoxycholate|NN|SUPP for|for|IN|_ 30|30|CD|_ min|min|NN|_ .|.|.|_
0.2|0.2|CD|_ ppm|ppm|NN|_ deoxynivalenol|deoxynivalenol|NN|_
0.2|0.2|CD|_ ppm|ppm|NN|_ nivalenol|nivalenol|NN|_
1|1|CD|_ ml|ml|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ with|with|IN|_ the|the|DT|_ mycotoxin|mycotoxin|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ Hybrid-RTM|hybrid-rtm|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gene|gene|NN|_ All|all|DT|_ ,|,|,|_ Seoul|Seoul|NNP|_ ,|,|,|_ Korea|Korea|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocols|protocol|NNS|_ .|.|.|_ A|a|DT|_ MICOBExpressTM|micobexpresstm|NN|_ bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Texas|Texas|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ remove|remove|VB|_ bacterial|bacterial|JJ|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_
2|2|CD|_ ppm|ppm|NN|_ deoxynivalenol|deoxynivalenol|NN|_
2|2|CD|_ ppm|ppm|NN|_ nivalenol|nivalenol|NN|_
acetonitrile|acetonitrile|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ with|with|IN|_ 0.2|0.2|CD|_ ppm|ppm|NN|_ deoxynivalenol|deoxynivalenol|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ with|with|IN|_ 0.2|0.2|CD|_ ppm|ppm|NN|_ nivalenol|nivalenol|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ with|with|IN|_ 2|2|CD|_ ppm|ppm|NN|_ deoxynivalenol|deoxynivalenol|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ with|with|IN|_ 2|2|CD|_ ppm|ppm|NN|_ nivalenol|nivalenol|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ with|with|IN|_ acetonitrile|acetonitrile|NN|_
concentration|concentration|NN|_ :|:|:|_ 0.2|0.2|CD|_ ppm|ppm|NN|_
concentration|concentration|NN|_ :|:|:|_ 2|2|CD|_ ppm|ppm|NN|_
condition|condition|NN|_ :|:|:|_ acetonitrile|acetonitrile|NN|_ -LRB-|-lrb-|-LRB-|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
condition|condition|NN|_ :|:|:|_ myxotoxin|myxotoxin|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ LB|lb|NN|_ liquid|liquid|NN|_ for|for|IN|_ 16|16|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ constant|constant|JJ|_ shaking|shake|VBG|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ 100|100|CD|_ µl|µl|NN|_ of|of|IN|_ each|each|DT|_ myxotoxin|myxotoxin|NN|_ dissolved|dissolve|VBN|_ in|in|IN|_ acetonitrile|acetonitrile|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ culture|culture|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.2|0.2|CD|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ ppm|ppm|NN|_ .|.|.|_ Additional|additional|JJ|_ incubation|incubation|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ 2|2|CD|_ h.|h.|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_ ASM1942v1|asm1942v1|NN|_
Mapped|map|VBD|_ reads|read|VBZ|_ per|per|IN|_ annotated|annotated|JJ|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ by|by|IN|_ Bam2readcount|bam2readcount|NN|_ .|.|.|_
Reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ gene|gene|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBN|_ sequence|sequence|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ normalization|normalization|NN|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ DH10B|dh10b|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ txt|txt|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
The|The|NNP|_ reads|read|VBZ|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ software|software|NN|_ .|.|.|_
toxin|toxin|NN|_ :|:|:|_ deoxynivalenol|deoxynivalenol|NN|_
toxin|toxin|NN|_ :|:|:|_ nivalenol|nivalenol|NN|_
Culture|culture|NN|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
genotype|genotype|NN|_ :|:|:|_ PNPase|pnpase|NN|_ mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ RNase|rnase|NN|_ II|ii|CD|_ mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ RNase|rnase|NN|_ R|r|NN|_ mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ Wild-type|wild-type|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Exponential|Exponential|NNP|_ Phase|phase|NN|_
Overnight|overnight|NN|_ cultures|culture|NNS|_ from|from|IN|_ isolated|isolate|VBN|_ colonies|colony|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ to|to|TO|_ an|a|DT|_ initial|initial|JJ|_ OD600|od600|NN|_ ~|~|NN|_ 0.03|0.03|CD|_ and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ thymine|thymine|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ When|when|WRB|_ required|require|VBN|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ present|present|JJ|_ at|at|IN|_ the|the|DT|_ following|follow|VBG|_ concentrations|concentration|NNS|_ :|:|:|_ kanamycin|kanamycin|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ tetracycline|tetracycline|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_ ml-1|ml-1|NN|_ ;|;|:|_ streptomycin|streptomycin|NN|_
∆|∆|CD|_ pnp|pnp|NN|GEN _|_|CD|_ RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ by|by|IN|_ the|the|DT|_ company|company|NN|_ Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ in|in|IN|_ Germany|Germany|NNP|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ following|follow|VBG|_ cell|cell|NN|_ lysis|lysis|NN|_ and|and|CC|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Andrade|Andrade|NNP|_ ,|,|,|_ Pobre|Pobre|NNP|_ et|et|FW|_ al.|al.|FW|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ precipitation|precipitation|NN|_ step|step|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ 300|300|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|SUPP acetate|acetate|NN|SUPP ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ MilliQ-water|MilliQ-water|NNP|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ RNA|rna|NN|_ samples|sample|NNS|_ was|be|VBD|_ evaluated|evaluate|VBN|_ by|by|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ treatment|treatment|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ remove|remove|VB|_ contaminant|contaminant|NN|_ DNA|dna|NN|_ .|.|.|_
∆|∆|SYM|_ rnb|rnb|FW|GEN _|_|FW|_ RNA-Seq|rna-seq|NN|_
∆|∆|CD|_ rnr|rnr|NN|GEN _|_|CD|_ RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12-MG1693|k12-mg1693|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ ...|...|:|_
Vertis|Vertis|NNP|_ Biotechnologie|Biotechnologie|NNP|_ AG|AG|NNP|_ bioinformatics|bioinformatic|NNS|_ department|department|NN|_ did|do|VBD|_ a|a|DT|_ preliminary|preliminary|JJ|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ high-throughput|high-throughput|JJ|_ sequencing|sequencing|NN|_ results|result|NNS|_ which|which|WDT|_ included|include|VBD|_ the|the|DT|_ mapping|mapping|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_ genome|genome|NN|_ database|database|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
We|we|PRP|_ then|then|RB|_ used|use|VBD|_ the|the|DT|_ mapped|map|VBN|_ files|file|NNS|_ to|to|TO|_ run|run|VB|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ estimates|estimate|VBZ|_ the|the|DT|_ relative|relative|JJ|_ abundance|abundance|NN|_ of|of|IN|_ the|the|DT|_ transcripts|transcript|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ after|after|IN|_ Cuffdiff|Cuffdiff|NNP|_ to|to|TO|_ find|find|VB|_ significant|significant|JJ|_ changes|change|NNS|_ in|in|IN|_ transcript|transcript|NN|_ expression|expression|NN|_ when|when|WRB|_ comparing|compare|VBG|_ two|two|CD|_ samples|sample|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ ,|,|,|_ Williams|Williams|NNP|_ et|et|FW|_ al.|al.|FW|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WT|WT|NNP|_ _|_|NNP|_ RNA-Seq|RNA-Seq|NNP|_
common|common|JJ|_ reference|reference|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Normalization|normalization|NN|_ is|be|VBZ|_ performed|perform|VBN|_ by|by|IN|_ TREBAX|trebax|NN|_ ,|,|,|_ using|use|VBG|_ MA-plots|ma-plot|NNS|_ .|.|.|_ MA-plots|ma-plot|NNS|_ can|can|MD|GEN reveal|reveal|VB|_ the|the|DT|_ spot|spot|NN|_ artifacts|artifact|NNS|_ globally|globally|RB|_ and|and|CC|_ show|show|VB|_ the|the|DT|_ intensity-dependent|intensity-dependent|JJ|_ logarithmic|logarithmic|JJ|_ ratio|ratio|NN|_ of|of|IN|_ raw|raw|JJ|_ microarray|microarray|NN|_ data|datum|NNS|_ .|.|.|_ In|in|IN|_ MA-plots|ma-plot|NNS|_ ,|,|,|_ we|we|PRP|_ calculate|calculate|VBP|_ two|two|CD|_ parameters|parameter|NNS|_ ,|,|,|_ average|average|NN|_ of|of|IN|_ logarithmic|logarithmic|JJ|_ transferred|transfer|VBN|_ intensity|intensity|NN|_ As|as|IN|_ =|=|JJ|_ -LRB-|-lrb-|-LRB-|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ Ts|ts|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ Rs|rs|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
OD|od|NN|_ :|:|:|_ 0.1|0.1|CD|_
OD|od|NN|_ :|:|:|_ 0.3|0.3|CD|_
OD|od|NN|_ :|:|:|_ 0.4|0.4|CD|_
OD|od|NN|_ :|:|:|_ 0.5|0.5|CD|_
OD|od|NN|_ :|:|:|_ 0.6|0.6|CD|_
OD|od|NN|_ :|:|:|_ 1.0|1.0|CD|_
OD|od|NN|_ :|:|:|_ 1.3|1.3|CD|_
OD|od|NN|_ :|:|:|_ 1.7|1.7|CD|_
OD|od|NN|_ :|:|:|_ 2.7|2.7|CD|_
OD|od|NN|_ :|:|:|_ 4.5|4.5|CD|_
OD|od|NN|_ :|:|:|_ 4.7|4.7|CD|_
OD|od|NN|_ :|:|:|_ 4.8|4.8|CD|_
Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_
Reference|Reference|NNP|_ Design|Design|NNP|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t10|t10|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t10|t10|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t1|t1|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t11|t11|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t11|t11|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t1|t1|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t2|t2|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t2|t2|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t3|t3|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t3|t3|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t4|t4|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t4|t4|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t5|t5|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t5|t5|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t6|t6|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t6|t6|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t7|t7|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t7|t7|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t8|t8|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t8|t8|NN|_ .2|.2|NN|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t9|t9|NN|_ .1|.1|CD|_
Reference|Reference|NNP|_ Design|design|NN|_ timecourse|timecourse|NN|_ c|c|NN|_ _|_|CD|_ t9|t9|NN|_ .2|.2|NN|_
Strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
time|time|NN|_ 10|10|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 4.7|4.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 4.8|4.8|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 1.3|1.3|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 1.7|1.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 2.7|2.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 9|9|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_
All|all|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench5|workbench5|NN|_ with|with|IN|_ the|the|DT|_ length|length|NN|_ fraction|fraction|NN|_ of|of|IN|_ 0.9|0.9|CD|_ and|and|CC|_ the|the|DT|_ similarity|similarity|NN|_ of|of|IN|_ 0.99|0.99|CD|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ used|use|VBN|_ are|be|VBP|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ and|and|CC|_ its|its|PRP$|_ derivatives|derivative|NNS|_ .|.|.|_ Glycerol|glycerol|NN|_ stock|stock|NN|_ of|of|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 3|3|CD|_ mL|ml|NN|_ Luria|Luria|NNP|MED broth|broth|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 150|150|CD|_ μg|μg|NN|_ kanamycin|kanamycin|NN|_ and|and|CC|_ cultured|culture|VBN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ .|.|.|_
ArgR|argr|NN|TF -LRB-|-lrb-|-LRB-|_ -|-|:|_ arg|arg|NN|_ -RRB-|-rrb-|-RRB-|_ rep1|rep1|NN|_ and|and|CC|_ rep2|rep2|NN|_
ArgR|argr|NN|TF -LRB-|-lrb-|-LRB-|_ +|+|CC|_ arg|arg|NN|_ -RRB-|-rrb-|-RRB-|_ rep1|rep1|NN|_ and|and|CC|_ rep2|rep2|NN|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.4|1.4|CD|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ Anti-myc|anti-myc|NN|_ -LRB-|-lrb-|-LRB-|_ 9E10|9e10|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ ,|,|,|_ Dallas|Dallas|NNP|_ ,|,|,|_ TX|TX|NNP|_ -RRB-|-rrb-|-RRB-|_
ChIP-Seq|chip-seq|NN|_
Cultured|culture|VBN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ cross-linked|cross-link|VBN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ added|add|VBD|_ 2|2|CD|_ mL|ml|NN|_ of|of|IN|_ 2.5|2.5|CD|_ M|m|NN|_ glycine|glycine|NN|_ to|to|TO|_ quench|quench|VB|_ the|the|DT|_ unused|unused|JJ|_ formaldehyde|formaldehyde|NN|_ .|.|.|_ After|after|IN|_ washing|wash|VBG|_ three|three|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ Tris-buffered|tris-buffered|JJ|_ saline|saline|NN|_ -LRB-|-lrb-|-LRB-|_ TBS|tbs|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ washed|washed|JJ|_ cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 0.5|0.5|CD|_ mL|ml|NN|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ composed|compose|VBN|_ of|of|IN|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 1|1|CD|_ μg|μg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
substrain|substrain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ gff|gff|NN|_ file|file|NN|_ is|be|VBZ|_ generated|generate|VBN|_ by|by|IN|_ in-house|in-house|JJ|_ script|script|NN|_
The|the|DT|_ cross-linked|cross-linked|JJ|_ DNA-ArgR|dna-argr|NN|_ complexes|complex|NNS|_ in|in|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ were|be|VBD|_ then|then|RB|_ immunoprecipitated|immunoprecipitate|VBN|_ by|by|IN|_ adding|add|VBG|_ 10|10|CD|_ µL|µl|NN|_ of|of|IN|_ Anti-myc|anti-myc|NN|_ -LRB-|-lrb-|-LRB-|_ 9E10|9e10|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ ,|,|,|_ Dallas|Dallas|NNP|_ ,|,|,|_ TX|TX|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ mock-IP|mock-ip|JJ|_ control|control|NN|_ ,|,|,|_ 2|2|CD|_ µg|µg|NN|_ of|of|IN|_ normal|normal|JJ|_ mouse|mouse|NN|_ IgG|igg|NN|_ -LRB-|-lrb-|-LRB-|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ into|into|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ in|in|IN|_ parallel|parallel|NN|_ .|.|.|_ They|they|PRP|_ were|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ overnight|overnight|JJ|_ at|at|IN|_ 4oC|4oc|NN|_ with|with|IN|_ constant|constant|JJ|_ rotation|rotation|NN|_ .|.|.|_ The|the|DT|_ cross-linked|cross-linked|JJ|_ DNA-protein|dna-protein|NN|_ and|and|CC|_ antibody|antibody|NN|_ complexes|complex|NNS|_ were|be|VBD|_ selectively|selectively|RB|_ captured|capture|VBN|_ by|by|IN|_ adding|add|VBG|_ 50|50|CD|_ µL|µl|NN|_ of|of|IN|_ Dynabeads|Dynabeads|NNP|_ Pan|Pan|NNP|_ Mouse|Mouse|NNP|_ IgG|igg|NN|_ magnetic|magnetic|JJ|_ beads|bead|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Grand|Grand|NNP|_ Island|Island|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ DNAs|dna|NNS|_ were|be|VBD|_ end-polished|end-polished|JJ|_ using|use|VBG|_ T4|t4|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ligated|ligate|VBN|_ with|with|IN|_ the|the|DT|_ annealed|annealed|JJ|_ adaptor|adaptor|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ Phospho-AACTGCCCCGGGTTGCTCTTCCGATCT|phospho-aactgccccgggttgctcttccgatct|NN|_ and|and|CC|_ 5|5|CD|_ '|'|''|_ -|-|:|_ OH-AGATCGGAAGAGC-OH|oh-agatcggaagagc-oh|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ nick-repaired|nick-repaired|JJ|_ using|use|VBG|_ phi29|phi29|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ digested|digest|VBN|_ with|with|IN|_ λ|λ|NN|_ exonuclease|exonuclease|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ reported|report|VBN|_ previously|previously|RB|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ protein-DNA|protein-dna|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ reverse-cross-linked|reverse-cross-link|VBN|_ by|by|IN|_ heating|heating|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ overnight|overnight|JJ|_ and|and|CC|_ proteins|protein|NNS|_ were|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ 8|8|CD|_ µg|µg|NN|_ of|of|IN|_ protease|protease|NN|_ K|k|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ DNAs|dna|NNS|_ were|be|VBD|_ denatured|denature|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ and|and|CC|_ extended|extend|VBN|_ by|by|IN|_ P1|p1|NN|_ primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ OH-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT|oh-gtgactggagttcagacgtgtgctcttccgatct|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ further|further|JJ|_ ligated|ligate|VBN|_ with|with|IN|_ the|the|DT|_ annealed|annealed|JJ|_ adaptor|adaptor|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ OH-ACACTCTTTCCCTACACGACGCTCTTCCGATCT|oh-acactctttccctacacgacgctcttccgatct|NN|_ and|and|CC|_ 5|5|CD|_ '|'|''|_ -|-|:|_ OH-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG|oh-agatcggaagagcgtcgtgtagggaaagagtgtag|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ DNA|dna|NN|_ products|product|NNS|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ and|and|CC|_ were|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ by|by|IN|_ P2|p2|NN|_ primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT|oh-aatgatacggcgaccaccgagatctacactctttccctacacgacgctcttccgatct|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ P3|p3|NN|_ primer|primer|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ OH-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT|oh-caagcagaagacggcatacgagatnnnnnngtgactggagttcagacgtgt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ degenerative|degenerative|JJ|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ the|the|DT|_ underlined|underline|VBN|_ 6Ns|6n|NNS|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ P3|p3|NN|_ primer|primer|NN|_ indicates|indicate|VBZ|_ the|the|DT|_ index|index|NN|_ sequence|sequence|NN|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ next-generation|next-generation|JJ|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ PCR-amplified|pcr-amplified|JJ|_ DNA|dna|NN|_ products|product|NNS|_ were|be|VBD|_ then|then|RB|_ loaded|load|VBN|_ onto|onto|IN|_ 2|2|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ and|and|CC|_ extracted|extract|VBN|_ using|use|VBG|_ QIAquick|qiaquick|NN|_ gel|gel|NN|_ purification|purification|NN|_ columns|column|NNS|_ .|.|.|_
The|the|DT|_ cultured|culture|VBN|_ cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1:100|1:100|CD|_ dilution|dilution|NN|_ into|into|IN|_ 50|50|CD|_ mL|ml|NN|_ of|of|IN|_ the|the|DT|_ fresh|fresh|JJ|_ M9|m9|NN|_ medium|medium|NN|_ containing|contain|VBG|_ 2|2|CD|_ g|g|NN|_
To|to|TO|_ capture|capture|VB|_ target|target|NN|_ protein|protein|NN|_ binding|binding|NN|_ sites|site|NNS|_ corresponding|correspond|VBG|_ genomic|genomic|JJ|_ position|position|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ start|start|NN|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ MRSP|mrsp|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ stored|store|VBN|_ for|for|IN|_ visual|visual|JJ|_ inspection|inspection|NN|_ using|use|VBG|_ in-house|in-house|JJ|_ scripts|script|NNS|_ .|.|.|_
cDNA|cdna|NN|_ _|_|NN|_ A|a|NN|_ _|_|CD|_ cy3|cy3|NN|_
cDNA|cdna|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy5|cy5|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
gDNA|gdna|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy5|cy5|NN|_
gDNA|gdna|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy3|cy3|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ a|a|DT|_ 20|20|CD|_
Linearly|linearly|RB|_ scaled|scale|VBD|_ so|so|RB|_ that|that|IN|_ intensity|intensity|NN|_ values|value|NNS|_ in|in|IN|_ gDNA|gdna|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy5|cy5|NN|_ ,|,|,|_ cDNA|cdna|NN|_ _|_|NN|_ A|a|NN|_ _|_|NN|_ cy3|cy3|NN|_ ,|,|,|_ gDNA|gdna|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy3|cy3|NN|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy5|cy5|NN|_ are|be|VBP|_ comparable|comparable|JJ|_
Strain|strain|NN|_ MG1655|mg1655|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ RNeasy|rneasy|NN|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ MicroExpress|MicroExpress|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ RNA|rna|NN|_ was|be|VBD|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ with|with|IN|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ random|random|JJ|_ hexamers|hexamer|NNS|_ +|+|CC|_ dNTP|dntp|NN|_ mix|mix|NN|_ containing|contain|VBG|_ aminoallyl-dUTP|aminoallyl-dutp|NN|_ .|.|.|_
Beta|Beta|NNP|_ _|_|NNP|_ ChIP|ChIP|NNP|_ _|_|SYM|_ A|a|DT|_ _|_|SYM|_ cy5|cy5|CD|_
Beta|beta|JJ|_ _|_|NN|_ ChIP|chip|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy5|cy5|NN|_
Beta|beta|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy3|cy3|NN|_
Beta|beta|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ control|control|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy3|cy3|NN|_
Cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ ,|,|,|_ quenched|quench|VBN|_ with|with|IN|_ glycine|glycine|NN|_ ,|,|,|_ and|and|CC|_ lysed|lyse|VBN|_ .|.|.|_ Chromatin|chromatin|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ solublized|solublize|VBN|_ by|by|IN|_ sonication|sonication|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ ,|,|,|_ quenched|quench|VBN|_ with|with|IN|_ glycine|glycine|NN|_ ,|,|,|_ and|and|CC|_ lysed|lyse|VBN|_ .|.|.|_ Chromatin|chromatin|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ solublized|solublize|VBN|_ by|by|IN|_ sonication|sonication|NN|_ .|.|.|_ Crosslinked|crosslink|VBN|_ chromatin|chromatin|NN|_ was|be|VBD|_ then|then|RB|_ immunoprecipitated|immunoprecipitate|VBN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Linearly|linearly|RB|_ scaled|scale|VBN|_ so|so|IN|_ that|that|IN|_ intensity|intensity|NN|_ values|value|NNS|_ in|in|IN|_ Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy3|cy3|NN|_ ,|,|,|_ Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy5|cy5|NN|_ ,|,|,|_ Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ control|control|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy3|cy3|NN|_ ,|,|,|_ Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy5|cy5|NN|_ ,|,|,|_ Beta|beta|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy3|cy3|NN|_ ,|,|,|_ Beta|beta|NN|_ _|_|NN|_ ChIP|chip|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy5|cy5|NN|_ ,|,|,|_ Beta|beta|NN|_ _|_|NN|_ ChIP|chip|NN|_ _|_|CD|_ control|control|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy3|cy3|NN|_ ,|,|,|_ Beta|beta|NN|_ _|_|NN|_ ChIP|chip|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy5|cy5|NN|_ are|be|VBP|_ comparable|comparable|JJ|_
Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy5|cy5|NN|_
Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy5|cy5|NN|_
Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ A|a|DT|_ _|_|NN|_ cy3|cy3|NN|_
Sigma70|sigma70|NN|_ _|_|CD|_ ChIP|chip|NN|_ _|_|NN|_ control|control|NN|_ _|_|NN|_ B|b|NN|_ _|_|CD|_ cy3|cy3|NN|_
Strain|strain|NN|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Normalization|normalization|NN|_ is|be|VBZ|_ performed|perform|VBN|_ by|by|IN|_ TREBAX|trebax|NN|_ ,|,|,|_ using|use|VBG|_ MA-plots|ma-plot|NNS|_ .|.|.|_ MA-plots|ma-plot|NNS|_ can|can|MD|GEN reveal|reveal|VB|_ the|the|DT|_ spot|spot|NN|_ artifacts|artifact|NNS|_ globally|globally|RB|_ and|and|CC|_ show|show|VB|_ the|the|DT|_ intensity-dependent|intensity-dependent|JJ|_ logarithmic|logarithmic|JJ|_ ratio|ratio|NN|_ of|of|IN|_ raw|raw|JJ|_ microarray|microarray|NN|_ data|datum|NNS|_ .|.|.|_ In|in|IN|_ MA-plots|ma-plot|NNS|_ ,|,|,|_ we|we|PRP|_ calculate|calculate|VBP|_ two|two|CD|_ parameters|parameter|NNS|_ ,|,|,|_ average|average|NN|_ of|of|IN|_ logarithmic|logarithmic|JJ|_ transferred|transfer|VBN|_ intensity|intensity|NN|_ As|as|IN|_ =|=|JJ|_ -LRB-|-lrb-|-LRB-|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ Ts|ts|NN|_ -RRB-|-rrb-|-RRB-|_ +|+|CC|_ log|log|NN|_ -LRB-|-lrb-|-LRB-|_ Rs|rs|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
OD|od|NN|_ :|:|:|_ 0.1|0.1|CD|_
OD|od|NN|_ :|:|:|_ 0.3|0.3|CD|_
OD|od|NN|_ :|:|:|_ 0.4|0.4|CD|_
OD|od|NN|_ :|:|:|_ 0.6|0.6|CD|_
OD|od|NN|_ :|:|:|_ 0.6|0.6|CD|_
OD|od|NN|_ :|:|:|_ 1.0|1.0|CD|_
OD|od|NN|_ :|:|:|_ 1.3|1.3|CD|_
OD|od|NN|_ :|:|:|_ 1.7|1.7|CD|_
OD|od|NN|_ :|:|:|_ 2.7|2.7|CD|_
OD|od|NN|_ :|:|:|_ 4.5|4.5|CD|_
OD|od|NN|_ 4.5|4.5|CD|_
OD|od|NN|_ :|:|:|_ 4.7|4.7|CD|_
OD|od|NN|_ :|:|:|_ 4.8|4.8|CD|_
OD|od|NN|_ :|:|:|_ OD|od|NN|_ 0.1|0.1|CD|_
Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t10|t10|NN|_ _|_|CD|_ t11|t11|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t10|t10|NN|_ _|_|CD|_ t11|t11|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t1|t1|NN|_ _|_|CD|_ t2|t2|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t1|t1|NN|_ _|_|CD|_ t2|t2|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t2|t2|NN|_ _|_|CD|_ t3|t3|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t2|t2|NN|_ _|_|CD|_ t3|t3|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t3|t3|NN|_ _|_|CD|_ t4|t4|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t3|t3|NN|_ _|_|CD|_ t4|t4|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t4|t4|NN|_ _|_|CD|_ t5|t5|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t4|t4|NN|_ _|_|CD|_ t5|t5|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t5|t5|NN|_ _|_|CD|_ t6|t6|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t5|t5|NN|_ _|_|CD|_ t6|t6|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t6|t6|NN|_ _|_|CD|_ t7|t7|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t6|t6|NN|_ _|_|CD|_ t7|t7|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t7|t7|NN|_ _|_|CD|_ t8|t8|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t7|t7|NN|_ _|_|CD|_ t8|t8|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t8|t8|NN|_ _|_|CD|_ t9|t9|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t8|t8|NN|_ _|_|CD|_ t9|t9|NN|_ .2|.2|NN|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t9|t9|NN|_ _|_|CD|_ t10|t10|NN|_ .1|.1|CD|_
Sequential|sequential|JJ|_ Design|design|NN|_ timecourse|timecourse|NN|_ t9|t9|NN|_ _|_|CD|_ t10|t10|NN|_ .2|.2|NN|_
Strain|strain|NN|_ W3110|w3110|NN|_
Strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
Strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
Strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
Strian|strian|NN|_ :|:|:|_ W3110|w3110|NN|_
time|time|NN|_ 10|10|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 4.7|4.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 4.8|4.8|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 1.0|1.0|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 1.3|1.3|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ OD|od|NN|_ =|=|JJ|_ 1.7|1.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 1.7|1.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ OD|od|NN|_ =|=|JJ|_ 2.7|2.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 2.7|2.7|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ 9|9|CD|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 4.5|4.5|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ HB101|hb101|NN|_ grown|grow|VBN|_ in|in|IN|_ Terrific|Terrific|NNP|_ broth|broth|NN|_ media|media|NNS|_ for|for|IN|_ 12|12|CD|_ hours|hour|NNS|_ were|be|VBD|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ in|in|IN|_ sdH2O|sdh2o|NN|_ and|and|CC|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ S-Basal|s-basal|JJ|_ complete|complete|JJ|_ medium|medium|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ in|in|IN|_ S-Basal|s-basal|JJ|_ complete|complete|JJ|_ medium|medium|NN|_ alone|alone|RB|_ or|or|CC|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ C.|C.|NNP|_ elegans|elegan|NNS|_ ,|,|,|_ Giardia|Giardia|NNP|_ conditioned|condition|VBD|_ meida|meida|NN|_ ,|,|,|_ and|and|CC|_ both|both|DT|_ C.|c.|FW|_ elegans|elegan|NNS|_ and|and|CC|_ Giardia|Giardia|NNP|_ conditioned|condition|VBN|_ media|media|NNS|_ .|.|.|_
Escherchia|escherchia|FW|_ coli|coli|FW|_ HB101|hb101|NN|_
Escherchia|escherchia|FW|_ coli|coli|FW|_ HB101|hb101|NN|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ and|and|CC|_ Giardia|Giardia|NNP|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_
Escherchia|Escherchia|NNP|_ coli|coli|NN|_ HB101|hb101|NN|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_
Escherchia|Escherchia|NNP|_ coli|coli|NN|_ HB101|hb101|NN|_ exposed|expose|VBN|_ to|to|TO|_ Giardia|Giardia|NNP|_ for|for|IN|_ 24|24|CD|_ hours|hour|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ -LSB-|-lsb-|-LRB-|_ supE44|supe44|NN|_ hsdS20|hsds20|NN|_ -LRB-|-lrb-|-LRB-|_ rB-mB|rb-mb|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ recA13|reca13|NN|_ ara-14|ara-14|NN|_ proA2|proa2|NN|_ lacY1|lacy1|NN|_ galK2|galk2|NN|_ rpsL20|rpsl20|NN|_ xyl-5|xyl-5|NN|_ mtl-1|mtl-1|NN|_ -RSB-|-rsb-|-RRB-|_
HB101|hb101|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
HB101|hb101|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ and|and|CC|_ Giardia|Giardia|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ and|and|CC|_ Giardia|Giardia|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ and|and|CC|_ Giardia|Giardia|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ C.|C.|NNP|_ elegans|elegan|NNS|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ Giardia|Giardia|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ Giardia|Giardia|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
HB101|hb101|NN|_ ,|,|,|_ exposed|expose|VBN|_ to|to|TO|_ Giardia|Giardia|NNP|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
strain|strain|NN|_ :|:|:|_ HB101|hb101|NN|_
The|the|DT|_ microarray|microarray|NN|_ data|datum|NNS|_ files|file|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ statistical|statistical|JJ|_ software|software|NN|_ R|r|NN|_ version|version|NN|_ 3.0.1|3.0.1|CD|_ and|and|CC|_ Bioconductor|Bioconductor|NNP|_ packages|package|NNS|_ .|.|.|_ The|the|DT|_ Single-Channel|Single-Channel|NNP|_ Array|Array|NNP|_ Normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ SCAN.UPC|scan.upc|NN|_ -RRB-|-rrb-|-RRB-|_ package|package|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ normalize|normalize|VB|_ the|the|DT|_ microarray|microarray|NN|_ data|datum|NNS|_ .|.|.|_ Batch|batch|NN|_ effects|effect|NNS|_ were|be|VBD|_ adjusted|adjust|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ Empirical|Empirical|NNP|_ Bayes|Bayes|NNP|_ method|method|NN|_ implemented|implement|VBN|_ in|in|IN|_ COMBAT|COMBAT|NNP|_ software|software|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ instructions|instruction|NNS|_ in|in|IN|_ the|the|DT|_ kit|kit|NN|_ .|.|.|_
CEL|cel|NN|_ files|file|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ with|with|IN|_ Distribution|distribution|NN|_ Free|Free|NNP|_ Weighted|Weighted|NNP|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ DFW|dfw|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ using|use|VBG|_ the|the|DT|_ statistical|statistical|JJ|_ language|language|NN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ R-2.7.2|r-2.7.2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Bioconductor|Bioconductor|NNP|_ 2.2|2.2|CD|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ BW25113|bw25113|NN|_ were|be|VBD|_ maintained|maintain|VBN|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ medium|medium|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_ for|for|IN|_ about|about|RB|_ 14|14|CD|_ h|h|NN|_ until|until|IN|_ they|they|PRP|_ reached|reach|VBD|_ the|the|DT|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase of|of|IN|_ cell|cell|NN|_ growth|growth|NN|_ before|before|IN|_ treatment|treatment|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ incubated|incubate|VBN|_ with|with|IN|_ GST-fused|gst-fused|JJ|_ Drosophila|drosophila|NN|_ immune|immune|JJ|_ proteins|protein|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ incubated|incubate|VBN|_ with|with|IN|_ GST-fused|gst-fused|JJ|_ Drosophila|drosophila|NN|_ immune|immune|JJ|_ proteins|protein|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ incubated|incubate|VBN|_ with|with|IN|_ GST-fused|gst-fused|JJ|_ Drosophila|drosophila|NN|_ immune|immune|JJ|_ proteins|protein|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ incubated|incubate|VBN|_ with|with|IN|_ GST-fused|gst-fused|JJ|_ Drosophila|drosophila|NN|_ immune|immune|JJ|_ proteins|protein|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
E.|e.|FW|_ coli|coli|FW|_ incubated|incubate|VBN|_ with|with|IN|_ GST|gst|NN|_ protein|protein|NN|_ alone|alone|RB|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ incubated|incubate|VBN|_ with|with|IN|_ GST|gst|NN|_ protein|protein|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ incubated|incubate|VBN|_ with|with|IN|_ GST|gst|NN|_ protein|protein|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ incubated|incubate|VBN|_ with|with|IN|_ GST|gst|NN|_ protein|protein|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
incubated|incubate|VBN|_ with|with|IN|_ :|:|:|_ Drosophila|drosophila|FW|_ immune|immune|JJ|_ proteins|protein|NNS|_
incubated|incubate|VBN|_ with|with|IN|_ :|:|:|_ GST|gst|NN|_ alone|alone|RB|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ μM|μm|NN|_ ;|;|:|_ control|control|NN|_ -RRB-|-rrb-|-RRB-|_
incubation|incubation|NN|_ duration|duration|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ x|x|CC|_ 10|10|CD|_ ^|^|SYM|_ 9|9|CD|_ -RRB-|-rrb-|-RRB-|_ suspended|suspend|VBN|_ with|with|IN|_ insect|insect|JJ|_ saline|saline|NN|_ -LRB-|-lrb-|-LRB-|_ 0.13|0.13|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 4.7|4.7|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ,|,|,|_ 1.9|1.9|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ was|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ GST|gst|NN|_ or|or|CC|_ GST-fused|gst-fused|JJ|_ Drosophila|drosophila|FW|_ immune|immune|JJ|_ proteins|protein|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ an|a|DT|_ RNeasy|rneasy|NN|_ micro|micro|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ K.K.|K.K.|NNP|_ ,|,|,|_ Tokyo|Tokyo|NNP|_ ,|,|,|_ Japan|Japan|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
cDNA|cdna|NN|_ were|be|VBD|_ synthesized|synthesize|VBN|_ from|from|IN|_ the|the|DT|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ of|of|IN|_ Total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ SuperScript|SuperScript|NNP|_ II|II|NNP|_ Double-Strand|Double-Strand|NNP|_ Synthesis|synthesis|NN|_ Kit|kit|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Cold|Cold|NNP|_ Shock|shock|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Cold|Cold|NNP|_ Shock|shock|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 15|15|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hour|hour|NN|_ then|then|RB|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Heat|heat|NN|_ Shock|shock|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ Heat|heat|NN|_ Shock|shock|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 4|4|CD|_ hour|hour|NN|_ then|then|RB|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Low|low|JJ|_ pH|ph|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ Low|low|JJ|_ pH|ph|NN|_ was|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ pH4|ph4|NN|_ .5|.5|CD|_ then|then|RB|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ minimal|minimal|JJ|_ C|c|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ minimal|minimal|JJ|_ C&N|c&n|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ minimal|minimal|JJ|_ C&N|C&N|NNP|_ Source|Source|NNP|_ was|be|VBD|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ quater|quater|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ minimal|minimal|JJ|_ C|c|NN|_ and|and|CC|_ N|n|NN|_ source|source|NN|_ MOPS|mop|NNS|MED media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ C-N|c-n|NN|_ -|-|:|_ MOPS|mop|NNS|MED -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ minimal|minimal|JJ|_ C|c|NN|_ Source|source|NN|_ was|be|VBD|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ minimal|minimal|JJ|_ C|c|NN|_ source|source|NN|_ MOPS|mop|NNS|MED media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ C|c|NN|_ -|-|:|_ MOPS|mop|NNS|MED -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ minimal|minimal|JJ|_ N|n|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ minimal|minimal|JJ|_ N|n|NN|_ Source|source|NN|_ was|be|VBD|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ minimal|minimal|JJ|_ N|n|NN|_ source|source|NN|_ MOPS|mop|NNS|MED media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ N|n|NN|_ -|-|:|_ MOPS|mop|NNS|MED -RRB-|-rrb-|-RRB-|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Osmotic|osmotic|JJ|_ stress|stress|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Osmotic|osmotic|JJ|_ Stress|stress|NN|_ was|be|VBD|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 45|45|CD|_ ml|ml|NN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ 4M|4m|NN|_ Sodium|sodium|NN|_ Chloride|chloride|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Oxidative|oxidative|JJ|_ stress|stress|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Oxidative|oxidative|JJ|_ Stress|stress|NN|_ was|be|VBD|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 49|49|CD|_ ml|ml|NN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 400μl|400μl|NN|_ 7|7|CD|_ %|%|NN|_ Hydrogen|hydrogen|NN|_ peroxide|peroxide|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|MG1655|NNP|_ Standard|Standard|NNP|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ Standard|Standard|NNP|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ O.D.|o.d.|NN|_ 600nm|600nm|CD|_ 0.6|0.6|CD|_ ~|~|NN|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ UV|uv|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ UV|uv|NN|_ was|be|VBD|_ exposed|expose|VBN|_ to|to|TO|_ UV|uv|NN|_ light|light|NN|_ for|for|IN|_ 15|15|CD|_ minutes|minute|NNS|_ then|then|RB|_ grown|grow|VBN|_ untill|untill|JJ|_ reach|reach|NN|_ to|to|TO|_ half|half|NN|_ of|of|IN|_ O.D.|O.D.|NNP|_ 600nm|600nm|NNP|_ of|of|IN|_ Standard|Standard|NNP|_ sample|sample|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ standard|standard|JJ|_ _|_|NN|_ condition|condition|NN|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ standard|standard|JJ|_ _|_|NN|_ condition|condition|NN|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|CD|_ ColdShock|ColdShock|NNP|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|CD|_ ColdShock|ColdShock|NNP|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NN|_ HeatShock|heatshock|NN|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NNP|_ Low|Low|NNP|_ _|_|NNP|_ pH|ph|NN|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ C&N|c&n|NN|_ _|_|NN|_ source|source|NN|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ C&N|c&n|NN|_ _|_|NN|_ source|source|NN|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ C|c|NN|_ _|_|NN|_ source|source|NN|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ C|c|NN|_ _|_|NN|_ source|source|NN|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|CD|_ N|n|NN|_ _|_|NN|_ source|source|NN|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|CD|_ N|n|NN|_ _|_|NN|_ source|source|NN|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NNP|_ Osmotic|Osmotic|NNP|_ _|_|NNP|_ Stress|stress|NN|_ _|_|NN|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|CD|_ Osmotic|osmotic|JJ|_ _|_|NN|_ Stress|stress|NN|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NNP|_ Oxidative|oxidative|JJ|_ _|_|NN|_ Stress|stress|NN|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ under|under|IN|_ _|_|NNP|_ Oxidative|oxidative|JJ|_ _|_|NN|_ Stress|stress|NN|_ _|_|CD|_ rep2|rep2|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ UV|uv|NN|_ _|_|NN|_ Treatment|treatment|NN|_ _|_|CD|_ rep1|rep1|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ UV|uv|NN|_ _|_|NN|_ Treatment|treatment|NN|_ _|_|CD|_ rep2|rep2|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ RMA|rma|NN|_ -LRB-|-lrb-|-LRB-|_ Robust|robust|JJ|_ Multi-Array|multi-array|JJ|_ Analysis|analysis|NN|_ ;|;|:|_ Irizarry|Irizarry|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Biostatistics|biostatistic|NNS|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 249|249|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ -LRB-|-lrb-|-LRB-|_ Bolstad|Bolstad|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Bioinformatics|bioinformatic|NNS|_ 19|19|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 185|185|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ background|background|NN|_ correction|correction|NN|_ as|as|IN|_ implemented|implement|VBN|_ in|in|IN|_ the|the|DT|_ NimbleGen|NimbleGen|NNP|_ Deva|Deva|NNP|_ software|software|NN|_ ,|,|,|_ version|version|NN|_ 1.2|1.2|CD|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ NimbleGen|NimbleGen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ with|with|IN|_ the|the|DT|_ RNase-Free|rnase-free|JJ|_ DNase|dnase|NN|_ set|set|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ concentration|concentration|NN|_ was|be|VBD|_ measured|measure|VBN|_ by|by|IN|_ SpectorPhotometer|spectorphotometer|NN|_ -LRB-|-lrb-|-LRB-|_ NonoDrop|nonodrop|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ Cold|Cold|NNP|_ Shock|shock|NN|_
treatment|treatment|NN|_ :|:|:|_ Heat|Heat|NNP|_ Shock|shock|NN|_
treatment|treatment|NN|_ :|:|:|_ Low|low|JJ|_ pH|ph|NN|_
treatment|treatment|NN|_ :|:|:|_ minimal|minimal|JJ|_ C&N|c&n|NN|_ source|source|NN|_
treatment|treatment|NN|_ :|:|:|_ minimal|minimal|JJ|_ C|c|NN|_ source|source|NN|_
treatment|treatment|NN|_ :|:|:|_ minimal|minimal|JJ|_ N|n|NN|_ source|source|NN|_
treatment|treatment|NN|_ :|:|:|_ Osmotic|osmotic|JJ|_ stress|stress|NN|_
treatment|treatment|NN|_ :|:|:|_ Oxidative|oxidative|JJ|_ stress|stress|NN|_
treatment|treatment|NN|_ :|:|:|_ Standard|Standard|NNP|_
treatment|treatment|NN|_ :|:|:|_ UV|uv|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ M63|m63|NN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ cell|cell|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ controlled|control|VBN|_ ~|~|SYM|_ 10|10|CD|_ ^|^|SYM|_ 8|8|CD|_ cells|cell|NNS|_
condition|condition|NN|_ :|:|:|_ exponential|exponential|JJ|_ growth|growth|NN|_ ,|,|,|_ 36.9|36.9|CD|_ ºC|ºc|NN|_
condition|condition|NN|_ :|:|:|_ exponential|exponential|JJ|_ growth|growth|NN|_ ,|,|,|_ 41.2|41.2|CD|_ ºC|ºc|NN|_
condition|condition|NN|_ :|:|:|_ exponential|exponential|JJ|_ growth|growth|NN|_ ,|,|,|_ 43.2|43.2|CD|_ ºC|ºc|NN|_
condition|condition|NN|_ :|:|:|_ exponential|exponential|JJ|_ growth|growth|NN|_ ,|,|,|_ 44.8|44.8|CD|_ ºC|ºc|NN|_
condition|condition|NN|_ :|:|:|_ heat|heat|NN|_ shock|shock|NN|_ response|response|NN|_ ,|,|,|_ 44.8|44.8|CD|_ ºC|ºc|NN|_
E.|E.|NNP|_ coli|coli|NN|_ 37L|37l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 37L|37l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 37L|37l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 41ºC|41ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 41ºC|41ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 41ºC|41ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 41B|41b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 43ºC|43ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 43ºC|43ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 43ºC|43ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 43B|43b|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ evolutionary|evolutionary|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ evolved|evolve|VBD|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ 45L|45l|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ancestor|ancestor|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ancestor|ancestor|NN|_ strain|strain|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ancestor|ancestor|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ancestor|ancestor|NN|_ strain|strain|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ heat|heat|NN|_ shock|shock|NN|_ at|at|IN|_ 45ºC|45ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ancestor|ancestor|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ancestor|ancestor|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ancestor|ancestor|NN|_ strain|strain|NN|_ ,|,|,|_ under|under|IN|_ 37ºC|37ºc|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ Anc|anc|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|e.|FW|_ coli|coli|FW|_ Anc|anc|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ long|long|RB|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|e.|FW|_ coli|coli|FW|_ Anc|anc|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|e.|FW|_ coli|coli|FW|_ Anc|anc|NN|_ strain|strain|NN|_ ,|,|,|_ heat|heat|NN|_ shock|shock|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|e.|FW|_ coli|coli|FW|_ Anc|anc|NN|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 1|1|CD|_
E.|e.|FW|_ coli|coli|FW|_ Anc|anc|NN|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 2|2|CD|_
E.|e.|FW|_ coli|coli|FW|_ Anc|anc|NN|_ strain|strain|NN|_ ,|,|,|_ regular|regular|JJ|_ temperature|temperature|NN|_ ,|,|,|_ rep|rep|NN|GEN 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ written|write|VBN|_ in|in|IN|_ R|r|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ finite|finite|JJ|_ hybridisation|hybridisation|NN|_ -LRB-|-lrb-|-LRB-|_ FH|fh|NN|_ -RRB-|-rrb-|-RRB-|_ model|model|NN|_ -LRB-|-lrb-|-LRB-|_ Ono|Ono|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2008|2008|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ thermodynamic|thermodynamic|JJ|_ model|model|NN|_ of|of|IN|_ non-specific|non-specific|JJ|_ binding|binding|NN|_ -LRB-|-lrb-|-LRB-|_ NSB|nsb|NN|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ short|short|JJ|_ nucleotide|nucleotide|NN|_ microarrays|microarray|NNS|_ -LRB-|-lrb-|-LRB-|_ Furusawa|Furusawa|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ DH1ΔleuB|dh1δleub|NN|_ :|:|:|_ :|:|:|_ gfpuv5-kmr|gfpuv5-kmr|JJ|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ put|put|VBN|_ into|into|IN|_ cold|cold|JJ|_ phenol-ethanol|phenol-ethanol|JJ|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ of|of|IN|_ phenol|phenol|NN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ ethanol|ethanol|NN|_ -RRB-|-rrb-|-RRB-|_ prepared|prepare|VBN|_ in|in|IN|_ advance|advance|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ 7,000|7,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ pelleted|pelleted|JJ|_ cells|cell|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ --|--|:|_ 80|80|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ use|use|VB|_ .|.|.|_
The|the|DT|_ normalized|normalize|VBN|_ data|datum|NNS|_ can|can|MD|GEN be|be|VB|_ found|find|VBN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ in|in|IN|_ the|the|DT|_ file|file|NN|_ \|\|NN|_ GSE61749|gse61749|NN|_ _|_|CD|_ Normalized|normalize|VBN|_ _|_|SYM|_ data.txt|data.txt|FW|_ \|\|FW|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ values|value|NNS|_ presented|present|VBN|_ in|in|IN|_ this|this|DT|_ file|file|NN|_ are|be|VBP|_ log10|log10|NN|_ mRNA|mrna|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ pM|pm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
7|7|CD|_ h|h|NN|_ 7HI|7HI|NNP|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
7|7|CD|_ h|h|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
7|7|CD|_ h|h|NN|_ isatin|isatin|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
7|7|CD|_ h|h|NN|_ suspension|suspension|NN|_ cells|cell|NNS|_
EHEC|ehec|NN|_ LB|lb|NN|_ 7|7|CD|_ h|h|NN|_ 7HI|7HI|NNP|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
EHEC|ehec|NN|_ LB|lb|NN|_ 7|7|CD|_ h|h|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
EHEC|ehec|NN|_ LB|lb|NN|_ 7|7|CD|_ h|h|NN|_ isatin|isatin|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
EHEC|ehec|NN|_ LB|lb|NN|_ 7|7|CD|_ h|h|NN|_ suspension|suspension|NN|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ EHEC|ehec|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 7h|7h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ 0.1|0.1|CD|_ %|%|NN|_ DMF|dmf|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ EHEC|ehec|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 7h|7h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ 1000|1000|CD|_ micro|micro|JJ|_ M|m|NN|_ 7-hydroxyindole|7-hydroxyindole|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ EHEC|ehec|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 7h|7h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ 250|250|CD|_ micro|micro|JJ|_ M|m|NN|_ isatin|isatin|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ suspension|suspension|NN|_ cells|cell|NNS|_ of|of|IN|_ EHEC|ehec|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 7|7|CD|_ h|h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ and|and|CC|_ 0.1|0.1|CD|_ %|%|NN|_ DMF|dmf|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_
To|to|TO|_ lyse|lyse|VB|_ the|the|DT|_ cells|cell|NNS|_ ,|,|,|_ 1.0|1.0|CD|_ mL|ml|NN|_ RLT|rlt|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 0.2|0.2|CD|_ mL|ml|NN|_ 0.1|0.1|CD|_ mm|mm|NN|_ zirconia|zirconia|NN|_
cDNA|cdna|NN|_ library|library|NN|_ of|of|IN|_ the|the|DT|_ nascent|nascent|JJ|_ RNA|rna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ according|accord|VBG|_ to|to|TO|_ Churchman|Churchman|NNP|_ and|and|CC|_ Weissman|Weissman|NNP|_ ,|,|,|_ Nature|Nature|NNP|_ 2011|2011|CD|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 21248844|21248844|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Each|each|DT|_ tube|tube|NN|_ of|of|IN|_ the|the|DT|_ cell|cell|NN|_ pellet|pellet|NN|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 650|650|CD|_ ml|ml|NN|_ TES|tes|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH|ph|NN|_ 7.5|7.5|CD|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ TritonX|tritonx|NN|_ 100|100|CD|_ ,|,|,|_ 0.3|0.3|CD|_ mM|mm|NN|KWSUPP PMSF|pmsf|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ -LRB-|-lrb-|-LRB-|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 100|100|CD|_ kU|ku|NN|_ Ready-Lyse|Ready-Lyse|NNP|_ Lysozyme|Lysozyme|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 50|50|CD|_ µg|µg|NN|_ RNaseA|rnasea|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ allowing|allow|VBG|_ rapid|rapid|JJ|_ cell|cell|NN|_ lysis|lysis|NN|_ .|.|.|_ To|to|TO|_ digest|digest|VB|_ the|the|DT|_ nucleoide|nucleoide|NN|_ ,|,|,|_ 62.5|62.5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 250|250|CD|_ µg|µg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ nascent|nascent|JJ|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_
Pause|pause|NN|_ sites|site|NNS|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ wild-type|wild-type|JJ|_ strain|strain|NN|_ identified|identify|VBN|_ by|by|IN|_ RNET-seq|rnet-seq|NN|_
Pause|pause|NN|_ sites|site|NNS|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ΔgreAB|δgreab|NN|_ strain|strain|NN|_ identified|identify|VBN|_ by|by|IN|_ RNET-seq|rnet-seq|NN|_
RNA-Seq|rna-seq|NN|_
The|the|DT|_ 200|200|CD|_ ml|ml|NN|_ eluate|eluate|NN|_ from|from|IN|_ the|the|DT|_ Ni-NTA|ni-nta|NN|_ agarose|agarose|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ PCI|pci|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 70|70|CD|_ ˚C|˚c|NN|_ .|.|.|_ The|the|DT|_ mixture|mixture|NN|_ was|be|VBD|_ centrifuged|centrifuge|VBN|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ and|and|CC|_ DNA|dna|NN|_ were|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ from|from|IN|_ the|the|DT|_ supernatant|supernatant|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ 30|30|CD|_ ml|ml|NN|_ DNase|dnase|NN|_ I|i|CD|_ buffer|buffer|NN|_ with|with|IN|_ 5|5|CD|_ U|U|NNP|_ DNaseI|dnasei|NN|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ Bio|Bio|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 20|20|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ RT.|RT.|NNP|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ separated|separate|VBN|_ from|from|IN|_ the|the|DT|_ digested|digest|VBN|_ DNA|dna|NN|_ by|by|IN|_ the|the|DT|_ PCI|pci|NN|_ extraction|extraction|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ dissolved|dissolve|VBN|_ in|in|IN|_ diethylpyrocarbonate-treated|diethylpyrocarbonate-treated|JJ|_ water|water|NN|_ and|and|CC|_ used|use|VBN|_ for|for|IN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ .|.|.|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ ~|~|NN|_ 300|300|CD|_ ml|ml|NN|_ LB|lb|NN|MED broth|broth|NN|MED +25|+25|CD|_ mg|mg|NN|_
The|the|DT|_ fastq|fastq|NN|_ files|file|NNS|_ of|of|IN|_ 36-bp|36-bp|JJ|_ sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ generated|generate|VBN|_ with|with|IN|_ the|the|DT|_ CASAVA|CASAVA|NNP|_ v1|v1|NN|_ .8|.8|CD|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ bulk|bulk|NN|_ RNET-seq|rnet-seq|NN|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ specific|specific|JJ|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ the|the|DT|_ Trimmomatic|trimmomatic|JJ|_ v0|v0|NN|_ .25|.25|CD|_ to|to|TO|_ obtain|obtain|VB|_ reads|read|VBZ|_ ≥|≥|SYM|_ 21-nt|21-nt|CD|_ from|from|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ .|.|.|_ The|the|DT|_ reads|read|VBZ|_ ≥|≥|SYM|_ 21-nt|21-nt|JJ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ strain|strain|NN|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779.1|007779.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Bowtie2|bowtie2|NN|_ v2|v2|NN|_ .1.0|.1.0|CD|_ with|with|IN|_ the|the|DT|_ default|default|NN|_ parameter|parameter|NN|_ .|.|.|_ A|a|DT|_ gene|gene|NN|_ annotation|annotation|NN|_ file|file|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ ftp|ftp|NN|GEN server|server|NN|_ of|of|IN|_ Ensembl|ensembl|NN|_ .|.|.|_
The|the|DT|_ processed|process|VBN|_ data|datum|NNS|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ csv|csv|NN|_ -RRB-|-rrb-|-RRB-|_ includes|include|VBZ|_ information|information|NN|_ about|about|IN|_ genomic|genomic|JJ|_ position|position|NN|_ ,|,|,|_ reference|reference|NN|_
To|to|TO|_ analyze|analyze|VB|_ RNAP|rnap|NN|_ pausing|pause|VBG|_ on|on|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ chromosome|chromosome|NN|_ ,|,|,|_ we|we|PRP|_ counted|count|VBD|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ every|every|DT|_ genomic|genomic|JJ|_ nucleotide|nucleotide|NN|_ position|position|NN|_ using|use|VBG|_ the|the|DT|_ mpileup|mpileup|NN|_ command|command|NN|_ of|of|IN|_ SAM|SAM|NNP|_ tools|tool|NNS|_ v0|v0|VBP|_ .1.18|.1.18|CD|_ with|with|IN|_ --|--|:|_ A|a|DT|_ --|--|:|_ B|b|NN|_ parameters|parameter|NNS|_ .|.|.|_ Pausing|pause|VBG|_ sites|site|NNS|_ were|be|VBD|_ defined|define|VBN|_ P|p|NN|_ -LRB-|-lrb-|-LRB-|_ φ|φ|NN|_ ,|,|,|_ δ|δ|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ where|where|WRB|_ φ|φ|NN|_ is|be|VBZ|_ the|the|DT|_ minimal|minimal|JJ|_ fraction|fraction|NN|_ of|of|IN|_ having|have|VBG|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ ends|end|VBZ|_ in|in|IN|_ the|the|DT|_ mapped|map|VBN|_ reads|read|VBZ|_ and|and|CC|_ δ|δ|NN|_ is|be|VBZ|_ the|the|DT|_ minimal|minimal|JJ|_ read|read|NN|_ depth|depth|NN|_ for|for|IN|_ any|any|DT|_ genomic|genomic|JJ|_ position|position|NN|_ .|.|.|_ We|we|PRP|_ chose|choose|VBD|_ δ|δ|NN|_ to|to|TO|_ be|be|VB|_ 100|100|CD|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ 160|160|CD|_ for|for|IN|_ ΔgreAB|δgreab|NN|_ ,|,|,|_ which|which|WDT|_ normalized|normalize|VBD|_ these|these|DT|_ respective|respective|JJ|_ numbers|number|NNS|_ for|for|IN|_ each|each|DT|_ strain|strain|NN|_ since|since|IN|_ there|there|EX|_ were|be|VBD|_ 1.6-fold|1.6-fold|RB|_ more|more|RBR|_ total|total|JJ|_ reads|read|VBZ|_ in|in|IN|_ the|the|DT|_ ΔgreAB|δgreab|NN|_ strain|strain|NN|_ .|.|.|_ The|the|DT|_ high|high|JJ|_ φ|φ|NN|_ parameter|parameter|NN|_ allowed|allow|VBD|_ us|we|PRP|_ to|to|TO|_ define|define|VB|_ a|a|DT|_ reliable|reliable|JJ|_ pause-inducing|pause-inducing|JJ|_ element|element|NN|_ for|for|IN|_ WT|WT|NNP|_ or|or|CC|_ ΔgreAB|δgreab|NN|_ cells|cell|NNS|_ .|.|.|_
W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|FW|_ gal490|gal490|FW|_
W3110|w3110|NN|_ rpoC-6xHis|rpoc-6xhis|NN|_ :|:|:|_ :|:|:|_ kan|kan|NN|_ greA|grea|NN|GEN :|:|:|_ :|:|:|_ tet|tet|NN|_ ,|,|,|_ greB|greb|NN|GEN :|:|:|_ :|:|:|_ amp|amp|NN|_
10|10|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ sample|sample|NN|_ was|be|VBD|_ subjected|subject|VBN|_ to|to|TO|_ purification|purification|NN|_ for|for|IN|_ discarding|discard|VBG|_ rRNA|rrna|NN|_ via|via|IN|_ the|the|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ Following|follow|VBG|_ purification|purification|NN|_ ,|,|,|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ interrupted|interrupt|VBN|_ into|into|IN|_ short|short|JJ|_ fragments|fragment|NNS|_ using|use|VBG|_ divalent|divalent|JJ|_ cations|cation|NNS|_ under|under|IN|_ elevated|elevated|JJ|_ temperature|temperature|NN|_ and|and|CC|_ the|the|DT|_ short|short|JJ|_ fragments|fragment|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ a|a|DT|_ SuperScript|SuperScript|NNP|_ Double-Stranded|Double-Stranded|NNP|_ cDNA|cdna|NN|_ Synthesis|synthesis|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ These|these|DT|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ a|a|DT|_ QIAquick|qiaquick|NN|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ went|go|VBD|_ through|through|IN|_ end|end|NN|_ reparation|reparation|NN|_ ,|,|,|_ adding|add|VBG|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ligation|ligation|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ adaptors|adaptor|NNS|_ .|.|.|_ These|these|DT|_ products|product|NNS|_ were|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ and|and|CC|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ size|size|NN|_ of|of|IN|_ 200-250|200-250|CD|_ bp|bp|NN|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ PCR|pcr|NN|_ amplification|amplification|NN|_ to|to|TO|_ construct|construct|VB|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_
All|all|PDT|_ those|those|DT|_ uniquely|uniquely|RB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ level|level|NN|_ by|by|IN|_ the|the|DT|_ RPKM|rpkm|NN|_ method|method|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ able|able|JJ|_ to|to|TO|_ eliminate|eliminate|VB|_ the|the|DT|_ influence|influence|NN|_ of|of|IN|_ different|different|JJ|_ gene|gene|NN|_ length|length|NN|_ and|and|CC|_ sequencing|sequencing|NN|_ discrepancy|discrepancy|NN|_ on|on|IN|_ the|the|DT|_ calculation|calculation|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ and|and|CC|_ thus|thus|RB|_ the|the|DT|_ calculated|calculate|VBN|_ gene|gene|NN|_ expression|expression|NN|_ level|level|NN|_ can|can|MD|GEN be|be|VB|_ directly|directly|RB|_ used|use|VBN|_ for|for|IN|_ comparing|compare|VBG|_ the|the|DT|_ difference|difference|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ among|among|IN|_ samples|sample|NNS|_ .|.|.|_
Bacterium|Bacterium|NNP|_
Base|Base|NNP|_ calling|call|VBG|_ performed|perform|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ GA|GA|NNP|_ pipeline|pipeline|NN|_ 1.6|1.6|CD|_ .|.|.|_
cas|ca|NNS|_ _|_|VBP|_ RNAA|rnaa|NN|_
con|con|NN|_ _|_|CD|_ RNAA|rnaa|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM666v1|asm666v1|NN|_ ;|;|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
In|in|IN|_ order|order|NN|_ to|to|TO|_ generate|generate|VB|_ the|the|DT|_ VBNC|vbnc|JJ|_ state|state|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ ,|,|,|_ 20|20|CD|_ mL|ml|NN|_ of|of|IN|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cell|cell|NN|_ suspensions|suspension|NNS|_ in|in|IN|_ a|a|DT|_ 50|50|CD|_ mL|ml|NN|_ sterile|sterile|JJ|_ glass|glass|NN|_ tube|tube|NN|_ was|be|VBD|_ treated|treat|VBN|_ by|by|IN|_ HPCD|hpcd|NN|_ at|at|IN|_ 5|5|CD|_ MPa|mpa|NN|_ and|and|CC|_ 25|25|CD|_ ℃|℃|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ NCTC|nctc|NN|_ 12900|12900|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ excel|excel|VB|_ spreadsheet|spreadsheet|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ of|of|IN|_ sample|sample|NN|_
The|the|DT|_ clean|clean|JJ|_ reads|read|VBZ|_ obtained|obtain|VBN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ sequence|sequence|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ using|use|VBG|_ SOAP2|soap2|NN|_
The|the|DT|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ filtered|filtered|VBN|_ for|for|IN|_ removing|remove|VBG|_ dirty|dirty|JJ|_ raw|raw|JJ|_ reads|read|VBZ|_ which|which|WDT|_ contain|contain|VBP|_ adapters|adapter|NNS|_ ,|,|,|_ unknown|unknown|JJ|_ or|or|CC|_ low|low|JJ|_ quality|quality|NN|_ bases|basis|NNS|_ .|.|.|_
The|the|DT|_ strain|strain|NN|_ was|be|VBD|_ stocked|stock|VBN|_ in|in|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ TSB|tsb|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 25|25|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP at|at|IN|_ -80|-80|CD|_ ℃|℃|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ activated|activate|VBN|_ by|by|IN|_ streaking|streak|VBG|_ onto|onto|IN|_ TSA|TSA|NNP|_ plate|plate|NN|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 24|24|CD|_ h.|h.|NN|_ And|and|CC|_ then|then|RB|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ colony|colony|NN|_ was|be|VBD|_ picked|pick|VBN|_ and|and|CC|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ TSB|TSB|NNP|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ for|for|IN|_ 12|12|CD|_ h|h|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ This|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ TSB|tsb|NN|_ at|at|IN|_ a|a|DT|_ dilution|dilution|NN|_ of|of|IN|_ 1:100|1:100|CD|_ and|and|CC|_ grew|grow|VBD|_ to|to|TO|_ the|the|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD550|od550|NN|_ =|=|JJ|_ 0.93|0.93|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ VBNC|vbnc|NN|_ cells|cell|NNS|_ and|and|CC|_ the|the|DT|_ exponential-phase|exponential-phase|NN|_ cells|cell|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ Ⅰ|ⅰ|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ residual|residual|JJ|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ None|none|NN|_
treatment|treatment|NN|_ :|:|:|_ Treated|treat|VBN|_ by|by|IN|_ HPCD|hpcd|NN|_ at|at|IN|_ 5|5|CD|_ MPa|mpa|NN|_ and|and|CC|_ 25|25|CD|_ ℃|℃|NN|_ for|for|IN|_ 40|40|CD|_ min|min|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_ grown|grow|VBN|_ to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_
Bacterial|bacterial|JJ|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
GPR|gpr|NN|_ files|file|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ further|further|RB|_ with|with|IN|_ Acuity|acuity|NN|_ 4.0|4.0|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Molecular|molecular|JJ|_ Devices|Devices|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ starting|start|VBG|_ with|with|IN|_ lowess|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_ Normalized|normalize|VBN|_ log2|log2|NN|_ ratio|ratio|NN|_ data|datum|NNS|_ from|from|IN|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ technical|technical|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ dye|dye|VB|_ swap|swap|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ averaged|average|VBN|_ and|and|CC|_ the|the|DT|_ statistical|statistical|JJ|_ significance|significance|NN|_ -LRB-|-lrb-|-LRB-|_ p-value|p-value|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ calculated|calculate|VBN|_ .|.|.|_
recA730|reca730|NN|_ _|_|CD|_ vs|vs|CC|_ _|_|CD|_ recA730|reca730|NN|_ ,|,|,|_ dcd|dcd|NN|GEN
recA730|reca730|NN|_ _|_|CD|_ vs|vs|CC|_ _|_|CD|_ recA730|reca730|NN|_ ,|,|,|_ ndk|ndk|NN|GEN
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Protect|Protect|NNP|_ Bacteria|bacterium|NNS|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_ derivative|derivative|JJ|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_ derivative|derivative|NN|_ ,|,|,|_ dcd|dcd|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_ derivative|derivative|NN|_ ,|,|,|_ ndk|ndk|NN|GEN :|:|:|_ :|:|:|_ cam|cam|FW|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_ derivative|derivative|NN|_ ,|,|,|_ recA730|reca730|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_ derivative|derivative|NN|_ ,|,|,|_ recA730|reca730|NN|_ ,|,|,|_ dcd|dcd|NN|GEN :|:|:|_ :|:|:|_ kan|kan|FW|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_ derivative|derivative|NN|_ ,|,|,|_ recA730|reca730|NN|_ ,|,|,|_ ndk|ndk|NN|GEN :|:|:|_ :|:|:|_ cam|cam|FW|_
WT|wt|FW|_ _|_|FW|_ vs|vs|CC|_ _|_|FW|_ dcd|dcd|FW|GEN
WT|WT|NNP|_ _|_|CD|_ vs|vs|CC|_ _|_|CD|_ ndk|ndk|NN|GEN
WT|wt|VBD|_ _|_|CD|_ vs|vs|CC|_ _|_|CD|_ recA730|reca730|NN|_
50|50|CD|_ OD600|od600|NN|_ of|of|IN|_ bacteria|bacterium|NNS|_ have|have|VBP|_ been|be|VBN|_ grown|grow|VBN|_ to|to|TO|_ the|the|DT|_ desired|desire|VBN|_ growth|growth|NN|_ stage|stage|NN|_ and|and|CC|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ .|.|.|_ They|they|PRP|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ 500|500|CD|_ µl|µl|NN|_ of|of|IN|_ the|the|DT|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ ,|,|,|_ pH7|ph7|NN|_ .5|.5|CD|_ ,|,|,|_ 150|150|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP DTT|dtt|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP PMSF|pmsf|NN|_ ,|,|,|_ 0.2|0.2|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X100|x100|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Coverage|Coverage|NNP|_ calculation|calculation|NN|_ and|and|CC|_ normalisation|normalisation|NN|_ -LRB-|-lrb-|-LRB-|_ via|via|IN|_ READemption|reademption|NN|_ -RRB-|-rrb-|-RRB-|_
Demultiplexing|demultiplexing|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|_ ProQ|ProQ|NNP|_ coIP|coIP|NNP|_
Escherichia|escherichia|FW|_ ProQ|ProQ|NNP|_ Lysate|Lysate|NNP|_
Escherichia|escherichia|FW|_ WT|WT|NNP|_ coIP|coIP|NNP|_
Escherichia|escherichia|FW|_ WT|WT|NNP|_ Lysate|Lysate|NNP|_
Fastq|Fastq|NNP|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 007779.1|007779.1|CD|_
LB|LB|NNP|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 220|220|CD|_ rpm|rpm|NN|_ ,|,|,|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ ,|,|,|_ 2.0|2.0|CD|_ ,|,|,|_ 2.0|2.0|CD|_ +6|+6|CD|_ h|h|NN|_
Read|Read|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ segemehl|segemehl|NN|_ -LRB-|-lrb-|-LRB-|_ via|via|IN|_ READemption|reademption|NN|_ -RRB-|-rrb-|-RRB-|_
rip|rip|JJ|_ antibody|antibody|NN|_ :|:|:|_ Monoclonal|monoclonal|JJ|_ ANTI-FLAG|anti-flag|NN|_ ^|^|NN|_ =|=|JJ|_ AE|ae|NN|_ M2|m2|NN|_ antibody|antibody|NN|_ produced|produce|VBN|_ in|in|IN|_ mouse|mouse|NN|_ ,|,|,|_ Sigma|Sigma|NNP|_ ,|,|,|_ F1804-200UG|f1804-200ug|NN|_ ,|,|,|_ SLBG5673V|slbg5673v|NN|_
RIP-Seq|rip-seq|JJ|_
RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ Vertis|Vertis|NNP|_ AG|AG|NNP|_ -LRB-|-lrb-|-LRB-|_ Freising-Weihenstephan|Freising-Weihenstephan|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ polyadenylated|polyadenylated|JJ|_ with|with|IN|_ poly|poly|NN|_ -LRB-|-lrb-|-LRB-|_ A|a|NN|_ -RRB-|-rrb-|-RRB-|_ polymerase|polymerase|NN|_ ,|,|,|_ 5|5|CD|_ '|'|''|_ -|-|:|_ triphosphates|triphosphate|NNS|_ were|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ followed|follow|VBN|_ by|by|IN|_ ligation|ligation|NN|_ of|of|IN|_ a|a|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ adapter|adapter|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ use|use|NN|_ of|of|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ barcoded|barcoded|JJ|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MVL|m-mvl|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ The|the|DT|_ resulting|result|VBG|_ cDNA|cdna|NN|_ was|be|VBD|_ PCR-amplified|pcr-amplified|JJ|_ with|with|IN|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ the|the|DT|_ Agencourt|Agencourt|NNP|_ AMPure|AMPure|NNP|_ XP|xp|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ Genomics|Genomics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Size|size|NN|_ filtering|filter|VBG|_ :|:|:|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 12|12|CD|_ nt|nt|NNS|_ -LRB-|-lrb-|-LRB-|_ via|via|IN|_ READemption|reademption|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wiggle|wiggle|NN|_
The|the|DT|_ equivalent|equivalent|NN|_ of|of|IN|_ 5|5|CD|_ OD600|od600|NN|_ was|be|VBD|_ saved|save|VBN|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ with|with|IN|_ TriZOL|trizol|NN|_ before|before|IN|_ adding|add|VBG|_ antibodies|antibody|NNS|_ -LRB-|-lrb-|-LRB-|_ lysate|lysate|NN|_ RNA|rna|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ coIP|coip|NN|_ samples|sample|NNS|_ ,|,|,|_ beads|bead|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ the|the|DT|_ lysis|lysis|NN|_ buffer|buffer|NN|_ ,|,|,|_ mixed|mix|VBN|_ with|with|IN|_ an|a|DT|_ equal|equal|JJ|_ volume|volume|NN|_ of|of|IN|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ :|:|:|_ isopropanol|isopropanol|NN|_ -LRB-|-lrb-|-LRB-|_ 25:24:1|25:24:1|CD|_ ,|,|,|_ pH4|ph4|NN|_ .5|.5|CD|_ ,|,|,|_ Roth|Roth|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 20|20|CD|_ s|s|NNS|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ .|.|.|_ After|after|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ the|the|DT|_ aqueous|aqueous|JJ|_ phase|phase|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ with|with|IN|_ isopropanol|isopropanol|NN|_ -LRB-|-lrb-|-LRB-|_ coIP|coip|NN|_ RNA|rna|NN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ coIP|coip|NN|_ sample|sample|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ remove|remove|VB|_ the|the|DT|_ residual|residual|JJ|_ DNA|dna|NN|_ and|and|CC|_ reisolated|reisolate|VBN|_ with|with|IN|_ phenol|phenol|NN|_ :|:|:|_ chloroform|chloroform|NN|_ :|:|:|_ isopropanol|isopropanol|NN|_ .|.|.|_ The|the|DT|_ spike-in|spike-in|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ P-CUCGUCCGACGUCACCUAGA|p-cucguccgacgucaccuaga|NN|_ ,|,|,|_ IBA|iba|NN|_ -RRB-|-rrb-|-RRB-|_ had|have|VBD|_ been|be|VBN|_ added|add|VBN|_ to|to|TO|_ 40|40|CD|_ pg|pg|NN|_
Adapter|Adapter|NNP|_ cutting|cut|VBG|_ using|use|VBG|_ cutadapt|cutadapt|NN|_ ,|,|,|_ version|version|NN|_ 1.2.1|1.2.1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ e|e|SYM|_ 0.1|0.1|CD|_ -|-|:|_ O|o|NN|_ 1|1|CD|_ -|-|:|_ m|m|NN|_ 12|12|CD|_
AT1|at1|NN|_ biological|biological|JJ|_ replicate|replicate|VB|_
E.|e.|FW|_ coli|coli|FW|_ MC4100|mc4100|NN|_ strain|strain|NN|_ was|be|VBD|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.4|0.4|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ strain|strain|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_ ,|,|,|_ downloaded|download|VBN|_ from|from|IN|_ NCBI|NCBI|NNP|_
Genome|Genome|NNP|_ mapping|mapping|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ ,|,|,|_ version|version|NN|_ 0.12.9|0.12.9|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ ,|,|,|_ parameters|parameter|NNS|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ :|:|:|_ -|-|:|_ v|v|LS|_ 3|3|CD|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_
LB|lb|NN|_ mRNA|mrna|NN|_
LB|lb|NN|_ mRNA|mrna|NN|_ biological|biological|JJ|_ replicate|replicate|VBP|_
LB|lb|NN|_ mRNA|mrna|NN|_ technical|technical|JJ|_ replicate|replicate|VB|_
LB|LB|NNP|_ RPF|RPF|NNP|_
LB|LB|NNP|_ RPF|RPF|NNP|_ biological|biological|JJ|_ replicate|replicate|VBP|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
Quality|quality|JJ|_ trimming|trim|VBG|_ using|use|VBG|_ FASTX-toolkit|fastx-toolkit|NN|_ ,|,|,|_ version|version|NN|_ 0.0.13.2|0.0.13.2|CD|_ ,|,|,|_ parameters|parameter|NNS|_ -|-|:|_ v|v|LS|_ -|-|:|_ t|t|NN|_ 20|20|CD|_ -|-|:|_ l|l|NN|_ 10|10|CD|_
Read|read|VBP|_ counts|count|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ for|for|IN|_ each|each|DT|_ nucleotide|nucleotide|NN|_
Read|Read|NNP|_ using|use|VBG|_ bedtools|bedtool|NNS|_ ,|,|,|_ version|version|NN|_ 2.17.0|2.17.0|CD|_ ,|,|,|_ parameter|parameter|NN|_ :|:|:|_ -|-|:|_ s|s|NNS|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 1-5|1-5|CD|_ the|the|DT|_ middle|middle|NN|_ nucleotide|nucleotide|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ was|be|VBD|_ taken|take|VBN|_ ,|,|,|_ for|for|IN|_ samples|sample|NNS|_ 6-9|6-9|CD|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ was|be|VBD|_ assigned|assign|VBN|_ to|to|TO|_ the|the|DT|_ nucleotide|nucleotide|NN|_ 5|5|CD|_ '|'|''|_ of|of|IN|_ the|the|DT|_ first|first|JJ|_ nucleotide|nucleotide|NN|_ see|see|VB|_ -LCB-|-lcb-|-LRB-|_ Kertesz|Kertesz|NNP|_ ,|,|,|_ 2010|2010|CD|_ -RCB-|-rcb-|-RRB-|_ for|for|IN|_ details|detail|NNS|_
RNA-Seq|rna-seq|JJ|_
RNA-size|rna-size|NN|_ selection|selection|NN|_ and|and|CC|_ generation|generation|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ -LCB-|-lcb-|-LRB-|_ Ingolia|Ingolia|NNP|_ ,|,|,|_ 2009|2009|CD|_ -RCB-|-rcb-|-RRB-|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ AT1|at1|NN|_ digested|digest|VBD|_ total|total|JJ|_ RNA|rna|NN|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ ribosome|ribosome|NN|_ protected|protect|VBD|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ V1|v1|NN|_ digested|digest|VBD|_ total|total|JJ|_ RNA|rna|NN|_
strain|strain|NN|_ :|:|:|_ MC4100|mc4100|NN|_
strain|strain|NN|_ :|:|:|_ MC4101|mc4101|NN|_
strain|strain|NN|_ :|:|:|_ MC4102|mc4102|NN|_
strain|strain|NN|_ :|:|:|_ MC4103|mc4103|NN|_
strain|strain|NN|_ :|:|:|_ MC4104|mc4104|NN|_
strain|strain|NN|_ :|:|:|_ MC4105|mc4105|NN|_
strain|strain|NN|_ :|:|:|_ MC4106|mc4106|NN|_
strain|strain|NN|_ :|:|:|_ MC4107|mc4107|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Column|Column|NNP|_ 1|1|CD|_ names|name|NNS|_ the|the|DT|_ nucleotide|nucleotide|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ ,|,|,|_ column|column|NN|_ 2|2|CD|_ gives|give|VBZ|_ counts|count|NNS|_ for|for|IN|_ the|the|DT|_ forward|forward|JJ|_ strand|strand|NN|_ ,|,|,|_ column|column|NN|_ 3|3|CD|_ for|for|IN|_ the|the|DT|_ reverse|reverse|JJ|_ strand|strand|NN|_ ,|,|,|_ columns|column|NNS|_ are|be|VBP|_ tab|tab|NN|_ separated|separated|JJ|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ in|in|IN|_ mRNA|mrna|NN|_ ,|,|,|_ depleting|deplete|VBG|_ small|small|JJ|_ RNAs|rna|NNS|_ with|with|IN|_ GeneJET|genejet|NN|_ ™|™|NN|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Fermentas|fermentas|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ with|with|IN|_ two|two|CD|_ cycle|cycle|NN|_ of|of|IN|_ MICROBExpress|microbexpress|NN|_ ™|™|CD|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ probe|probe|VB|_ the|the|DT|_ RNA|rna|NN|_ structure|structure|NN|_ two|two|CD|_ µg|µg|NN|_ of|of|IN|_ enriched|enriched|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 45|45|CD|_ µl|µl|NN|_ of|of|IN|_ DEPC|depc|NN|_ water|water|NN|_ and|and|CC|_ denatured|denature|VBN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ ,|,|,|_ refolded|refold|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ after|after|IN|_ addition|addition|NN|_ of|of|IN|_ 10x|10x|CD|_ RNA-structure|rna-structure|NN|_ buffer|buffer|NN|_ with|with|IN|_ pH|ph|NN|_ 7.0|7.0|CD|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ ,|,|,|_ 1|1|CD|_ M|m|NN|_ KCl|kcl|NN|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ digested|digest|VBN|_ for|for|IN|_ 1|1|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ either|either|CC|_ 0.05|0.05|CD|_ U|U|NNP|_ RNase|rnase|NN|_ V1|v1|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ 2|2|CD|_ µg|µg|NN|_ RNase|rnase|NN|_ A|a|NN|_ and|and|CC|_ 5|5|CD|_ U|U|NNP|_ RNase|rnase|NN|_ T1|t1|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reaction|reaction|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ extracting|extract|VBG|_ the|the|DT|_ RNA|rna|NN|_ with|with|IN|_ phenol-chlorophorm|phenol-chlorophorm|NN|_ .|.|.|_ The|the|DT|_ RNase|rnase|NN|_ A|a|NN|_
V1|v1|NN|_ biological|biological|JJ|_ replicate|replicate|VBP|_
At|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ cultures|culture|NNS|_ induced|induce|VBN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ .|.|.|_ Cells|cell|NNS|_ harvested|harvest|VBN|_ 20|20|CD|_ min|min|NN|_ after|after|IN|_ induction|induction|NN|_
Cells|cell|NNS|_ harvested|harvest|VBN|_ at|at|IN|_ OD450|od450|NN|_ =|=|JJ|_ 0.3|0.3|CD|_
Culture|culture|NN|_ samples|sample|NNS|_ for|for|IN|_ microarray|microarray|NN|_ analysis|analysis|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ ice-cold|ice-cold|JJ|_ 5|5|CD|_ %|%|NN|_ water-saturated|water-saturated|JJ|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ solution|solution|NN|_ ,|,|,|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 6,600|6,600|CD|_ g|g|NN|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ flash|flash|VBP|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ N2|n2|NN|_ before|before|IN|_ storing|store|VBG|_ at|at|IN|_ -80|-80|CD|_ degrees|degree|NNS|_ C|c|NN|_ until|until|IN|_ required|require|VBN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ stored|store|VBN|_ cell|cell|NN|_ pellets|pellet|NNS|_ using|use|VBG|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ ,|,|,|_ and|and|CC|_ labeled|label|VBN|_ Cy3|cy3|NN|_ and|and|CC|_ Cy5|cy5|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ 16|16|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ with|with|IN|_ 10|10|CD|_ ug|ug|NN|_ random|random|JJ|_ hexamer|hexamer|NN|_ -LRB-|-lrb-|-LRB-|_ Integrated|Integrated|NNP|_ DNA|DNA|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Coralville|Coralville|NNP|_ ,|,|,|_ IA|IA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Data|Data|NNP|_ filtered|filter|VBD|_ for|for|IN|_ PCR|pcr|NN|_ success|success|NN|_ ,|,|,|_ >|>|JJR|_ 3x|3x|NN|_ local|local|JJ|_ background|background|NN|_ and|and|CC|_ spot|spot|NN|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ GenePix|GenePix|NNP|_ Flag|Flag|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Normalized|normalize|VBN|_ using|use|VBG|_ Lowess|Lowess|NNP|_ smoothing|smooth|VBG|_ from|from|IN|_ MA|MA|NNP|_ plot|plot|NN|_
delta|delta|NN|_ hfq|hfq|NN|GEN
Delta|delta|NN|_ hfq|hfq|NN|GEN
Delta|delta|NN|_ rseA|rsea|NN|GEN
EC12n097|ec12n097|NN|_ delta|delta|NN|_ rseA|rsea|NN|GEN
EC12n098|ec12n098|NN|_ delta|delta|NN|_ rseA|rsea|NN|GEN
EC12n099|ec12n099|NN|_ delta|delta|NN|_ rseA|rsea|NN|GEN
EC18n018|ec18n018|NN|_ hfq|hfq|NN|GEN +|+|CC|_ rpoE|rpoe|NN|GEN overexpression|overexpression|NN|_ 20|20|CD|_ min|min|NN|_
EC18n019|ec18n019|NN|_ hfq|hfq|NN|GEN -|-|:|_ rpoE|rpoe|NN|GEN overexpression|overexpression|NN|_ 20|20|CD|_ min|min|NN|_
EC18n035|ec18n035|NN|_ delta|delta|NN|_ rseA|rsea|NN|GEN
EC18n036|ec18n036|NN|_ delta|delta|NN|_ rseA|rsea|NN|GEN
EC18n037|ec18n037|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC18n038|ec18n038|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC18n039|ec18n039|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC18n040|ec18n040|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC18n136|ec18n136|NN|_ hfq|hfq|NN|GEN +|+|CC|_ rpoE|rpoe|NN|GEN overexpression|overexpression|NN|_ 20|20|CD|_ min|min|NN|_
Ec18n137|ec18n137|NN|_ hfq|hfq|NN|GEN -|-|:|_ rpoE|rpoe|NN|GEN overexpression|overexpression|NN|_ 20|20|CD|_ min|min|NN|_
EC18n139|ec18n139|NN|_ hfq|hfq|NN|GEN +|+|CC|_ rpoE|rpoe|NN|GEN overexpression|overexpression|NN|_ 20|20|CD|_ min|min|NN|_
EC18n140|ec18n140|NN|_ hfq|hfq|NN|GEN -|-|:|_ rpoE|rpoe|NN|GEN overexpression|overexpression|NN|_ 20|20|CD|_ min|min|NN|_
EC19n075|ec19n075|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC19n076|ec19n076|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC19n098|ec19n098|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC19n099|ec19n099|NN|_ delta|delta|NN|_ hfq|hfq|NN|GEN
EC19n100|ec19n100|NN|_ delta|delta|NN|_ rseA|rsea|NN|GEN
EC19n101|ec19n101|NN|_ delta|delta|NN|_ rseA|rsea|NN|GEN
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Hfq|hfq|NN|_ -|-|:|_ RpoE|rpoe|NN|_ overexpression|overexpression|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
hfq|hfq|NN|GEN +|+|CC|_ Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
M9|m9|NN|_ minimal|minimal|JJ|_ complete|complete|JJ|_ media|media|NNS|_ ,|,|,|_ cultures|culture|NNS|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ at|at|IN|_ 30|30|CD|_ degrees|degree|NNS|_ C|c|NN|_ in|in|IN|_ a|a|DT|_ gyratory|gyratory|JJ|_ water|water|NN|_ bath|bath|NN|_ shaking|shake|VBG|_ at|at|IN|_ 240|240|CD|_ rpm|rpm|NN|_
MG1655|mg1655|NN|_ rpoHp3|rpohp3|NN|Pr :|:|:|_ :|:|:|_ lacZ|lacz|NN|GEN delta|delta|NN|_ lacX74|lacx74|NN|_
MG1655|mg1655|NN|_ rpoHp3|rpohp3|NN|Pr :|:|:|_ :|:|:|_ lacZ|lacz|NN|GEN delta|delta|NN|_ lacX74|lacx74|NN|_ hfq1|hfq1|NN|_ :|:|:|_ :|:|:|_ omega|omega|NN|_ -LRB-|-lrb-|-LRB-|_ Km|km|NN|_ ;|;|:|_ BclI|bcli|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ hfq|hfq|SYM|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_
MG1655|mg1655|NN|_ rpoHp3|rpohp3|NN|Pr :|:|:|_ :|:|:|_ lacZ|lacz|NN|GEN delta|delta|NN|_ lacX74|lacx74|NN|_ hfq2|hfq2|NN|_ :|:|:|_ :|:|:|_ omega|omega|NN|_ -LRB-|-lrb-|-LRB-|_ Km|km|NN|_ ;|;|:|_ KpnI|kpni|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ hfq|hfq|NN|GEN +|+|CC|_ -RRB-|-rrb-|-RRB-|_
MG1655|mg1655|NN|_ rpoHp3|rpohp3|NN|Pr :|:|:|_ :|:|:|_ lacZ|lacz|NN|GEN delta|delta|NN|_ lacX74|lacx74|NN|_ nadB|nadb|NN|GEN :|:|:|_ :|:|:|_ Tn10|tn10|NN|_ drseA|drsea|NN|_
RpoE|rpoe|NN|_ induced|induce|VBN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_
Wild|Wild|NNP|_ type|type|NN|_ control|control|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Cells|cell|NNS|_ were|be|VBD|_ crosslinked|crosslink|VBN|_ in|in|IN|_ 1|1|CD|_ %|%|NN|_ formadehyde|formadehyde|NN|_ for|for|IN|_ 25|25|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ followed|follow|VBN|_ by|by|IN|_ 5|5|CD|_ minutes|minute|NNS|_ of|of|IN|_ quenching|quench|VBG|_ with|with|IN|_ glycine|glycine|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ 3X|3x|NN|_ with|with|IN|_ ice|ice|NN|_ cold|cold|JJ|_ TBS|tbs|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ enyzmatically|enyzmatically|RB|_ lysed|lyse|VBN|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ protease|protease|NN|_ inhibitors|inhibitor|NNS|_ prior|prior|RB|_ to|to|TO|_ fragmentation|fragmentation|NN|_ using|use|VBG|_ sonication|sonication|NN|_ .|.|.|_ Protein|protein|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ c-Myc|c-myc|NN|_ Antibody|antibody|NN|_ -LRB-|-lrb-|-LRB-|_ 9E10|9e10|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotech|Biotech|NNP|_ ,|,|,|_ sc-40|sc-40|JJ|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Monoclonal|monoclonal|JJ|_ Antibody|antibody|NN|_ ,|,|,|_ Neoclone|neoclone|NN|_ ,|,|,|_ #N0004|#n0004|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ RNA|rna|NN|_ Sigma|Sigma|NNP|_ 70|70|CD|_ Monoclonal|monoclonal|JJ|_ Antibody|antibody|NN|_ ,|,|,|_ Neoclone|neoclone|NN|_ ,|,|,|_ #WP004|#wp004|NN|_
ChIPExo-ArcA|chipexo-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-myc|anti-myc|JJ|_
ChIPExo-ArcA|chipexo-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-myc|anti-myc|JJ|_
ChIPExo-ArcA|chipexo-arca|NN|_ _|_|CD|_ ArcA8myc|arca8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-myc|anti-myc|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr1delAr2|delar1delar2|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr1delAr2|delar1delar2|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr1delAr2|delar1delar2|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr1|delar1|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr1|delar1|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr1|delar1|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr2|delar2|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr2|delar2|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delAr2|delar2|NN|_ _|_|CD|_ glycerol|glycerol|NN|SUPP _|_|NN|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 4|4|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|SYM|_ O2|o2|CD|_ _|_|SYM|_ 5|5|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_ _|_|NN|_ rif|rif|NN|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ anti-crp|anti-crp|JJ|_ _|_|NN|_ rif|rif|NN|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_ _|_|NN|_ rif|rif|NN|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 4|4|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|SYM|_ O2|o2|CD|_ _|_|SYM|_ 5|5|CD|_ _|_|SYM|_ anti-crp|anti-crp|JJ|_
ChIPExo-Crp|chipexo-crp|JJ|_ _|_|NN|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 6|6|CD|_ _|_|NN|_ anti-crp|anti-crp|JJ|_
ChIPExo-Fnr|chipexo-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ anti-myc|anti-myc|JJ|_
ChIPExo-Fnr|chipexo-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ anti-myc|anti-myc|JJ|_
ChIPExo-Fnr|chipexo-fnr|JJ|_ _|_|NN|_ Fnr8myc|fnr8myc|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|NN|_ anaerobic|anaerobic|JJ|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-myc|anti-myc|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ anti-rpod|anti-rpod|JJ|_
ChIPExo-RpoD|chipexo-rpod|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ anti-rpod|anti-rpod|JJ|_
ChIP-Seq|chip-seq|NN|_
Chromosomal|chromosomal|JJ|_ DNA|dna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Library|Library|NNP|_ construction|construction|NN|_ was|be|VBD|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Rhee|Rhee|NNP|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ doi|doi|FW|_ :|:|:|_ 10.1016|10.1016|CD|_
Peak-calls|peak-call|NNS|_ were|be|VBD|_ done|do|VBN|_ using|use|VBG|_ GPS|gps|NN|_ within|within|IN|_ the|the|DT|_ GEMS|gem|NNS|_ software|software|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ adapted|adapt|VBD|_ for|for|IN|_ ChIP-exo|ChIP-exo|NNP|_ data|datum|NNS|_
strain|strain|NN|_ :|:|:|_ ArcA8myc|arca8myc|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1|delar1|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1delAr2|delar1delar2|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr2|delar2|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|crp|NN|_
strain|strain|NN|_ :|:|:|_ Fnr8myc|fnr8myc|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ gff|gff|NN|_ files|file|NNS|_ containing|contain|VBG|_ a|a|DT|_ pileup|pileup|NN|_ of|of|IN|_ 5|5|CD|_ '|'|''|_ tags|tag|NNS|_ .|.|.|_ GFF|gff|NN|_ column|column|NN|_ headers|header|NNS|_ \|\|VBP|_ Genbank|Genbank|NNP|_ fna|fna|NNP|_ ID|ID|NNP|_ ,|,|,|_ file|file|NN|_ name|name|NN|_ ,|,|,|_ left|leave|VBD|_ genomic|genomic|JJ|_ position|position|NN|_ ,|,|,|_ right|right|JJ|_ genomic|genomic|JJ|_ position|position|NN|_ ,|,|,|_ value|value|NN|_ ,|,|,|_ strand|strand|NN|_ ,|,|,|_ extra|extra|JJ|_ value|value|NN|_ ,|,|,|_ information|information|NN|_ \|\|SYM|_
The|the|DT|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.3|.2.3|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ shake|shake|NN|_ flasks|flask|NNS|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ under|under|IN|_ either|either|CC|_ aerobic|aerobic|JJ|_ or|or|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplement|supplement|NN|_ with|with|IN|_ either|either|CC|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ ,|,|,|_ or|or|CC|_ glycerol|glycerol|NN|SUPP as|as|IN|_ the|the|DT|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ was|be|VBD|_ used|use|VBN|_ depending|depend|VBG|_ on|on|IN|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Gene|gene|NN|_ expression|expression|NN|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ ,|,|,|_ paired-end|paired-end|JJ|_ RNA-seq|rna-seq|NN|_ protocol|protocol|NN|_ using|use|VBG|_ the|the|DT|_ dUTP|dutp|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Levin|Levin|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ Kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
Reads|Reads|NNPS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ in|in|IN|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Datasets|dataset|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ cuffdiff|cuffdiff|NN|_ in|in|IN|_ the|the|DT|_ cufflinks|cufflink|NNS|_ package|package|NN|_ to|to|TO|_ generate|generate|VB|_ FPKM|fpkm|NN|_ -LRB-|-lrb-|-LRB-|_ Framents|Framents|NNP|_ Per|per|IN|_ Kilobase|Kilobase|NNP|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ mapped|map|VBN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ all|all|DT|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr1delAr2|delar1delar2|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr1delAr2|delar1delar2|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr1delAr2|delar1delar2|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr1|delar1|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr1|delar1|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr1|delar1|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr2|delar2|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr2|delar2|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delAr2|delar2|NN|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ delta-crp|delta-crp|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_ _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 3|3|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 1|1|CD|_
RNAseq|rnaseq|NN|_ _|_|CD|_ wt|wt|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP _|_|CD|_ NH4Cl|nh4cl|NN|_ _|_|CD|_ O2|o2|CD|_ _|_|NN|_ 2|2|CD|_
rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ primed|prime|VBN|_ using|use|VBG|_ random|random|JJ|_ hexamers|hexamer|NNS|_ and|and|CC|_ reverse|reverse|VB|_ transcribed|transcribe|VBN|_ using|use|VBG|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1|delar1|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr1delAr2|delar1delar2|NN|_
strain|strain|NN|_ :|:|:|_ Crp|Crp|NNP|_ _|_|SYM|_ delAr2|delar2|NN|_
strain|strain|NN|_ :|:|:|_ delta|delta|NN|_ Crp|crp|NN|_
strain|strain|NN|_ :|:|:|_ wt|wt|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ is|be|VBZ|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ cuff|cuff|NN|_ diff|diff|NN|_ analysis|analysis|NN|_ format|format|NN|_
The|the|DT|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ MiSeq|miseq|NN|_ Reporter|reporter|NN|_ 2.4.60.8|2.4.60.8|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ demultiplexing|demultiplex|VBG|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNAs|rna|NNS|_ using|use|VBG|_ Epicentre|Epicentre|NNP|_ 's|'s|POS|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_
DNeasy|dneasy|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
gDNA|gdna|NN|_ 520|520|CD|_
gDNA|gdna|NN|_ 521|521|CD|_
gDNA|gdna|NN|_ B02|b02|NN|_
gDNA|gdna|NN|_ B05|b05|NN|_
gDNA|gdna|NN|_ C01|c01|NN|_
gDNA|gdna|NN|_ C02|c02|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|SYM|_ 520|520|CD|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|SYM|_ 521|521|CD|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ B02|b02|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ B05|b05|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ C01|c01|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ C02|c02|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ F01|f01|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ F02|f02|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H01|h01|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H02|h02|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H03|h03|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H04|h04|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H05|h05|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H12|h12|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H23|h23|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ H27|h27|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ S04|s04|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ S05|s05|NN|_
gDNA|gdna|NN|_ _|_|CD|_ EColi|ecolus|NNS|_ _|_|VBP|_ S13|s13|NN|_
gDNA|gdna|NN|_ F01|f01|NN|_
gDNA|gdna|NN|_ F02|f02|NN|_
gDNA|gdna|NN|_ from|from|IN|_ E.coli|e.coli|JJ|_ K12|k12|NN|_ cyanine|cyanine|NN|_ 3|3|CD|_
gDNA|gdna|NN|_ H01|h01|NN|_
gDNA|gdna|NN|_ H02|h02|NN|_
gDNA|gdna|NN|_ H03|h03|NN|_
gDNA|gdna|NN|_ H04|h04|NN|_
gDNA|gdna|NN|_ H05|h05|NN|_
gDNA|gdna|NN|_ H12|h12|NN|_
gDNA|gdna|NN|_ H23|h23|NN|_
gDNA|gdna|NN|_ H27|h27|NN|_
gDNA|gdna|NN|_ K12|k12|NN|_
gDNA|gdna|NN|_ S04|s04|NN|_
gDNA|gdna|NN|_ S05|s05|NN|_
gDNA|gdna|NN|_ S13|s13|NN|_
Local|local|JJ|_ Background|background|NN|_ Substracted|Substracted|NNP|_ Signal|Signal|NNP|_ Corrected|Corrected|NNP|_ for|for|IN|_ unequal|unequal|JJ|_ Dye|dye|NN|_ incorporation|incorporation|NN|_ or|or|CC|_ unequal|unequal|JJ|_ load|load|NN|_ of|of|IN|_ labelled|label|VBN|_ product|product|NN|_
strain|strain|NN|_ 520|520|CD|_
strain|strain|NN|_ 521|521|CD|_
strain|strain|NN|_ B02|b02|NN|_
strain|strain|NN|_ B05|b05|NN|_
strain|strain|NN|_ C01|c01|NN|_
strain|strain|NN|_ C02|c02|NN|_
strain|strain|NN|_ F01|f01|NN|_
strain|strain|NN|_ F02|f02|NN|_
strain|strain|NN|_ H01|h01|NN|_
strain|strain|NN|_ H02|h02|NN|_
strain|strain|NN|_ H03|h03|NN|_
strain|strain|NN|_ H04|h04|NN|_
strain|strain|NN|_ H05|h05|NN|_
strain|strain|NN|_ H12|h12|NN|_
strain|strain|NN|_ H23|h23|NN|_
strain|strain|NN|_ H27|h27|NN|_
strain|strain|NN|_ S04|s04|NN|_
strain|strain|NN|_ S05|s05|NN|_
strain|strain|NN|_ S13|s13|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δfis|Δfis|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CSH50|csh50|NN|_ Δhns|δhns|NNS|_
Fis|Fis|NNP|TF --|--|:|_ 120|120|CD|_ min|min|NN|_
Fis|Fis|NNP|TF --|--|:|_ 180|180|CD|_ min|min|NN|_
Fis|Fis|NNP|TF --|--|:|_ 420|420|CD|_ min|min|NN|_
Fis|Fis|NNP|TF --|--|:|_ 60|60|CD|_ min|min|NN|_
GATC|gatc|NN|_
GATC|gatc|NN|_ software|software|NN|_ for|for|IN|_ read|read|NN|_ mapping|mapping|NN|_ on|on|IN|_ MG1655|mg1655|NN|_
gene|gene|NN|_ expression|expression|NN|_ sum|sum|NN|_ normalized|normalize|VBD|_ to|to|TO|_ 1|1|CD|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_
Gene|Gene|NNP|_ wise|wise|JJ|_ natural|natural|JJ|_ spline|spline|NN|_ interpolation|interpolation|NN|_ of|of|IN|_ temporal|temporal|JJ|_ data|datum|NNS|_ from|from|IN|_ initial|initial|JJ|_ time|time|NN|_ points|point|NNS|_ to|to|TO|_ a|a|DT|_ dataset|dataset|NN|_ of|of|IN|_ 10|10|CD|_ minutes|minute|NNS|_ steps|step|NNS|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Expression|expression|NN|_ values|value|NNS|_ at|at|IN|_ the|the|DT|_ time|time|NN|_ points|point|NNS|_ of|of|IN|_ the|the|DT|_ raw|raw|JJ|_ data|datum|NNS|_ are|be|VBP|_ not|not|RB|_ affected|affect|VBN|_ by|by|IN|_ the|the|DT|_ interpolation|interpolation|NN|_ .|.|.|_
genotype|genotype|NN|_ :|:|:|_ delta-fis|delta-fis|JJ|_
genotype|genotype|NN|_ :|:|:|_ delta-hns|delta-hn|NNS|_
genotype|genotype|NN|_ :|:|:|_ wildtype|wildtype|JJ|_
Hns|hn|NNS|_ --|--|:|_ 120|120|CD|_ min|min|NN|_
Hns|hn|VBZ|_ -180|-180|CD|_ min|min|NN|_
Hns|hn|NNS|_ --|--|:|_ 420|420|CD|_ min|min|NN|_
Hns|hn|NNS|_ --|--|:|_ 60|60|CD|_ min|min|NN|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ airated|airate|VBN|_ ,|,|,|_ constant|constant|JJ|_ pH|ph|NN|_ 7.5|7.5|CD|_
RNA|rna|NN|_ extraction|extraction|NN|_ Kit|kit|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ CSH50|csh50|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ time|time|NN|_ ,|,|,|_ rows|row|NNS|_ =|=|JJ|_ genes|gene|NNS|_ ,|,|,|_ cols|col|NNS|_ =|=|JJ|_ time|time|NN|_ points|point|NNS|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ minutes|minute|NNS|_
time|time|NN|_ :|:|:|_ 180|180|CD|_ minutes|minute|NNS|_
time|time|NN|_ :|:|:|_ 300|300|CD|_ minutes|minute|NNS|_
time|time|NN|_ :|:|:|_ 420|420|CD|_ minutes|minute|NNS|_
time|time|NN|_ :|:|:|_ 60|60|CD|_ minutes|minute|NNS|_
verified|verify|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ pipeline|pipeline|NN|_
Wt|wt|NN|_ --|--|:|_ 120|120|CD|_ min|min|NN|_
Wt|wt|NN|_ --|--|:|_ 180|180|CD|_ min|min|NN|_
Wt|wt|NN|_ --|--|:|_ 300|300|CD|_ min|min|NN|_
Wt|wt|NN|_ --|--|:|_ 420|420|CD|_ min|min|NN|_
Wt|wt|NN|_ --|--|:|_ 60|60|CD|_ min|min|NN|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ an|a|DT|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED supplemented|supplement|VBN|_ with|with|IN|_ 2|2|CD|_ g|g|NN|_
Data|Data|NNP|_ analysis|analysis|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ R|r|NN|_ language|language|NN|_ and|and|CC|_ environment|environment|NN|_ for|for|IN|_ a|a|DT|_ statistical|statistical|JJ|_ computing|computing|NN|_ and|and|CC|_ Bioconductor|bioconductor|NN|_ .|.|.|_ Array|array|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ with|with|IN|_ gcRMA|gcrma|NN|_ method|method|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ tynA|tyna|NN|GEN -|-|:|_ 1h|1h|NN|_ after|after|IN|_ induction|induction|NN|_ of|of|IN|_ tynA|tyna|NN|GEN expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ tynA|tyna|NN|GEN -|-|:|_ 4h|4h|NN|_ after|after|IN|_ the|the|DT|_ induction|induction|NN|_ of|of|IN|_ tynA|tyna|NN|GEN expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ tynA|tyna|NN|GEN -|-|:|_ at|at|IN|_ time|time|NN|_ of|of|IN|_ induction|induction|NN|_ of|of|IN|_ tynA|tyna|NN|GEN expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ wt|wt|JJ|_ 1h|1h|NN|_ after|after|IN|_ the|the|DT|_ induction|induction|NN|_ of|of|IN|_ tynA|tyna|NN|GEN expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ wt|wt|JJ|_ 4h|4h|NN|_ after|after|IN|_ the|the|DT|_ induction|induction|NN|_ of|of|IN|_ tynA|tyna|NN|GEN expression|expression|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_ wt|wt|JJ|_ at|at|IN|_ time|time|NN|_ of|of|IN|_ induction|induction|NN|_ of|of|IN|_ tynA|tyna|NN|GEN expression|expression|NN|_
genotype|genotype|NN|_ :|:|:|_ tynA|tyna|NN|GEN -|-|:|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Prokaryotic|Prokaryotic|NNP|_ Target|target|NN|_ Preparation|preparation|NN|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ GeneChip|genechip|NN|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Technical|Technical|NNP|_ Manual|Manual|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ Mini-Kit|mini-kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ `|`|``|_ s|be|VBZ|_ instruction|instruction|NN|_ and|and|CC|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ using|use|VBG|_ RNAse-Free|rnase-free|JJ|_ DNAse|dnase|NN|_ Set|set|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
tynA|tyna|SYM|GEN -|-|:|_ at|at|IN|_ T0|t0|NN|_
tynA|tyna|NN|GEN -|-|:|_ at|at|IN|_ T1h|t1h|NN|_
tynA|tyna|NN|GEN -|-|:|_ at|at|IN|_ T4h|t4h|NN|_
wt|wt|JJ|_ at|at|IN|_ T0|t0|NN|_
wt|wt|JJ|_ at|at|IN|_ T1h|t1h|NN|_
wt|wt|JJ|_ at|at|IN|_ T4h|t4h|NN|_
acetate|acetate|NN|SUPP
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-myc|anti-myc|JJ|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-rpoB|anti-rpob|NN|_ -LRB-|-lrb-|-LRB-|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotech|Biotech|NNP|_ ,|,|,|_ sc-56766|sc-56766|NN|_ -RRB-|-rrb-|-RRB-|_
chip|chip|NN|_ antibody|antibody|NN|_ cat|cat|NN|_ .|.|.|_ #|#|#|_ :|:|:|_ sc-28207|sc-28207|JJ|_
chip|chip|NN|_ antibody|antibody|NN|_ vendor|vendor|NN|_ :|:|:|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotech|Biotech|NNP|_
ChIP-exo|ChIP-exo|NNP|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ ASM584v2|asm584v2|NN|_ genome|genome|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ using|use|VBG|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ S|s|NN|_
ChIP-Seq|chip-seq|JJ|_
ChIP-seq|chip-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
cra-8myc|cra-8myc|NN|_ tagged|tag|VBD|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP
cra-8myc|cra-8myc|NN|_ tagged|tag|VBD|_ strain|strain|NN|_ _|_|NN|_ fructose|fructose|NN|_
cra-8myc|cra-8myc|NN|_ tagged|tag|VBD|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP
Cra|Cra|NNP|TF acetate|acetate|NN|SUPP 1|1|CD|_
Cra|Cra|NNP|TF acetate|acetate|NN|SUPP 2|2|CD|_
Cra|Cra|NNP|TF fructose|fructose|NN|_ 1|1|CD|_
Cra|Cra|NNP|TF fructose|fructose|NN|_ 2|2|CD|_
Cra|cra|NN|TF glucose|glucose|NN|SUPP 1|1|CD|_
Cra|cra|NN|TF glucose|glucose|NN|SUPP 2|2|CD|_
Crosslinked|crosslink|VBN|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ ul|ul|NN|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 40|40|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ in|in|IN|_ 0.25|0.25|CD|_ ml|ml|NN|_ of|of|IN|_ DMSO|dmso|NN|_ and|and|CC|_ 0.75|0.75|CD|_ ml|ml|NN|_ of|of|IN|_ TDW|tdw|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lyzed|lyze|VBN|_ with|with|IN|_ 1|1|CD|_ ul|ul|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37C|37c|NN|_ on|on|IN|_ a|a|DT|_ rocker|rocker|NN|_ .|.|.|_ 0.55|0.55|CD|_ ml|ml|NN|_ of|of|IN|_ 2X|2x|NN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ sonicated|sonicate|VBN|_ to|to|TO|_ fragmentize|fragmentize|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_ 0.3|0.3|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ buffer|buffer|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 140|140|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ make|make|VB|_ the|the|DT|_ volume|volume|NN|_ up|up|IN|_ to|to|TO|_ 1.4|1.4|CD|_ ml|ml|NN|_ .|.|.|_ Only|only|RB|_ 0.7|0.7|CD|_ ml|ml|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transfered|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ tube|tube|NN|_ ,|,|,|_ and|and|CC|_ 15|15|CD|_ ul|ul|NN|_ of|of|IN|_ Anti-c-myc|anti-c-myc|JJ|_ mouse|mouse|NN|_ antibody|antibody|NN|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 4C|4c|NN|_ to|to|TO|_ make|make|VB|_ Antibody-TF|antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ 50|50|CD|_ ul|ul|NN|_ of|of|IN|_ Dynabeads|Dynabeads|NNP|_ Pan|Pan|NNP|_ mouse|mouse|NN|_ IgG|igg|NN|_ were|be|VBD|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ bead|bead|NN|_ washing|wash|VBG|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ mg|mg|NN|_ BSA|bsa|NN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ PBS|PBS|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ Cell|cell|NN|_ lysate|lysate|NN|_ with|with|IN|_ beads|bead|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ or|or|CC|_ overnight|overnight|JJ|_ at|at|IN|_ 4C|4c|NN|_ to|to|TO|_ make|make|VB|_ Dynabead-antibody-TF|dynabead-antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ The|the|DT|_ beads|bead|NNS|_ were|be|VBD|_ pulled|pull|VBN|_ down|down|RP|_ on|on|IN|_ a|a|DT|_ magnet|magnet|NN|_ stand|stand|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ 2|2|CD|_ times|time|NNS|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ I|i|NN|_ and|and|CC|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 500|500|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ wash|wash|NN|_ buffer|buffer|NN|_ III|iii|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 250|250|CD|_ mM|mm|NN|KWSUPP LiCl|licl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ wash|wash|NN|_ buffer|buffer|NN|_ IV|iv|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ bead-bound|bead-bound|JJ|_ TF-DNA|tf-dna|NN|_ complex|complex|NN|_ was|be|VBD|_ then|then|RB|_ end-repaired|end-repaired|JJ|_ ,|,|,|_ dA-tailed|da-tailed|JJ|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ adapter|adapter|NN|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ nick-repair|nick-repair|JJ|_ reagent|reagent|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ lambda|lambda|NN|_ exonuclease|exonuclease|NN|_ and|and|CC|_ RecJ|recj|NN|_ exonuclease|exonuclease|NN|_ .|.|.|_ Then|then|RB|_ DNA|dna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ away|away|RB|_ from|from|IN|_ Dynabeads|Dynabeads|NNPS|_ by|by|IN|_ incubating|incubate|VBG|_ in|in|IN|_ 200|200|CD|_ ul|ul|NN|_ of|of|IN|_ elution|elution|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65C|65c|CD|_ overnight|overnight|JJ|_ .|.|.|_ Protein|protein|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ treating|treat|VBG|_ 4|4|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ K|k|NN|_ and|and|CC|_ being|be|VBG|_ incubated|incubate|VBN|_ at|at|IN|_ 55C|55c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ by|by|IN|_ Phenol-Chloroform-IAA|phenol-chloroform-iaa|NN|_ extraction|extraction|NN|_ .|.|.|_ Purified|purify|VBN|_ DNA|dna|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ bulid|bulid|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ another|another|DT|_ dA-tailing|da-tailing|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ ligation|ligation|NN|_ ,|,|,|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ overhang|overhang|NN|_ removal|removal|NN|_ stpes|stpe|NNS|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ enrichment|enrichment|NN|_ .|.|.|_
Crosslinked|crosslinked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ ul|ul|NN|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 40|40|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ in|in|IN|_ 0.25|0.25|CD|_ ml|ml|NN|_ of|of|IN|_ DMSO|dmso|NN|_ and|and|CC|_ 0.75|0.75|CD|_ ml|ml|NN|_ of|of|IN|_ TDW|tdw|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lyzed|lyze|VBN|_ with|with|IN|_ 1|1|CD|_ ul|ul|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37oC|37oc|NN|_ on|on|IN|_ a|a|DT|_ rocker|rocker|NN|_ .|.|.|_ 0.55|0.55|CD|_ ml|ml|NN|_ of|of|IN|_ 2X|2x|NN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ sonicated|sonicate|VBN|_ to|to|TO|_ fragmentize|fragmentize|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_ 0.3|0.3|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ buffer|buffer|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 140|140|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ make|make|VB|_ the|the|DT|_ volume|volume|NN|_ up|up|IN|_ to|to|TO|_ 1.4|1.4|CD|_ ml|ml|NN|_ .|.|.|_ Only|only|RB|_ 0.7|0.7|CD|_ ml|ml|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transfered|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ tube|tube|NN|_ ,|,|,|_ and|and|CC|_ 10|10|CD|_ ul|ul|NN|_ of|of|IN|_ Anti-rpoB|anti-rpob|JJ|_ mouse|mouse|NN|_ antibody|antibody|NN|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 4|4|CD|_ oC|oc|NN|_ to|to|TO|_ make|make|VB|_ Antibody-TF|antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ 50|50|CD|_ ul|ul|NN|_ of|of|IN|_ Dynabeads|Dynabeads|NNP|_ Pan|Pan|NNP|_ mouse|mouse|NN|_ IgG|igg|NN|_ were|be|VBD|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ bead|bead|NN|_ washing|wash|VBG|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ mg|mg|NN|_ BSA|bsa|NN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ PBS|PBS|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ Cell|cell|NN|_ lysate|lysate|NN|_ with|with|IN|_ beads|bead|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ or|or|CC|_ overnight|overnight|JJ|_ at|at|IN|_ 4oC|4oc|NN|_ to|to|TO|_ make|make|VB|_ Dynabead-antibody-TF|dynabead-antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ The|the|DT|_ beads|bead|NNS|_ were|be|VBD|_ pulled|pull|VBN|_ down|down|RP|_ on|on|IN|_ a|a|DT|_ magnet|magnet|NN|_ stand|stand|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ 2|2|CD|_ times|time|NNS|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ I|i|NN|_ and|and|CC|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 500|500|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ wash|wash|NN|_ buffer|buffer|NN|_ III|iii|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 250|250|CD|_ mM|mm|NN|KWSUPP LiCl|licl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ wash|wash|NN|_ buffer|buffer|NN|_ IV|iv|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ bead-bound|bead-bound|JJ|_ TF-DNA|tf-dna|NN|_ complex|complex|NN|_ was|be|VBD|_ then|then|RB|_ end-repaired|end-repaired|JJ|_ ,|,|,|_ dA-tailed|da-tailed|JJ|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ adapter|adapter|NN|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ nick-repair|nick-repair|JJ|_ reagent|reagent|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ lambda|lambda|NN|_ exonuclease|exonuclease|NN|_ and|and|CC|_ RecJ|recj|NN|_ exonuclease|exonuclease|NN|_ .|.|.|_ Then|then|RB|_ DNA|dna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ away|away|RB|_ from|from|IN|_ Dynabeads|Dynabeads|NNPS|_ by|by|IN|_ incubating|incubate|VBG|_ in|in|IN|_ 200|200|CD|_ ul|ul|NN|_ of|of|IN|_ elution|elution|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65oC|65oc|NN|_ overnight|overnight|JJ|_ .|.|.|_ Protein|protein|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ treating|treat|VBG|_ 4|4|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ K|k|NN|_ and|and|CC|_ being|be|VBG|_ incubated|incubate|VBN|_ at|at|IN|_ 55|55|CD|_ oC|oc|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ by|by|IN|_ Phenol-Chloroform-IAA|phenol-chloroform-iaa|NN|_ extraction|extraction|NN|_ .|.|.|_ Purified|purify|VBN|_ DNA|dna|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ bulid|bulid|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ another|another|DT|_ dA-tailing|da-tailing|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ ligation|ligation|NN|_ ,|,|,|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ overhang|overhang|NN|_ removal|removal|NN|_ stpes|stpe|NNS|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ enrichment|enrichment|NN|_ .|.|.|_
cultured|culture|VBN|_ in|in|IN|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ acetate|acetate|NN|SUPP
cultured|culture|VBN|_ in|in|IN|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ fructose|fructose|NN|_
cultured|culture|VBN|_ in|in|IN|_ :|:|:|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ crosslinked|crosslink|VBN|_ in|in|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ 25|25|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ on|on|IN|_ a|a|DT|_ rocker|rocker|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ each|each|DT|_ time|time|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ cra-8myc|cra-8myc|NN|_ tagged|tag|VBD|_ strains|strain|NNS|_ was|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ each|each|DT|_ peak|peak|NN|_ detected|detect|VBN|_ with|with|IN|_ MACE|MACE|NNP|_ ,|,|,|_ binding|bind|VBG|_ intensity|intensity|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ averaging|average|VBG|_ read|read|VBN|_ counts|count|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ dividing|divide|VBG|_ by|by|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
genotype|genotype|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-cra|delta-cra|NN|_ Knock-out|knock-out|JJ|_ strain|strain|NN|_
genotype|genotype|NN|_ :|:|:|_ delta-crp|delta-crp|JJ|_ Knock-out|knock-out|JJ|_ strain|strain|NN|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_
MACE|mace|VBP|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
Read|read|VBP|_ count|count|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ from|from|IN|_ sequence|sequence|NN|_ alignment|alignment|NN|_ ,|,|,|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ strongest|strongest|JJS|_ intensity|intensity|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
RpoB|rpob|NN|_ ∆|∆|CD|_ cra|cra|NN|GEN 1|1|CD|_
RpoB|rpob|NN|_ ∆|∆|CD|_ cra|cra|NN|GEN 2|2|CD|_
RpoB|rpob|NN|_ ∆|∆|CD|_ crp|crp|NN|GEN 1|1|CD|_
RpoB|rpob|NN|_ ∆|∆|CD|_ crp|crp|NN|GEN 2|2|CD|_
RpoB|rpob|NN|_ WT|wt|NN|_ 1|1|CD|_
RpoB|rpob|NN|_ WT|wt|NN|_ 2|2|CD|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ in|in|IN|_ gff|gff|NN|_ format|format|NN|_ which|which|WDT|_ has|have|VBZ|_ 8|8|CD|_ columns|column|NNS|_ :|:|:|_ sequence|sequence|NN|_ id|id|NN|_ ,|,|,|_ source|source|NN|_ -LRB-|-lrb-|-LRB-|_ empty|empty|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ feature|feature|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ acetate|acetate|NN|SUPP
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ fructose|fructose|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glucose|glucose|NN|SUPP
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ and|and|CC|_ Δcra|Δcra|NNP|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ fructose|fructose|NN|_ and|and|CC|_ acetate|acetate|NN|SUPP .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
genotype|genotype|NN|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WT|WT|NNP|_ _|_|NNP|_ acetate|acetate|NN|SUPP
WT|WT|NNP|_ acetate|acetate|NN|SUPP 1|1|CD|_
WT|wt|JJ|_ acetate|acetate|NN|SUPP 2|2|CD|_
WT|wt|JJ|_ _|_|NN|_ fructose|fructose|NN|_
WT|wt|JJ|_ fructose|fructose|NN|_ 1|1|CD|_
WT|wt|JJ|_ fructose|fructose|NN|_ 2|2|CD|_
WT|wt|JJ|_ _|_|NN|_ glucose|glucose|NN|SUPP
WT|wt|JJ|_ glucose|glucose|NN|SUPP 1|1|CD|_
WT|wt|JJ|_ glucose|glucose|NN|SUPP 2|2|CD|_
Δcra|δcra|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP
Δcra|δcra|NN|_ acetate|acetate|NN|SUPP 1|1|CD|_
Δcra|δcra|NN|_ acetate|acetate|NN|SUPP 2|2|CD|_
Δcra|δcra|NN|_ _|_|NN|_ fructose|fructose|NN|_
Δcra|δcra|NN|_ fructose|fructose|NN|_ 1|1|CD|_
Δcra|δcra|NN|_ fructose|fructose|NN|_ 2|2|CD|_
Δcra|δcra|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP
Δcra|δcra|NN|_ glucose|glucose|NN|SUPP 1|1|CD|_
Δcra|δcra|NN|_ glucose|glucose|NN|SUPP 2|2|CD|_
A|a|DT|_ total|total|NN|_ of|of|IN|_ six|six|CD|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ .|.|.|_ oxyR-8myc|oxyr-8myc|NN|_ ,|,|,|_ soxR-8myc|soxr-8myc|NN|_ ,|,|,|_ and|and|CC|_ soxS-8myc|soxs-8myc|NN|_ tagged|tag|VBD|_ cells|cell|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-myc|anti-myc|JJ|_
chip|chip|NN|_ antibody|antibody|NN|_ cat|cat|NN|_ .|.|.|_ #|#|#|_ :|:|:|_ sc-28207|sc-28207|JJ|_
chip|chip|NN|_ antibody|antibody|NN|_ vendor|vendor|NN|_ :|:|:|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotech|Biotech|NNP|_
ChIP-exo|ChIP-exo|NNP|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ ASM584v2|asm584v2|NN|_ genome|genome|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ using|use|VBG|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ S|s|NN|_
ChIP-Seq|chip-seq|JJ|_
ChIP-seq|chip-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Crosslinked|crosslink|VBN|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ ul|ul|NN|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 40|40|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ in|in|IN|_ 0.25|0.25|CD|_ ml|ml|NN|_ of|of|IN|_ DMSO|dmso|NN|_ and|and|CC|_ 0.75|0.75|CD|_ ml|ml|NN|_ of|of|IN|_ TDW|tdw|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lyzed|lyze|VBN|_ with|with|IN|_ 1|1|CD|_ ul|ul|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37oC|37oc|NN|_ on|on|IN|_ a|a|DT|_ rocker|rocker|NN|_ .|.|.|_ 0.55|0.55|CD|_ ml|ml|NN|_ of|of|IN|_ 2X|2x|NN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ sonicated|sonicate|VBN|_ to|to|TO|_ fragmentize|fragmentize|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_ 0.3|0.3|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ buffer|buffer|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 140|140|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ make|make|VB|_ the|the|DT|_ volume|volume|NN|_ up|up|IN|_ to|to|TO|_ 1.4|1.4|CD|_ ml|ml|NN|_ .|.|.|_ Only|only|RB|_ 0.7|0.7|CD|_ ml|ml|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transfered|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ tube|tube|NN|_ ,|,|,|_ and|and|CC|_ 15|15|CD|_ ul|ul|NN|_ of|of|IN|_ Anti-c-myc|anti-c-myc|JJ|_ mouse|mouse|NN|_ antibody|antibody|NN|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 4|4|CD|_ oC|oc|NN|_ to|to|TO|_ make|make|VB|_ Antibody-TF|antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ 50|50|CD|_ ul|ul|NN|_ of|of|IN|_ Dynabeads|Dynabeads|NNP|_ Pan|Pan|NNP|_ mouse|mouse|NN|_ IgG|igg|NN|_ were|be|VBD|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ bead|bead|NN|_ washing|wash|VBG|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ mg|mg|NN|_ BSA|bsa|NN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ PBS|PBS|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ Cell|cell|NN|_ lysate|lysate|NN|_ with|with|IN|_ beads|bead|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ or|or|CC|_ overnight|overnight|JJ|_ at|at|IN|_ 4oC|4oc|NN|_ to|to|TO|_ make|make|VB|_ Dynabead-antibody-TF|dynabead-antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ The|the|DT|_ beads|bead|NNS|_ were|be|VBD|_ pulled|pull|VBN|_ down|down|RP|_ on|on|IN|_ a|a|DT|_ magnet|magnet|NN|_ stand|stand|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ 2|2|CD|_ times|time|NNS|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ I|i|NN|_ and|and|CC|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 500|500|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ wash|wash|NN|_ buffer|buffer|NN|_ III|iii|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 250|250|CD|_ mM|mm|NN|KWSUPP LiCl|licl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ wash|wash|NN|_ buffer|buffer|NN|_ IV|iv|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ bead-bound|bead-bound|JJ|_ TF-DNA|tf-dna|NN|_ complex|complex|NN|_ was|be|VBD|_ then|then|RB|_ end-repaired|end-repaired|JJ|_ ,|,|,|_ dA-tailed|da-tailed|JJ|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ adapter|adapter|NN|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ nick-repair|nick-repair|JJ|_ reagent|reagent|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ lambda|lambda|NN|_ exonuclease|exonuclease|NN|_ and|and|CC|_ RecJ|recj|NN|_ exonuclease|exonuclease|NN|_ .|.|.|_ Then|then|RB|_ DNA|dna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ away|away|RB|_ from|from|IN|_ Dynabeads|Dynabeads|NNPS|_ by|by|IN|_ incubating|incubate|VBG|_ in|in|IN|_ 200|200|CD|_ ul|ul|NN|_ of|of|IN|_ elution|elution|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65oC|65oc|NN|_ overnight|overnight|JJ|_ .|.|.|_ Protein|protein|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ treating|treat|VBG|_ 4|4|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ K|k|NN|_ and|and|CC|_ being|be|VBG|_ incubated|incubate|VBN|_ at|at|IN|_ 55|55|CD|_ oC|oc|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ by|by|IN|_ Phenol-Chloroform-IAA|phenol-chloroform-iaa|NN|_ extraction|extraction|NN|_ .|.|.|_ Purified|purify|VBN|_ DNA|dna|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ bulid|bulid|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ another|another|DT|_ dA-tailing|da-tailing|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ ligation|ligation|NN|_ ,|,|,|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ overhang|overhang|NN|_ removal|removal|NN|_ stpes|stpe|NNS|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ enrichment|enrichment|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ crosslinked|crosslink|VBN|_ in|in|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ 25|25|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ on|on|IN|_ a|a|DT|_ rocker|rocker|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ each|each|DT|_ time|time|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ each|each|DT|_ peak|peak|NN|_ detected|detect|VBN|_ with|with|IN|_ MACE|MACE|NNP|_ ,|,|,|_ binding|bind|VBG|_ intensity|intensity|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ averaging|average|VBG|_ read|read|VBN|_ counts|count|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ dividing|divide|VBG|_ by|by|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
genotype|genotype|NN|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ ChIP-seq|ChIP-seq|NNP|_ -LRB-|-lrb-|-LRB-|_ ChIP-exo|ChIP-exo|NNP|_ -RRB-|-rrb-|-RRB-|_
MACE|MACE|NNP|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
oxyR-8myc-tagged|oxyr-8myc-tagged|JJ|_ _|_|NN|_ PQ|pq|NN|_ treated|treat|VBN|_
OxyR|oxyr|NN|TF PQ|pq|NN|_ 1|1|CD|_
OxyR|oxyr|NN|TF PQ|pq|NN|_ 2|2|CD|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ from|from|IN|_ sequence|sequence|NN|_ alignment|alignment|NN|_ ,|,|,|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ strongest|strongest|JJS|_ intensity|intensity|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
soxR-8myc-tagged|soxr-8myc-tagged|JJ|_ _|_|NN|_ PQ|pq|NN|_ treated|treat|VBN|_
SoxR|soxr|NN|TF PQ|pq|NN|_ 1|1|CD|_
SoxR|soxr|NN|TF PQ|pq|NN|_ 2|2|CD|_
soxS-8myc-tagged|soxs-8myc-tagged|JJ|_ _|_|NN|_ PQ|pq|NN|_ treated|treat|VBN|_
SoxS|soxs|NN|TF PQ|pq|NN|_ 1|1|CD|_
SoxS|soxs|NN|TF PQ|pq|NN|_ 2|2|CD|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ in|in|IN|_ gff|gff|NN|_ format|format|NN|_ which|which|WDT|_ has|have|VBZ|_ 8|8|CD|_ columns|column|NNS|_ :|:|:|_ sequence|sequence|NN|_ id|id|NN|_ ,|,|,|_ source|source|NN|_ -LRB-|-lrb-|-LRB-|_ empty|empty|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ feature|feature|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ ΔoxyR|δoxyr|NN|_ ,|,|,|_ ΔsoxR|δsoxr|NN|_ ,|,|,|_ and|and|CC|_ ΔsoxS|δsoxs|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
genotype|genotype|NN|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 250|250|CD|_ uM|um|NN|_ of|of|IN|_ paraquat|paraquat|NN|SUPP at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_
WT|WT|NNP|_ PQ|PQ|NNP|_
WT|WT|NNP|_ PQ|PQ|NNP|_ 1|1|CD|_
WT|WT|NNP|_ PQ|PQ|NNP|_ 2|2|CD|_
ΔoxyR|δoxyr|NN|_ PQ|pq|NN|_
ΔoxyR|δoxyr|NN|_ PQ|pq|NN|_ 1|1|CD|_
ΔoxyR|δoxyr|NN|_ PQ|pq|NN|_ 2|2|CD|_
ΔsoxR|δsoxr|NN|_ PQ|pq|NN|_
ΔsoxR|δsoxr|NN|_ PQ|pq|NN|_ 1|1|CD|_
ΔsoxR|δsoxr|NN|_ PQ|pq|NN|_ 2|2|CD|_
ΔsoxS|δsoxs|NN|_ PQ|pq|NN|_
ΔsoxS|δsoxs|VBZ|_ PQ|pq|NN|_ 1|1|CD|_
ΔsoxS|δsoxs|NN|_ PQ|pq|NN|_ 2|2|CD|_
16,000|16,000|CD|_ g|g|NN|_ for|for|IN|_ 40|40|CD|_ s|s|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ ,|,|,|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_
1.8|1.8|CD|_ ml|ml|NN|_ -LRB-|-lrb-|-LRB-|_ ca.|ca.|FW|_ 3E|3e|FW|_ +9|+9|NN|_ cells|cell|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ pipetted|pipet|VBN|_ into|into|IN|_ 2.0|2.0|CD|_ ml|ml|NN|_ tubes|tube|NNS|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_
68908|68908|CD|_
68909|68909|CD|_
68910|68910|CD|_
68911|68911|CD|_
68912|68912|CD|_
68913|68913|CD|_
68915|68915|CD|_
68916|68916|CD|_
68917|68917|CD|_
68919|68919|CD|_
68920|68920|CD|_
68921|68921|CD|_
68922|68922|CD|_
68923|68923|CD|_
68924|68924|CD|_
68925|68925|CD|_
68926|68926|CD|_
68927|68927|CD|_
68928|68928|CD|_
68929|68929|CD|_
68930|68930|CD|_
68931|68931|CD|_
68932|68932|CD|_
68933|68933|CD|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ on|on|IN|_ days|day|NNS|_ 1|1|CD|_ and|and|CC|_ 3|3|CD|_ of|of|IN|_ glucose|glucose|NN|SUPP starvation|starvation|NN|_ ,|,|,|_ with|with|IN|_ samples|sample|NNS|_ taken|take|VBN|_ from|from|IN|_ the|the|DT|_
chilled|chill|VBN|_ in|in|IN|_ a|a|DT|_ dry|dry|JJ|_ ice|ice|NN|_
D1-ae10|d1-ae10|NN|_
D1-ae11|d1-ae11|NN|_
D1-ae12|d1-ae12|NN|_
D1|d1|NN|_ +|+|CC|_ ae7|ae7|NN|_
D1|d1|NN|_ +|+|CC|_ ae8|ae8|NN|_
D1|d1|NN|_ +|+|CC|_ ae9|ae9|NN|_
D1|d1|NN|_ +|+|CC|_ AN|a|DT|_
D1|d1|NN|_ +|+|CC|_ AN2|an2|NN|_
D1|d1|NN|_ +|+|CC|_ AN3|an3|NN|_
D1-AN4|d1-an4|NN|_
D1-AN5|d1-an5|NN|_
D1-AN6|d1-an6|NN|_
D3|d3|NN|_ +|+|CC|_ ae19|ae19|NN|_
D3|d3|NN|_ +|+|CC|_ ae20|ae20|NN|_
D3|d3|NN|_ +|+|CC|_ ae21|ae21|NN|_
D3-ae22|d3-ae22|NN|_
D3-ae23|d3-ae23|NN|_
D3-ae24|d3-ae24|NN|_
D3|d3|NN|_ +|+|CC|_ AN13|an13|NN|_
D3|d3|NN|_ +|+|CC|_ AN14|an14|NN|_
D3|d3|NN|_ +|+|CC|_ AN15|an15|NN|_
D3-AN16|d3-an16|NN|_
D3-AN17|d3-an17|NN|_
D3-AN18|d3-an18|NN|_
day|day|NN|_ :|:|:|_ .|.|.|_ strain|strain|NN|_ :|:|:|_ .|.|.|_ oxygen|oxygen|NN|_ :|:|:|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Feature|feature|NN|_ pixel|pixel|NN|_ median|median|NN|_ minus|minus|CC|_ background|background|NN|_ pixel|pixel|NN|_ mean|mean|NN|_ ;|;|:|_
further|further|RB|_ processing|process|VBG|_
isolated|isolate|VBN|_ by|by|IN|_ chloroform|chloroform|NN|_ extraction|extraction|NN|_ and|and|CC|_ precipitation|precipitation|NN|_ by|by|IN|_ isopropanol|isopropanol|NN|_ .|.|.|_ Precipitated|precipitate|VBN|_ RNA|rna|NN|_
normalization|normalization|NN|_ subtracting|subtract|VBG|_ array-median|array-median|JJ|_ log2|log2|NN|_ ratio|ratio|NN|_ .|.|.|_
pool|pool|NN|_ of|of|IN|_ aliquots|aliquot|NNS|_ from|from|IN|_ all|all|DT|_ samples|sample|NNS|_
ratio|ratio|NN|_ set|set|VBN|_ to|to|TO|_ missing|miss|VBG|_ where|where|WRB|_ SNR|snr|NN|_ -LRB-|-lrb-|-LRB-|_ feature|feature|NN|_ mean|mean|NN|_ -|-|:|_ backround|backround|NN|_ mean|mean|VB|_
Reference|Reference|NNP|_ Pool|Pool|NNP|_
re-suspended|re-suspended|JJ|_ in|in|IN|_ 200|200|CD|_ ul|ul|NN|_ Trizol|trizol|NN|_ and|and|CC|_ combined|combine|VBN|_ for|for|IN|_ a|a|DT|_ total|total|JJ|_ volume|volume|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ ,|,|,|_ then|then|RB|_ promptly|promptly|RB|_
same|same|JJ|_ cultures|culture|NNS|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ viability|viability|NN|_ assay|assay|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ experimental|experimental|JJ|_ condition|condition|NN|_ ,|,|,|_ 15|15|CD|_ aliquots|aliquot|NNS|_ of|of|IN|_
triplicate|triplicate|NN|_ samples|sample|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ combining|combine|VBG|_ cells|cell|NNS|_ from|from|IN|_ 5|5|CD|_ tubes|tube|NNS|_ each|each|DT|_ .|.|.|_ Each|each|DT|_ pellet|pellet|NN|_ was|be|VBD|_
was|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 70|70|CD|_ percent|percent|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ resuspended|resuspend|VBN|_ in|in|IN|_ 30|30|CD|_ ul|ul|NN|_ water|water|NN|_ ,|,|,|_ and|and|CC|_ held|hold|VBN|_ at|at|IN|_ 4|4|CD|_ deg|deg|NN|_ .|.|.|_ C|c|NN|_ for|for|IN|_
were|be|VBD|_ immediately|immediately|RB|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ deg|deg|NN|_ .|.|.|_ C.|c.|NN|_ For|for|IN|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-myc|anti-myc|JJ|_ -LRB-|-lrb-|-LRB-|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotech|Biotech|NNP|_ ,|,|,|_ sc-28207|sc-28207|NN|_ -RRB-|-rrb-|-RRB-|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RpoS|anti-rpos|NN|_ -LRB-|-lrb-|-LRB-|_ neoclone|neoclone|NN|_ ,|,|,|_ WP009|wp009|NN|_ -RRB-|-rrb-|-RRB-|_
ChIP-exo|ChIP-exo|NNP|_ GadE|GadE|NNP|TF pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
ChIP-exo|ChIP-exo|NNP|_ GadE|GadE|NNP|TF pH5|ph5|NN|_ .5|.5|CD|_ 2|2|CD|_
ChIP-exo|chip-exo|JJ|_ GadW|gadw|NN|TF pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
ChIP-exo|chip-exo|JJ|_ GadW|gadw|NN|TF pH5|ph5|NN|_ .5|.5|CD|_ 2|2|CD|_
ChIP-exo|chip-exo|JJ|_ GadX|gadx|NN|TF pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
ChIP-exo|chip-exo|JJ|_ GadX|gadx|NN|TF pH5|ph5|NN|_ .5|.5|CD|_ 2|2|CD|_
ChIP-exo|chip-exo|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ ASM584v2|asm584v2|NN|_ genome|genome|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ using|use|VBG|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ S|s|NN|_
ChIP-exo|chip-exo|JJ|_ RpoS|rpos|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
ChIP-exo|chip-exo|JJ|_ RpoS|rpos|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 2|2|CD|_
ChIP-Seq|chip-seq|JJ|_
ChIP-seq|chip-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|WT|NNP|_ ,|,|,|_ GadE-8-myc|gade-8-myc|NN|_ ,|,|,|_ GadW-8-myc|gadw-8-myc|NN|_ ,|,|,|_ and|and|CC|_ GadX-8-myc|gadx-8-myc|NN|_ tagged|tag|VBD|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ each|each|DT|_ peak|peak|NN|_ detected|detect|VBN|_ with|with|IN|_ MACE|MACE|NNP|_ ,|,|,|_ binding|bind|VBG|_ intensity|intensity|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ averaging|average|VBG|_ read|read|VBN|_ counts|count|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ dividing|divide|VBG|_ by|by|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
genotype|genotype|NN|_ :|:|:|_ gadE-8myc|gade-8myc|NN|_
genotype|genotype|NN|_ :|:|:|_ gadW-8myc|gadw-8myc|NN|_
genotype|genotype|NN|_ :|:|:|_ gadX-8myc|gadx-8myc|NN|_
genotype|genotype|NN|_ :|:|:|_ WT|WT|NNP|_
Immunoprecipitated|immunoprecipitate|VBD|_ DNA|dna|NN|_
MACE|mace|NN|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
Read|read|VBP|_ count|count|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ from|from|IN|_ sequence|sequence|NN|_ alignment|alignment|NN|_ ,|,|,|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ strongest|strongest|JJS|_ intensity|intensity|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ in|in|IN|_ gff|gff|NN|_ format|format|NN|_ which|which|WDT|_ has|have|VBZ|_ 8|8|CD|_ columns|column|NNS|_ :|:|:|_ sequence|sequence|NN|_ id|id|NN|_ ,|,|,|_ source|source|NN|_ -LRB-|-lrb-|-LRB-|_ empty|empty|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ feature|feature|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ ,|,|,|_ gadE|gade|NN|GEN ,|,|,|_ gadW|gadw|NN|GEN and|and|CC|_ gadX|gadx|NN|GEN mutant|mutant|JJ|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP at|at|IN|_ pH|ph|NN|_ 5.5|5.5|CD|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
genotype|genotype|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WT|WT|NNP|_ pH5|ph5|NN|_ .5|.5|CD|_
WT|wt|JJ|_ pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
WT|wt|JJ|_ pH5|ph5|NN|_ .5|.5|NN|_ 2|2|CD|_
ΔgadE|δgade|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
ΔgadE|δgade|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
ΔgadE|δgade|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 2|2|CD|_
ΔgadW|δgadw|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
ΔgadW|δgadw|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
ΔgadW|δgadw|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 2|2|CD|_
ΔgadX|δgadx|NN|_ pH5|ph5|NN|_ .5|.5|CD|_
ΔgadX|δgadx|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 1|1|CD|_
ΔgadX|δgadx|NN|_ pH5|ph5|NN|_ .5|.5|CD|_ 2|2|CD|_
Background|background|NN|_ subtractions|subtraction|NNS|_ and|and|CC|_ normalization|normalization|NN|_ of|of|IN|_ extracted|extract|VBN|_ data|datum|NNS|_ were|be|VBD|_ performed|perform|VBN|_ through|through|IN|_ R|r|NN|_ using|use|VBG|_ the|the|DT|_ Bioconductor|Bioconductor|NNP|_ package|package|NN|_ as|as|IN|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Yang|Yang|NNP|_ ,|,|,|_ Y.H.|Y.H.|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Normalization|normalization|NN|_ for|for|IN|_ cDNA|cdna|NN|_ microarray|microarray|NN|_ data|datum|NNS|_ :|:|:|_ a|a|DT|_ robust|robust|JJ|_ composite|composite|JJ|_ method|method|NN|_ addressing|address|VBG|_ single|single|JJ|_ and|and|CC|_ multiple|multiple|JJ|_ slide|slide|NN|_ systematic|systematic|JJ|_ variation|variation|NN|_ ,|,|,|_ Nucleic|nucleic|JJ|_ Acid|acid|NN|_ Res|Res|NNP|_ 30|30|CD|_ ,|,|,|_ e15|e15|NN|_ ,|,|,|_ 2002|2002|CD|_ ;|;|:|_ Smyth|Smyth|NNP|_ ,|,|,|_ G.K.|G.K.|NNP|_ in|in|IN|_ Bioinformatics|Bioinformatics|NNP|_ and|and|CC|_ Computational|Computational|NNP|_ Biology|Biology|NNP|_ Solutions|Solutions|NNPS|_ using|use|VBG|_ R|r|NN|_ and|and|CC|_ Bioconductor|bioconductor|NN|_ .|.|.|_ 397-420|397-420|CD|_ ,|,|,|_ Springer|Springer|NNP|_ ,|,|,|_ New|New|NNP|_ York|York|NNP|_ ,|,|,|_ 2005|2005|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cultures|culture|NNS|_ of|of|IN|_ both|both|DT|_ strains|strain|NNS|_ were|be|VBD|_ started|start|VBN|_ with|with|IN|_ a|a|DT|_ 2|2|CD|_ %|%|NN|_ overnight|overnight|JJ|_ inoculum|inoculum|NN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED containing|contain|VBG|_ 35ug|35ug|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_ growth|growth|NN|_ phase|phase|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ transition|transition|NN|_ growth|growth|NN|_ phase|phase|NN|_
pControl|pcontrol|NN|_ _|_|CD|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ _|_|NN|_ 1|1|CD|_ ml|ml|NN|_ cell|cell|NN|_ pellet|pellet|NN|_
pControl|pcontrol|NN|_ _|_|CD|_ stationary|stationary|JJ|_ growth|growth|NN|_ phase|phase|NN|_ _|_|NN|_ 1|1|CD|_ ml|ml|NN|_ cell|cell|NN|_ pellet|pellet|NN|_
pControl|pcontrol|NN|_ _|_|CD|_ transition|transition|NN|_ growth|growth|NN|_ phase|phase|NN|_ _|_|NN|_ 1|1|CD|_ ml|ml|NN|_ cell|cell|NN|_ pellet|pellet|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pControl|pcontrol|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pLPLσ|plplσ|NN|_
pLPLσ|plplσ|NN|_ _|_|CD|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ _|_|NN|_ 1|1|CD|_ ml|ml|NN|_ cell|cell|NN|_ pellet|pellet|NN|_
pLPLσ|plplσ|NN|_ _|_|CD|_ stationary|stationary|JJ|_ growth|growth|NN|_ phase|phase|NN|_ _|_|NN|_ 1|1|CD|_ ml|ml|NN|_ cell|cell|NN|_ pellet|pellet|NN|_
pLPLσ|plplσ|NN|_ _|_|CD|_ transition|transition|NN|_ growth|growth|NN|_ phase|phase|NN|_ _|_|NN|_ 1|1|CD|_ ml|ml|NN|_ cell|cell|NN|_ pellet|pellet|NN|_
Replicate|replicate|VB|_ 1|1|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ 4.5|4.5|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_
Replicate|replicate|VB|_ 1|1|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ 4.5|4.5|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dye|dye|VB|_ swap|swap|NN|_
Replicate|replicate|VB|_ 1|1|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ 6h|6h|NN|_ -RRB-|-rrb-|-RRB-|_
Replicate|replicate|VB|_ 1|1|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ 6h|6h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dye|dye|VB|_ swap|swap|NN|_
Replicate|replicate|VB|_ 1|1|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ 9h|9h|NN|_ -RRB-|-rrb-|-RRB-|_
Replicate|replicate|VB|_ 1|1|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ 9h|9h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dye|dye|VB|_ swap|swap|NN|_
Replicate|replicate|VB|_ 2|2|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ 4.5|4.5|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_
Replicate|replicate|VB|_ 2|2|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ 4.5|4.5|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dye|dye|VB|_ swap|swap|NN|_
Replicate|replicate|VB|_ 2|2|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ 6h|6h|NN|_ -RRB-|-rrb-|-RRB-|_
Replicate|replicate|VB|_ 2|2|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ 6h|6h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dye|dye|VB|_ swap|swap|NN|_
Replicate|replicate|VB|_ 2|2|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ 9h|9h|NN|_ -RRB-|-rrb-|-RRB-|_
Replicate|replicate|VB|_ 2|2|LS|_ -|-|:|_ timepoint|timepoint|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ 9h|9h|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ dye|dye|VB|_ swap|swap|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ optical|optical|JJ|_ density|density|NN|_ was|be|VBD|_ measured|measure|VBN|_ every|every|DT|_ 30|30|CD|_ min|min|NN|_ and|and|CC|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ heterologous|heterologous|JJ|_ sigma|sigma|NN|_ factor|factor|NN|_ was|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_ at|at|IN|_ an|a|DT|_ optical|optical|JJ|_ density|density|NN|_ of|of|IN|_ 0.1|0.1|CD|_ .|.|.|_ Samples|sample|NNS|_ for|for|IN|_ RNA|rna|NN|_ extractions|extraction|NNS|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ taken|take|VBN|_ after|after|IN|_ 4.5|4.5|CD|_ ,|,|,|_ 6|6|CD|_ and|and|CC|_ 9|9|CD|_ hours|hour|NNS|_ after|after|IN|_ induction|induction|NN|_ .|.|.|_ Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ .|.|.|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4.5|4.5|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 9|9|CD|_ hrs|hr|NNS|_ after|after|IN|_ induction|induction|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufactures|manufacture|VBZ|_ recommendations|recommendation|NNS|_ .|.|.|_
10-HT874-PS-60min1|10-ht874-ps-60min1|NN|_
11-HT874-PS-60min2|11-ht874-ps-60min2|NN|_
12-HT874-PS-60min3|12-ht874-ps-60min3|NN|_
1-HT873-PA1|1-ht873-pa1|NN|_
1-HT873-PA1|1-ht873-pa1|NN|_ -|-|:|_
2-HT873-PA2|2-ht873-pa2|NN|_
2-HT873-PA2|2-ht873-pa2|NN|_ -|-|:|_
3-HT873-PA3|3-ht873-pa3|NN|_
3-HT873-PA3|3-ht873-pa3|NN|_ -|-|:|_
4-HT873-PS-60min1|4-ht873-ps-60min1|NN|_
5-HT873-PS-60min2|5-ht873-ps-60min2|NN|_
6-HT873-PS-60min3|6-ht873-ps-60min3|JJ|_
7-HT874-PA1|7-ht874-pa1|NN|_
7-HT874-PA1|7-ht874-pa1|NN|_ -|-|:|_
873-Con1|873-con1|NN|_ --|--|:|_
873-Con2|873-con2|NN|_ --|--|:|_
873-Con3|873-con3|NN|_ --|--|:|_
873-PA1|873-pa1|NN|_ --|--|:|_
873-PA2|873-pa2|NN|_ --|--|:|_
873-PA3|873-pa3|NN|_ --|--|:|_
875-Con1|875-con1|NN|_ --|--|:|_
875-Con2|875-con2|NN|_ --|--|:|_
875-Con3|875-con3|NN|_ --|--|:|_
875-PA1|875-pa1|NN|_ --|--|:|_
875-PA2|875-pa2|NN|_ --|--|:|_
875-PA3|875-pa3|NN|_ --|--|:|_
8-HT874-PA2|8-ht874-pa2|NN|_
8-HT874-PA2|8-ht874-pa2|NN|_ -|-|:|_
9-HT874-PA3|9-ht874-pa3|NN|_
9-HT874-PA3|9-ht874-pa3|NN|_ -|-|:|_
Data|Data|NNP|_ was|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ RMA|rma|NN|_ using|use|VBG|_ the|the|DT|_ program|program|NN|_ Partek|Partek|NNP|_ 6.6|6.6|CD|_
E.|E.|NNP|_ coli|coli|NN|_ strains|strain|NNS|_ HT874|ht874|NN|_ ,|,|,|_ HT873|ht873|NN|_ ,|,|,|_ HT875|ht875|NN|_ ,|,|,|_ HT873|ht873|NN|_ treated|treat|VBN|_ with|with|IN|_ or|or|CC|_ no|no|DT|_ polyamines|polyamine|NNS|_ by|by|IN|_ Trizol|trizol|NN|_ protocol|protocol|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
HT873-Con1|ht873-con1|NN|_
HT873-Con2|ht873-con2|NN|_
HT873-Con3|ht873-con3|NN|_
HT873-PA1|ht873-pa1|NN|_
HT873-PA2|ht873-pa2|NN|_
HT873-PA3|ht873-pa3|NN|_
HT875-Con1|ht875-con1|NN|_
HT875-Con2|ht875-con2|NN|_
HT875-Con3|ht875-con3|NN|_
HT875-PA1|ht875-pa1|NN|_
HT875-PA2|ht875-pa2|NN|_
HT875-PA3|ht875-pa3|NN|_
RNA|rna|NN|_ were|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ wild|wild|JJ|_ type|type|NN|_ and|and|CC|_ mutants|mutant|NNS|_ .|.|.|_ Trizol|trizol|NN|_ extraction|extraction|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ to|to|TO|_ standard|standard|JJ|_ affymetrix|affymetrix|NN|_ labeling|labeling|NN|_ protocols|protocol|NNS|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ HT873|ht873|NN|_
strain|strain|NN|_ :|:|:|_ HT874|ht874|NN|_
strain|strain|NN|_ :|:|:|_ HT875|ht875|NN|_
treatment|treatment|NN|_ :|:|:|_ Con1|con1|NN|_
treatment|treatment|NN|_ :|:|:|_ Con2|con2|NN|_
treatment|treatment|NN|_ :|:|:|_ Con3|con3|NN|_
treatment|treatment|NN|_ :|:|:|_ PA1|pa1|NN|_
treatment|treatment|NN|_ :|:|:|_ PA2|pa2|NN|_
treatment|treatment|NN|_ :|:|:|_ PA3|pa3|NN|_
treatment|treatment|NN|_ :|:|:|_ PS-60min|ps-60min|JJ|_
50|50|CD|_ ng|ng|NN|_ of|of|IN|_ the|the|DT|_ fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ sequencing|sequencing|NN|_ library|library|NN|_ using|use|VBG|_ TruSeq|TruSeq|NNP|_ ®|®|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Sample|Sample|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
All|All|NNP|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench5|workbench5|NN|_ with|with|IN|_ the|the|DT|_ length|length|NN|_ fraction|fraction|NN|_ of|of|IN|_ 0.9|0.9|CD|_ and|and|CC|_ the|the|DT|_ similarity|similarity|NN|_ of|of|IN|_ 0.99|0.99|CD|_ .|.|.|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.4|1.4|CD|_
cell|cell|NN|_ type|type|NN|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
From|from|IN|_ the|the|DT|_ cells|cell|NNS|_ cultured|culture|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ ,|,|,|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNAsnapTM|rnasnaptm|NN|_ method|method|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ the|the|DT|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ ribo-zeroTM|ribo-zerotm|JJ|_ magnetic|magnetic|JJ|_ kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ in|in|IN|_ accordance|accordance|NN|_ with|with|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instruction|instruction|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ rRNA|rrna|NN|_ removal|removal|NN|_ was|be|VBD|_ confirmed|confirm|VBN|_ using|use|VBG|_ ExperionTM|experiontm|NN|_ system|system|NN|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ 4|4|CD|_ µg|µg|NN|_ of|of|IN|_ the|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ to|to|TO|_ sizes|size|NNS|_ of|of|IN|_ ~|~|NN|_ 300|300|CD|_ bp|bp|NN|_ using|use|VBG|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Grand|Grand|NNP|_ Island|Island|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Glycerol|Glycerol|NNP|_ stocks|stock|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ LB|lb|NN|MED media|media|NNS|MED grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|NN|_ with|with|IN|_ constant|constant|JJ|_ agitation|agitation|NN|_ overnight|overnight|JJ|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ fresh|fresh|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ and|and|CC|_ then|then|RB|_ cultured|culture|VBN|_ at|at|IN|_ 37|37|CD|_ ℃|℃|CD|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ nm|nm|NN|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
No|no|DT|_ treatment|treatment|NN|_
RNA-Seq|rna-seq|NN|_
RNA-seq|rna-seq|NN|_ 37C|37c|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
RNA-seq|rna-seq|NN|_ 37C|37c|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_ is|be|VBZ|_ generated|generate|VBN|_ by|by|IN|_ in-house|in-house|JJ|_ script|script|NN|_
The|the|DT|_ expression|expression|NN|_ levels|level|NNS|_ were|be|VBD|_ based|base|VBN|_ upon|upon|IN|_ the|the|DT|_ RPKM|RPKM|NNP|_ metric|metric|JJ|_ obtained|obtain|VBN|_ from|from|IN|_ strand-specific|strand-specific|JJ|_ manner|manner|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 22|22|CD|_ °C|°c|NN|_ or|or|CC|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ as|as|IN|_ indicated|indicate|VBN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ Lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10mM|10mm|NN|_ tris|tris|NN|_ ,|,|,|_ 20|20|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ ,|,|,|_ 50mM|50mm|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 10mM|10mm|NN|_ EDTA|edta|NN|_ ,|,|,|_ 10|10|CD|_ mg|mg|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-Flag|anti-flag|JJ|_
ChIP-Seq|chip-seq|NN|_
Crosslinking|crosslinking|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ 1|1|CD|_ %|%|NN|_ of|of|IN|_ forlmaldehyde|forlmaldehyde|NN|_
deltamatP|deltamatp|NN|_ 22|22|CD|_ °C|°c|NN|_
E.|E.|NNP|_ coli|coli|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
genotype|genotype|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 22|22|CD|_ °C|°c|NN|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ v1|v1|NN|_ .8|.8|CD|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
MACS|mac|NNS|_ v2|v2|VBP|_ .0.10.20131216|.0.10.20131216|CD|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ peak|peak|JJ|_ calling|call|VBG|_ with|with|IN|_ parameters|parameter|NNS|_ --|--|:|_ llocal|llocal|JJ|_ =|=|JJ|_ 10000|10000|CD|_ -|-|:|_ g|g|NN|_ 4639675|4639675|CD|_ --|--|:|_ bw|bw|NN|_ 300|300|CD|_ -|-|:|_ p|p|NN|_ 0.05|0.05|CD|_ --|--|:|_ slocal|slocal|JJ|_ =|=|JJ|_ 1000|1000|CD|_ --|--|:|_ keep-dup|keep-dup|NN|_ =|=|JJ|_ 20|20|CD|_
MatP|matp|NN|_ 37|37|CD|_ °C|°c|NN|_
MukB|mukb|NN|_ 22|22|CD|_ °C|°c|NN|_
MukB|mukb|NN|_ 37|37|CD|_ °C|°c|NN|_
MukBDA|mukbda|NN|_ 22|22|CD|_ °C|°c|NN|_
MukB|mukb|NN|_ deltamatP|deltamatp|NN|_ 22|22|CD|_ °C|°c|NN|_
MukBEQ|mukbeq|NN|_ 22|22|CD|_ °C|°c|NN|_
MukBEQ|mukbeq|NN|_ deltamatP|deltamatp|NN|_ 22|22|CD|_ °C|°c|NN|_
Reads|read|NNS|_ were|be|VBD|_ adapter|adapter|NN|_ removed|remove|VBN|_ and|and|CC|_ trimmed|trim|VBN|_ to|to|TO|_ 40Bp|40bp|NN|_ using|use|VBG|_ trimmomatic|trimmomatic|JJ|_ 0.32|0.32|CD|_ with|with|IN|_ parameters|parameter|NNS|_ ILLUMINACLIP|ILLUMINACLIP|NNP|_ :|:|:|_
Sequences|sequence|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ v2|v2|NN|_ .2.2|.2.2|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ N|n|NN|_ 0|0|CD|_ --|--|:|_ sensitive|sensitive|JJ|_ --|--|:|_ minins|minin|NNS|_ 130|130|CD|_ --|--|:|_ maxins|maxin|NNS|_ 780|780|CD|_ -|-|:|_ q|q|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ --|--|:|_ no-discordant|no-discordant|JJ|_ --|--|:|_ no-unal|no-unal|JJ|_
Sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|ultra|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ #E7370|#E7370|NNP|_ ,|,|,|_ NEB|NEB|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ samples|sample|NNS|_ 1|1|CD|_ to|to|TO|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ WaferGen|WaferGen|NNP|_ PrepX|PrepX|NNP|_ ILM|ILM|NNP|_ ChiP-Seq|ChiP-Seq|NNP|_ Library|Library|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ #|#|#|_ 400075|400075|CD|_ ,|,|,|_ WaferGen|WaferGen|NNP|_ -RRB-|-rrb-|-RRB-|_ on|on|IN|_ the|the|DT|_ Apollo|Apollo|NNP|_ 324|324|CD|_ System|System|NNP|_ for|for|IN|_ samples|sample|NNS|_ 4|4|CD|_ to|to|TO|_ 10|10|CD|_ -LRB-|-lrb-|-LRB-|_ 22|22|CD|_ C|c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ MACS|macs|NN|_ v2|v2|NN|_ .0.10.20131216|.0.10.20131216|CD|_ peaks|peak|VBZ|_ file|file|NN|_
WT|wt|NN|_ 22|22|CD|_ °C|°c|NN|_
WT|wt|NN|_ 37|37|CD|_ °C|°c|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ strain|strain|NN|_ REL606|rel606|NN|_ was|be|VBD|_ revived|revive|VBN|_ from|from|IN|_ a|a|DT|_ freezer|freezer|NN|_ stock|stock|NN|_ via|via|IN|_ overnight|overnight|JJ|_ growth|growth|NN|_ in|in|IN|_ 10|10|CD|_ ml|ml|NN|_ Davis|Davis|NNP|_ Minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ limiting|limit|VBG|_ glucose|glucose|NN|SUPP at|at|IN|_ 0.5|0.5|CD|_ g|g|NN|_
Exact|exact|JJ|_ details|detail|NNS|_ for|for|IN|_ the|the|DT|_ full|full|JJ|_ computational|computational|JJ|_ pipeline|pipeline|NN|_ are|be|VBP|_ available|available|JJ|_ at|at|IN|_ https|http|NNS|_ :|:|:|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_ plus|plus|CC|_ small|small|JJ|_ RNAs|rna|NNS|_ as|as|IN|_ annotated|annotated|JJ|_ in|in|IN|_ Rfam|Rfam|NNP|_ 11.0|11.0|CD|_ database|database|NN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 168|168|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 168|168|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 168|168|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 168|168|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 24|24|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 24|24|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 24|24|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 24|24|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 336|336|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 336|336|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 336|336|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 336|336|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 3|3|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 3|3|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 3|3|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 3|3|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 48|48|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 48|48|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 48|48|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 48|48|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 4|4|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 4|4|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 4|4|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 4|4|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 5|5|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 5|5|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 5|5|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 5|5|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 6|6|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 6|6|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 6|6|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 6|6|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 8|8|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 1|1|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 8|8|CD|_ hour|hour|NN|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VB|_ 2|2|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 8|8|CD|_ hourt|hourt|NN|_ ime|ime|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_
Glucose|glucose|NN|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ 8|8|CD|_ hourt|hourt|NN|_ ime|ime|NN|_ point|point|NN|_ ,|,|,|_ biological|biological|JJ|_ replicate|replicate|VBP|_ 3|3|CD|_ ,|,|,|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
Mapped|map|VBD|_ R1|r1|NN|_ reads|read|VBZ|_ in|in|IN|_ single-end|single-end|JJ|_ mode|mode|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ 2.1.0|2.1.0|CD|_ with|with|IN|_ the|the|DT|_ --|--|:|_ k|k|NN|_ 1|1|CD|_ option|option|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ rRNA-depleted|rrna-depleted|JJ|_ total|total|JJ|_ RNA|rna|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 168|168|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 24|24|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 336|336|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 3|3|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 48|48|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 4|4|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|SYM|_ 5|5|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 6|6|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_
REL606|rel606|NN|_ _|_|CD|_ glucose-limited|glucose-limited|JJ|_ minimal|minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ 8|8|CD|_ hr|hr|NN|_ _|_|NN|_ rRNA|rrna|NN|_ not|not|RB|_ depleted|deplete|VBN|_
RNA-Seq|rna-seq|NN|_
RNAsnap|rnasnap|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Magnesium|magnesium|NN|_ RNA|rna|NN|_ Fragmentation|fragmentation|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ RNA|rna|NN|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ using|use|VBG|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ and|and|CC|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ Small|small|JJ|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ Multiplex|Multiplex|NNP|_ Compatible|Compatible|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ fragments|fragment|NNS|_ greater|greater|JJR|_ than|than|IN|_ 100|100|CD|_ bp|bp|NN|_ were|be|VBD|_ excised|excise|VBN|_ from|from|IN|_ a|a|DT|_ 4|4|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ after|after|IN|_ library|library|NN|_ preparation|preparation|NN|_ and|and|CC|_ recovered|recover|VBD|_ using|use|VBG|_ the|the|DT|_ Zymoclean|Zymoclean|NNP|_ Gel|gel|NN|_ DNA|dna|NN|_ Recovery|recovery|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ REL606|rel606|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Read|Read|NNP|_ counts|count|VBZ|_ aligned|align|VBN|_ to|to|TO|_ genes|gene|NNS|_ and|and|CC|_ noncoding|noncoding|JJ|_ Rfam|rfam|NN|_ features|feature|NNS|_ in|in|IN|_ CSV|CSV|NNP|_ format|format|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ R1|r1|NN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ 0.6.0|0.6.0|CD|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 168|168|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 24|24|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 336|336|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 3|3|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 48|48|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 5|5|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ hours|hour|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ hours|hour|NNS|_
Trimmed|trim|VBD|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ from|from|IN|_ reads|read|VBZ|_ using|use|VBG|_ Flexbar|Flexbar|NNP|_ 2.31|2.31|CD|_
After|after|IN|_ normalization|normalization|NN|_ ,|,|,|_ the|the|DT|_ expression|expression|NN|_ of|of|IN|_ a|a|DT|_ gene|gene|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ a|a|DT|_ RMA-summarization|rma-summarization|NN|_ procedure|procedure|NN|_ within|within|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_
agno3|agno3|NN|_ concentration|concentration|NN|_ in|in|IN|_ µm|µm|NN|_ :|:|:|_ 0|0|CD|_
agno3|agno3|NN|_ concentration|concentration|NN|_ in|in|IN|_ µm|µm|NN|_ :|:|:|_ 5|5|CD|_
agno3|agno3|NN|_ concentration|concentration|NN|_ in|in|IN|_ µm|µm|NN|_ :|:|:|_ 6.5|6.5|CD|_
agno3|agno3|NN|_ concentration|concentration|NN|_ in|in|IN|_ µm|µm|NN|_ :|:|:|_ 8.5|8.5|CD|_
At|at|IN|_ 3|3|CD|_ h|h|NN|_ of|of|IN|_ culture|culture|NN|_ ,|,|,|_ 60|60|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ at|at|IN|_ OD595|od595|CD|_ nm|nm|NN|_ =|=|JJ|_ 0.73|0.73|CD|_ ±|±|SYM|_ 0.07|0.07|CD|_ ,|,|,|_ 0.63|0.63|CD|_ ±|±|SYM|_ 0.02|0.02|CD|_ ,|,|,|_ 0.12|0.12|CD|_ ±|±|SYM|_ 0.01|0.01|CD|_ and|and|CC|_ 0.11|0.11|CD|_ ±|±|NN|_ 0.02|0.02|CD|_ for|for|IN|_ cultures|culture|NNS|_ subjected|subject|VBN|_ to|to|TO|_ 0|0|CD|_ ,|,|,|_ 5.0|5.0|CD|_ ,|,|,|_ 6.5|6.5|CD|_ and|and|CC|_ 8.5|8.5|CD|_ µM|µm|NN|_ AgNO3|agno3|NN|_ ,|,|,|_ respectively|respectively|RB|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ sampled|sample|VBN|_ and|and|CC|_ centrifuged|centrifuge|VBN|_ -LRB-|-lrb-|-LRB-|_ 4000|4000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ resuspended|resuspend|VBN|_ with|with|IN|_ 1|1|CD|_ mL|ml|NN|_ of|of|IN|_ TE|TE|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Tris-HCl|tris-hcl|NN|_ 10|10|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ EDTA|edta|NN|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ 1|1|CD|_ mg|mg|NN|_ lysozyme|lysozyme|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ a|a|DT|_ RNeasy|rneasy|NN|_ midi|midi|JJ|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ including|include|VBG|_ the|the|DT|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ described|describe|VBN|_ in|in|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ quantity|quantity|NN|_ and|and|CC|_ integrity|integrity|NN|_ were|be|VBD|_ checked|check|VBN|_ by|by|IN|_ Nanodrop|Nanodrop|NNP|_ ®|®|NNP|_ and|and|CC|_ Agilent|Agilent|NNP|_ BioAnalyzer|BioAnalyzer|NNP|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Ecoli|Ecoli|NNP|_ _|_|SYM|_ Ag0|ag0|NN|_ .0|.0|CD|_ _|_|NN|_ rep1|rep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag0|ag0|NN|_ .0|.0|CD|_ _|_|NN|_ rep2|rep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag0|ag0|NN|_ .0|.0|CD|_ _|_|NN|_ rep3|rep3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag5|ag5|NN|_ .0|.0|CD|_ _|_|NN|_ rep1|rep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag5|ag5|NN|_ .0|.0|CD|_ _|_|NN|_ rep2|rep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag5|ag5|NN|_ .0|.0|CD|_ _|_|NN|_ rep3|rep3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag6|ag6|NN|_ .5|.5|CD|_ _|_|NN|_ rep1|rep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag6|ag6|NN|_ .5|.5|CD|_ _|_|NN|_ rep2|rep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag6|ag6|NN|_ .5|.5|CD|_ _|_|NN|_ rep3|rep3|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag8|ag8|NN|_ .5|.5|CD|_ _|_|NN|_ rep1|rep1|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag8|ag8|NN|_ .5|.5|CD|_ _|_|NN|_ rep2|rep2|NN|_
Ecoli|ecolus|NNS|_ _|_|VBP|_ Ag8|ag8|NN|_ .5|.5|CD|_ _|_|NN|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ 0|0|CD|_ µM|µm|NN|_ AgNO3|agno3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ 0|0|CD|_ µM|µm|NN|_ AgNO3|agno3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ 5|5|CD|_ µM|µm|NN|_ AgNO3|agno3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ 6.5|6.5|CD|_ µM|µm|NN|_ AgNO3|agno3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ,|,|,|_ 8.5|8.5|CD|_ µM|µm|NN|_ AgNO3|agno3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Ionic|ionic|JJ|_ silver|silver|NN|_ stock|stock|NN|_ solutions|solution|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ AgNO3|agno3|NN|_ powder|powder|NN|_ -LRB-|-lrb-|-LRB-|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ Bioblock|Bioblock|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Saulou|Saulou|NNP|_ ,|,|,|_ Jamme|Jamme|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ in|in|IN|_ darkness|darkness|NN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ tested|test|VBN|_ concentrations|concentration|NNS|_ -LRB-|-lrb-|-LRB-|_ 5.0|5.0|CD|_ ,|,|,|_ 6.5|6.5|CD|_ ,|,|,|_ and|and|CC|_ 8.5|8.5|CD|_ µM|µm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ diluting|dilute|VBG|_ the|the|DT|_ corresponding|corresponding|JJ|_ AgNO3|agno3|NN|_ stock|stock|NN|_ solution|solution|NN|_ directly|directly|RB|_ into|into|IN|_ the|the|DT|_ M9|m9|NN|_ growth|growth|NN|_ medium|medium|NN|_ .|.|.|_ Control|Control|NNP|_ experiment|experiment|NN|_ was|be|VBD|_ simultaneously|simultaneously|RB|_ performed|perform|VBN|_ by|by|IN|_ adding|add|VBG|_ deionised|deionised|JJ|_ water|water|NN|_ into|into|IN|_ the|the|DT|_ M9|m9|NN|_ broth|broth|NN|_ .|.|.|_ In|in|IN|_ both|both|DT|_ cases|case|NNS|_ ,|,|,|_ a|a|DT|_ stabilization|stabilization|NN|_ period|period|NN|_ of|of|IN|_ 24|24|CD|_ h|h|NN|_ -LRB-|-lrb-|-LRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 120|120|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ before|before|IN|_ cell|cell|NN|_ inoculation|inoculation|NN|_ .|.|.|_
Raw|raw|NN|_ probe|probe|NN|_ intensities|intensity|NNS|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ pair|pair|NN|_ files|file|NNS|_ three|three|CD|_ replicates|replicate|VBZ|_ for|for|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ with|with|IN|_ respectively|respectively|RB|_ 0|0|CD|_ ,|,|,|_ 5.0|5.0|CD|_ ,|,|,|_ 6.5|6.5|CD|_ and|and|CC|_ 8.5|8.5|CD|_ µM|µm|NN|_ of|of|IN|_ AgNO3|agno3|NN|_ in|in|IN|_ the|the|DT|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ processed|process|VBN|_ and|and|CC|_ analyzed|analyze|VBN|_ with|with|IN|_ R|r|NN|_ computing|computing|NN|_ environment|environment|NN|_ using|use|VBG|_ the|the|DT|_ affy|affy|NN|_ and|and|CC|_ limma|limma|NN|_ package|package|NN|_ of|of|IN|_ Bioconductor|Bioconductor|NNP|_ .|.|.|_ Raw|raw|NN|_ data|datum|NNS|_ were|be|VBD|_ submitted|submit|VBN|_ to|to|TO|_ a|a|DT|_ RMA-base|rma-base|NN|_ background|background|NN|_ correction|correction|NN|_ -LSB-|-lsb-|-LRB-|_ Irizarry|Irizarry|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ 2003|2003|CD|_ ,|,|,|_ Biostatistics|biostatistic|NNS|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 249-264|249-264|CD|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ After|after|IN|_ background|background|NN|_ correction|correction|NN|_ ,|,|,|_ intra-replicate|intra-replicate|JJ|_ quantil|quantil|NN|_ normalization|normalization|NN|_ was|be|VBD|_ performed|perform|VBN|_ for|for|IN|_ each|each|DT|_ growth|growth|NN|_ condition|condition|NN|_ .|.|.|_ A|a|DT|_ set|set|NN|_ of|of|IN|_ probes|probe|NNS|_ in|in|IN|_ the|the|DT|_ background|background|NN|_ for|for|IN|_ which|which|WDT|_ the|the|DT|_ ranks|rank|NNS|_ were|be|VBD|_ roughly|roughly|RB|_ invariant|invariant|JJ|_ across|across|IN|_ all|all|PDT|_ the|the|DT|_ twelve|twelve|CD|_ arrays|array|NNS|_ was|be|VBD|_ selected|select|VBN|_ .|.|.|_ The|the|DT|_ median|median|JJ|_ value|value|NN|_ of|of|IN|_ the|the|DT|_ invariant|invariant|JJ|_ probeset|probeset|NN|_ intensities|intensity|NNS|_ on|on|IN|_ each|each|DT|_ array|array|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ scaling|scaling|NN|_ factor|factor|NN|_ for|for|IN|_ normalization|normalization|NN|_ between|between|IN|_ growth|growth|NN|_ conditions|condition|NNS|_ .|.|.|_
The|the|DT|_ laboratory|laboratory|NN|_ strain|strain|NN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 24|24|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ under|under|IN|_ continuous|continuous|JJ|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 120|120|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ in|in|IN|_ 200|200|CD|_ mL|ml|NN|_ M9|m9|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Merck|Merck|NNP|_ Prolabo|Prolabo|NNP|_ -RRB-|-rrb-|-RRB-|_ complemented|complement|VBN|_ with|with|IN|_ 2.5|2.5|CD|_ g|g|NN|_
15|15|CD|_ ml|ml|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 30|30|CD|_ ml|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ bacterial|bacterial|JJ|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ Ltd|Ltd|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
An|a|DT|_ RNeasy|rneasy|NN|_ midikit|midikit|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ prepare|prepare|VB|_ total|total|JJ|_ RNA|rna|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ Ltd.|Ltd.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Any|any|DT|_ contaminating|contaminate|VBG|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ a|a|DT|_ DNAase|dnaase|NN|_ column|column|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ Ltd|Ltd|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Data|Data|NNP|_ was|be|VBD|_ analysed|analyse|VBN|_ using|use|VBG|_ GeneSpring|GeneSpring|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_
Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_
Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_ +2.5|+2.5|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|_ nitrite|nitrite|JJ|_
pGIT1|pgit1|NN|_
pGIT1|pgit1|NN|_ .1|.1|CD|_
pGIT1|pgit1|NN|_ .1|.1|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT1|pgit1|NN|_ .2|.2|NN|_
pGIT1|pgit1|NN|_ .2|.2|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT1|pgit1|NN|_ .3|.3|NN|_
pGIT1|pgit1|NN|_ .3|.3|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT1|pgit1|NN|_ .4|.4|CD|_
pGIT1|pgit1|NN|_ .4|.4|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT1|pgit1|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT8|pgit8|NN|_
pGIT8|pgit8|NN|_ .1|.1|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT8|pgit8|NN|_ .2|.2|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT8|pgit8|NN|_ .3|.3|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT8|pgit8|NN|_ .4|.4|NN|_ +|+|CC|_ NO2|no2|NN|_
pGIT8|pgit8|NN|_ +|+|CC|_ NO2|no2|NN|_
Pool|Pool|NNP|_ of|of|IN|_ eight|eight|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_
Strain|Strain|NNP|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT1|pgit1|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ in|in|IN|_ multicopy|multicopy|JJ|_ ,|,|,|_ titrates|titrate|VBZ|_ out|out|RP|_ NsrR|nsrr|NN|TF to|to|TO|_ phenocopy|phenocopy|VB|_ an|a|DT|_ NsrR|nsrr|NN|TF -|-|:|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT1|pgit1|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ in|in|IN|_ multicopy|multicopy|JJ|_ ,|,|,|_ titrates|titrate|VBZ|_ out|out|RP|_ NsrR|nsrr|NN|TF to|to|TO|_ phenocopy|phenocopy|VB|_ an|a|DT|_ NsrR|nsrr|NN|TF -|-|:|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_ Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT1|pgit1|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ in|in|IN|_ multicopy|multicopy|JJ|_ ,|,|,|_ titrates|titrate|VBZ|_ out|out|RP|_ NsrR|nsrr|NN|TF to|to|TO|_ phenocopy|phenocopy|VB|_ an|a|DT|_ NsrR|nsrr|NN|TF -|-|:|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_ Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT1|pgit1|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ in|in|IN|_ multicopy|multicopy|JJ|_ ,|,|,|_ titrates|titrate|VBZ|_ out|out|RP|_ NsrR|nsrr|NN|TF to|to|TO|_ phenocopy|phenocopy|VB|_ an|a|DT|_ NsrR|nsrr|NN|TF -|-|:|_ mutation|mutation|NN|_ -RRB-|-rrb-|-RRB-|_ Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_ +2.5|+2.5|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|_ nitrite|nitrite|JJ|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT8|pgit8|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ 1|1|CD|_ base|base|NN|_ pair|pair|NN|_ deletion|deletion|NN|_ in|in|IN|_ the|the|DT|_ NsrR-binding|nsrr-binding|JJ|_ site|site|NN|_ of|of|IN|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ -RRB-|-rrb-|-RRB-|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT8|pgit8|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ 1|1|CD|_ base|base|NN|_ pair|pair|NN|_ deletion|deletion|NN|_ in|in|IN|_ the|the|DT|_ NsrR-binding|nsrr-binding|JJ|_ site|site|NN|_ of|of|IN|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ -RRB-|-rrb-|-RRB-|_ Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_ +|+|CC|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|_ nitrite|nitrite|JJ|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT8|pgit8|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ 1|1|CD|_ base|base|NN|_ pair|pair|NN|_ deletion|deletion|NN|_ in|in|IN|_ the|the|DT|_ NsrR-binding|nsrr-binding|JJ|_ site|site|NN|_ of|of|IN|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ -RRB-|-rrb-|-RRB-|_ Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_ +2.5|+2.5|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|_ nitrite|nitrite|JJ|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT8|pgit8|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ 1|1|CD|_ base|base|NN|_ pair|pair|NN|_ deletion|deletion|NN|_ in|in|IN|_ the|the|DT|_ NsrR-binding|nsrr-binding|JJ|_ site|site|NN|_ of|of|IN|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ -RRB-|-rrb-|-RRB-|_ Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_ +|+|CC|_ .5|.5|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|_ nitrite|nitrite|JJ|_
Strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ pGIT8|pgit8|NN|_ -LRB-|-lrb-|-LRB-|_ carries|carry|VBZ|_ 1|1|CD|_ base|base|NN|_ pair|pair|NN|_ deletion|deletion|NN|_ in|in|IN|_ the|the|DT|_ NsrR-binding|nsrr-binding|JJ|_ site|site|NN|_ of|of|IN|_ the|the|DT|_ ytfE|ytfe|NN|GEN promoter|promoter|NN|_ -RRB-|-rrb-|-RRB-|_ Growth|growth|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ to|to|TO|_ early|early|JJ|_ exponential|exponential|JJ|_ growth|growth|NN|_ Media|Media|NNP|_ :|:|:|_ Minimal|minimal|JJ|_ salts|salt|NNS|_ +|+|CC|_ 20|20|CD|_ mM|mm|NN|KWSUPP trimethylamine-N-oxide|trimethylamine-n-oxide|NN|_ Pool|Pool|NNP|_ of|of|IN|_ eight|eight|CD|_ independent|independent|JJ|_ cultures|culture|NNS|_
b2618|b2618|NN|_ _|_|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
b2618|b2618|NN|_ _|_|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
b2618|b2618|NN|_ _|_|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
b2618|b2618|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
bcp|bcp|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
bcp|bcp|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r2|r2|NN|_
bcp|bcp|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r3|r3|NN|_
bcp|bcp|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 120|120|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ K12|k12|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r2|r2|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 120|120|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r2|r2|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r2|r2|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r2|r2|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ W1863|w1863|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ W1863|w1863|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ W1863|w1863|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r1|r1|NN|_
ccdB|ccdb|NN|_ _|_|CD|_ W1863|w1863|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r1|r1|NN|_
cells|cell|NNS|_ 12|12|CD|_ min|min|NN|_ after|after|IN|_ treatment|treatment|NN|_ by|by|IN|_ norfloxacin|norfloxacin|NN|_
cells|cell|NNS|_ 24|24|CD|_ min|min|NN|_ after|after|IN|_ treatment|treatment|NN|_ by|by|IN|_ norfloxacin|norfloxacin|NN|_
cells|cell|NNS|_ 36|36|CD|_ min|min|NN|_ after|after|IN|_ treatment|treatment|NN|_ by|by|IN|_ norfloxacin|norfloxacin|NN|_
cells|cell|NNS|_ 48|48|CD|_ min|min|NN|_ after|after|IN|_ treatment|treatment|NN|_ by|by|IN|_ norfloxacin|norfloxacin|NN|_
cells|cell|NNS|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ treatment|treatment|NN|_ by|by|IN|_ norfloxacin|norfloxacin|NN|_
cells|cell|NNS|_ prior|prior|RB|_ to|to|TO|_ treatment|treatment|NN|_ by|by|IN|_ norfloxacin|norfloxacin|NN|_
cpxR|cpxr|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
cpxR|cpxr|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
cpxR|cpxr|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
cpxR|cpxr|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
crcB|crcb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
crcB|crcb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
crcB|crcb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
crcB|crcb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
crp|crp|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
crp|crp|VBP|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
crp|crp|VBP|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
crp|crp|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
cspF|cspf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
cspF|cspf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
cspF|cspf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
cspF|cspf|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
dam|dam|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
dam|dam|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r2|r2|NN|_
dam|dam|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r3|r3|NN|_
dam|dam|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
dinI|dini|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r1|r1|NN|_
dinI|dini|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r2|r2|FW|_
dinI|dini|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r3|r3|FW|_
dinI|dini|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
dinP|dinp|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r1|r1|FW|_
dinP|dinp|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r2|r2|FW|_
dinP|dinp|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r3|r3|FW|_
dinP|dinp|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
dnaA|dnaa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
dnaA|dnaa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
dnaA|dnaa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
dnaA|dnaa|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
dnaN|dnan|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
dnaN|dnan|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
dnaN|dnan|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
dnaN|dnan|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
dnaT|dnat|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
dnaT|dnat|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
dnaT|dnat|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
dnaT|dnat|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 120|120|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 30|30|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 90|90|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 120|120|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 30|30|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ K12|k12|NN|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 90|90|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 120|120|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 30|30|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 90|90|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 120|120|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 30|30|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ MG1063|mg1063|NN|_ -LRB-|-lrb-|-LRB-|_ recA56|reca56|NN|_ =|=|JJ|_ recA|reca|NN|GEN -|-|:|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 90|90|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 30|30|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ ccdB|ccdb|NN|_ upregulation|upregulation|NN|_ 90|90|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 30|30|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 60|60|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
E.coli|e.coli|NN|_ W1863|w1863|NN|_ wt|wt|JJ|_ lambda|lambda|NN|_ -|-|:|_ with|with|IN|_ lacZ|lacz|NN|GEN upregulation|upregulation|NN|_ 90|90|CD|_ minutes|minute|NNS|_ after|after|IN|_ induction|induction|NN|_
emrR|emrr|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
emrR|emrr|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
emrR|emrr|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
era|era|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
era|era|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r2|r2|NN|_
era|era|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
era|era|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
fis|fi|VBZ|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
fis|fi|VBZ|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
fis|fi|VBZ|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
fis|fis|FW|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
fklB|fklb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
fklB|fklb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
fklB|fklb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
fklB|fklb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
folA|fola|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
folA|fola|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
folA|fola|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
folA|fola|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
galF|galf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
galF|galf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
galF|galf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
galF|galf|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
gcvR|gcvr|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
gcvR|gcvr|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
gcvR|gcvr|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
gcvR|gcvr|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
GeneChips|genechip|NNS|_ were|be|VBD|_ washed|wash|VBN|_ and|and|CC|_ stained|stain|VBN|_ with|with|IN|_ an|a|DT|_ FS450|fs450|NN|_ fluidics|fluidic|NNS|_ machine|machine|NN|_ and|and|CC|_ scanned|scan|VBN|_ using|use|VBG|_ a|a|DT|_ GeneChip|GeneChip|NNP|_ Scanner|Scanner|NNP|_ 3000|3000|CD|_
gyrA|gyrA|NNP|GEN __|__|VBD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
gyrA|gyra|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
gyrA|gyra|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
gyrA|gyra|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
gyrI|gyri|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
gyrI|gyri|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
gyrI|gyri|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
gyrI|gyri|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
hlpA|hlpa|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
hlpA|hlpa|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
hlpA|hlpa|NN|_ __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
hlpA|hlpa|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
holD|hold|VBP|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
holD|hold|VBP|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
holD|hold|VBP|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
holD|hold|VBP|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
hscA|hsca|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r1|r1|FW|_
hscA|hsca|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
hscA|hsca|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
hscA|hsca|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
IHF|ihf|NN|TF ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r1|r1|FW|_
IHF|ihf|NN|TF ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
IHF|ihf|NN|TF upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T2|t2|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T3|t3|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T3|t3|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T4|t4|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T5|t5|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T5|t5|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ H2|h2|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T2|t2|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T3|t3|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T3|t3|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T4|t4|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T4|t4|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T5|t5|NN|_ .5|.5|CD|_ _|_|NN|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T5|t5|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T6|t6|NN|_ _|_|CD|_ r1|r1|NN|_
ik|ik|NN|_ _|_|NN|_ L2|l2|NN|_ _|_|CD|_ T8|t8|NN|_ _|_|CD|_ r1|r1|NN|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2.5|2.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 3.5|3.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 3|3|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 4.5|4.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 4|4|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 5.5|5.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 5|5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 6|6|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.2|0.2|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 8|8|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 2.5|2.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 3.5|3.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 3|3|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 4.5|4.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 4|4|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 5.5|5.5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 5|5|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 6|6|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
K12|k12|NN|_ EMG2|emg2|NN|_ on|on|IN|_ LB|lb|NN|_ with|with|IN|_ 0.4|0.4|CD|_ percent|percent|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 8|8|CD|_ hours|hour|NNS|_ post-incubation|post-incubation|JJ|_
lacZ|lacz|NN|GEN _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 120|120|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ K12|k12|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ K12|k12|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r2|r2|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 120|120|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r2|r2|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r2|r2|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ MG1063|mg1063|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r2|r2|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ W1863|w1863|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ W1863|w1863|NN|_ _|_|CD|_ 30|30|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ W1863|w1863|NN|_ _|_|NN|_ 60|60|CD|_ _|_|NN|_ r1|r1|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ W1863|w1863|NN|_ _|_|NN|_ 90|90|CD|_ _|_|NN|_ r1|r1|NN|_
ldrA|ldra|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
ldrA|ldra|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
ldrA|ldra|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
ldrA|ldra|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
lexA|lexa|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r1|r1|FW|_
lexA|lexa|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r2|r2|FW|_
lexA|lexa|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r3|r3|FW|_
lexA|lexa|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
lon|lon|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r1|r1|NN|_
lon|lon|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r2|r2|NN|_
lon|lon|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r3|r3|NN|_
lon|lon|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
luc2|luc2|NN|_ _|_|CD|_ U|U|NNP|_ _|_|NNP|_ N0000|N0000|NNP|_ _|_|VBD|_ r1|r1|NN|_
luc2|luc2|NN|_ _|_|CD|_ U|U|NNP|_ _|_|NNP|_ N0000|N0000|NNP|_ _|_|VBD|_ r2|r2|NN|_
luc2|luc2|NN|_ _|_|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r1|r1|NN|_
luc2|luc2|NN|_ _|_|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r2|r2|NN|_
luciferase|luciferase|NN|_ 0.025|0.025|CD|_ ug|ug|NN|_
luciferase|luciferase|NN|_ no|no|DT|_ drug|drug|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0000|N0000|NNP|_ _|_|NNP|_ r1|r1|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0000|N0000|NNP|_ _|_|NNP|_ r2|r2|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0000|N0000|NNP|_ _|_|NNP|_ r3|r3|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r1|r1|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r2|r2|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r3|r3|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r2|r2|NN|_
luc|luc|NN|_ ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r3|r3|NN|_
luc|luc|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ 0.000|0.000|CD|_ ug|ug|NN|_
luc|luc|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
luc|luc|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
mazF|mazf|NN|GEN _|_|CD|_ chpA|chpa|NN|_ upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
mazF|mazf|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r1|r1|NN|_
mazF|mazf|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r2|r2|NN|_
mazF|mazf|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r3|r3|NN|_
mcrB|mcrb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
mcrB|mcrb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
mcrB|mcrb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
mcrB|mcrb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
mcrC|mcrc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
mcrC|mcrc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
mcrC|mcrc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
mcrC|mcrc|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
menB|menb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
menB|menb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
menB|menb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
menB|menb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
menC|menc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
menC|menc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
menC|menc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
menC|menc|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
minD|mind|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
minD|mind|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
minD|mind|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
minD|mind|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
minE|mine|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r1|r1|NN|_
minE|mine|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|NNP|_ r2|r2|NN|_
minE|mine|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
minE|mine|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
murI|muri|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r1|r1|FW|_
murI|muri|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
murI|muri|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
murI|muri|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
nrdA|nrda|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
nrdA|nrda|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
nrdA|nrda|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
nrdA|nrda|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
nrdB|nrdb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
nrdB|nrdb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
nrdB|nrdb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
nupC|nupc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
nupC|nupc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
nupC|nupc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r3|r3|NN|_
nupC|nupc|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
pyrC|pyrc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
pyrC|pyrc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
pyrC|pyrc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
pyrC|pyrc|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
recA|reca|NN|GEN deletion|deletion|NN|_ 0.05|0.05|CD|_ ug|ug|NN|_
recA|reca|NN|GEN deletion|deletion|NN|_ 0|0|CD|_ ug|ug|NN|_
recA|reca|NN|GEN deletion|deletion|NN|_ 1.0|1.0|CD|_ ug|ug|NN|_
recA|reca|NN|GEN _|_|NN|_ D|d|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r1|r1|NN|_
recA|reca|NN|GEN _|_|NN|_ D|d|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r2|r2|NN|_
recA|reca|NN|GEN _|_|NN|_ D|d|NN|_ _|_|CD|_ N0050|n0050|NN|_ _|_|CD|_ r1|r1|NN|_
recA|reca|NN|GEN _|_|NN|_ D|d|NN|_ _|_|CD|_ N0050|n0050|NN|_ _|_|CD|_ r2|r2|NN|_
recA|reca|NN|GEN _|_|NN|_ D|d|NN|_ _|_|CD|_ N1000|n1000|NN|_ _|_|CD|_ r1|r1|NN|_
recA|reca|NN|GEN _|_|NN|_ D|d|NN|_ _|_|CD|_ N1000|n1000|NN|_ _|_|CD|_ r2|r2|NN|_
recA|reca|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|NNP|_ r1|r1|NN|_
recA|reca|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r2|r2|FW|_
recA|reca|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r3|r3|FW|_
recA|reca|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
relE|rele|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r1|r1|NN|_
relE|rele|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r2|r2|NN|_
relE|rele|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r3|r3|NN|_
relE|rele|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
rimI|rimi|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r1|r1|FW|_
rimI|rimi|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
rimI|rimi|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
rimI|rimi|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
RNAEasy|rnaeasy|NN|_ with|with|IN|_ RNAProtect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_
rstB|rstb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
rstB|rstb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
rstB|rstb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
rstB|rstb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
ruvA|ruva|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r1|r1|NN|_
ruvA|ruva|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r2|r2|NN|_
ruvA|ruva|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r3|r3|FW|_
ruvA|ruva|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
ruvC|ruvc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
ruvC|ruvc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
ruvC|ruvc|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
ruvC|ruvc|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
sbcB|sbcb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
sbcB|sbcb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
sbcB|sbcb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
sbcB|sbcb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
sulA|sula|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r1|r1|FW|_
sulA|sula|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r2|r2|FW|_
sulA|sula|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r3|r3|FW|_
sulA|sula|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
T0|t0|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r1|r1|NN|_
T0|t0|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r2|r2|NN|_
T0|t0|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r3|r3|NN|_
T12|t12|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r1|r1|NN|_
T12|t12|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r2|r2|NN|_
T12|t12|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r3|r3|NN|_
T24|t24|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r1|r1|NN|_
T24|t24|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r2|r2|NN|_
T24|t24|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r3|r3|NN|_
T24|t24|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r1|r1|NN|_
T24|t24|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r2|r2|NN|_
T24|t24|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|SYM|_ r3|r3|FW|_
T36|t36|FW|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r1|r1|NN|_
T36|t36|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|SYM|_ r2|r2|FW|_
T36|t36|FW|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r3|r3|NN|_
T48|t48|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r1|r1|NN|_
T48|t48|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r2|r2|NN|_
T48|t48|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r3|r3|NN|_
T60|t60|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r1|r1|NN|_
T60|t60|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r2|r2|NN|_
T60|t60|NN|_ _|_|CD|_ N0000|n0000|NN|_ _|_|CD|_ r3|r3|NN|_
T60|t60|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r1|r1|NN|_
T60|t60|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r2|r2|NN|_
T60|t60|NN|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r3|r3|NN|_
umuD|umud|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r1|r1|NN|_
umuD|umud|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r2|r2|NN|_
umuD|umud|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r3|r3|NN|_
umuD|umud|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
untreated|untreated|JJ|_ cells|cell|NNS|_ after|after|IN|_ 24|24|CD|_ min|min|NN|_
untreated|untreated|JJ|_ cells|cell|NNS|_ after|after|IN|_ 60|60|CD|_ min|min|NN|_
uspA|uspa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r1|r1|FW|_
uspA|uspa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
uspA|uspa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
uspA|uspa|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
uvrA|uvra|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r1|r1|NN|_
uvrA|uvra|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|VBD|_ r2|r2|NN|_
uvrA|uvra|NN|GEN ___|___|CD|_ U|U|NNP|_ _|_|NNP|_ N0025|N0025|NNP|_ _|_|SYM|_ r3|r3|FW|_
uvrA|uvra|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ amp|amp|NN|_ 50ug|50ug|JJ|_
wild-type|wild-type|JJ|_ 1.0|1.0|CD|_ ug|ug|NN|_
wild-type|wild-type|JJ|_ cells|cell|NNS|_ with|with|IN|_ 0.025|0.025|CD|_ ug|ug|NN|_
wild-type|wild-type|JJ|_ cells|cell|NNS|_ with|with|IN|_ 0.050|0.050|CD|_ ug|ug|NN|_
wild-type|wild-type|JJ|_ cells|cell|NNS|_ with|with|IN|_ 0.075|0.075|CD|_ ug|ug|NN|_
wild-type|wild-type|JJ|_ cells|cell|NNS|_ without|without|IN|_ norfloxacin|norfloxacin|JJ|_
WT|wt|JJ|_ _|_|NN|_ D|d|NN|_ _|_|CD|_ N1000|n1000|NN|_ _|_|CD|_ r1|r1|NN|_
WT|wt|JJ|_ _|_|NN|_ D|d|NN|_ _|_|CD|_ N1000|n1000|NN|_ _|_|CD|_ r2|r2|NN|_
WT|wt|JJ|_ _|_|NN|_ N0000|n0000|NN|_ _|_|CD|_ r1|r1|NN|_
WT|wt|JJ|_ _|_|NN|_ N0000|n0000|NN|_ _|_|CD|_ r2|r2|NN|_
WT|wt|JJ|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|SYM|_ r1|r1|FW|_
WT|wt|FW|_ _|_|SYM|_ N0025|n0025|CD|_ _|_|CD|_ r2|r2|NN|_
WT|wt|JJ|_ _|_|NN|_ N0050|n0050|NN|_ _|_|CD|_ r1|r1|NN|_
WT|wt|JJ|_ _|_|NN|_ N0050|n0050|NN|_ _|_|CD|_ r2|r2|NN|_
WT|wt|JJ|_ _|_|NN|_ N0075|n0075|NN|_ _|_|CD|_ r1|r1|NN|_
WT|wt|JJ|_ _|_|NN|_ N0075|n0075|NN|_ _|_|CD|_ r2|r2|NN|_
yebF|yebf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
yebF|yebf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
yebF|yebf|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
yebF|yebf|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
yoeB|yoeb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
yoeB|yoeb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r2|r2|NN|_
yoeB|yoeb|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
yoeB|yoeb|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ mg|mg|NN|_
zipA|zipa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|VBD|_ r1|r1|NN|_
zipA|zipa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r2|r2|FW|_
zipA|zipa|NN|GEN __|__|CD|_ U|U|NNP|_ _|_|NNP|_ N0075|N0075|NNP|_ _|_|SYM|_ r3|r3|FW|_
zipA|zipa|NN|GEN upregulation|upregulation|NN|_ ,|,|,|_ 0.075|0.075|CD|_ ug|ug|NN|_
BW25113|bw25113|NN|_ W|w|NN|_
BW25113|bw25113|NN|_ ymgB|ymgb|NN|_ LBglu|lbglu|NN|_ 24h|24h|JJ|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
channel|channel|NN|_ 1|1|CD|_
Channel|Channel|NNP|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 24h|24h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LBglu|lbglu|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ BW25113|bw25113|NN|_ ymgB|ymgb|NN|_ mutant|mutant|NN|_ after|after|IN|_ 24h|24h|NN|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LBglu|lbglu|NN|_ with|with|IN|_ glass|glass|NN|_ wool|wool|NN|_
To|to|TO|_ lyse|lyse|VB|_ the|the|DT|_ cells|cell|NNS|_ ,|,|,|_ 1.0|1.0|CD|_ mL|ml|NN|_ RLT|rlt|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 0.2|0.2|CD|_ mL|ml|NN|_ 0.1|0.1|CD|_ mm|mm|NN|_ zirconia|zirconia|NN|_
agent|agent|NN|_ :|:|:|_ control|control|NN|_
agent|agent|NN|_ :|:|:|_ glycolaldehyde|glycolaldehyde|NN|_
Data|Data|NNP|_ were|be|VBD|_ analyzed|analyze|VBN|_ by|by|IN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ V.|V.|NNP|_ 11.5.1.1|11.5.1.1|CD|_ .|.|.|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
M9|m9|NN|_ mineral|mineral|NN|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ D|d|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ xylose|xylose|NN|_ as|as|IN|_ the|the|DT|_ only|only|JJ|_ carbon|carbon|NN|_ source|source|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ ml|ml|NN|_ in|in|IN|_ 500|500|CD|_ ml|ml|NN|_ shake|shake|NN|_ flasks|flask|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ wild-type|wild-type|JJ|_ cells|cell|NNS|_ or|or|CC|_ synthetic|synthetic|JJ|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ cultivated|cultivate|VBN|_ on|on|IN|_ xylose|xylose|NN|_ M9|m9|NN|_ medium|medium|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ adjust|adjust|VB|_ an|a|DT|_ OD|od|NN|_ of|of|IN|_ ~|~|NN|_ 0.1|0.1|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ under|under|IN|_ shaking|shake|VBG|_ until|until|IN|_ OD|od|NN|_ reached|reach|VBD|_ ~|~|NN|_ 1|1|CD|_ .|.|.|_ Then|then|RB|_ they|they|PRP|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ two|two|CD|_ 50|50|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ further|further|JJ|_ cultivated|cultivate|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ shake|shake|NN|_ flasks|flask|NNS|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ or|or|CC|_ absence|absence|NN|_ of|of|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP glycolaldehyde|glycolaldehyde|NN|_ .|.|.|_ After|after|IN|_ 30|30|CD|_ min|min|NN|_ of|of|IN|_ incubation|incubation|NN|_ ,|,|,|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ cell|cell|NN|_ suspension|suspension|NN|_ was|be|VBD|_ withdrawn|withdraw|VBN|_ and|and|CC|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 1500|1500|CD|_ x|x|CC|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ Eppendorf|eppendorf|NN|_ 5415D|5415d|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ the|the|DT|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ directly|directly|RB|_ subject|subject|JJ|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ Experiment|experiment|NN|_ were|be|VBD|_ repeated|repeat|VBN|_ three|three|CD|_ times|time|NNS|_ .|.|.|_
PEN205|pen205|NN|_
PEN205|pen205|NN|_ strain|strain|NN|_ first|first|JJ|_ repetition|repetition|NN|_
PEN205|pen205|NN|_ strain|strain|NN|_ second|second|JJ|_ repetition|repetition|NN|_
PEN205|pen205|NN|_ strain|strain|NN|_ third|third|JJ|_ repetition|repetition|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ RNeasy|rneasy|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|NN|_ RNA|rna|NN|_ .|.|.|_ Quantity|quantity|NN|_ and|and|CC|_ quality|quality|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ NanoDrop|NanoDrop|NNP|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Bioanalyzer|bioanalyzer|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_
wild-type|wild-type|JJ|_ MG1655|mg1655|NN|_
wild-type|wild-type|JJ|_ MG1655|mg1655|NN|_ +|+|CC|_ glycolaldehyde|glycolaldehyde|NN|_ 10|10|CD|_ mM|mm|NN|KWSUPP
WT|wt|JJ|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Glycolaldehyde|glycolaldehyde|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ whenever|whenever|WRB|_ the|the|DT|_ culture|culture|NN|_ OD600nm|od600nm|NN|_ reached|reach|VBD|_ ~|~|NN|_ 1|1|CD|_ .|.|.|_
WT|WT|NNP|_ strain|strain|NN|_ treated|treat|VBN|_ with|with|IN|_ glycolaldehyde|glycolaldehyde|NN|_ first|first|JJ|_ repetition|repetition|NN|_
WT|wt|JJ|_ strain|strain|NN|_ treated|treat|VBN|_ with|with|IN|_ glycolaldehyde|glycolaldehyde|NN|_ second|second|JJ|_ repetition|repetition|NN|_
WT|wt|JJ|_ strain|strain|NN|_ treated|treat|VBN|_ with|with|IN|_ glycolaldehyde|glycolaldehyde|NN|_ third|third|JJ|_ repetition|repetition|NN|_
WT|wt|JJ|_ strain|strain|NN|_ without|without|IN|_ glycolaldehyde|glycolaldehyde|NN|_ first|first|JJ|_ repetition|repetition|NN|_
WT|wt|JJ|_ strain|strain|NN|_ without|without|IN|_ glycolaldehyde|glycolaldehyde|NN|_ second|second|JJ|_ repetition|repetition|NN|_
WT|wt|JJ|_ strain|strain|NN|_ without|without|IN|_ glycolaldehyde|glycolaldehyde|NN|_ third|third|JJ|_ repetition|repetition|NN|_
Cells|cell|NNS|_ were|be|VBD|_ disrupted|disrupt|VBN|_ by|by|IN|_ sonication|sonication|NN|_ and|and|CC|_ NsrR|nsrr|NN|TF bound|bind|VBD|_ DNA|dna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ anti-Flag|anti-flag|JJ|_ antibody|antibody|NN|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ Monoclonal|monoclonal|JJ|_ ANTI-FLAG|anti-flag|NN|_ M5|m5|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma-Aldrich|Sigma-Aldrich|NNP|_ ,|,|,|_ catalog|catalog|NN|_ number|number|NN|_ :|:|:|_ F4042|f4042|NN|_ -RRB-|-rrb-|-RRB-|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ none|none|NN|_
ChIP-Seq|chip-seq|NN|_
ChIP-seq|chip-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ CFT073|cft073|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.12.8|0.12.8|CD|_ -RRB-|-rrb-|-RRB-|_
DNA|dna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ End-It|end-it|JJ|_ DNA|dna|NN|_ End|end|NN|_ Repair|Repair|NNP|_ Kit|kit|NN|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ A|a|DT|_ overhangs|overhang|NNS|_ were|be|VBD|_ added|add|VBN|_ with|with|IN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ Klenow|klenow|NN|_ fragment|fragment|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Adapters|adapter|NNS|_ from|from|IN|_ the|the|DT|_ IlluminaTruSeq|illuminatruseq|NN|_ DNA|dna|NN|_ sample|sample|NN|_ preparation|preparation|NN|_ kit|kit|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ using|use|VBG|_ LigFast|LigFast|NNP|_ -LRB-|-lrb-|-LRB-|_ Promega|Promega|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ DNAs|dna|NNS|_ were|be|VBD|_ amplified|amplify|VBN|_ by|by|IN|_ PCR|pcr|NN|_ using|use|VBG|_ primers|primer|NNS|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ IlluminaTruSeq|illuminatruseq|NN|_ DNA|dna|NN|_ sample|sample|NN|_ preparation|preparation|NN|_ kit|kit|NN|_ and|and|CC|_ Phusion|phusion|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Products|Products|NNPS|_ of|of|IN|_ the|the|DT|_ ligation|ligation|NN|_ reaction|reaction|NN|_ and|and|CC|_ PCR|pcr|NN|_ amplification|amplification|NN|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ 300-400|300-400|CD|_ bp|bp|NN|_ were|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ 2|2|CD|_ %|%|NN|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ DNA|dna|NN|_ concentrations|concentration|NNS|_ were|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ Qubit|Qubit|NNP|_ ™|™|SYM|_ dsDNA|dsdna|NN|_ HS|hs|NN|_ Assay|assay|NN|_ Kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CFT073|cft073|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CFT073|cft073|NN|_ -LRB-|-lrb-|-LRB-|_ AE014075|ae014075|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_
NsrR|nsrr|NN|TF _|_|NN|_ ChIPSeq|chipseq|NN|_ _|_|CD|_ rep1|rep1|NN|_
NsrR|nsrr|NN|TF _|_|NN|_ ChIPSeq|chipseq|NN|_ _|_|CD|_ rep2|rep2|NN|_
NsrR|nsrr|NN|TF _|_|NN|_ ChIPSeq|chipseq|NN|_ _|_|CD|_ rep3|rep3|NN|_
NsrR|nsrr|NN|TF _|_|NN|_ input|input|NN|_
peaks|peak|NNS|_ were|be|VBD|_ called|call|VBN|_ using|use|VBG|_ MACS2|macs2|NN|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
samples|sample|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ in|in|IN|_ rich|rich|JJ|MED media|media|NNS|MED
strain|strain|NN|_ :|:|:|_ CFT073|cft073|NN|_ nsrR|nsrr|NN|GEN :|:|:|_ :|:|:|_ 3X-Flag|3x-flag|NN|_ tag|tag|NN|GEN
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ bed|bed|NN|_ format|format|NN|_ peak|peak|NN|_ file|file|NN|_ generated|generate|VBN|_ from|from|IN|_ MACS2|macs2|NN|_
uropathogenic|uropathogenic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ UPEC|upec|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism CFT073|cft073|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CFT073|cft073|NN|_ -LRB-|-lrb-|-LRB-|_ AE014075|ae014075|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ deltahmp|deltahmp|JJ|_ deltanrfA|deltanrfa|NN|_ deltanorVW|deltanorvw|NN|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ NO|no|NN|_ -RRB-|-rrb-|-RRB-|_ 1|1|CD|_
-LRB-|-lrb-|-LRB-|_ +|+|CC|_ NO|no|NN|_ -RRB-|-rrb-|-RRB-|_ 1|1|CD|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ NO|no|NN|_ -RRB-|-rrb-|-RRB-|_ 2|2|CD|_
-LRB-|-lrb-|-LRB-|_ +|+|CC|_ NO|no|NN|_ -RRB-|-rrb-|-RRB-|_ 2|2|CD|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ NO|no|NN|_ -RRB-|-rrb-|-RRB-|_ 3|3|CD|_
-LRB-|-lrb-|-LRB-|_ +|+|CC|_ NO|no|NN|_ -RRB-|-rrb-|-RRB-|_ 3|3|CD|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ CFT073|cft073|NN|_ genome|genome|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.12.8|0.12.8|CD|_ -RRB-|-rrb-|-RRB-|_
Samples|sample|NNS|_ were|be|VBD|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP using|use|VBG|_ glucose|glucose|NN|SUPP as|as|IN|_ the|the|DT|_ carbon|carbon|NN|_ source|source|NN|_ .|.|.|_ 20mM|20mm|NN|_ nitrate|nitrate|NN|SUPP was|be|VBD|_ added|add|VBN|_ to|to|TO|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_ NO|no|NN|_ -RRB-|-rrb-|-RRB-|_ cultures|culture|NNS|_ for|for|IN|_ inducing|induce|VBG|_ nitrosative|nitrosative|JJ|_ stress|stress|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ CFT073|cft073|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ TPM|tpm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|sample|NN|_ ;|;|:|_ column1|column1|NN|_ :|:|:|_ transcript|transcript|NN|_ id|id|NN|_ ;|;|:|_ column2|column2|NN|_ :|:|:|_ TPM|tpm|NN|_ value|value|NN|_
Total|Total|NNP|_ Rna|Rna|NNP|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cultures|culture|NNS|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Protect|protect|VB|_ Bacteria|bacterium|NNS|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ For|for|IN|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ MICROBExpressTM|MICROBExpressTM|NNP|_ Bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ Enrichment|Enrichment|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ cleaned|clean|VBN|_ with|with|IN|_ the|the|DT|_ Zymo|Zymo|NNP|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ ConcentratorTM|concentratortm|NN|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ a|a|DT|_ second|second|JJ|_ cycle|cycle|NN|_ of|of|IN|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ ethanol|ethanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_
TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ RSEM|rsem|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1.2.19|1.2.19|CD|_ -RRB-|-rrb-|-RRB-|_
uropathogenic|uropathogenic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ UPEC|upec|NN|_ -RRB-|-rrb-|-RRB-|_ grown|grow|VBN|_ with|with|IN|_ nitrosative|nitrosative|JJ|_ stress|stress|NN|_
uropathogenic|uropathogenic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ UPEC|upec|NN|_ -RRB-|-rrb-|-RRB-|_ grown|grow|VBN|_ without|without|IN|_ nitrosative|nitrosative|JJ|_ stress|stress|NN|_
DnaK|dnak|NN|_ deletant|deletant|JJ|_ _|_|NN|_ 37C|37c|NN|_
E.coli|e.coli|NN|_ gene|gene|NN|_ expression|expression|NN|_ data|datum|NNS|_ in|in|IN|_ deletion|deletion|NN|_ of|of|IN|_ chaperone|chaperone|NN|_ DnaK|dnak|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ BW25113|bw25113|NN|_
The|the|DT|_ signal|signal|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ from|from|IN|_ strains|strain|NNS|_ using|use|VBG|_ NucleoSpin|NucleoSpin|NNP|_ RNAII|RNAII|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Macherey-Nagel|Macherey-Nagel|NNP|_ Corporation|Corporation|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ instruction|instruction|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ examined|examine|VBN|_ in|in|IN|_ a|a|DT|_ 1.5|1.5|CD|_ %|%|NN|_ denaturing|denature|VBG|_ agarose|agarose|NN|_ gel|gel|NN|_ ,|,|,|_ quantitated|quantitate|VBN|_ by|by|IN|_ absorbance|absorbance|NN|_ at|at|IN|_ 260|260|CD|_ nm|nm|NN|_ and|and|CC|_ stored|store|VBN|_ until|until|IN|_ further|further|JJ|_ use|use|NN|_ for|for|IN|_ microarray|microarray|NN|_ .|.|.|_
WT|WT|NNP|_ _|_|NNP|_ 37C|37C|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ 10|10|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ 2|2|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ 4|4|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ 6|6|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ 8|8|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ before|before|IN|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ with|with|IN|_ a|a|DT|_ precise|precise|JJ|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN and|and|CC|_ 10|10|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ with|with|IN|_ a|a|DT|_ precise|precise|JJ|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN and|and|CC|_ 2|2|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ with|with|IN|_ a|a|DT|_ precise|precise|JJ|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN and|and|CC|_ 4|4|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ with|with|IN|_ a|a|DT|_ precise|precise|JJ|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN and|and|CC|_ 6|6|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ with|with|IN|_ a|a|DT|_ precise|precise|JJ|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN and|and|CC|_ 8|8|CD|_ minutes|minute|NNS|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ with|with|IN|_ a|a|DT|_ precise|precise|JJ|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN before|before|IN|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t0|t0|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t0|t0|NN|_ ,|,|,|_ rep2|rep2|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t10|t10|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t10|t10|NN|_ ,|,|,|_ rep2|rep2|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t2|t2|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t2|t2|NN|_ ,|,|,|_ rep2|rep2|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t4|t4|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t4|t4|NN|_ ,|,|,|_ rep2|rep2|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t6|t6|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t6|t6|NN|_ ,|,|,|_ rep2|rep2|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t8|t8|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ wild|wild|JJ|_ type|type|NN|_ at|at|IN|_ t8|t8|NN|_ ,|,|,|_ rep2|rep2|NN|_
M1655|m1655|NN|_ with|with|IN|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN at|at|IN|_ t0|t0|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ with|with|IN|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN at|at|IN|_ t10|t10|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ with|with|IN|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN at|at|IN|_ t2|t2|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ with|with|IN|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN at|at|IN|_ t4|t4|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ with|with|IN|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN at|at|IN|_ t6|t6|NN|_ ,|,|,|_ rep1|rep1|NN|_
M1655|m1655|NN|_ with|with|IN|_ deletion|deletion|NN|_ in|in|IN|_ soxR|soxr|NN|GEN at|at|IN|_ t8|t8|NN|_ ,|,|,|_ rep1|rep1|NN|_
Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ of|of|IN|_ EZ|ez|NN|_ Rich|rich|JJ|_ Defined|defined|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 125|125|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37oC|37oc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ in|in|IN|_ a|a|DT|_ reciprocating|reciprocate|VBG|_ water|water|NN|_ bath|bath|NN|_ .|.|.|_
Paraquat|Paraquat|NNP|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ growing|grow|VBG|_ cultures|culture|NNS|_ at|at|IN|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 250|250|CD|_ ?|?|.|_ M.|M.|NNP|_ Samples|Samples|NNP|_ -LRB-|-lrb-|-LRB-|_ 1.4|1.4|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ taken|take|VBN|_ every|every|DT|_ 2|2|CD|_ minutes|minute|NNS|_ following|follow|VBG|_ paraquat|paraquat|NN|SUPP treatment|treatment|NN|_ for|for|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ time|time|NN|_ course|course|NN|_ ,|,|,|_ and|and|CC|_ flash-frozen|flash-frozen|JJ|_ by|by|IN|_ immersion|immersion|NN|_ of|of|IN|_ the|the|DT|_ tubes|tube|NNS|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ for|for|IN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ 13,000|13,000|CD|_ rpm|rpm|NN|_ ,|,|,|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ Robust|robust|JJ|_ Multi-Array|multi-array|JJ|_ average|average|NN|_ as|as|IN|_ implemented|implement|VBN|_ in|in|IN|_ Bioconductor|Bioconductor|NNP|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ I|i|CD|_
agitation|agitation|NN|_ speed|speed|NN|_ :|:|:|_ 1200|1200|CD|_ rpm|rpm|NN|_
agitation|agitation|NN|_ speed|speed|NN|_ :|:|:|_ 600|600|CD|_ rpm|rpm|NN|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Data|Data|NNP|_ filtering|filter|VBG|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ in-house|in-house|JJ|_ script|script|NN|_ with|with|IN|_ the|the|DT|_ set|set|VBN|_ value|value|NN|_ as|as|IN|_ follows|follow|VBZ|_ :|:|:|_ Removal|removal|NN|_ if|if|IN|_ %|%|NN|_ of|of|IN|_ N|n|NN|_ nucleotide|nucleotide|NN|_ is|be|VBZ|_ more|more|JJR|_ than|than|IN|_ 10|10|CD|_ %|%|NN|_ ,|,|,|_ if|if|IN|_ more|more|JJR|_ than|than|IN|_ 40|40|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ nucleotide|nucleotide|NN|_ is|be|VBZ|_ Q20|q20|NN|_ or|or|CC|_ less|less|JJR|_ ,|,|,|_ if|if|IN|_ average|average|JJ|_ quality|quality|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ is|be|VBZ|_ less|less|JJR|_ than|than|IN|_ Q20|q20|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Expression|expression|NN|_ of|of|IN|_ introduced|introduce|VBN|_ enzymes|enzyme|NNS|_ for|for|IN|_ 3-HP|3-hp|NN|_ productionm|productionm|NN|_ was|be|VBD|_ induced|induce|VBN|_ by|by|IN|_ 0.05|0.05|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ and|and|CC|_ 50|50|CD|_ µM|µm|NN|_ vitamin|vitamin|NN|_ B12|b12|NN|_ when|when|WRB|_ the|the|DT|_ cell|cell|NN|_ reached|reach|VBN|_ at|at|IN|_ the|the|DT|_ early-exponential|early-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ .|.|.|_ T|t|NN|_
fermentation|fermentation|NN|_ time|time|NN|_ :|:|:|_ 20h|20h|JJ|_
fermentation|fermentation|NN|_ time|time|NN|_ :|:|:|_ 30h|30h|CD|_
fermentation|fermentation|NN|_ time|time|NN|_ :|:|:|_ 40h|40h|JJ|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ http|http|NN|_ :|:|:|_
Illumina|Illumina|NNP|_ Casava|Casava|NNP|_ 1.8.2|1.8.2|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecall|VBG|_ with|with|IN|_ default|default|NN|_ parameter|parameter|NN|_ .|.|.|_
Read|Read|NNP|_ alignment|alignment|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.6.2|0.6.2|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ parameter|parameter|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.coli|e.coli|VB|_ W3110|w3110|NN|_ whole|whole|JJ|_ genome|genome|NN|_ .|.|.|_
SH0003|sh0003|NN|_ 30h|30h|CD|_
SH0012|sh0012|NN|_ 20h|20h|JJ|_
SH0012|sh0012|NN|_ 30h|30h|CD|_
Sh0012|sh0012|NN|_ 40h|40h|CD|_
SH0012|sh0012|NN|_ and|and|CC|_ SH0003|sh0003|NN|_ were|be|VBD|_ fermented|ferment|VBN|_ in|in|IN|_ a|a|DT|_ 5.0|5.0|CD|_ L|l|NN|_ jar-fermenter|jar-fermenter|NN|_ with|with|IN|_ a|a|DT|_ 2.0|2.0|CD|_ working|work|VBG|_ voulume|voulume|NN|_ of|of|IN|_ modified|modify|VBN|_ R|r|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 20g|20g|JJ|_
SH0012|sh0012|NN|_ no|no|DT|_ rpm|rpm|NN|_ change|change|NN|_
SH0012|sh0012|NN|_ no|no|DT|_ vitamin|vitamin|NN|_ B12|b12|NN|_
strain|strain|NN|_ :|:|:|_ SH0003|sh0003|NN|_
strain|strain|NN|_ :|:|:|_ SH0012|sh0012|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
The|the|DT|_ bacterial|bacterial|JJ|_ cells|cell|NNS|_ from|from|IN|_ 5L|5l|NN|_ fermentation|fermentation|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 20h|20h|CD|_ ,|,|,|_ 30h|30h|CD|_ ,|,|,|_ 40h|40h|NN|_ and|and|CC|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ to|to|TO|_ pellet|pellet|VB|_ the|the|DT|_ cells|cell|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ then|then|RB|_ mixed|mix|VBN|_ with|with|IN|_ 500mL|500ml|NN|_ of|of|IN|_ RNA|rna|NN|_ protectant|protectant|NN|_ bacterial|bacterial|JJ|_ reagents|reagent|NNS|_ to|to|TO|_ stabilize|stabilize|VB|_ RNA|rna|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ use|use|NN|_ .|.|.|_ Total|total|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ and|and|CC|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ to|to|TO|_ remove|remove|VB|_ DNA|dna|NN|_ .|.|.|_
The|the|DT|_ RNA-Seq|rna-seq|JJ|_ library|library|NN|_ was|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ RNA|rna|NN|_ Preparation|preparation|NN|_ Kit|kit|NN|_ .|.|.|_
Transcript|Transcript|NNP|_ assembly|assembly|NN|_ an|a|DT|_ quantification|quantification|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ protocols|protocol|NNS|_ from|from|IN|_ Trapnell|Trapnell|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ and|and|CC|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Fragments|fragment|NNS|_ Per|per|IN|_ Kilobases|kilobase|NNS|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ .|.|.|_
Cells|cell|NNS|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|MED media|media|NNS|MED at|at|IN|_ 37C|37c|NN|_ were|be|VBD|_ harvested|harvest|VBN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ expressing|express|VBG|_ dr1558|dr1558|NN|_ replicate|replicate|VB|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ expressing|express|VBG|_ dr1558|dr1558|NN|_ replicate|replicate|VB|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ expressing|express|VBG|_ dr1558|dr1558|NN|_ replicate|replicate|VB|_ 3|3|CD|_
E.|E.|NNP|_ coli|coli|NN|_ harboring|harboring|NN|_ pRadGro|pradgro|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ harboring|harboring|NN|_ pRadGro|pradgro|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ harboring|harboring|NN|_ pRadGro|pradgro|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
Ec-pR|ec-pr|NN|_ VS|vs|NN|_ Ec-1558|ec-1558|NN|_ rep1|rep1|NN|_
Ec-pR|ec-pr|NN|_ VS|vs|NN|_ Ec-1558|ec-1558|NN|_ rep2|rep2|NN|_
Ec-pR|ec-pr|NN|_ VS|vs|NN|_ Ec-1558|ec-1558|NN|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Non-treatment|non-treatment|JJ|_
strain|strain|NN|_ information|information|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ harboring|harboring|NN|_ empty|empty|JJ|_ vector|vector|NN|_ -LRB-|-lrb-|-LRB-|_ pRADgro|pradgro|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ control|control|NN|_ strain|strain|NN|_
strain|strain|NN|_ information|information|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ harboring|harbor|VBG|_ pRADgro|pradgro|NN|_ :|:|:|_ :|:|:|_ dr1558|dr1558|CD|_
The|the|DT|_ genes|gene|NNS|_ were|be|VBD|_ considered|consider|VBN|_ differentially|differentially|RB|_ expressed|express|VBN|_ when|when|WRB|_ the|the|DT|_ logarithmic|logarithmic|JJ|_ gene|gene|NN|_ expression|expression|NN|_ ratios|ratio|NNS|_ had|have|VBD|_ a|a|DT|_ 2-fold|2-fold|JJ|_ difference|difference|NN|_ in|in|IN|_ the|the|DT|_ expression|expression|NN|_ level|level|NN|_ .|.|.|_ The|the|DT|_ significance|significance|NN|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Student|student|NN|_ 's|'s|POS|_ t|t|NN|_ test|test|NN|_ .|.|.|_ P-values|p-value|NNS|_ of|of|IN|_ less|less|JJR|_ than|than|IN|_ 0.01|0.01|CD|_ were|be|VBD|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
The|the|DT|_ genes|gene|NNS|_ were|be|VBD|_ filtered|filter|VBN|_ by|by|IN|_ removing|remove|VBG|_ the|the|DT|_ flag-out|flag-out|JJ|_ genes|gene|NNS|_ in|in|IN|_ each|each|DT|_ experiment|experiment|NN|_ .|.|.|_ The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ normalized|normalize|VBN|_ through|through|IN|_ LOWESS|lowess|NN|_ regression|regression|NN|_ for|for|IN|_ 3|3|CD|_ datasets|dataset|NNS|_ obtained|obtain|VBN|_ from|from|IN|_ 3|3|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ RiboEX|RiboEX|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ GeneAll|GeneAll|NNP|_ ,|,|,|_ Korea|Korea|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ treated|treat|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ ,|,|,|_ and|and|CC|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Rneasy|Rneasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
0|0|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
0|0|CD|_ '|'|''|_ in|in|IN|_ min|min|NN|_ med|med|VBD|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25ug|25ug|JJ|_ total|total|JJ|_ RNA|rna|NN|_
0|0|CD|_ '|'|''|_ minimal|minimal|JJ|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
0|0|CD|_ '|'|''|_ minimal|minimal|JJ|_ +02|+02|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
0|0|CD|_ '|'|''|_ minimal|minimal|JJ|_ medium|medium|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_
Adaptor|adaptor|NN|_ Sequences|sequence|NNS|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
All|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ processed|process|VBN|_ following|follow|VBG|_ NEB|NEB|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ from|from|IN|_ the|the|DT|_ NEBNext|nebnext|NN|_ ®|®|NN|_ ChIP-Seq|chip-seq|JJ|_ library|library|NN|_ preparation|preparation|NN|_ kit|kit|NN|_ .|.|.|_
bacterial|bacterial|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ _|_|VBP|_ input|input|NN|_
bacterial|bacterial|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ _|_|VBP|_ RecA-ChIP-seq|reca-chip-seq|JJ|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ 1X|1x|NN|_ PBS|PBS|NNP|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ then|then|RB|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 250|250|CD|_ μl|μl|NN|_ ChIP|chip|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 600|600|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ 4|4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X|X|NNP|_ ,|,|,|_ Complete|complete|JJ|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ EDTA-free|edta-free|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Sonication|sonication|NN|_ of|of|IN|_ crosslinked|crosslink|VBN|_ samples|sample|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Diagenode|Diagenode|NNP|_ Bioruptor|Bioruptor|NNP|_ ®|®|NN|_ at|at|IN|_ 30s|30s|CD|_ intervals|interval|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ high|high|JJ|_ amplitude|amplitude|NN|_ .|.|.|_ After|after|IN|_ sonication|sonication|NN|_ ,|,|,|_ 350|350|CD|_ μl|μl|NN|_ of|of|IN|_ ChIP|chip|NN|_ buffer|buffer|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ by|by|IN|_ gentle|gentle|JJ|_ pipetting|pipetting|NN|_ and|and|CC|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ lysate|lysate|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ stored|store|VBN|_ as|as|IN|_ `|`|``|_ input|input|NN|_ '|'|''|_ .|.|.|_ Immunoprecipitation|immunoprecipitation|NN|_ was|be|VBD|_ performed|perform|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ using|use|VBG|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ casamino|casamino|NN|SUPP acids|acid|NNS|SUPP ,|,|,|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP 5μM|5μm|NN|_ CaCl2|cacl2|NN|_ and|and|CC|_ 1mM|1mm|NN|_ MgSO4|mgso4|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ and|and|CC|_ OD600nm|od600nm|NN|_ of|of|IN|_ 0.2-0.25|0.2-0.25|CD|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-RecA|anti-reca|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ cat|cat|NN|_ .|.|.|_ #|#|#|_ :|:|:|_ ab63797|ab63797|CD|_
chip|chip|NN|_ antibody|antibody|NN|_ vendor|vendor|NN|_ :|:|:|_ Abcam|Abcam|NNP|_
ChIP-Seq|ChIP-Seq|NNP|_
Data|Data|NNP|_ collapsed|collapse|VBD|_ using|use|VBG|_ fastx|fastx|NN|_ collapser|collapser|NN|_ to|to|TO|_ remove|remove|VB|_ identical|identical|JJ|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
DL4899|dl4899|NN|_
DL4900|dl4900|NN|_
DL4900|dl4900|NN|_ _|_|NN|_ input|input|NN|_
DL5215|dl5215|NN|_
DL5322|dl5322|NN|_
DL5324|dl5324|NN|_
DL5326|dl5326|NN|_
DL5328|dl5328|NN|_
DL5330|dl5330|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ MG1655|mg1655|NN|_ NC000913|nc000913|NN|_ .3|.3|NN|_
Protein|protein|NN|_ DNA|dna|NN|_ interactions|interaction|NNS|_ were|be|VBD|_ crosslinked|crosslink|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 22.5|22.5|CD|_ C|c|NN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ and|and|CC|_ quenched|quench|VBN|_ using|use|VBG|_ glycine|glycine|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ M|m|NN|_
reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ genome|genome|NN|_ using|use|VBG|_ Novoalign|novoalign|JJ|_ version|version|NN|_ 2.07|2.07|CD|_ -LRB-|-lrb-|-LRB-|_ www.novocraft.com|www.novocraft.com|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Example|example|NN|_ :|:|:|_ -LRB-|-lrb-|-LRB-|_ novoalign|novoalign|JJ|_ -|-|:|_ f|f|FW|_ DL4900|dl4900|FW|_ _|_|SYM|_ clip|clip|VB|_ _|_|SYM|_ clp.fasta|clp.fasta|SYM|_ -|-|:|_ d|d|NN|_ NC000913|nc000913|NN|_ .3|.3|NN|_ .|.|.|_ nix|nix|SYM|_ -|-|:|_ r|r|NN|_ Random|Random|NNP|_ >|>|JJR|_ DL4900.novo|dl4900.novo|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ 246pal|246pal|JJ|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χ|χ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ codBχ|codbχ|NN|_ -|-|:|_ prpEχ|prpeχ|NN|_ -|-|:|_ mhpCχ|mhpcχ|NN|_ -|-|:|_ cynXχ|cynxχ|NN|_ -|-|:|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ 246pal|246pal|JJ|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χχ|χχ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ codBχ|codbχ|NN|_ -|-|:|_ prpEχ|prpeχ|NN|_ -|-|:|_ mhpCχ|mhpcχ|NN|_ -|-|:|_ cynXχ|cynxχ|NN|_ -|-|:|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ 246pal|246pal|JJ|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ codBχ|codbχ|NN|_ -|-|:|_ prpEχ|prpeχ|NN|_ -|-|:|_ mhpCχ|mhpcχ|NN|_ -|-|:|_ cynXχ|cynxχ|NN|_ -|-|:|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ 246pal|246pal|JJ|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ 246pal|246pal|JJ|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χχχχ|χχχχ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ codBχ|codbχ|NN|_ -|-|:|_ prpEχ|prpeχ|NN|_ -|-|:|_ mhpCχ|mhpcχ|NN|_ -|-|:|_ cynXχ|cynxχ|NN|_ -|-|:|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ 246pal|246pal|JJ|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χχχχχ|χχχχχ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ codBχ|codbχ|NN|_ -|-|:|_ prpEχ|prpeχ|NN|_ -|-|:|_ mhpCχ|mhpcχ|NN|_ -|-|:|_ cynXχ|cynxχ|NN|_ -|-|:|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ details|detail|NNS|_ :|:|:|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ 246pal|246pal|JJ|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacZY|laczy|NN|_ :|:|:|_ :|:|:|_ χχχχχχ|χχχχχχ|NN|_ mhpA|mhpa|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ codBχ|codbχ|NN|_ -|-|:|_ prpEχ|prpeχ|NN|_ -|-|:|_ mhpCχ|mhpcχ|NN|_ -|-|:|_ cynXχ|cynxχ|NN|_ -|-|:|_ rph|rph|NN|GEN +|+|CC|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ txt|txt|NN|_ files|file|NNS|_ including|include|VBG|_ count|count|NN|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ whole|whole|JJ|_ genome|genome|NN|_
yPileup|ypileup|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ count|count|NN|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ whole|whole|JJ|_ genome|genome|NN|_ -|-|:|_ Example|example|NN|_ :|:|:|_ pyPileup.py|pypileup.py|NN|_ --|--|:|_ file|file|NN|_ _|_|NN|_ type|type|NN|_ =|=|JJ|_ novo|novo|FW|_ -|-|:|_ f|f|LS|_ DL4900.novo|dl4900.novo|NN|_ --|--|:|_ tab|tab|NN|_ =|=|JJ|_ NC000913|nc000913|NN|_ .3|.3|NN|_ .|.|.|_ tab|tab|NN|_ --|--|:|_ chr|chr|NN|_ =|=|JJ|_ Wholechom.txt.gz|wholechom.txt.gz|NN|_ --|--|:|_ ignorestrand|ignorestrand|JJ|_
15|15|CD|_ '|'|''|_ 10|10|CD|_ ug|ug|NN|_
15|15|CD|_ '|'|''|_ 15|15|CD|_ ug|ug|NN|_
15|15|CD|_ '|'|''|_ +50|+50|CD|_ ug|ug|NN|_
Aeration|Aeration|NNP|_ was|be|VBD|_ initiated|initiate|VBN|_ at|at|IN|_ 1|1|CD|_ l|l|NN|_
alignment|alignment|NN|_ :|:|:|_ STAR|star|NN|_ 2.4.0|2.4.0|CD|_ i|i|FW|_
batch|batch|NN|_ culture|culture|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep1|rep1|NN|_ ,|,|,|_ 0.5|0.5|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep1|rep1|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep1|rep1|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep1|rep1|NN|_ ,|,|,|_ 1|1|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep1|rep1|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep1|rep1|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep2|rep2|NN|_ ,|,|,|_ 0.5|0.5|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep2|rep2|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep2|rep2|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep2|rep2|NN|_ ,|,|,|_ 1|1|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep2|rep2|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep2|rep2|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep3|rep3|NN|_ ,|,|,|_ 0.5|0.5|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep3|rep3|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep3|rep3|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep3|rep3|NN|_ ,|,|,|_ 1|1|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep3|rep3|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_
batch|batch|NN|_ culture|culture|NN|_ rep3|rep3|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_
Cell|cell|NN|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 3-liter|3-liter|NN|_ stirred|stir|VBD|_ tank|tank|NN|_ bioreactor|bioreactor|NN|_ anaerobically|anaerobically|RB|_ .|.|.|_ The|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ contained|contain|VBD|_ Na2H2PO4|na2h2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ g|g|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
gene|gene|NN|_ counting|counting|NN|_ :|:|:|_ HTSeq-Count|htseq-count|JJ|_ 0.6.0|0.6.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC007779|nc007779|NN|_ .1|.1|NN|_ -LRB-|-lrb-|-LRB-|_ UCSC|ucsc|NN|_ Archaeal|archaeal|NN|_ Genome|Genome|NNP|_ Browser|Browser|NNP|_ -RRB-|-rrb-|-RRB-|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
replicate|replicate|VBP|_ :|:|:|_ 3|3|CD|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Samples|sample|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ RNAprotect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ preparation|preparation|NN|_ .|.|.|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ TruSeq|truseq|NN|_ ™|™|CD|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ Kitv2|kitv2|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ file|file|NN|_ format|format|NN|_ is|be|VBZ|_ .|.|.|_ xlsx|xlsx|NN|_ .|.|.|_ The|the|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ of|of|IN|_ all|all|DT|_ samples|sample|NNS|_ .|.|.|_
time|time|NN|_ :|:|:|_ 0.5|0.5|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
15|15|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
15|15|CD|_ '|'|''|_ in|in|IN|_ min|min|NN|_ med|med|VBD|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ +50|+50|CD|_ ug|ug|NN|_
15|15|CD|_ '|'|''|_ vs|vs|CC|_ 0|0|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_
agent|agent|NN|_ :|:|:|_ control|control|NN|_
agent|agent|NN|_ :|:|:|_ CORM-401|corm-401|NN|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_ 10.10.1.1|10.10.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
Continuous|continuous|JJ|_ aerobically|aerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ CORM-401|corm-401|NN|_ samples|sample|NNS|_ or|or|CC|_ samples|sample|NNS|_ prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ CORM-401|corm-401|NN|_
Continuous|continuous|JJ|_ anaerobically|anaerobically|RB|_ grown|grow|VBN|_ cultures|culture|NNS|_ in|in|IN|_ Evans|Evans|NNP|_ medium|medium|NN|_ ,|,|,|_ CORM-401|corm-401|NN|_ samples|sample|NNS|_ or|or|CC|_ samples|sample|NNS|_ prior|prior|RB|_ to|to|TO|_ addition|addition|NN|_ of|of|IN|_ CORM-401|corm-401|NN|_
culture|culture|NN|_ conditions|condition|NNS|_ :|:|:|_ aerobic|aerobic|JJ|_
culture|culture|NN|_ conditions|condition|NNS|_ :|:|:|_ anaerobic|anaerobic|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Slide|slide|VBP|_ 46|46|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 46|46|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 46|46|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 46|46|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|slide|VBP|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 48|48|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 53|53|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|slide|NN|_ 53|53|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|slide|NN|_ 53|53|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 53|53|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 54|54|CD|_ _|_|SYM|_ Aerobic|aerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 58|58|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 10|10|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 20|20|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 40|40|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 59|59|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 2|2|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 80|80|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 10|10|CD|_
Slide|Slide|NNP|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 20|20|CD|_
Slide|Slide|NNP|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 2.5|2.5|CD|_
Slide|Slide|NNP|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 40|40|CD|_
Slide|slide|NN|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 5|5|CD|_
Slide|Slide|NNP|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|NN|_ Cy3|cy3|NN|_ 0|0|CD|_ Cy5|cy5|NN|_ 80|80|CD|_
Slide|Slide|NNP|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 2.5|2.5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
Slide|Slide|NNP|_ 70|70|CD|_ _|_|SYM|_ Anaerobic|anaerobic|JJ|_ culture|culture|NN|_ _|_|NN|_ CORM-401|corm-401|NN|_ _|_|CD|_ biol|biol|NN|_ rep|rep|NN|GEN 1|1|CD|_ _|_|CD|_ Cy3|cy3|NN|_ 5|5|CD|_ Cy5|cy5|NN|_ 0|0|CD|_
strain|strain|NN|_ :|:|:|_ Wild|Wild|NNP|_ type|type|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_
time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 2.5|2.5|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 40|40|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 80|80|CD|_ min|min|NN|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
K12|k12|NN|_ WT|wt|JJ|_ 3110|3110|CD|_
MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ Kit|kit|NN|_
Overnight|overnight|JJ|_ culture|culture|NN|_
phoU|phou|NN|GEN _|_|NN|_ 1|1|CD|_
phoU|phou|NN|GEN _|_|NN|_ 2|2|CD|_
phoU|phou|NN|GEN _|_|CD|_ 3|3|CD|_
phoU|phou|NN|GEN gene|gene|NN|_ mutant|mutant|JJ|_
phoU|phou|NN|GEN gene|gene|NN|_ mutant|mutant|NN|_ ;|;|:|_ minimal|minimal|JJ|_ medium|medium|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ GCOS|gcos|NN|_ 1.4|1.4|CD|_ software|software|NN|_ .|.|.|_ All|all|DT|_ probe|probe|NN|_ sets|set|VBZ|_ scaling|scale|VBG|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ a|a|DT|_ target|target|NN|_ signal|signal|NN|_ value|value|NN|_ of|of|IN|_ 500|500|CD|_ .|.|.|_ No|no|DT|_ normalization|normalization|NN|_ was|be|VBD|_ performed|perform|VBN|_ .|.|.|_
wildtype|wildtype|JJ|_ strain|strain|NN|_ ;|;|:|_ minimal|minimal|JJ|_ medium|medium|NN|_
WT3110|wt3110|NN|_ _|_|NN|_ 1|1|CD|_
WT3110|wt3110|NN|_ _|_|NN|_ 2|2|CD|_
WT3110|wt3110|NN|_ _|_|CD|_ 3|3|CD|_
30|30|CD|_ '|'|''|_ 10|10|CD|_ ug|ug|NN|_
30|30|CD|_ '|'|''|_ 15|15|CD|_ ug|ug|NN|_
30|30|CD|_ '|'|''|_ +50|+50|CD|_ ug|ug|NN|_
30|30|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
30|30|CD|_ '|'|''|_ in|in|IN|_ min|min|NN|_ med|med|VBD|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ +50|+50|CD|_ ug|ug|NN|_
30|30|CD|_ '|'|''|_ vs|vs|CC|_ 0|0|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ HPA|hpa|NN|_ 0mM|0mm|NN|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ HPA|hpa|NN|_ 3mM|3mm|NN|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 3|3|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ heptanoic|heptanoic|JJ|_ acid|acid|NN|_
BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ without|without|IN|_ heptanoic|heptanoic|JJ|_ acid|acid|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
K12|k12|NN|_ MG1655|mg1655|NN|_ with|with|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP of|of|IN|_ heptanoic|heptanoic|JJ|_ acid|acid|NN|_
K12|k12|NN|_ MG1655|mg1655|NN|_ without|without|IN|_ heptanoic|heptanoic|JJ|_ acid|acid|NN|_
metabolic|metabolic|JJ|_ response|response|NN|_ :|:|:|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ very|very|RB|_ susceptible|susceptible|JJ|_ to|to|TO|_ heptanoic|heptanoic|JJ|_ acid|acid|NN|_ ,|,|,|_ because|because|IN|_ several|several|JJ|_ acid|acid|NN|_ resistance|resistance|NN|_ systems|system|NNS|_ stay|stay|VBP|_ inactive|inactive|JJ|_ under|under|IN|_ this|this|DT|_ stress|stress|NN|_ condition|condition|NN|_
metabolic|metabolic|JJ|_ response|response|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ activates|activate|VBZ|_ various|various|JJ|_ acid|acid|NN|_ resistance|resistance|NN|_ systems|system|NNS|_ under|under|IN|_ heptanoic|heptanoic|JJ|_ acid|acid|NN|_ stress|stress|NN|_
MG1655|mg1655|NN|_ HPA|hpa|NN|_ 0mM|0mm|NN|_
MG1655|mg1655|NN|_ HPA|hpa|NN|_ 10mM|10mm|NN|_
strain|strain|NN|_ :|:|:|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
stress|stress|NN|_ :|:|:|_ control|control|NN|_
stress|stress|NN|_ :|:|:|_ heptanoic|heptanoic|JJ|_ acid|acid|NN|_
The|the|DT|_ average|average|JJ|_ fluorescence|fluorescence|NN|_ intensity|intensity|NN|_ for|for|IN|_ each|each|DT|_ spot|spot|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ and|and|CC|_ local|local|JJ|_ background|background|NN|_ was|be|VBD|_ subtracted|subtract|VBN|_ .|.|.|_ All|all|DT|_ data|datum|NNS|_ normalization|normalization|NN|_ and|and|CC|_ selection|selection|NN|_ of|of|IN|_ fold-changed|fold-changed|JJ|_ genes|gene|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ GeneSpringGX|GeneSpringGX|NNP|_ 7.3.1|7.3.1|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technology|Technology|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Normalization|normalization|NN|_ for|for|IN|_ Agilent|Agilent|NNP|_ one-color|one-color|JJ|_ method|method|NN|_ was|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ Data|Data|NNP|_ transformation|transformation|NN|_ :|:|:|_ Set|set|VB|_ measurements|measurement|NNS|_ less|less|JJR|_ than|than|IN|_ 5.0|5.0|CD|_ to|to|TO|_ 5.0|5.0|CD|_ and|and|CC|_ Per|per|IN|_ Chip|chip|NN|_ :|:|:|_ Normalize|normalize|VB|_ to|to|TO|_ 50th|50th|JJ|_ percentage|percentage|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_
When|when|WRB|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ cultivated|cultivate|VBN|_ to|to|TO|_ the|the|DT|_ exponential|exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ Riesenberg|Riesenberg|NNP|_ medium|medium|NN|_ ,|,|,|_ 3|3|CD|_ or|or|CC|_ 10|10|CD|_ mM|mm|NN|KWSUPP heptanoic|heptanoic|JJ|_ acid|acid|NN|_ was|be|VBD|_ treated|treat|VBN|_ to|to|TO|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_ After|after|IN|_ 3|3|CD|_ h|h|NN|_ incubation|incubation|NN|_ ,|,|,|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ for|for|IN|_ transcriptome|transcriptome|NN|_ analysis|analysis|NN|_
aspC|aspc|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
aspC|aspc|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
aspC|aspc|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ Vol|vol|NN|_ of|of|IN|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ in|in|IN|_ ethanol|ethanol|NN|_ and|and|CC|_ frozen|freeze|VBN|_ at|at|IN|_ -80|-80|CD|_ C.|C.|NNP|_ Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
cysA|cysa|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
cysA|cysa|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
cysA|cysa|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
cysG|cysg|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
cysG|cysg|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
cysH|cysh|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
cysH|cysh|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
dcd|dcd|NN|GEN KO|KO|NNP|_ LB|LB|NNP|_ rep1|rep1|NN|_
dcd|dcd|NN|GEN KO|KO|NNP|_ LB|LB|NNP|_ rep2|rep2|NN|_
dcd|dcd|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep1|rep1|NN|_
dcd|dcd|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep2|rep2|NN|_
entF|entf|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
entF|entf|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
entF|entf|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW25113|bw25113|NN|_
fadr|fadr|NN|_ KO|ko|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
fadr|fadr|NN|_ KO|ko|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
fadr|fadr|NN|_ KO|ko|NN|_ M9|m9|NN|_ rep1|rep1|NN|_
fadr|fadr|NN|_ KO|ko|NN|_ M9|m9|NN|_ rep2|rep2|NN|_
fepA|fepa|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
fepA|fepa|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
fepA|fepa|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep1|rep1|NN|_
fepA|fepa|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep2|rep2|NN|_
fliY|fliy|NN|_ KO|ko|NN|_ rep1|rep1|NN|_
fliY|fliy|NN|_ KO|ko|NN|_ rep2|rep2|NN|_
fliY|fliy|NN|_ KO|ko|NN|_ rep3|rep3|NN|_
For|for|IN|_ RNA-Seq|rna-seq|NN|_ analysis|analysis|NN|_ ,|,|,|_ the|the|DT|_ fastq|fastq|NN|_ file|file|NN|_ produced|produce|VBN|_ from|from|IN|_ the|the|DT|_ machine|machine|NN|_ was|be|VBD|_ demultiplexed|demultiplex|VBN|_ into|into|IN|_ a|a|DT|_ separate|separate|JJ|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
For|for|IN|_ the|the|DT|_ first|first|JJ|_ batch|batch|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ WT|WT|NNP|_ _|_|NNP|_ LB|LB|NNP|_ _|_|SYM|_ 1|1|CD|_ to|to|TO|_ lacA|lacA|NNP|GEN _|_|NNP|_ M9|M9|NNP|_ _|_|SYM|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ fresh|fresh|JJ|_ colonies|colony|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ were|be|VBD|_ taken|take|VBN|_ and|and|CC|_ inoculated|inoculate|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ LB|lb|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 8|8|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ 20|20|CD|_ µL|µl|NN|_ of|of|IN|_ grown|grown|JJ|_ culture|culture|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ to|to|TO|_ 3|3|CD|_ ml|ml|NN|_ LB|lb|NN|_
gabT|gabt|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
gabT|gabt|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
gabT|gabt|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
galE|gale|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
galE|gale|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
galE|gale|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ RefSeq|RefSeq|NNP|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_
genotype|genotype|NN|_
HTSeq|htseq|NN|_ is|be|VBZ|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
Index|Index|NNP|_ sequences|sequence|NNS|_ accompanying|accompany|VBG|_ with|with|IN|_ reads|read|VBZ|_ were|be|VBD|_ compared|compare|VBN|_ with|with|IN|_ pre-designed|pre-designed|JJ|_ barcodes|barcode|NNS|_ ,|,|,|_ allowing|allow|VBG|_ two|two|CD|_ base|base|NN|_ mismatches|mismatch|NNS|_ at|at|IN|_ most|most|JJS|_ .|.|.|_
kefB|kefb|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
kefB|kefb|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
kefB|kefb|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
khc|khc|NN|_ KO|ko|NN|_ rep1|rep1|NN|_
khc|khc|NN|_ KO|ko|NN|_ rep2|rep2|NN|_
khc|khc|NN|_ KO|ko|NN|_ rep3|rep3|NN|_
lacA|laca|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
lacA|laca|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
lacA|laca|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep1|rep1|NN|_
lacA|laca|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep2|rep2|NN|_
Library|Library|NNP|_ constructed|construct|VBN|_ using|use|VBG|_ KAPA|KAPA|NNP|_ Kit|kit|NN|_ .|.|.|_
lplA|lpla|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
lplA|lpla|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
lplA|lpla|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
media|media|NNS|_ :|:|:|_ LB|lb|NN|_
media|media|NNS|_ :|:|:|_ M9|m9|NN|_
mgtA|mgta|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
mgtA|mgta|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
mgtA|mgta|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
mhpD|mhpd|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
mhpD|mhpd|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
mhpD|mhpd|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
Parent|Parent|NNP|_ LB|LB|NNP|_ rep1|rep1|NN|_
Parent|Parent|NNP|_ LB|LB|NNP|_ rep2|rep2|NN|_
Parent|Parent|NNP|_ M9|M9|NNP|_ rep1|rep1|NN|_
Parent|Parent|NNP|_ M9|M9|NNP|_ rep2|rep2|NN|_
ppk|ppk|NN|GEN KO|KO|NNP|_ LB|LB|NNP|_ rep1|rep1|NN|_
ppk|ppk|NN|GEN KO|KO|NNP|_ LB|LB|NNP|_ rep2|rep2|NN|_
ppk|ppk|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep1|rep1|NN|_
ppk|ppk|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep2|rep2|NN|_
putP|putp|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
putP|putp|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
putP|putp|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
rfbA|rfba|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
rfbA|rfba|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
rfbA|rfba|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
RNA-Seq|rna-seq|NN|_
sdhC|sdhc|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
sdhC|sdhc|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
sdhC|sdhc|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
strain|strain|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ htcount|htcount|NN|_ :|:|:|_ expression|expression|NN|_ count|count|NN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ and|and|CC|_ its|its|PRP$|_ name|name|NN|_ .|.|.|_
The|the|DT|_ low-quality|low-quality|NN|_ of|of|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trimmomatic|trimmomatic|JJ|_ -LRB-|-lrb-|-LRB-|_ v0|v0|JJ|_ .30|.30|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
treatment|treatment|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ on|on|IN|_ most|most|JJS|_ recent|recent|JJ|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ U00096|u00096|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ using|use|VBG|_ TopHat|TopHat|NNP|_ -LRB-|-lrb-|-LRB-|_ v2|v2|NN|_ .0.10|.0.10|CD|_ -RRB-|-rrb-|-RRB-|_ coupled|couple|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .0.0|.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
trpD|trpd|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
trpD|trpd|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
trpD|trpd|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
ugpC|ugpc|NN|GEN KO|ko|NN|_ rep1|rep1|NN|_
ugpC|ugpc|NN|GEN KO|ko|NN|_ rep2|rep2|NN|_
ugpC|ugpc|NN|GEN KO|ko|NN|_ rep3|rep3|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ aspC|aspc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysA|cysa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysG|cysg|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ cysH|cysh|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ dcd|dcd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ entF|entf|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fadR|fadr|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fepA|fepa|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fepA|fepa|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ fliY|fliy|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ gabT|gabt|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ galE|gale|NN|GEN KO|KO|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ kefB|kefb|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ khc|khc|NN|_ KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lacA|laca|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lacA|laca|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ lplA|lpla|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mgtA|mgta|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ mhpD|mhpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ppk|ppk|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ putP|putp|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ rfbA|rfba|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ sdhC|sdhc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ trpD|trpd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ ugpC|ugpc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ LB|LB|NNP|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ WT|WT|NNP|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ wzc|wzc|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ LB|lb|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
Whole|whole|JJ|_ cell|cell|NN|_ ,|,|,|_ yghD|yghd|NN|GEN KO|ko|NN|_ ,|,|,|_ M9|m9|NN|_ and|and|CC|_ 0.3|0.3|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP
WT|wt|JJ|_ rep1|rep1|NN|_
WT|wt|JJ|_ rep2|rep2|NN|_
WT|wt|JJ|_ rep3|rep3|NN|_
wzc|wzc|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
wzc|wzc|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
wzc|wzc|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep1|rep1|NN|_
wzc|wzc|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep2|rep2|NN|_
yghD|yghd|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep1|rep1|NN|_
yghD|yghd|NN|GEN KO|ko|NN|_ LB|lb|NN|_ rep2|rep2|NN|_
yghD|yghd|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep1|rep1|NN|_
yghD|yghd|NN|GEN KO|ko|NN|_ M9|m9|NN|_ rep2|rep2|NN|_
5-azacytidine-treated|5-azacytidine-treated|JJ|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extract|extract|NN|_ software|software|NN|_ performed|perform|VBN|_ background|background|NN|_ normalization|normalization|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ correction|correction|NN|_ for|for|IN|_ dye|dye|VB|_ bias|bias|NN|_ .|.|.|_ Non-E|non-e|NN|_ .|.|.|_ coli|coli|NN|_ K-12|k-12|NN|_ probes|probe|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ the|the|DT|_ dataset|dataset|NN|_ ,|,|,|_ as|as|IN|_ the|the|DT|_ BW25113|bw25113|NN|_ strain|strain|NN|_ is|be|VBZ|_ a|a|DT|_ K-12|k-12|NN|_ strain|strain|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ the|the|DT|_ absence|absence|NN|_ and|and|CC|_ presence|presence|NN|_ of|of|IN|_ 0.005|0.005|CD|_ mg|mg|NN|_
early|early|JJ|GrowthPhase stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 1|1|CD|_
early|early|JJ|GrowthPhase stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 2|2|CD|_
early|early|JJ|GrowthPhase stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 3|3|CD|_
early|early|JJ|GrowthPhase stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 4|4|CD|_
early|early|JJ|GrowthPhase stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase 5|5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 250|250|CD|_ RPM|rpm|NNS|_
log|log|VBP|_ phase|phase|NN|_ 1|1|CD|_
log|log|NN|_ phase|phase|NN|_ 2|2|CD|_
log|log|VBP|_ phase|phase|NN|_ 3|3|CD|_
log|log|NN|_ phase|phase|NN|_ 4|4|CD|_
log|log|VBP|_ phase|phase|NN|_ 5|5|CD|_
phase|phase|NN|_ :|:|:|_ early|early|JJ|GrowthPhase stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ the|the|DT|_ MasterPure|masterpure|NN|_ RNA|rna|NN|_ Isolation|isolation|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ enriched|enriched|JJ|_ for|for|IN|_ mRNA|mrna|NN|_ using|use|VBG|_ the|the|DT|_ mRNA|mrna|NN|_ Prokaryotic|prokaryotic|JJ|_ mRNA|mrna|NN|_ Isolation|isolation|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ polyadenylated|polyadenylated|JJ|_ with|with|IN|_ kit|kit|NN|_ all|all|DT|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_
untreated|untreated|JJ|_
150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_
240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_
360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|LB|NNP|_
90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|LB|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 150|150|CD|_ minutes|minute|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 240|240|CD|_ minutes|minute|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 360|360|CD|_ minutes|minute|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 90|90|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ fis|fis|NN|GEN :|:|:|_ :|:|:|_ kan|kan|NN|_ grown|grow|VBN|_ 150|150|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ fis|fis|NN|GEN :|:|:|_ :|:|:|_ kan|kan|NN|_ grown|grow|VBN|_ 240|240|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ fis|fis|NN|GEN :|:|:|_ :|:|:|_ kan|kan|NN|_ grown|grow|VBN|_ 360|360|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ fis|fis|NN|GEN :|:|:|_ :|:|:|_ kan|kan|NN|_ grown|grow|VBN|_ 90|90|CD|_ minutes|minute|NNS|_
fis|fis|NN|GEN 150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
fis|fi|VBZ|GEN 150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
fis|fi|VBZ|GEN 150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
fis|fi|VBZ|GEN 240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
fis|fi|VBZ|GEN 240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
fis|fi|VBZ|GEN 240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
fis|fi|VBZ|GEN 360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
fis|fi|VBZ|GEN 360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
fis|fi|VBZ|GEN 360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
fis|fi|VBZ|GEN 90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
fis|fi|VBZ|GEN 90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
fis|fi|VBZ|GEN 90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
fis|fi|VBZ|GEN Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ Kit|kit|NN|_ per|per|IN|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_
Saturated|Saturated|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ LB|LB|NNP|_ toan|toan|NN|_ OD.of|od.of|NN|_ 0.05|0.05|CD|_ OD600|od600|NN|_ ,|,|,|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ MAS|mas|NN|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ MAS|mas|NN|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ Data|datum|NNS|_ from|from|IN|_ this|this|DT|_ sample|sample|NN|_ were|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ Affy|Affy|NNP|_ Ecoli|Ecoli|NNP|_ anti-sense|anti-sense|JJ|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ 2001|2001|CD|_ ;|;|:|_ platform|platform|NN|_ ID|id|NN|_ GPL4940|gpl4940|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ but|but|CC|_ because|because|IN|_ the|the|DT|_ analysis|analysis|NN|_ software|software|NN|_ failed|fail|VBD|_ to|to|TO|_ recognize|recognize|VB|_ the|the|DT|_ correct|correct|JJ|_ platform|platform|NN|_ ,|,|,|_ we|we|PRP|_ reformatted|reformat|VBD|_ the|the|DT|_ data|datum|NNS|_ to|to|TO|_ match|match|VB|_ the|the|DT|_ newer|newer|JJR|_ -LRB-|-lrb-|-LRB-|_ and|and|CC|_ mostly|mostly|RB|_ equivalent|equivalent|JJ|_ -RRB-|-rrb-|-RRB-|_ platform|platform|NN|_ GPL199|gpl199|NN|_ -LRB-|-lrb-|-LRB-|_ Affy|Affy|NNP|_ Ecoli|Ecoli|NNP|_ anti-sense|anti-sense|JJ|_ chip|chip|NN|_ version|version|NN|_ 2|2|CD|_ ,|,|,|_ 2002|2002|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Because|because|IN|_ ,|,|,|_ however|however|RB|_ ,|,|,|_ not|not|RB|_ all|all|DT|_ of|of|IN|_ the|the|DT|_ probes|probe|NNS|_ on|on|IN|_ the|the|DT|_ new|new|JJ|_ platform|platform|NN|_ were|be|VBD|_ present|present|JJ|_ on|on|IN|_ the|the|DT|_ old|old|JJ|_ platform|platform|NN|_ ,|,|,|_ data|datum|NNS|_ for|for|IN|_ some|some|DT|_ probes|probe|NNS|_ were|be|VBD|_ unavailable|unavailable|JJ|_ and|and|CC|_ labeled|label|VBN|_ in|in|IN|_ the|the|DT|_ `|`|``|_ remapped|remapped|NN|_ '|'|''|_ dataset|dataset|NN|_ as|as|IN|_ `|`|``|_ NULL|NULL|NNP|_ '|'|''|_ to|to|TO|_ indicate|indicate|VB|_ they|they|PRP|_ were|be|VBD|_ missing|miss|VBG|_ .|.|.|_ While|while|IN|_ the|the|DT|_ following|follow|VBG|_ data|datum|NNS|_ are|be|VBP|_ therefore|therefore|RB|_ formatted|format|VBN|_ using|use|VBG|_ ID|ID|NNP|_ _|_|SYM|_ REFs|ref|NNS|_ that|that|WDT|_ match|match|VBP|_ GPL199|gpl199|NN|_ ,|,|,|_ the|the|DT|_ CEL|CEL|NNP|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ not|not|RB|_ `|`|``|_ remapped|remap|VBN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ thus|thus|RB|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ actual|actual|JJ|_ array|array|NN|_ used|use|VBN|_ -LRB-|-lrb-|-LRB-|_ GPL4940|gpl4940|NN|_ ,|,|,|_ Ecoli|ecoli|JJ|_ antisense|antisense|JJ|_ chip|chip|NN|_ ,|,|,|_ 2001|2001|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_
240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_
360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|LB|NNP|_
90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ in|in|IN|_ LB|LB|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 150|150|CD|_ minutes|minute|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 240|240|CD|_ minutes|minute|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 360|360|CD|_ minutes|minute|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 90|90|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ wt|wt|JJ|_ grown|grown|JJ|_ 150|150|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ wt|wt|JJ|_ grown|grown|JJ|_ 240|240|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ wt|wt|JJ|_ grown|grown|JJ|_ 360|360|CD|_ minutes|minute|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ wt|wt|JJ|_ grown|grown|JJ|_ 90|90|CD|_ minutes|minute|NNS|_
MasterPure|masterpure|NN|_ RNA|rna|NN|_ purification|purification|NN|_ Kit|kit|NN|_ per|per|IN|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_
Saturated|Saturated|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ LB|lb|NN|_ to|to|TO|_ an|a|DT|_ OD.of|od.of|JJ|_ 0.05|0.05|CD|_ OD600|od600|NN|_ ,|,|,|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_
Saturated|Saturated|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ LB|LB|NNP|_ toan|toan|NN|_ OD.of|od.of|NN|_ 0.05|0.05|CD|_ OD600|od600|NN|_ ,|,|,|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ MAS|mas|NN|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ MAS|mas|NN|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ Data|datum|NNS|_ from|from|IN|_ this|this|DT|_ sample|sample|NN|_ were|be|VBD|_ collected|collect|VBN|_ using|use|VBG|_ Affy|Affy|NNP|_ Ecoli|Ecoli|NNP|_ anti-sense|anti-sense|JJ|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ 2001|2001|CD|_ ;|;|:|_ platform|platform|NN|_ ID|id|NN|_ GPL4940|gpl4940|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ but|but|CC|_ because|because|IN|_ the|the|DT|_ analysis|analysis|NN|_ software|software|NN|_ failed|fail|VBD|_ to|to|TO|_ recognize|recognize|VB|_ the|the|DT|_ correct|correct|JJ|_ platform|platform|NN|_ ,|,|,|_ we|we|PRP|_ reformatted|reformat|VBD|_ the|the|DT|_ data|datum|NNS|_ to|to|TO|_ match|match|VB|_ the|the|DT|_ newer|newer|JJR|_ -LRB-|-lrb-|-LRB-|_ and|and|CC|_ mostly|mostly|RB|_ equivalent|equivalent|JJ|_ -RRB-|-rrb-|-RRB-|_ platform|platform|NN|_ GPL199|gpl199|NN|_ -LRB-|-lrb-|-LRB-|_ Affy|Affy|NNP|_ Ecoli|Ecoli|NNP|_ anti-sense|anti-sense|JJ|_ chip|chip|NN|_ version|version|NN|_ 2|2|CD|_ ,|,|,|_ 2002|2002|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Because|because|IN|_ ,|,|,|_ however|however|RB|_ ,|,|,|_ not|not|RB|_ all|all|DT|_ of|of|IN|_ the|the|DT|_ probes|probe|NNS|_ on|on|IN|_ the|the|DT|_ new|new|JJ|_ platform|platform|NN|_ were|be|VBD|_ present|present|JJ|_ on|on|IN|_ the|the|DT|_ old|old|JJ|_ platform|platform|NN|_ ,|,|,|_ data|datum|NNS|_ for|for|IN|_ some|some|DT|_ probes|probe|NNS|_ were|be|VBD|_ unavailable|unavailable|JJ|_ and|and|CC|_ labeled|label|VBN|_ in|in|IN|_ the|the|DT|_ `|`|``|_ remapped|remapped|NN|_ '|'|''|_ dataset|dataset|NN|_ as|as|IN|_ `|`|``|_ NULL|NULL|NNP|_ '|'|''|_ to|to|TO|_ indicate|indicate|VB|_ they|they|PRP|_ were|be|VBD|_ missing|miss|VBG|_ .|.|.|_ While|while|IN|_ the|the|DT|_ following|follow|VBG|_ data|datum|NNS|_ are|be|VBP|_ therefore|therefore|RB|_ formatted|format|VBN|_ using|use|VBG|_ ID|ID|NNP|_ _|_|SYM|_ REFs|ref|NNS|_ that|that|WDT|_ match|match|VBP|_ GPL199|gpl199|NN|_ ,|,|,|_ the|the|DT|_ CEL|CEL|NNP|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ raw|raw|JJ|_ data|data|NN|_ -LRB-|-lrb-|-LRB-|_ not|not|RB|_ `|`|``|_ remapped|remap|VBN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ thus|thus|RB|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ actual|actual|JJ|_ array|array|NN|_ used|use|VBN|_ -LRB-|-lrb-|-LRB-|_ GPL4940|gpl4940|NN|_ ,|,|,|_ Ecoli|ecoli|JJ|_ antisense|antisense|JJ|_ chip|chip|NN|_ ,|,|,|_ 2001|2001|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
wildtype|wildtype|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
wt|wt|JJ|_ 150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
wt|wt|JJ|_ 150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
wt|wt|JJ|_ 150|150|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
wt|wt|JJ|_ 240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
wt|wt|JJ|_ 240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
wt|wt|JJ|_ 240|240|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
wt|wt|JJ|_ 360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
wt|wt|JJ|_ 360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
wt|wt|JJ|_ 360|360|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
wt|wt|JJ|_ 90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep1|rep1|NN|_
wt|wt|JJ|_ 90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep2|rep2|NN|_
wt|wt|JJ|_ 90|90|CD|_ minutes|minute|NNS|_ growth|growth|NN|_ rep3|rep3|NN|_
All|all|DT|_ raw|raw|JJ|_ FastQ|fastq|NN|_ files|file|NNS|_ generated|generate|VBN|_ were|be|VBD|_ filtered|filter|VBN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Enterohemorrhagic|enterohemorrhagic|JJ|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ EDL933|edl933|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655.2|002655.2|CD|_
genotype|genotype|NN|_ :|:|:|_ -LCB-|-lcb-|-LRB-|_ delta|delta|NN|_ -RCB-|-rcb-|-RRB-|_ hns|hn|VBZ|GEN
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
hns|hn|NNS|GEN _|_|VBP|_ 1|1|CD|_
hns|hn|NNS|GEN _|_|VBP|_ 2|2|CD|_
Illumina|Illumina|NNP|_ Casava1|Casava1|NNP|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED and|and|CC|_ grown|grow|VBN|_ to|to|TO|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_ at|at|IN|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ about|about|IN|_ 0.8|0.8|CD|_ .|.|.|_
phase|phase|NN|_ :|:|:|_ logarithmic|logarithmic|JJ|_ phase|phase|NN|_
Reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ model|model|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ a|a|DT|_ normalized|normalize|VBN|_ metric|metric|JJ|_ to|to|TO|_ present|present|VB|_ the|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ levels|level|NNS|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Nature|Nature|NNP|_ methods|method|NNS|_ 2008|2008|CD|_ ,|,|,|_ 5|5|CD|_ :|:|:|_ 621-628|621-628|CD|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboPure-BacteriaTM|RiboPure-BacteriaTM|NNP|_ Bacteria|bacterium|NNS|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ applied|apply|VBN|_ to|to|TO|_ eliminate|eliminate|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPKM|rpkm|NN|_
The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 4000|4000|CD|_ ×|×|CD|_ g|g|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ and|and|CC|_ then|then|RB|_ washed|wash|VBN|_ with|with|IN|_ PBS|PBS|NNP|_ .|.|.|_
Transcripts|transcript|NNS|_ evaluation|evaluation|NN|_ of|of|IN|_ differential|differential|JJ|_ expression|expression|NN|_ were|be|VBD|_ accomplished|accomplish|VBN|_ using|use|VBG|_ MARS|mars|NN|_ -LRB-|-lrb-|-LRB-|_ MA-plot-based|ma-plot-based|JJ|_ method|method|NN|_ with|with|IN|_ Random|Random|NNP|_ sampling|sampling|NN|_ model|model|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ DEGseq|degseq|NN|_ package|package|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ Bioinformatics|bioinformatic|NNS|_ 2010|2010|CD|_ ,|,|,|_ 26|26|CD|_ :|:|:|_ 136-138|136-138|CD|_ -RRB-|-rrb-|-RRB-|_
wt|wt|JJ|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|NN|_ 2|2|CD|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
genotype|genotype|NN|_ :|:|:|_ del|del|DT|_ rpoS|rpos|NN|GEN
genotype|genotype|NN|_ :|:|:|_ del|del|DT|_ rsd|rsd|NN|GEN
genotype|genotype|NN|_ :|:|:|_ del|del|DT|_ rsd|rsd|NN|GEN ;|;|:|_ del|del|DT|_ ssrS|ssrs|NN|GEN
genotype|genotype|NN|_ :|:|:|_ del|del|DT|_ ssrS|ssrs|NN|GEN
genotype|genotype|NN|_ :|:|:|_ Wild-type|wild-type|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Early|early|JJ|_ Exponential|exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ Stationary|stationary|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid-Exponential|mid-exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stationary|stationary|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Transition|transition|NN|_ to|to|TO|_ Stationary|stationary|JJ|_
Libraries|library|NNS|_ for|for|IN|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 1000|1000|CD|_ sequencing|sequencing|NN|_ using|use|VBG|_ the|the|DT|_ Truseq|Truseq|NNP|_ kit|kit|NN|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ protocols|protocol|NNS|_ recommended|recommend|VBN|_ by|by|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ .|.|.|_
M9|m9|NN|_ defined|define|VBN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 0.6|0.6|CD|_ %|%|NN|_ Na2HPO4|na2hpo4|NN|_ ,|,|,|_ 0.3|0.3|CD|_ %|%|NN|_ KH2PO4|kh2po4|NN|_ ,|,|,|_ 0.05|0.05|CD|_ %|%|NN|_ NaCl|nacl|NN|_ ,|,|,|_ 0.01|0.01|CD|_ %|%|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mM|mm|NN|KWSUPP MgSO4|mgso4|NN|_ ,|,|,|_ 5|5|CD|_ x|x|CC|_ 10|10|CD|_ −|−|NN|_ 4|4|CD|_ %|%|NN|_ Thiamin|thiamin|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP and|and|CC|_ 0.1|0.1|CD|_ %|%|NN|_ amino|amino|NN|SUPP acids|acid|NNS|SUPP was|be|VBD|_ used|use|VBN|_ for|for|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ .|.|.|_
Overnight|Overnight|NNP|_ cultures|culture|NNS|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 100|100|CD|_ mL|ml|NN|_ fresh|fresh|JJ|_ M9|m9|NN|_ glucose|glucose|NN|SUPP to|to|TO|_ a|a|DT|_ final|final|JJ|_ OD600|od600|NN|_ of|of|IN|_ 0.02|0.02|CD|_ .|.|.|_ The|the|DT|_ flasks|flask|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ at|at|IN|_ the|the|DT|_ early|early|JJ|_ exponential|exponential|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ mid-exponential|mid-exponential|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.8|0.8|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transition|transition|NN|_ to|to|TO|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 16|16|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ late|late|JJ|_ stationary|stationary|JJ|_ -LRB-|-lrb-|-LRB-|_ 48|48|CD|_ hrs|hr|NNS|_ ,|,|,|_ OD600|od600|NN|_ ~|~|NN|_ 1.6|1.6|CD|_ -RRB-|-rrb-|-RRB-|_ phases|phase|NNS|_ of|of|IN|_ growth|growth|NN|_ .|.|.|_
Raw|raw|NN|_ sequence|sequence|NN|_ data|datum|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ the|the|DT|_ fastq|fastq|NN|_ format|format|NN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ matching|match|VBG|_ program|program|NN|_ BWA|bwa|NN|_ .|.|.|_ Reads|read|NNS|_ mapping|map|VBG|_ uniquely|uniquely|RB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ selected|select|VBN|_ and|and|CC|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ computed|compute|VBN|_ using|use|VBG|_ custom|custom|NN|_ scripts|script|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNAse|dnase|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 18068-015|18068-015|CD|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ Further|further|JJ|_ precipitation|precipitation|NN|_ of|of|IN|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ cleanup|cleanup|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ Ambion|Ambion|NNP|_ MICROBExpress|MICROBExpress|NNPS|_ bacterial|bacterial|JJ|_ mRNA|mrna|NN|_ purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ cat|cat|NN|_ .|.|.|_ no|no|DT|_ .|.|.|_ AM1905|am1905|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ finally|finally|RB|_ suspended|suspend|VBN|_ in|in|IN|_ 10|10|CD|_ μL|μl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ .|.|.|_
rpoS|rpos|NN|GEN _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 1|1|CD|_
rpoS|rpos|NN|GEN _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 2|2|CD|_
rpoS|rpos|NN|GEN _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 1|1|CD|_
rpoS|rpos|NN|GEN _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 2|2|CD|_
rpoS|rpos|NN|GEN _|_|CD|_ ME|me|NN|_ _|_|NN|_ 1|1|CD|_
rpoS|rpos|NN|GEN _|_|CD|_ ME|me|NN|_ _|_|NN|_ 2|2|CD|_
rpoS|rpos|NN|GEN _|_|CD|_ S|s|NN|_ _|_|NN|_ 1|1|CD|_
rpoS|rpos|NN|GEN _|_|CD|_ S|s|NN|_ _|_|NN|_ 2|2|CD|_
rpoS|rpos|NN|GEN _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 1|1|CD|_
rpoS|rpos|NN|GEN _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 2|2|CD|_
rsd|rsd|NN|GEN _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 1|1|CD|_
rsd|rsd|NN|GEN _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 2|2|CD|_
rsd|rsd|NN|GEN _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 1|1|CD|_
rsd|rsd|NN|GEN _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 2|2|CD|_
rsd|rsd|NN|GEN _|_|CD|_ ME|me|NN|_ _|_|NN|_ 1|1|CD|_
rsd|rsd|NN|GEN _|_|CD|_ ME|me|NN|_ _|_|NN|_ 2|2|CD|_
rsd|rsd|NN|GEN _|_|CD|_ S|s|NN|_ _|_|NN|_ 1|1|CD|_
rsd|rsd|NN|GEN _|_|CD|_ S|s|NN|_ _|_|NN|_ 2|2|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 1|1|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 2|2|CD|_
rsdssrS|rsdssrs|NN|_ _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 1|1|CD|_
rsdssrS|rsdssrs|NN|_ _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 2|2|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ ME|me|NN|_ _|_|NN|_ 1|1|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ ME|me|NN|_ _|_|NN|_ 2|2|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ S|s|NN|_ _|_|NN|_ 1|1|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ S|s|NN|_ _|_|NN|_ 2|2|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 1|1|CD|_
rsdssrS|rsdssrs|NN|_ _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 2|2|CD|_
rsd|rsd|NN|GEN _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 1|1|CD|_
rsd|rsd|NN|GEN _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 2|2|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 1|1|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ EE|ee|NN|_ _|_|NN|_ 2|2|CD|_
ssrS|ssrs|NN|GEN _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 1|1|CD|_
ssrS|ssrs|NN|GEN _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 2|2|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ ME|me|NN|_ _|_|NN|_ 1|1|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ ME|me|NN|_ _|_|NN|_ 2|2|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ S|s|NN|_ _|_|NN|_ 1|1|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ S|s|NN|_ _|_|NN|_ 2|2|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 1|1|CD|_
ssrS|ssrs|NN|GEN _|_|CD|_ TS|ts|NN|_ _|_|NN|_ 2|2|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ ;|;|:|_ genes|gene|NNS|_ in|in|IN|_ rows|row|NNS|_ and|and|CC|_ samples|sample|NNS|_ in|in|IN|_ columns|column|NNS|_ ;|;|:|_ each|each|DT|_ entry|entry|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ given|give|VBN|_ gene|gene|NN|_ in|in|IN|_ the|the|DT|_ given|give|VBN|_ sample|sample|NN|_ .|.|.|_
These|these|DT|_ counts|count|NNS|_ were|be|VBD|_ fed|feed|VBN|_ into|into|IN|_ the|the|DT|_ DESeq|deseq|NN|_ package|package|NN|_ in|in|IN|_ Bioconductor|Bioconductor|NNP|_ to|to|TO|_ estimate|estimate|VB|_ differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ the|the|DT|_ mutants|mutant|NNS|_ and|and|CC|_ the|the|DT|_ wildtype|wildtype|JJ|_ .|.|.|_
wt|wt|JJ|_ _|_|NN|_ EE|ee|NN|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|NN|_ EE|ee|NN|_ _|_|NN|_ 2|2|CD|_
wt|wt|JJ|_ _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|NN|_ LS|ls|NN|_ _|_|NN|_ 2|2|CD|_
wt|wt|JJ|_ _|_|CD|_ ME|me|NN|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|CD|_ ME|me|NN|_ _|_|NN|_ 2|2|CD|_
wt|wt|JJ|_ _|_|NN|_ S|s|NN|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|NN|_ S|s|NN|_ _|_|NN|_ 2|2|CD|_
wt|wt|JJ|_ _|_|NN|_ TS|ts|NN|_ _|_|NN|_ 1|1|CD|_
wt|wt|JJ|_ _|_|NN|_ TS|ts|NN|_ _|_|NN|_ 2|2|CD|_
chip|chip|NN|_ antibody|antibody|NN|_ manufacturer|manufacturer|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ Monoclonal|monoclonal|JJ|_ anti-FLAG|anti-flag|JJ|_ antibody|antibody|NN|_ ,|,|,|_ Murine|murine|JJ|_ IgG|igg|NN|_
ChIP-exo|chip-exo|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ BWA|bwa|NN|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
E.|E.|NNP|_ coli|coli|NN|_ and|and|CC|_ S.|S.|NNP|_ Typhimurium|Typhimurium|NNP|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ at|at|IN|_ mid-exponential|mid-exponential|JJ|_ growth|growth|NN|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ formaldehyde|formaldehyde|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 20|20|CD|_ min|min|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ .|.|.|_ The|the|DT|_ crosslinking|crosslinking|NN|_ reaction|reaction|NN|_ was|be|VBD|_ then|then|RB|_ quenched|quench|VBN|_ by|by|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ glycine|glycine|NN|_ -LRB-|-lrb-|-LRB-|_ 0.33|0.33|CD|_ M|m|NN|_ final|final|JJ|_ concentrationg|concentrationg|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ with|with|IN|_ gentle|gentle|JJ|_ mixing|mix|VBG|_ .|.|.|_ Cells|cell|NNS|_ where|where|WRB|_ then|then|RB|_ lysed|lyse|VBN|_ on|on|IN|_ ice|ice|NN|_ with|with|IN|_ lysozyme|lysozyme|NN|_ and|and|CC|_ sonication|sonication|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Kornberg|Kornberg|NNP|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 1.1|1.1|CD|_ %|%|NN|_ -LSB-|-lsb-|-LRB-|_ wt|wt|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 016856.1|016856.1|CD|_
Library|Library|NNP|_ strategy|strategy|NN|_ :|:|:|_ ChIP-exo|ChIP-exo|NNP|_
OTHER|OTHER|NNP|_
Peaks|Peaks|NNPS|_ on|on|IN|_ opposing|oppose|VBG|_ strands|strand|NNS|_ were|be|VBD|_ paired|pair|VBN|_ with|with|IN|_ Genetrack|genetrack|NN|_ -LRB-|-lrb-|-LRB-|_ u|u|NN|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ d|d|NN|_ =|=|JJ|_ 80|80|CD|_ ,|,|,|_ b|b|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ m|m|NN|_ =|=|JJ|_ mode|mode|NN|_ -RRB-|-rrb-|-RRB-|_
Peaks|peak|NNS|_ were|be|VBD|_ called|call|VBN|_ with|with|IN|_ GeneTrack|genetrack|NN|_ 1.0.3|1.0.3|CD|_ -LRB-|-lrb-|-LRB-|_ s|s|NN|_ =|=|JJ|_ 5|5|CD|_ ,|,|,|_ e|e|SYM|_ =|=|JJ|_ 10|10|CD|_ -RRB-|-rrb-|-RRB-|_
Peconic|Peconic|NNP|_ LLC|LLC|NNP|_ performed|perform|VBD|_ data|datum|NNS|_ processing|processing|NN|_
Samples|sample|NNS|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ on-bead|on-bead|JJ|_ enzymatic|enzymatic|JJ|_ reactions|reaction|NNS|_ of|of|IN|_ the|the|DT|_ ChIP-exo|ChIP-exo|NNP|_ procedure|procedure|NN|_ and|and|CC|_ Illumina|Illumina|NNP|_ Tru-seq|tru-seq|JJ|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ construction|construction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Rhee|Rhee|NNP|_ and|and|CC|_ Pugh|Pugh|NNP|_ ,|,|,|_ 2012|2012|CD|_
Singleton|Singleton|NNP|_ peaks|peak|VBZ|_ -LRB-|-lrb-|-LRB-|_ standard|standard|JJ|_ deviation|deviation|NN|_ =|=|JJ|_ 0|0|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ peaks|peak|VBZ|_ without|without|IN|_ matched|match|VBN|_ peaks|peak|NNS|_ on|on|IN|_ the|the|DT|_ opposing|oppose|VBG|_ strand|strand|NN|_ where|where|WRB|_ discarded|discard|VBN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
S.|S.|NNP|_ Typhimurium|Typhimurium|NNP|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 10mM|10mm|NN|_ glucose|glucose|NN|SUPP -RRB-|-rrb-|-RRB-|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ =|=|JJ|_ ~|~|NN|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ and|and|CC|_ shaking|shake|VBG|_ 250rpm|250rpm|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraphs|bedgraph|NNS|_ files|file|NNS|_ representing|represent|VBG|_ the|the|DT|_ extracted|extract|VBN|_ peak|peak|NN|_ data|datum|NNS|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ chromosome|chromosome|NN|_ chromosomeStartPosition|chromosomestartposition|NN|_ chromosomeStopPosition|chromosomestopposition|NN|_ readCoverage|readcoverage|NN|_ -LRB-|-lrb-|-LRB-|_ positive|positive|JJ|_ values|value|NNS|_ on|on|IN|_ +|+|CC|_ strand|strand|NN|_ ,|,|,|_ negative|negative|JJ|_ on|on|IN|_ -|-|:|_ strand|strand|NN|_ -RRB-|-rrb-|-RRB-|_
UvrY|uvry|NN|TF -|-|:|_ ChIP-exo|ChIP-exo|NNP|_
UvrY|uvry|NN|TF -LRB-|-lrb-|-LRB-|_ Response|response|NN|_ regulator|regulator|NN|_ of|of|IN|_ the|the|DT|_ BarA|bara|NN|_
Bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 200|200|CD|_ rpm|rpm|NN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ -LRB-|-lrb-|-LRB-|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ None|none|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ RpoS|rpos|NN|_ -LRB-|-lrb-|-LRB-|_ Neoclone|neoclone|JJ|_ cat|cat|NN|_ .|.|.|_ no|no|DT|_ .|.|.|_ WP009|wp009|NN|_ -RRB-|-rrb-|-RRB-|_
ChIP-Seq|chip-seq|NN|_
Cross-linked|cross-linked|JJ|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ ,|,|,|_ washed|wash|VBN|_ thrice|thrice|RB|_ with|with|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ resuspended|resuspend|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|tris|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 20|20|CD|_ %|%|NN|_ sucrose|sucrose|NN|_ ,|,|,|_ 50|50|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 20|20|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Files|file|NNS|_ were|be|VBD|_ coverted|covert|VBN|_ to|to|TO|_ .|.|.|_ bam|bam|NN|_ format|format|NN|_ using|use|VBG|_ samtools|samtool|NNS|_
Formaldehyde|Formaldehyde|NNP|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ %|%|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ ,|,|,|_ glycine|glycine|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ M|m|NN|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_ del|del|FW|_ ssrS|ssrs|FW|GEN
genotype|genotype|NN|_ :|:|:|_ MG1655|mg1655|NN|_ wild-type|wild-type|JJ|_
Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Raw|raw|NN|_ sequence|sequence|NN|_ data|datum|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ the|the|DT|_ fastq|fastq|NN|_ format|format|NN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ matching|match|VBG|_ program|program|NN|_ BWA|bwa|NN|_ .|.|.|_ Reads|read|NNS|_ mapping|map|VBG|_ uniquely|uniquely|RB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ selected|select|VBN|_ .|.|.|_
Raw|raw|NN|_ sequence|sequence|NN|_ data|datum|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ the|the|DT|_ fastq|fastq|NN|_ format|format|NN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ matching|match|VBG|_ program|program|NN|_ BWA|bwa|NN|_ .|.|.|_ Reads|read|NNS|_ mapping|map|VBG|_ uniquely|uniquely|RB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ selected|select|VBN|_ .|.|.|_ Files|file|NNS|_ were|be|VBD|_ coverted|covert|VBN|_ to|to|TO|_ .|.|.|_ bam|bam|NN|_ format|format|NN|_ using|use|VBG|_ samtools|samtool|NNS|_ .|.|.|_ The|the|DT|_ MACS|macs|NN|_ 2.1.0|2.1.0|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ call|call|VB|_ peaks|peak|NNS|_ .|.|.|_ Peaks|peak|NNS|_ overlapping|overlap|VBG|_ in|in|IN|_ both|both|CC|_ replicates|replicate|VBZ|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
Raw|raw|NN|_ sequence|sequence|NN|_ data|datum|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ the|the|DT|_ fastq|fastq|NN|_ format|format|NN|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ Burrows-Wheeler|Burrows-Wheeler|NNP|_ matching|match|VBG|_ program|program|NN|_ BWA|bwa|NN|_ .|.|.|_ Reads|read|NNS|_ mapping|map|VBG|_ uniquely|uniquely|RB|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ selected|select|VBN|_ .|.|.|_ Files|file|NNS|_ were|be|VBD|_ coverted|covert|VBN|_ to|to|TO|_ .|.|.|_ bam|bam|NN|_ format|format|NN|_ using|use|VBG|_ samtools|samtool|NNS|_ .|.|.|_ The|the|DT|_ MACS|macs|NN|_ 2.1.0|2.1.0|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ call|call|VB|_ peaks|peak|NNS|_ .|.|.|_ Peaks|peak|NNS|_ overlapping|overlap|VBG|_ in|in|IN|_ both|both|CC|_ replicates|replicate|VBZ|_ were|be|VBD|_ selected|select|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ quality|quality|NN|_ using|use|VBG|_ Trimmomatic-0.32|trimmomatic-0.32|NN|_ with|with|IN|_ a|a|DT|_ cutoff|cutoff|JJ|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 20|20|CD|_
ssrS|ssrs|NN|GEN _|_|NN|_ 1|1|CD|_ _|_|NN|_ input|input|NN|_
ssrS|ssrs|NN|GEN _|_|NN|_ 1|1|CD|_ _|_|CD|_ IP|IP|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ narrowPeak|narrowpeak|NN|_ files|file|NNS|_ output|output|NN|_ by|by|IN|_ macs2|macs2|NN|_ ,|,|,|_ giving|give|VBG|_ peak|peak|JJ|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ positions|position|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ fold-change|fold-change|NN|_ ,|,|,|_ -|-|:|_ log10pvalue|log10pvalue|NN|_ ,|,|,|_ -|-|:|_ log10qvalue|log10qvalue|NN|_ ,|,|,|_ and|and|CC|_ relative|relative|JJ|_ summit|summit|NN|_ position|position|NN|_ to|to|TO|_ peak|peak|VB|_ start|start|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ narrowPeak|narrowpeak|NN|_ files|file|NNS|_ output|output|NN|_ by|by|IN|_ MACS|mac|NNS|_ ,|,|,|_ giving|give|VBG|_ peak|peak|JJ|_ start|start|NN|_ and|and|CC|_ end|end|NN|_ positions|position|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ fold-change|fold-change|NN|_ ,|,|,|_ -|-|:|_ log10pvalue|log10pvalue|NN|_ ,|,|,|_ -|-|:|_ log10qvalue|log10qvalue|NN|_ ,|,|,|_ and|and|CC|_ relative|relative|JJ|_ summit|summit|NN|_ position|position|NN|_ to|to|TO|_ peak|peak|VB|_ start|start|NN|_
The|the|DT|_ MACS|macs|NN|_ 2.1.0|2.1.0|CD|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ call|call|VB|_ peaks|peak|NNS|_ .|.|.|_
The|the|DT|_ MACS2|macs2|NN|_ software|software|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ call|call|VB|_ peaks|peak|NNS|_ .|.|.|_
wt|wt|JJ|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ input|input|NN|_
wt|wt|JJ|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IP|IP|NNP|_
wt|wt|JJ|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ input|input|NN|_
wt|wt|JJ|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IP|IP|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 70|70|CD|_ %|%|NN|_ N2|n2|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ O2|o2|CD|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3-0.35|0.3-0.35|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ glucose|glucose|NN|SUPP media|media|NNS|_ containing|contain|VBG|_ 10|10|CD|_ µM|µm|NN|_ FeSO4|feso4|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ a|a|DT|_ stop|stop|NN|_ solution|solution|NN|_ of|of|IN|_ phenol|phenol|NN|_ and|and|CC|_ ethanol|ethanol|NN|_ -LRB-|-lrb-|-LRB-|_ Khodursky|Khodursky|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ Methods|method|NNS|_ in|in|IN|_ Molecular|molecular|JJ|_ Biology|Biology|NNP|_ 2003|2003|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ spun|spin|VBD|_ down|down|RP|_ ,|,|,|_ and|and|CC|_ flash|flash|NN|_ frozen|frozen|JJ|_ and|and|CC|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
culture|culture|NN|_ condition|condition|NN|_ :|:|:|_ Aerobic|aerobic|JJ|_ cultures|culture|NNS|_
culture|culture|NN|_ condition|condition|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
∆|∆|CD|_ fur|fur|NN|GEN Aerobic|aerobic|JJ|_ A|a|NN|_
∆|∆|CD|_ fur|fur|NN|GEN Aerobic|aerobic|JJ|_ B|b|NN|_
∆|∆|CD|_ fur|fur|NN|GEN Anaerobic|anaerobic|JJ|_ A|a|NN|_
∆|∆|CD|_ fur|fur|NN|GEN Anaerobic|anaerobic|JJ|_ B|b|NN|_
Fur-minus|fur-minus|NN|_ _|_|CD|_ cDNA|cdna|NN|_ _|_|CD|_ Aerobic|aerobic|JJ|_
Fur-minus|fur-minus|NN|_ _|_|CD|_ cDNA|cdna|NN|_ _|_|CD|_ Anaerobic|anaerobic|JJ|_
Fur-minus|fur-minus|NN|_ _|_|CD|_ RyhB-minus|RyhB-minus|NNP|_ _|_|NNP|_ cDNA|cdna|NN|_ _|_|CD|_ Aerobic|aerobic|JJ|_
Fur-minus|fur-minus|NN|_ _|_|CD|_ RyhB-minus|RyhB-minus|NNP|_ _|_|NNP|_ cDNA|cdna|NN|_ _|_|CD|_ Anaerobic|anaerobic|JJ|_
∆|∆|NN|_ fur|fur|NN|GEN ∆|∆|CD|_ ryhB|ryhb|NN|GEN Aerobic|aerobic|JJ|_ A|a|NN|_
∆|∆|CD|_ fur|fur|NN|GEN ∆|∆|CD|_ ryhB|ryhb|NN|GEN Aerobic|aerobic|JJ|_ B|b|NN|_
∆|∆|CD|_ fur|fur|NN|GEN ∆|∆|CD|_ ryhB|ryhb|NN|GEN Anaerobic|anaerobic|JJ|_ A|a|NN|_
∆|∆|CD|_ fur|fur|NN|GEN ∆|∆|CD|_ ryhB|ryhb|NN|GEN Anaerobic|anaerobic|JJ|_ B|b|NN|_
genotype|genotype|NN|_
Raw|raw|NN|_ probe|probe|NN|_ intensities|intensity|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ across|across|IN|_ all|all|DT|_ samples|sample|NNS|_ using|use|VBG|_ the|the|DT|_ Robust|Robust|NNP|_ Multichip|Multichip|NNP|_ Average|Average|NNP|_ -LRB-|-lrb-|-LRB-|_ RMA|RMA|NNP|_ -RRB-|-rrb-|-RRB-|_ algorithm|algorithm|NN|_ in|in|IN|_ the|the|DT|_ NimbleScan|NimbleScan|NNP|_ software|software|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.5|2.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RMA|rma|NN|_ normalized|normalize|VBD|_ probe|probe|NN|_ data|datum|NNS|_ was|be|VBD|_ uploaded|upload|VBN|_ into|into|IN|_ the|the|DT|_ Mochiview|Mochiview|NNP|_ visualization|visualization|NN|_ software|software|NN|_ where|where|WRB|_ data|datum|NNS|_ cooresponding|coorespond|VBG|_ to|to|TO|_ the|the|DT|_ plus|plus|NN|_ and|and|CC|_ minus|minus|CC|_ strands|strand|NNS|_ were|be|VBD|_ subtracted|subtract|VBN|_ to|to|TO|_ get|get|VB|_ a|a|DT|_ strand-specific|strand-specific|JJ|_ probe|probe|NN|_ intesenity|intesenity|NN|_ per|per|IN|_ base|base|NN|_ as|as|IN|_ reported|report|VBN|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ .|.|.|_
∆|∆|SYM|_ ryhB|ryhb|NN|GEN Aerobic|aerobic|JJ|_
∆|∆|CD|_ ryhB|ryhb|NN|GEN Anaerobic|anaerobic|JJ|_
RyhB-minus_cDNA_Aerobic_WIG.txt|ryhb-minus_cdna_aerobic_wig.txt|NN|_
RyhB-minus_cDNA_Anaerobic_WIG.txt|ryhb-minus_cdna_anaerobic_wig.txt|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Khodursky|Khodursky|NNP|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ Methods|method|NNS|_ in|in|IN|_ Molecular|molecular|JJ|_ Biology|Biology|NNP|_ 2003|2003|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Wild-type|wild-type|JJ|_ Aerobic|Aerobic|NNP|_ A|A|NNP|_
Wild-type|wild-type|JJ|_ Aerobic|aerobic|JJ|_ B|b|NN|_
Wild-type|wild-type|JJ|_ Anaerobic|anaerobic|JJ|_ A|a|NN|_
Wild-type|wild-type|JJ|_ Anaerobic|anaerobic|JJ|_ B|b|NN|_
Wild-type|wild-type|JJ|_ _|_|NN|_ cDNA|cdna|NN|_ _|_|CD|_ Aerobic|aerobic|JJ|_
Wild-type|wild-type|JJ|_ _|_|NN|_ cDNA|cdna|NN|_ _|_|CD|_ Anaerobic|anaerobic|JJ|_
Cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ glucose|glucose|NN|SUPP media|media|NNS|_ containing|contain|VBG|_ 10|10|CD|_ µM|µm|NN|_ FeSO4|feso4|NN|_
Custom|Custom|NNP|_ anti-Fur|anti-fur|JJ|_ antibodies|antibody|NNS|_ were|be|VBD|_ purified|purify|VBN|_ over|over|IN|_ a|a|DT|_ His6-Fur|his6-fur|NN|_ bound|bind|VBD|_ HiTrap|HiTrap|NNP|_ NHS-activated|NHS-activated|NNP|_ HP|HP|NNP|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ GE|GE|NNP|_ Healthcare|Healthcare|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 21478858|21478858|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Western|western|NN|_ blot|blot|NN|_ analyses|analysis|NNS|_ showed|show|VBD|_ that|that|IN|_ the|the|DT|_ purified|purify|VBN|_ antibody|antibody|NN|_ was|be|VBD|_ specific|specific|JJ|_ for|for|IN|_ Fur|Fur|NNP|TF .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
∆|∆|CD|_ fur|fur|NN|GEN Anaerobic|anaerobic|JJ|_ -LSB-|-lsb-|-LRB-|_ IP|IP|NNP|_ vs|vs|CC|_ nput|nput|NN|_ -RSB-|-rsb-|-RRB-|_
genotype|genotype|NN|_
Input|Input|NNP|_ ∆|∆|NNP|_ fur|fur|NN|GEN Anaerobic|anaerobic|JJ|_
ip|ip|NN|_ antibody|antibody|NN|_ :|:|:|_ affinity|affinity|NN|_ purified|purify|VBN|_ anti-Fur|anti-fur|JJ|_ antibody|antibody|NN|_
IP|IP|NNP|_ ∆|∆|NNP|_ fur|fur|NN|GEN Anaerobic|anaerobic|JJ|_
NimbleScan|nimblescan|NN|_ software|software|NN|_ package|package|NN|_ ,|,|,|_ version|version|NN|_ 2.5|2.5|CD|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ NimbleGen|NimbleGen|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ extract|extract|VB|_ the|the|DT|_ scanned|scan|VBN|_ data|datum|NNS|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ subsequently|subsequently|RB|_ qunatile|qunatile|JJ|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ statistical|statistical|JJ|_ program|program|NN|_ R|r|NN|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ data|datum|NNS|_ table|table|NN|_ contains|contain|VBZ|_ the|the|DT|_ log2|log2|NN|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ IP|IP|NNP|_
sample|sample|NN|_ type|type|NN|_ :|:|:|_ input|input|NN|_ control|control|NN|_
Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Aerobic|aerobic|JJ|_ cultures|culture|NNS|_
Anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_
Anaerobic|anaerobic|JJ|_ ,|,|,|_ Iron|iron|JJ|_ Deficient|deficient|JJ|_ cultures|culture|NNS|_
Call|call|VB|_ peaks|peak|NNS|_ to|to|TO|_ and|and|CC|_ FDR|FDR|NNP|_ 0.1|0.1|CD|_ ,|,|,|_ MOSAiCs|MOSAiCs|NNP|_
Cell|cell|NN|_ pellets|pellet|NNS|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ initial|initial|JJ|_ 250|250|CD|_ mL|ml|NN|_ of|of|IN|_ culture|culture|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ thawed|thaw|VBN|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 250|250|CD|_ μL|μl|NN|_ of|of|IN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8|8|CD|_ ,|,|,|_ 300|300|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ TritonX-100|tritonx-100|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sonicated|sonicate|VBN|_ using|use|VBG|_ a|a|DT|_ microtip|microtip|NN|_ sonicator|sonicator|NN|_ set|set|VBN|_ at|at|IN|_ 10|10|CD|_ %|%|NN|_ output|output|NN|_ for|for|IN|_ 20|20|CD|_ second|second|JJ|_ intervals|interval|NNS|_ with|with|IN|_ periods|period|NNS|_ of|of|IN|_ cooling|cool|VBG|_ in|in|IN|_ between|between|IN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ for|for|IN|_ one|one|CD|_ hour|hour|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ with|with|IN|_ RNase|rnase|NN|_ A|a|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ ng|ng|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ aerobically|aerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 70|70|CD|_ %|%|NN|_ N2|n2|NN|_ ,|,|,|_ 25|25|CD|_ %|%|NN|_ O2|o2|CD|_ ,|,|,|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ anaerobically|anaerobically|RB|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ N2|n2|NN|_ and|and|CC|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3-0.35|0.3-0.35|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ Custom|Custom|NNP|_ anti-Fur|anti-fur|JJ|_ polyclonal|polyclonal|JJ|_ antibody|antibody|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ none|none|NN|_
ChIP-Seq|chip-seq|JJ|_
Combined|combine|VBN|_ input|input|NN|_
Custom|Custom|NNP|_ anti-Fur|anti-fur|JJ|_ antibodies|antibody|NNS|_ were|be|VBD|_ purified|purify|VBN|_ over|over|IN|_ a|a|DT|_ His6-Fur|his6-fur|NN|_ bound|bind|VBD|_ HiTrap|HiTrap|NNP|_ NHS-activated|NHS-activated|NNP|_ HP|HP|NNP|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ GE|GE|NNP|_ Healthcare|Healthcare|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ PMID|pmid|NN|_ :|:|:|_ 21478858|21478858|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Western|western|NN|_ blot|blot|NN|_ analyses|analysis|NNS|_ showed|show|VBD|_ that|that|IN|_ the|the|DT|_ purified|purify|VBN|_ antibody|antibody|NN|_ was|be|VBD|_ specific|specific|JJ|_ for|for|IN|_ Fur|Fur|NNP|TF .|.|.|_
Deconvolute|deconvolute|JJ|_ peaks|peak|NNS|_ in|in|IN|_ close|close|JJ|_ proximity|proximity|NN|_ ,|,|,|_ dPeak|dpeak|NN|_
DNA|dna|NN|_ samples|sample|NNS|_ were|be|VBD|_ submitted|submit|VBN|_ to|to|TO|_ the|the|DT|_ University|University|NNP|_ of|of|IN|_ Wisconsin-Madison|Wisconsin-Madison|NNP|_ DNA|DNA|NNP|_ Sequencing|sequencing|NN|_ Facility|facility|NN|_ for|for|IN|_ ChIP-seq|ChIP-seq|NNP|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ All|all|DT|_ libraries|library|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ reagents|reagent|NNS|_ from|from|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ Paired|Paired|NNP|_ End|End|NNP|_ Sample|Sample|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ Illumina|Illumina|NNP|_ protocol|protocol|NN|_ ``|``|``|_ Preparing|prepare|VBG|_ Samples|sample|NNS|_ for|for|IN|_ ChIP|chip|NN|_ Sequencing|sequencing|NN|_ of|of|IN|_ DNA|dna|NN|_ ''|''|''|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ part|part|NN|_ #|#|#|_ 11257047|11257047|CD|_ RevA|reva|NN|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ except|except|IN|_ products|product|NNS|_ of|of|IN|_ the|the|DT|_ ligation|ligation|NN|_ reaction|reaction|NN|_ were|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ using|use|VBG|_ 2|2|CD|_ %|%|NN|_ SizeSelect|sizeselect|NN|_ agarose|agarose|NN|_ gels|gel|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ targeting|target|VBG|_ 50|50|CD|_ bp|bp|NN|_ fragments|fragment|NNS|_ .|.|.|_ After|after|IN|_ library|library|NN|_ construction|construction|NN|_ and|and|CC|_ amplification|amplification|NN|_ ,|,|,|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ were|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|agilent|JJ|_ DNA|dna|NN|_ 1000|1000|CD|_ series|series|NN|_ chip|chip|NN|_ assay|assay|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ QuantIT|quantit|NN|_ PicoGreen|picogreen|NN|_ dsDNA|dsdna|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ ,|,|,|_ and|and|CC|_ libraries|library|NNS|_ were|be|VBD|_ standardized|standardized|JJ|_ to|to|TO|_ 10μM|10μm|NN|_ .|.|.|_ Cluster|cluster|NN|_ generation|generation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ cBot|cBot|NNP|_ Single|single|JJ|_ Read|Read|NNP|_ Cluster|Cluster|NNP|_ Generation|Generation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ placed|place|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ cBot|cBot|NNP|_ .|.|.|_ For|for|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ replicates|replicate|VBZ|_ A|a|NN|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ read|read|NN|_ ,|,|,|_ 50|50|CD|_ bp|bp|NN|_ run|run|NN|_ was|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ SBS|SBS|NNP|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ v4|v4|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ SCS|scs|NN|_ 2.6|2.6|CD|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ IIx|IIx|NNP|_ .|.|.|_ For|for|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ replicates|replicate|VBZ|_ B|b|NN|_ and|and|CC|_ C|c|NN|_ ,|,|,|_ the|the|DT|_ input|input|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ anaerobic|anaerobic|JJ|_ ,|,|,|_ iron|iron|NN|_ deficient|deficient|JJ|_ samples|sample|NNS|_ ,|,|,|_ a|a|DT|_ single|single|JJ|_ read|read|NN|_ ,|,|,|_ 50|50|CD|_ bp|bp|NN|_ run|run|NN|_ was|be|VBD|_ performed|perform|VBN|_ ,|,|,|_ using|use|VBG|_ standard|standard|JJ|_ SBS|SBS|NNP|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ v3|v3|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ SCS|scs|NN|_ 1.8.2|1.8.2|CD|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2000|hiseq2000|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Aerobic|Aerobic|NNP|_ A|A|NNP|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Aerobic|Aerobic|NNP|_ B|B|NNP|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Aerobic|Aerobic|NNP|_ C|C|NNP|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Anaerobic|Anaerobic|NNP|_ A|A|NNP|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Anaerobic|anaerobic|JJ|_ B|b|NN|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Anaerobic|Anaerobic|NNP|_ C|C|NNP|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Anaerobic|Anaerobic|NNP|_ ,|,|,|_ Iron|Iron|NNP|_ Deficient|Deficient|NNP|_ A|A|NNP|_
Fur|Fur|NNP|TF IP|IP|NNP|_ ChIP-Seq|ChIP-Seq|NNP|_ Anaerobic|Anaerobic|NNP|_ ,|,|,|_ Iron|Iron|NNP|_ Deficient|deficient|JJ|_ B|b|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ version|version|NN|_ U00096|u00096|NN|_ .2|.2|NN|_
genotype|genotype|NN|_
growth|growth|NN|_ medium|medium|NN|_ :|:|:|_ Combined|combine|VBN|_ input|input|NN|_
growth|growth|NN|_ medium|medium|NN|_ :|:|:|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ glucose|glucose|NN|SUPP media|media|NNS|_ containing|contain|VBG|_ 10|10|CD|_ µM|µm|NN|_ FeSO4|feso4|NN|_
growth|growth|NN|_ medium|medium|NN|_ :|:|:|_ MOPS|mop|NNS|MED minimal|minimal|JJ|_ glucose|glucose|NN|SUPP media|media|NNS|_ containing|contain|VBG|_ 1|1|CD|_ µM|µm|NN|_ FeSO4|feso4|NN|_
Input|input|NN|_ ChIP-Seq|chip-seq|NN|_
Map|map|NN|_ reads|read|VBZ|_ to|to|TO|_ theEscherichia|theescherichia|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ ,|,|,|_ Bowtie|bowtie|NN|_ 2|2|CD|_
Reformat|reformat|VB|_ Illumina|Illumina|NNP|_ files|file|NNS|_ to|to|TO|_ Sanger|Sanger|NNP|_ format|format|NN|_ ,|,|,|_ FASTQ|FASTQ|NNP|_ Groomer|Groomer|NNP|_
Require|require|VB|_ peaks|peak|NNS|_ to|to|TO|_ be|be|VB|_ present|present|JJ|_ in|in|IN|_ at|at|IN|_ least|least|JJS|_ 2|2|CD|_ replicates|replicate|VBZ|_ and|and|CC|_ conform|conform|VB|_ to|to|TO|_ a|a|DT|_ peak|peak|JJ|_ shape|shape|NN|_ by|by|IN|_ visual|visual|JJ|_ inspection|inspection|NN|_
Scale|Scale|NNP|_ data|datum|NNS|_ set|set|VBN|_ to|to|TO|_ 20|20|CD|_ million|million|CD|_ reads|read|VBZ|_
Sodium|sodium|NN|_ phosphate|phosphate|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed|process|VBN|_ data|datum|NNS|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ pair|pair|NN|_ after|after|IN|_ the|the|DT|_ total|total|JJ|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ were|be|VBD|_ scaled|scale|VBN|_ to|to|TO|_ 20|20|CD|_ million|million|CD|_ reads|read|VBZ|_ per|per|IN|_ experiment|experiment|NN|_
5|5|CD|_ '|'|''|_ 10|10|CD|_ ug|ug|NN|_
5|5|CD|_ '|'|''|_ 15|15|CD|_ ug|ug|NN|_
5|5|CD|_ '|'|''|_ +50|+50|CD|_ ug|ug|NN|_
Bacteria|bacterium|NNS|_ were|be|VBD|_ lyzed|lyze|VBN|_ with|with|IN|_ lyzozyme|lyzozyme|NN|_ and|and|CC|_ sonicated|sonicate|VBN|_ to|to|TO|_ shear|shear|NN|_ DNA|dna|NN|_ .|.|.|_ TopoIV-DNA|topoiv-dna|JJ|_ complexes|complex|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ antibody|antibody|NN|_ .|.|.|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ antiFlag|antiflag|NN|_ M2|m2|NN|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ none|none|NN|_
ChIP-Seq|chip-seq|NN|_
ChIP-seq|chip-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ NC|nc|FW|_ _|_|SYM|_ 000913|000913|CD|_ genome|genome|NN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.6.2|0.6.2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ parC|parc|NN|GEN :|:|:|_ :|:|:|_ flag|flag|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ parE|pare|NN|GEN :|:|:|_ :|:|:|_ flag|flag|NN|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ or|or|CC|_ minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ casaminoacids|casaminoacid|NNS|_ -LRB-|-lrb-|-LRB-|_ 0,1|0,1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ succinate|succinate|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0,1|0,1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD|od|NN|_ 0,2-0,4|0,2-0,4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ ChIP-seq|chip-seq|JJ|_ experiments|experiment|NNS|_ E.|e.|FW|_ coli|coli|FW|_ culture|culture|NN|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ formaldehyde|formaldehyde|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ %|%|NN|_ final|final|JJ|_ concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ for|for|IN|_ NorfliP|norflip|NN|_ experiments|experiment|NNS|_ TopoIV|topoiv|NN|_ was|be|VBD|_ crosslinked|crosslink|VBN|_ with|with|IN|_ Norfloxacin|norfloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µM|2µm|NN|_ -RRB-|-rrb-|-RRB-|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ LB|lb|NN|_ growth|growth|NN|_ OD|od|NN|_ 0,3|0,3|CD|_
growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ LB|lb|NN|_ growth|growth|NN|_ OD|od|NN|_ 0,5|0,5|CD|_
growth|growth|NN|_ conditions|condition|NNS|_ :|:|:|_ Minimal|minimal|JJ|_ Medium|medium|NN|_ A|a|DT|_ supplemented|supplement|VBN|_ with|with|IN|_ casaminoacids|casaminoacid|NNS|_ -LRB-|-lrb-|-LRB-|_ 0,1|0,1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ succinate|succinate|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0,2|0,2|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ OD|od|NN|_ 0,2|0,2|CD|_ at|at|IN|_ 40|40|CD|_ °C|°c|NN|_
Input|Input|NNP|_ ParC-flag|ParC-flag|NNP|_ 1|1|CD|_
Input|Input|NNP|_ ParE-flag|ParE-flag|NNP|_ 1|1|CD|_
Input|Input|NNP|_ ParE-flag|ParE-flag|NNP|_ 2|2|CD|_
Input|Input|NNP|_ ParE-flag|ParE-flag|NNP|_ G1|g1|NN|_
Input|Input|NNP|_ ParE-flag|ParE-flag|NNP|_ G2|g2|NN|_
Input|input|NN|_ ParE-flag|pare-flag|NN|_ S20min|s20min|NN|_
Input|input|NN|_ ParE-flag|pare-flag|NN|_ S40min|s40min|NN|_
IP|IP|NNP|_ ParC-flag|ParC-flag|NNP|_ 1|1|CD|_
IP|IP|NNP|_ ParE-flag|ParE-flag|NNP|_ 1|1|CD|_
IP|IP|NNP|_ ParE-flag|ParE-flag|NNP|_ 2|2|CD|_
IP|IP|NNP|_ ParE-flag|ParE-flag|NNP|_ G1|g1|NN|_
IP|IP|NNP|_ ParE-flag|ParE-flag|NNP|_ G2|g2|NN|_
IP|IP|NNP|_ ParE-flag|ParE-flag|NNP|_ S20min|S20min|NNP|_
IP|IP|NNP|_ ParE-flag|ParE-flag|NNP|_ S40min|S40min|NNP|_
Libraries|Libraries|NNPS|_ were|be|VBD|_ prepared|prepared|JJ|_ according|accord|VBG|_ to|to|TO|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ instructions|instruction|NNS|_ accompanying|accompany|VBG|_ the|the|DT|_ DNA|dna|NN|_ Sample|sample|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ FC-104-5001|fc-104-5001|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ DNA|dna|NN|_ was|be|VBD|_ end-repaired|end-repaired|JJ|_ using|use|VBG|_ a|a|DT|_ combination|combination|NN|_ of|of|IN|_ T4|t4|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DNA|dna|NN|_ Pol|pol|NN|_ I|I|PRP|_ large|large|JJ|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ Klenow|klenow|NN|_ polymerase|polymerase|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ T4|t4|NN|_ polynucleotide|polynucleotide|NN|_ kinase|kinase|NN|_ .|.|.|_ The|the|DT|_ blunt|blunt|JJ|_ ,|,|,|_ phosphorylated|phosphorylated|JJ|_ ends|end|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ Klenow|Klenow|NNP|_ fragment|fragment|NN|_ -LRB-|-lrb-|-LRB-|_ 32|32|CD|_ to|to|TO|_ 52|52|CD|_ exo|exo|NN|_ minus|minus|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ dATP|datp|NN|_ to|to|TO|_ yield|yield|VB|_ a|a|DT|_ protruding|protrude|VBG|_ 3|3|LS|_ -|-|:|_ `|`|``|_ A|a|DT|_ '|'|''|_ base|base|NN|_ for|for|IN|_ ligation|ligation|NN|_ of|of|IN|_ Illumina|Illumina|NNP|_ 's|'s|POS|_ adapters|adapter|NNS|_ which|which|WDT|_ have|have|VBP|_ a|a|DT|_ single|single|JJ|_ `|`|``|_ T|t|NN|_ '|'|''|_ base|base|NN|_ overhang|overhang|NN|_ at|at|IN|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ .|.|.|_ After|after|IN|_ adapter|adapter|NN|_ ligation|ligation|NN|_ DNA|dna|NN|_ was|be|VBD|_ PCR|pcr|NN|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ primers|primer|NNS|_ for|for|IN|_ 15|15|CD|_ cycles|cycle|NNS|_ and|and|CC|_ library|library|NN|_ fragments|fragment|NNS|_ of|of|IN|_ ~|~|NN|_ 250|250|CD|_ bp|bp|NN|_ -LRB-|-lrb-|-LRB-|_ insert|insert|NN|_ plus|plus|CC|_ adaptor|adaptor|NN|_ and|and|CC|_ PCR|pcr|NN|_ primer|primer|NN|_ sequences|sequence|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ band|band|NN|_ isolated|isolate|VBN|_ from|from|IN|_ an|a|DT|_ agarose|agarose|NN|_ gel|gel|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ DNA|dna|NN|_ was|be|VBD|_ captured|capture|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ flow|flow|NN|_ cell|cell|NN|_ for|for|IN|_ cluster|cluster|NN|_ generation|generation|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Genome|Genome|NNP|_ Analyzer|Analyzer|NNP|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocols|protocol|NNS|_ .|.|.|_
NorflIP|norflip|NN|_ Input|input|NN|_ ParC-flag|parc-flag|NN|_ 1|1|CD|_
NorflIP|norflip|NN|_ Input|input|NN|_ ParC-flag|parc-flag|NN|_ 2|2|CD|_
NorflIP|norflip|NN|_ Input|input|NN|_ ParE-flag|pare-flag|NN|_ 1|1|CD|_
NorflIP|norflip|NN|_ IP|IP|NNP|_ ParC-flag|ParC-flag|NNP|_ 1|1|CD|_
NorflIP|norflip|NN|_ IP|IP|NNP|_ ParC-flag|ParC-flag|NNP|_ 2|2|CD|_
NorflIP|norflip|NN|_ IP|IP|NNP|_ ParE-flag|ParE-flag|NNP|_ 1|1|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Enrichement|enrichement|NN|_ -LRB-|-lrb-|-LRB-|_ IP|IP|NNP|_
bla|bla|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
bla|bla|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
bla|bla|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
bla|bla|NN|_ _|_|NN|_ 1|1|CD|_ min|min|NN|_
bla|bla|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
bla|bla|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
bla|bla|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
bla|bla|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ as|as|IN|_ a|a|DT|_ function|function|NN|_ of|of|IN|_ time|time|NN|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP treatment|treatment|NN|_ at|at|IN|_ the|the|DT|_ specified|specify|VBN|_ times|time|NNS|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNAsnap|rnasnap|NN|_ protocol|protocol|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD|od|NN|_ _|_|NN|_ 600|600|CD|_ of|of|IN|_ 0.4|0.4|CD|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ Lennox|Lennox|NNP|_
Cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ rifampicin|rifampicin|NN|SUPP before|before|IN|_ sample|sample|NN|_ collection|collection|NN|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ kasugamycin|kasugamycin|NN|_ was|be|VBD|_ added|add|VBN|_ 15|15|CD|_ minutes|minute|NNS|_ before|before|IN|_ the|the|DT|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_
csv|csv|NN|_ files|file|NNS|_ contain|contain|VBP|_ 16|16|CD|_ columns|column|NNS|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ ,|,|,|_ each|each|DT|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ counts|count|NNS|_ from|from|IN|_ the|the|DT|_ top|top|NN|_ -LRB-|-lrb-|-LRB-|_ odd|odd|JJ|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ bottom|bottom|NN|_ -LRB-|-lrb-|-LRB-|_ even|even|RB|_ numbers|number|NNS|_ -RRB-|-rrb-|-RRB-|_ strand|strand|NN|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ pair|pair|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ Similarly|similarly|RB|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ ,|,|,|_ third|third|JJ|_ ,|,|,|_ fourth|fourth|JJ|_ ,|,|,|_ fifth|fifth|JJ|_ ,|,|,|_ sixth|sixth|JJ|_ ,|,|,|_ seventh|seventh|JJ|_ ,|,|,|_ and|and|CC|_ eigth|eigth|NN|_ pairs|pair|NNS|_ correspond|correspond|VBP|_ to|to|TO|_ counts|count|NNS|_ collected|collect|VBN|_ at|at|IN|_ 2|2|CD|_ ,|,|,|_ 4|4|CD|_ ,|,|,|_ 6|6|CD|_ ,|,|,|_ 8|8|CD|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ minutes|minute|NNS|_ after|after|IN|_ rifampicin|rifampicin|NN|SUPP addition|addition|NN|_ .|.|.|_ The|the|DT|_ ith|ith|NN|_ row|row|NN|_ in|in|IN|_ each|each|DT|_ column|column|NN|_ corresponds|correspond|VBZ|_ to|to|TO|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ alignments|alignment|NNS|_ at|at|IN|_ the|the|DT|_ ith|ith|NN|_ base|base|NN|_ in|in|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.2|000913.2|CD|_ .|.|.|_
DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ Dnase|Dnase|NNP|_ I.|I.|NNP|_ rRNA|rrna|NN|_ was|be|VBD|_ removed|remove|VBN|_ with|with|IN|_ the|the|DT|_ gram-negative|gram-negative|JJ|_ RiboZero|RiboZero|NNP|_ kit|kit|NN|_ .|.|.|_ Libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ the|the|DT|_ RNAUltra|rnaultra|NN|_ directional|directional|JJ|_ kit|kit|NN|_ from|from|IN|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_ For|for|IN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ ,|,|,|_ cDNA|cdna|NN|_ was|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ primers|primer|NNS|_ that|that|WDT|_ target|target|VBP|_ the|the|DT|_ signal-peptide-coding|signal-peptide-coding|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
genotype|genotype|NN|_
lacZ|lacz|NN|GEN _|_|NN|_ 0|0|CD|_ min|min|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ 10|10|CD|_ min|min|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ 15|15|CD|_ min|min|NN|_
lacZ|lacz|NN|GEN _|_|NN|_ 1|1|CD|_ min|min|NN|_
lacZ|lacz|NN|GEN _|_|NN|_ 2|2|CD|_ min|min|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ 4|4|CD|_ min|min|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ 6|6|CD|_ min|min|NN|_
lacZ|lacz|NN|GEN _|_|CD|_ 8|8|CD|_ min|min|NN|_
mg1655|mg1655|NN|_
mMaple3|mmaple3|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
mMaple3|mmaple3|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
mMaple3|mmaple3|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
mMaple3|mmaple3|NN|_ _|_|NN|_ 1|1|CD|_ min|min|NN|_
mMaple3|mmaple3|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
mMaple3|mmaple3|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
mMaple3|mmaple3|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
mMaple3|mmaple3|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
MutRep1|mutrep1|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
MutRep2|mutrep2|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|NN|_ 1|1|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|NN|_ 4|4|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|NN|_ 6|6|CD|_ min|min|NN|_
neo|neo|NN|_ _|_|NN|_ 8|8|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|NN|_ 0|0|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|CD|_ 10|10|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|CD|_ 15|15|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|NN|_ 1|1|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|NN|_ 2|2|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|CD|_ 4|4|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|CD|_ 6|6|CD|_ min|min|NN|_
phoA|phoa|NN|GEN _|_|CD|_ 8|8|CD|_ min|min|NN|_
RNA-Seq|rna-seq|NN|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ mg1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ a|a|DT|_ list|list|NN|_ of|of|IN|_ the|the|DT|_ designed|design|VBN|_ signal|signal|NN|_ peptide|peptide|NN|_ fusions|fusion|NNS|_ using|use|VBG|_ bowtie|bowtie|NN|_ 0.12.9|0.12.9|CD|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ sam|sam|NN|_ containing|contain|VBG|_ aligned|align|VBN|_ sequences|sequence|NNS|_
The|the|DT|_ sigPep.csv|sigpep.csv|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ specific|specific|JJ|_ signal|signal|NN|_ peptide|peptide|NN|_ fusion|fusion|NN|_ to|to|TO|_ each|each|DT|_ specific|specific|JJ|_ test|test|NN|_ gene|gene|NN|_ .|.|.|_ Entries|entry|NNS|_ with|with|IN|_ SP|sp|NN|_ _|_|CD|_ spkA|spka|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 15|15|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 2|2|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 4|4|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 6|6|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 8|8|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ rifampicin|rifampicin|NN|SUPP
WTKasRep1|wtkasrep1|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
WTKasRep1|wtkasrep1|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
WTKasRep1|wtkasrep1|NN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
WTKasRep1|wtkasrep1|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
WTKasRep1|wtkasrep1|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
WTKasRep1|wtkasrep1|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
WTKasRep1|wtkasrep1|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
WTKasRep2|wtkasrep2|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
WTRep1|wtrep1|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|CD|_ 10|10|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|CD|_ 20|20|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|CD|_ 4|4|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|CD|_ 6|6|CD|_ min|min|NN|_
WTRep2|wtrep2|NN|_ _|_|CD|_ 8|8|CD|_ min|min|NN|_
cDNA|cdna|NN|_ of|of|IN|_ EPEC|epec|NN|_ strain|strain|NN|_
CIP2G|cip2g|NN|_ _|_|CD|_ 00000|00000|CD|_
CIP2G|cip2g|NN|_ _|_|CD|_ 00045|00045|CD|_
CIP2G|cip2g|NN|_ _|_|CD|_ 00090|00090|CD|_
CIP2G|cip2g|NN|_ _|_|CD|_ 00135|00135|CD|_
CIP2G|cip2g|NN|_ _|_|CD|_ 00180|00180|CD|_
CIP4G|cip4g|NN|_ _|_|CD|_ 00000|00000|CD|_
CIP4G|cip4g|NN|_ _|_|CD|_ 00045|00045|CD|_
CIP4G|cip4g|NN|_ _|_|CD|_ 00090|00090|CD|_
CIP4G|cip4g|NN|_ _|_|CD|_ 00135|00135|CD|_
CIP4G|cip4g|NN|_ _|_|CD|_ 00180|00180|CD|_
CIPSG|cipsg|NN|_ _|_|CD|_ 00000|00000|CD|_
CIPSG|cipsg|NN|_ _|_|CD|_ 00045|00045|CD|_
CIPSG|cipsg|NN|_ _|_|CD|_ 00090|00090|CD|_
CIPSG|cipsg|NN|_ _|_|CD|_ 00135|00135|CD|_
CIPSG|cipsg|NN|_ _|_|CD|_ 00180|00180|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
RNA|rna|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ Reagent|Reagent|NNP|_ and|and|CC|_ a|a|DT|_ RiboPure|RiboPure|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ bioanalyser|bioanalyser|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Palo|Palo|NNP|_ Alto|Alto|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ EPEC|epec|NN|_
The|the|DT|_ scanned|scan|VBN|_ images|image|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ the|the|DT|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ to|to|TO|_ obtain|obtain|VB|_ background|background|NN|_ subtracted|subtract|VBN|_ and|and|CC|_ spatially|spatially|RB|_ detrended|detrend|VBD|_ Processed|processed|JJ|_ Signal|signal|NN|_ intensities|intensity|NNS|_ .|.|.|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 135|135|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 180|180|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 45|45|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 90|90|CD|_ min|min|NN|_
treatment|treatment|NN|_ :|:|:|_ 2ug|2ug|JJ|_
treatment|treatment|NN|_ :|:|:|_ 4ug|4ug|JJ|_
treatment|treatment|NN|_ :|:|:|_ saline|saline|NN|_
5|5|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
5|5|CD|_ '|'|''|_ in|in|IN|_ min|min|NN|_ med|med|VBD|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ +50|+50|CD|_ ug|ug|NN|_
5|5|CD|_ '|'|''|_ vs|vs|CC|_ 0|0|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_
60|60|CD|_ '|'|''|_ 10|10|CD|_ ug|ug|NN|_
60|60|CD|_ '|'|''|_ 15|15|CD|_ ug|ug|NN|_
60|60|CD|_ '|'|''|_ +|+|CC|_ 50|50|CD|_ ug|ug|NN|_
60|60|CD|_ '|'|''|_ 50|50|CD|_ ug|ug|NN|_
60|60|CD|_ '|'|''|_ +50|+50|CD|_ ug|ug|NN|_
60|60|CD|_ '|'|''|_ in|in|IN|_ min|min|NN|_ +.2|+.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ RNA|rna|NN|_
60|60|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
60|60|CD|_ '|'|''|_ in|in|IN|_ min|min|NN|_ med|med|VBD|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ +50|+50|CD|_ ug|ug|NN|_
60|60|CD|_ '|'|''|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ 50|50|CD|_ ug|ug|NN|_
60|60|CD|_ '|'|''|_ vs|vs|CC|_ 0|0|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_
60|60|CD|_ '|'|''|_ vs|vs|CC|_ 0|0|CD|_ '|'|''|_ in|in|IN|_ minimal|minimal|JJ|_ medium|medium|NN|_ +0.2|+0.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ II|ii|CD|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ HCS|hcs|NN|_ 2.0.5|2.0.5|CD|_ and|and|CC|_ RTA|RTA|NNP|_ 1.17.20|1.17.20|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ control|control|NN|_ condition|condition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism _|_|FW|_ nickel|nickel|NN|_ condition|condition|NN|_
Gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ based|base|VBN|_ on|on|IN|_ known|known|JJ|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Cufflinks|Cufflinks|NNP|_ 2.0.2|2.0.2|CD|_ ,|,|,|_ only|only|RB|_ PF|pf|NN|_ reads|read|VBZ|_ were|be|VBD|_ retained|retain|VBN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 007779|007779|CD|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ log|log|NN|_ phase|phase|NN|_
Library|Library|NNP|_ preparation|preparation|NN|_ were|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ Epicentre|Epicentre|NNP|_ ScriptseqTM|ScriptseqTM|NNP|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ preparation|preparation|NN|_ kit|kit|NN|_ with|with|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ ;|;|:|_ Strand|Strand|NNP|_ orientated|orientate|VBD|_ RNA-Seq|rna-seq|JJ|_
RNA-Seq|rna-seq|NN|_
RNA-seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ W3110|w3110|NN|_ genome|genome|NN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ 1.8.2|1.8.2|CD|_
Rodrigue|Rodrigue|NNP|_ _|_|SYM|_ 10-WT-Ni-3|10-wt-ni-3|NN|_
Rodrigue|Rodrigue|NNP|_ _|_|SYM|_ 1-WT-phiNi-1|1-wt-phini-1|NN|_
Rodrigue|Rodrigue|NNP|_ _|_|SYM|_ 2-WT-Ni-1|2-wt-ni-1|NN|_
Rodrigue|Rodrigue|NNP|_ _|_|SYM|_ 5-WT-Ni-2|5-wt-ni-2|NN|_
Rodrigue|Rodrigue|NNP|_ _|_|SYM|_ 6-WT-phiNi-2|6-wt-phini-2|JJ|_
Rodrigue|Rodrigue|NNP|_ _|_|SYM|_ 9-WT-phiNi-3|9-wt-phini-3|NN|_
strain|strain|NN|_ :|:|:|_ W3110|w3110|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ with|with|IN|_ coverage|coverage|NN|_ and|and|CC|_ FPKM|fpkm|NN|_ measurements|measurement|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ frozen|frozen|JJ|_ acid-phenol|acid-phenol|NN|_ method|method|NN|_ described|describe|VBN|_ by|by|IN|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ -LRB-|-lrb-|-LRB-|_ Maes|mae|NNS|_ and|and|CC|_ Messens|messen|NNS|_ ,|,|,|_ 1992|1992|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ RNase-free|rnase-free|JJ|_ DNaseI|dnasei|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Transcriptomic|transcriptomic|JJ|_ analyses|analysis|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ after|after|IN|_ growing|grow|VBG|_ bacteria|bacterium|NNS|_ in|in|IN|_ minimal|minimal|JJ|_ media|media|NNS|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP .|.|.|_ Several|several|JJ|_ Ni|ni|NN|_ concentrations|concentration|NNS|_ and|and|CC|_ exposure|exposure|NN|_ times|time|NNS|_ were|be|VBD|_ assayed|assay|VBN|_ .|.|.|_ rcnA|rcna|NN|GEN gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ taken|take|VBN|_ as|as|IN|_ an|a|DT|_ internal|internal|JJ|_ control|control|NN|_ to|to|TO|_ arbitrate|arbitrate|VB|_ between|between|IN|_ the|the|DT|_ different|different|JJ|_ conditions|condition|NNS|_ .|.|.|_ rcnA|rcna|NN|GEN is|be|VBZ|_ induced|induce|VBN|_ by|by|IN|_ Ni|ni|NN|_ when|when|WRB|_ cells|cell|NNS|_ are|be|VBP|_ overloaded|overload|VBN|_ with|with|IN|_ this|this|DT|_ ion|ion|NN|_ and|and|CC|_ must|must|MD|_ detoxify|detoxify|VB|_ the|the|DT|_ cytoplasm|cytoplasm|NN|_ by|by|IN|_ extruding|extrude|VBG|_ excess|excess|JJ|_ metal|metal|NN|_ via|via|IN|_ the|the|DT|_ RcnAB|rcnab|NN|_ efflux|efflux|NN|_ system|system|NN|_ .|.|.|_ rcnA|rcna|NN|GEN induction|induction|NN|_ was|be|VBD|_ maximised|maximise|VBN|_ after|after|IN|_ culture|culture|NN|_ incubation|incubation|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ and|and|CC|_ longer|longer|RBR|_ periods|period|NNS|_ of|of|IN|_ incubation|incubation|NN|_ lead|lead|NN|_ to|to|TO|_ a|a|DT|_ decline|decline|NN|_ in|in|IN|_ rcnA|rcna|NN|GEN expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ Fig|fig|NN|_ .|.|.|_ S1|s1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ RNA-Seq|rna-seq|NN|_ experiments|experiment|NNS|_ ,|,|,|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ O.D600nm|o.d600nm|NN|_ =|=|JJ|_ 0.3|0.3|CD|_ ,|,|,|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 50|50|CD|_ µM|µm|NN|_ NiCl2|nicl2|NN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ and|and|CC|_ were|be|VBD|_ frozen|freeze|VBN|_ prior|prior|RB|_ to|to|TO|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_
DicF|dicf|NN|_ rep1|rep1|NN|_
DicF|dicf|NN|_ rep2|rep2|NN|_
DicF|dicf|NN|_ rep3|rep3|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ supplemented|supplement|VBN|_ with|with|IN|_ 100ug|100ug|CD|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ until|until|IN|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ induce|induce|VB|_ expression|expression|NN|_ of|of|IN|_ the|the|DT|_ empty|empty|JJ|_ vector|vector|NN|_ or|or|CC|_ the|the|DT|_ small|small|JJ|_ RNA|rna|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ dicF|dicf|NN|GEN ,|,|,|_ lacIq|laciq|NN|_
Hot|hot|JJ|_ phenol|phenol|NN|_ RNA|rna|NN|_ extraction|extraction|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Aiba|Aiba|NNP|_ ,|,|,|_ Adhya|Adhya|NNP|_ and|and|CC|_ Crombrugge|Crombrugge|NNP|_ .|.|.|_ J.|J.|NNP|_ Bio|Bio|NNP|_ Chem|Chem|NNP|_ .|.|.|_ 1981|1981|CD|_ ,|,|,|_ 256|256|CD|_ :|:|:|_ p11905-11910|p11905-11910|JJ|_
protocol|protocol|NN|_ :|:|:|_ small|small|JJ|_ RNA|rna|NN|_ DicF|dicf|NN|_
protocol|protocol|NN|_ :|:|:|_ vector|vector|NN|_ control|control|NN|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Meta-Bacteria|Meta-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ mRNA-enriched|mrna-enriched|JJ|_ fraction|fraction|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ indexed|index|VBN|_ RNA-seq|rna-seq|NN|_ libraries|library|NNS|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ ™|™|CD|_ v2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ Biotechnologies|Biotechnologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ formatted|format|VBD|_ matrix|matrix|NN|_ table|table|NN|_ containing|contain|VBG|_ transcript|transcript|NN|_ coordinates|coordinate|VBZ|_ ,|,|,|_ normalized|normalize|VBD|_ abundance|abundance|NN|_ estimates|estimate|NNS|_ across|across|IN|_ the|the|DT|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ fold-changes|fold-change|VBZ|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ cells|cell|NNS|_ expressing|express|VBG|_ Vector|Vector|NNP|_ and|and|CC|_ DicF|dicf|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ tab|tab|NN|_ delimited|delimit|VBD|_ file|file|NN|_ with|with|IN|_ operons|operon|NNS|_ expressed|express|VBN|_ differently|differently|RB|_ between|between|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ txt|txt|NN|_ :|:|:|_ .|.|.|_ txt|txt|NN|_ raw|raw|JJ|_ output|output|NN|_ file|file|NN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP|_ .|.|.|_ xlsx|xlsx|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ with|with|IN|_ transcription|transcription|NN|_ start|start|NN|_ and|and|CC|_ stop|stop|VB|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ all|all|DT|_ genes|gene|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ in|in|IN|_ vector|vector|NN|_ and|and|CC|_ DicF|dicf|NN|_
The|the|DT|_ program|program|NN|_ Rockhopper|rockhopper|NN|_ -LRB-|-lrb-|-LRB-|_ described|describe|VBN|_ in|in|IN|_ Mc|mc|NN|_ Clure|clure|NN|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ Acids|Acids|NNP|_ Research|Research|NNP|_ .|.|.|_ 2013|2013|CD|_ ,|,|,|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ alignment|alignment|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ and|and|CC|_ quantification|quantification|NN|_ .|.|.|_ Genome|Genome|NNP|_ _|_|SYM|_ builg|builg|NN|_ :|:|:|_ K-12|k-12|NN|_ subst|subst|NN|_ .|.|.|_ MG1655|mg1655|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_
Total|Total|NNP|_ RNA|rna|NN|_ from|from|IN|_ bacterial|bacterial|JJ|_ culture|culture|NN|_
Vector|Vector|NNP|_ rep1|rep1|NN|_
Vector|Vector|NNP|_ rep2|rep2|NN|_
Vector|Vector|NNP|_ rep3|rep3|NN|_
Bacterial|bacterial|JJ|_ cell|cell|NN|_ pellet|pellet|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ given|give|VBN|_ 1|1|CD|_ %|%|NN|_ sub-culturing|sub-culturing|JJ|_ till|till|IN|_ OD|od|NN|_ at|at|IN|_ 600nm|600nm|NN|_ was|be|VBD|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Images|image|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Feature|feature|NN|_ extracted|extract|VBN|_ raw|raw|JJ|_ data|datum|NNS|_ was|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ Version|Version|NNP|_ software|software|NN|_ from|from|IN|_ Agilent|Agilent|NNP|_ .|.|.|_ Normalization|normalization|NN|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ using|use|VBG|_ the|the|DT|_ 75th|75th|JJ|_ percentile|percentile|NN|_ shift|shift|NN|_
MG1655|mg1655|NN|_ G181D|g181d|NN|_ NusA|nusa|NN|_ BR|br|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ G181D|g181d|NN|_ NusA|nusa|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ R258C|r258c|NN|_ NusA|nusa|NN|_ BR|br|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ R258C|r258c|NN|_ NusA|nusa|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ WT|WT|NNP|_ NusA|NusA|NNP|_ BR|BR|NNP|_ ,|,|,|_ control|control|NN|_
MG1655|mg1655|NN|_ WT|WT|NNP|_ NusA|NusA|NNP|_ ,|,|,|_ control|control|NN|_
plasmid|plasmid|NN|_ :|:|:|_ G181D|g181d|NN|_ NusA|nusa|NN|_
plasmid|plasmid|NN|_ :|:|:|_ R258C|r258c|NN|_ NusA|nusa|NN|_
plasmid|plasmid|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ NusA|nusa|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .|.|.|_ 74004|74004|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
Treated|treat|VBN|_ experimental|experimental|JJ|_ sets|set|NNS|_ transformed|transform|VBN|_ with|with|IN|_ plasmids|plasmid|NNS|_ containing|contain|VBG|_ WT|wt|JJ|_
Bacterial|bacterial|JJ|_ cell|cell|NN|_ pellet|pellet|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ given|give|VBN|_ 1|1|CD|_ %|%|NN|_ sub-culturing|sub-culturing|JJ|_ till|till|IN|_ OD|od|NN|_ at|at|IN|_ 600nm|600nm|NN|_ was|be|VBD|_ 0.4|0.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Images|image|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Feature|feature|NN|_ extracted|extract|VBN|_ raw|raw|JJ|_ data|datum|NNS|_ was|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ Version|Version|NNP|_ software|software|NN|_ from|from|IN|_ Agilent|Agilent|NNP|_ .|.|.|_ Normalization|normalization|NN|_ of|of|IN|_ the|the|DT|_ data|datum|NNS|_ was|be|VBD|_ done|do|VBN|_ in|in|IN|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ using|use|VBG|_ the|the|DT|_ 75th|75th|JJ|_ percentile|percentile|NN|_ shift|shift|NN|_
MG1655|mg1655|NN|_ G181D|g181d|NN|_ NusA|nusa|NN|_ BR1|br1|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ G181D|g181d|NN|_ NusA|nusa|NN|_ BR2|br2|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ R258C|r258c|NN|_ NusA|nusa|NN|_ BR1|br1|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ R258C|r258c|NN|_ NusA|nusa|NN|_ BR2|br2|NN|_ ,|,|,|_ treated|treat|VBN|_
MG1655|mg1655|NN|_ WT|WT|NNP|_ NusA|NusA|NNP|_ BR1|br1|NN|_ ,|,|,|_ control|control|NN|_
MG1655|MG1655|NNP|_ WT|WT|NNP|_ NusA|nusa|NN|_ BR2|br2|NN|_ ,|,|,|_ control|control|NN|_
plasmid|plasmid|NN|_ :|:|:|_ G181D|g181d|NN|_ NusA|nusa|NN|_
plasmid|plasmid|NN|_ :|:|:|_ R258C|r258c|NN|_ NuSA|nusa|NN|_
plasmid|plasmid|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ NusA|nusa|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .|.|.|_ 74004|74004|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
Treated|treat|VBN|_ experimental|experimental|JJ|_ sets|set|NNS|_ transformed|transform|VBN|_ with|with|IN|_ plasmids|plasmid|NNS|_ containing|contain|VBG|_ WT|wt|JJ|_
Bacterial|bacterial|JJ|_ cell|cell|NN|_ pellet|pellet|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ given|give|VBN|_ 1|1|CD|_ %|%|NN|_ sub-culturing|sub-culturing|JJ|_ till|till|IN|_ OD|od|NN|_ at|at|IN|_ 600nm|600nm|NN|_ was|be|VBD|_ 0.4|0.4|CD|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ BCM|BCM|NNP|_ treated-Replicate1|treated-replicate1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ BCM|BCM|NNP|_ treated-Replicate2|treated-replicate2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Vector|Vector|NNP|_ control-Replicate1|control-replicate1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ Vector|Vector|NNP|_ control-Replicate2|control-replicate2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ MG1655|mg1655|NN|_ ,|,|,|_ WT|WT|NNP|_ Rho|rho|NN|_ treated-Replicate1|treated-replicate1|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ,|,|,|_ WT|WT|NNP|_ Rho|rho|NN|_ treated-Replicate2|treated-replicate2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Images|image|NNS|_ Analysis|analysis|NN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ Version|Version|NNP|_ 11.5|11.5|CD|_ to|to|TO|_ obtain|obtain|VB|_ raw|raw|JJ|_ data.Probe|data.probe|NN|_ intensities|intensity|NNS|_ generated|generate|VBN|_ from|from|IN|_ feature|feature|NN|_ extraction|extraction|NN|_ raw|raw|JJ|_ data|datum|NNS|_ were|be|VBD|_ split|split|VBN|_ based|base|VBN|_ on|on|IN|_ channel|channel|NN|_ type|type|NN|_ and|and|CC|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .|.|.|_ 74004|74004|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
Treated|treat|VBN|_ experimental|experimental|JJ|_ sets|set|NNS|_ transformed|transform|VBN|_ with|with|IN|_ plasmids|plasmid|NNS|_ containing|contain|VBG|_ BCM|BCM|NNP|_
treatment|treatment|NN|_ :|:|:|_ BCM|BCM|NNP|_
treatment|treatment|NN|_ :|:|:|_ vector|vector|NN|_ control|control|NN|_
treatment|treatment|NN|_ :|:|:|_ WT|WT|NNP|_ Rho|rho|NN|_ plasmid|plasmid|NN|_
Bacterial|bacterial|JJ|_ cell|cell|NN|_ pellet|pellet|NN|_
Bacterial|bacterial|JJ|_ culture|culture|NN|_ grown|grow|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ given|give|VBN|_ 1|1|CD|_ %|%|NN|_ sub-culturing|sub-culturing|JJ|_ till|till|IN|_ OD|od|NN|_ at|at|IN|_ 600nm|600nm|NN|_ was|be|VBD|_ 0.4|0.4|CD|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ∆|∆|CD|_ Rac|rac|NN|_ G324D|g324d|NN|_ ,|,|,|_ treated-Replicate1-mutant|treated-replicate1-mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ∆|∆|CD|_ Rac|rac|NN|_ G324D|g324d|NN|_ ,|,|,|_ treated-Replicate2-mutant|treated-replicate2-mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ∆|∆|CD|_ Rac|rac|NN|_ N340S|n340s|NN|_ ,|,|,|_ treated-Replicate1-mutant|treated-replicate1-mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ∆|∆|CD|_ Rac|rac|NN|_ N340S|n340s|NN|_ ,|,|,|_ treated-Replicate2-mutant|treated-replicate2-mutant|JJ|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ∆|∆|CD|_ Rac|rac|NN|_ WT|WT|NNP|_ ,|,|,|_ control-Replicate1-Wildtype|control-replicate1-wildtype|JJ|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ ∆|∆|CD|_ Rac|rac|NN|_ WT|WT|NNP|_ ,|,|,|_ control-Replicate2-Wildtype|control-replicate2-wildtype|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ delta-rac|delta-rac|JJ|_
Images|image|NNS|_ Analysis|analysis|NN|_ using|use|VBG|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ Version|Version|NNP|_ 11.5|11.5|CD|_ to|to|TO|_ obtain|obtain|VB|_ raw|raw|JJ|_ data.Probe|data.probe|NN|_ intensities|intensity|NNS|_ generated|generate|VBN|_ from|from|IN|_ feature|feature|NN|_ extraction|extraction|NN|_ raw|raw|JJ|_ data|datum|NNS|_ were|be|VBD|_ split|split|VBN|_ based|base|VBN|_ on|on|IN|_ channel|channel|NN|_ type|type|NN|_ and|and|CC|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ .|.|.|_
plasmid|plasmid|NN|_ :|:|:|_ G324D|g324d|NN|_ Rho|rho|NN|_ mutant|mutant|JJ|_
plasmid|plasmid|NN|_ :|:|:|_ N340S|n340s|NN|_ Rho|rho|NN|_ mutant|mutant|JJ|_
plasmid|plasmid|NN|_ :|:|:|_ WT|WT|NNP|_ Rho|rho|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ DNAse|dnase|NN|_ treatment|treatment|NN|_ -LRB-|-lrb-|-LRB-|_ Cat.No|cat.no|NN|_ .|.|.|_ 74004|74004|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_
Treated|treat|VBN|_ experimental|experimental|JJ|_ sets|set|NNS|_ transformed|transform|VBN|_ with|with|IN|_ plasmids|plasmid|NNS|_ containing|contain|VBG|_ Rho|rho|NN|_ -LRB-|-lrb-|-LRB-|_ WT|wt|JJ|_
Adaptor|adaptor|NN|_ Sequences|sequence|NNS|_ were|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_ .|.|.|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
All|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ processed|process|VBN|_ following|follow|VBG|_ NEB|NEB|NNP|_ 's|'s|POS|_ protocol|protocol|NN|_ from|from|IN|_ the|the|DT|_ NEBNext|nebnext|NN|_ ®|®|NN|_ ChIP-Seq|chip-seq|JJ|_ library|library|NN|_ preparation|preparation|NN|_ kit|kit|NN|_ .|.|.|_
Bacterial|bacterial|JJ|_ Cell|cell|NN|_ Lysates|lysate|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ collected|collect|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ washed|wash|VBN|_ three|three|CD|_ times|time|NNS|_ in|in|IN|_ ice-cold|ice-cold|JJ|_ 1X|1x|NN|_ PBS|PBS|NNP|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ then|then|RB|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 250|250|CD|_ μl|μl|NN|_ ChIP|chip|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 200|200|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 600|600|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ 4|4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X|X|NNP|_ ,|,|,|_ Complete|complete|JJ|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ EDTA-free|edta-free|NN|_ -LRB-|-lrb-|-LRB-|_ Roche|Roche|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Sonication|sonication|NN|_ of|of|IN|_ crosslinked|crosslink|VBN|_ samples|sample|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ Diagenode|Diagenode|NNP|_ Bioruptor|Bioruptor|NNP|_ ®|®|NN|_ at|at|IN|_ 30s|30s|CD|_ intervals|interval|NNS|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ high|high|JJ|_ amplitude|amplitude|NN|_ .|.|.|_ After|after|IN|_ sonication|sonication|NN|_ ,|,|,|_ 350|350|CD|_ μl|μl|NN|_ of|of|IN|_ ChIP|chip|NN|_ buffer|buffer|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ by|by|IN|_ gentle|gentle|JJ|_ pipetting|pipetting|NN|_ and|and|CC|_ 100|100|CD|_ μl|μl|NN|_ of|of|IN|_ each|each|DT|_ lysate|lysate|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ stored|store|VBN|_ as|as|IN|_ `|`|``|_ input|input|NN|_ '|'|''|_ .|.|.|_ Immunoprecipitation|immunoprecipitation|NN|_ was|be|VBD|_ performed|perform|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ using|use|VBG|_ 1|1|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ to|to|TO|_ and|and|CC|_ OD600nm|od600nm|NN|_ of|of|IN|_ 0.2-0.25|0.2-0.25|CD|_
ChIP-Seq|chip-seq|NN|_
Data|Data|NNP|_ collapsed|collapse|VBD|_ using|use|VBG|_ fastx|fastx|NN|_ collapser|collapser|NN|_ to|to|TO|_ remove|remove|VB|_ identical|identical|JJ|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
DL4184C|dl4184c|NN|_ _|_|CD|_ ChIP-seq|ChIP-seq|NNP|_
DL4201C|DL4201C|NNP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_
DL4311C|DL4311C|NNP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_
DL4312C|DL4312C|NNP|_ _|_|SYM|_ ChIP-seq|ChIP-seq|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K12|k12|NN|_ MG1655|mg1655|NN|_ NC000913|nc000913|NN|_ .3|.3|NN|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ _|_|SYM|_ recG263|recg263|NN|_ :|:|:|_ :|:|:|_ KanR|kanr|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ proA|proa|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN +|+|CC|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ delta|delta|NN|_ _|_|SYM|_ recG263|recg263|NN|_ :|:|:|_ :|:|:|_ KanR|kanr|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ proA|proa|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ pal246|pal246|NN|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ proA|proa|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN +|+|CC|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_
genotype|genotype|NN|_ :|:|:|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ mhpR|mhpr|NN|GEN :|:|:|_ :|:|:|_ χχχ|χχχ|NN|_ proA|proa|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ tsx|tsx|NN|GEN :|:|:|_ :|:|:|_ ISceIcs|isceic|NNS|_ PBAD-sbcDC|pbad-sbcdc|NN|_ lacZ|lacz|NN|GEN :|:|:|_ :|:|:|_ pal246|pal246|NN|_ cynX|cynx|NN|GEN :|:|:|_ :|:|:|_ GmR|gmr|NN|_ lacIq|laciq|NN|_ lacZχ|laczχ|NN|_ -|-|:|_
Protein|protein|NN|_ DNA|dna|NN|_ interactions|interaction|NNS|_ were|be|VBD|_ crosslinked|crosslink|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 22.5|22.5|CD|_ C|c|NN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ and|and|CC|_ quenched|quench|VBN|_ using|use|VBG|_ glycine|glycine|NN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 0.5|0.5|CD|_ M|m|NN|_
reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NC000913|nc000913|NN|_ .3|.3|NN|_ -RRB-|-rrb-|-RRB-|_ genome|genome|NN|_ using|use|VBG|_ Novoalign|novoalign|JJ|_ version|version|NN|_ 2.07|2.07|CD|_ -LRB-|-lrb-|-LRB-|_ www.novocraft.com|www.novocraft.com|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Example|example|NN|_ :|:|:|_ -LRB-|-lrb-|-LRB-|_ novoalign|novoalign|JJ|_ -|-|:|_ f|f|FW|_ DL4900|dl4900|FW|_ _|_|SYM|_ clip|clip|VB|_ _|_|SYM|_ clp.fasta|clp.fasta|SYM|_ -|-|:|_ d|d|NN|_ NC000913|nc000913|NN|_ .3|.3|NN|_ .|.|.|_ nix|nix|SYM|_ -|-|:|_ r|r|NN|_ Random|Random|NNP|_ >|>|JJR|_ DL4900.novo|dl4900.novo|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ txt|txt|NN|_ files|file|NNS|_ including|include|VBG|_ count|count|NN|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ whole|whole|JJ|_ genome|genome|NN|_
yPileup|ypileup|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ generate|generate|VB|_ count|count|NN|_ data|datum|NNS|_ for|for|IN|_ the|the|DT|_ whole|whole|JJ|_ genome|genome|NN|_ -|-|:|_ Example|example|NN|_ :|:|:|_ pyPileup.py|pypileup.py|NN|_ --|--|:|_ file|file|NN|_ _|_|NN|_ type|type|NN|_ =|=|JJ|_ novo|novo|FW|_ -|-|:|_ f|f|LS|_ DL4184.novo|dl4184.novo|NN|_ --|--|:|_ tab|tab|NN|_ =|=|JJ|_ NC000913|nc000913|NN|_ .3|.3|NN|_ .|.|.|_ tab|tab|NN|_ --|--|:|_ chr|chr|NN|_ =|=|JJ|_ Wholechom.txt|wholechom.txt|NN|_ --|--|:|_ ignorestrand|ignorestrand|JJ|_
A|a|DT|_ minimal|minimal|JJ|_ growth|growth|NN|_ medium|medium|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ the|the|DT|_ study|study|NN|_ by|by|IN|_ Ihssen|Ihssen|NNP|_ and|and|CC|_ Egli|Egli|NNP|_ -LRB-|-lrb-|-LRB-|_ 2004|2004|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ all|all|DT|_ experiments|experiment|NNS|_ .|.|.|_ Bacterial|bacterial|JJ|_ stock|stock|NN|_ cultures|culture|NNS|_ were|be|VBD|_ streaked|streak|VBN|_ onto|onto|IN|_ agar|agar|NN|_ plates|plate|NNS|_ and|and|CC|_ incubated|incubate|VBN|_ overnight|overnight|JJ|_ .|.|.|_ One|one|CD|_ colony|colony|NN|_ was|be|VBD|_ then|then|RB|_ transferred|transfer|VBN|_ into|into|IN|_ 20|20|CD|_ ml|ml|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ ,|,|,|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ r.p.m.|r.p.m.|NNS|_ -RRB-|-rrb-|-RRB-|_ over|over|IN|_ night|night|NN|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ ONC|onc|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ served|serve|VBD|_ as|as|IN|_ the|the|DT|_ inoculum|inoculum|NN|_ for|for|IN|_ experiments|experiment|NNS|_ .|.|.|_ For|for|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ experiments|experiment|NNS|_ we|we|PRP|_ designed|design|VBD|_ and|and|CC|_ constructed|construct|VBD|_ 500|500|CD|_ ml|ml|NN|_ bioreactors|bioreactor|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ study|study|NN|_ by|by|IN|_ Huwiler|Huwiler|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ that|that|WDT|_ were|be|VBD|_ half-filled|half-filled|JJ|_ with|with|IN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP per|per|IN|_ l|l|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ a|a|DT|_ temperature|temperature|NN|_ controlled|controlled|JJ|_ water|water|NN|_ bath|bath|NN|_ .|.|.|_ Before|before|IN|_ continuous|continuous|JJ|_ cultivation|cultivation|NN|_ -LRB-|-lrb-|-LRB-|_ dilution|dilution|NN|_ rate|rate|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ --|--|:|_ 2|2|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ ONC|onc|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ batch-mode|batch-mode|NN|_ until|until|IN|_ reactors|reactor|NNS|_ became|become|VBD|_ visibly|visibly|RB|_ turbid|turbid|JJ|_ .|.|.|_ Subsequently|subsequently|RB|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ steady-state|steady-state|JJ|_ -LRB-|-lrb-|-LRB-|_ defined|define|VBN|_ as|as|IN|_ constant|constant|JJ|_ optical|optical|JJ|_ density|density|NN|_ over|over|IN|_ time|time|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ harvested|harvest|VBN|_ for|for|IN|_ experimentation|experimentation|NN|_ .|.|.|_ For|for|IN|_ starvation|starvation|NN|_ experiments|experiment|NNS|_ the|the|DT|_ medium|medium|NN|_ flow|flow|NN|_ was|be|VBD|_ stopped|stop|VBN|_ during|during|IN|_ steady-state|steady-state|JJ|_ and|and|CC|_ bacteria|bacterium|NNS|_ were|be|VBD|_ collected|collect|VBN|_ after|after|IN|_ 4|4|CD|_ h.|h.|NN|_ To|to|TO|_ avoid|avoid|VB|_ gene-expression|gene-expression|NN|_ signatures|signature|NNS|_ of|of|IN|_ stationary|stationary|JJ|_ cells|cell|NNS|_ from|from|IN|_ the|the|DT|_ ONC|ONC|NNP|_ ,|,|,|_ batch|batch|NN|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ 1000|1000|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ containing|contain|VBG|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ pre-warmed|pre-warmed|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP per|per|IN|_ l|l|NN|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ 37|37|CD|_ °C|°c|NN|_ ;|;|:|_ 250|250|CD|_ r.p.m.|r.p.m.|NNS|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ with|with|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ an|a|DT|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ pre-culture|pre-culture|JJ|_ that|that|IN|_ derived|derive|VBN|_ from|from|IN|_ the|the|DT|_ ONC|ONC|NNP|_ .|.|.|_
Differential|differential|JJ|_ expression|expression|NN|_ analysis|analysis|NN|_ with|with|IN|_ DESeq|deseq|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ and|and|CC|_ Huber|Huber|NNP|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ the|the|DT|_ default|default|NN|_ setting|set|VBG|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 011741|011741|CD|_ -LRB-|-lrb-|-LRB-|_ E.coli|e.coli|NN|_ strain|strain|NN|_ IAI1|iai1|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NC|nc|NN|_ _|_|SYM|_ 000913.2|000913.2|CD|_ -LRB-|-lrb-|-LRB-|_ E.coli|e.coli|NN|_ strain|strain|NN|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ TW09308|tw09308|NN|_ -LRB-|-lrb-|-LRB-|_ E.coli|e.coli|NN|_ strain|strain|NN|_ TW09308|tw09308|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ TW11588|tw11588|NN|_ -LRB-|-lrb-|-LRB-|_ E.coli|e.coli|NN|_ strain|strain|NN|_ TW11588|tw11588|NN|_ -RRB-|-rrb-|-RRB-|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Bacteria|bacterium|NNS|_ liquid|liquid|JJ|_ culture|culture|NN|_
Harvested|harvest|VBN|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|CD|_ ×|×|NN|_ 6|6|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ immediately|immediately|RB|_ combined|combine|VBN|_ with|with|IN|_ 6|6|CD|_ ml|ml|NN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Grand|Grand|NNP|_ Island|Island|NNP|_ ,|,|,|_ NY|NY|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 15|15|CD|_ min|min|NN|_ at|at|IN|_ 12000|12000|CD|_ r.p.m.|r.p.m.|NN|_ ,|,|,|_ washed|wash|VBN|_ with|with|IN|_ 1|1|CD|_ ml|ml|NN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 15000|15000|CD|_ r.p.m.|r.p.m.|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ re-suspended|re-suspended|JJ|_ in|in|IN|_ 0.5|0.5|CD|_ ml|ml|NN|_ RNAlater|rnalater|NN|_ and|and|CC|_ stored|store|VBD|_ at|at|IN|_ −|−|CD|_ 20|20|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ the|the|DT|_ RiboPure-Bacteria|RiboPure-Bacteria|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ To|to|TO|_ achieve|achieve|VB|_ high|high|JJ|_ RNA|rna|NN|_ yields|yield|NNS|_ several|several|JJ|_ reactions|reaction|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ done|do|VBN|_ in|in|IN|_ parallel|parallel|NN|_ and|and|CC|_ pooled|pool|VBD|_ at|at|IN|_ the|the|DT|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ procedure|procedure|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ DNase|dnase|NN|_ treatment|treatment|NN|_ step|step|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ included|include|VBN|_ to|to|TO|_ assure|assure|VB|_ no|no|DT|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contamination|contamination|NN|_ .|.|.|_ Messenger|messenger|NN|_ RNA|rna|NN|_ was|be|VBD|_ enriched|enrich|VBN|_ using|use|VBG|_ the|the|DT|_ RiboMinus|RiboMinus|NNP|_ Bacteria|bacterium|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
IAI1|iai1|NN|_ batch|batch|NN|_
IAI1|iai1|NN|_ chemostat|chemostat|NN|_
IAI1|iai1|NN|_ starvation|starvation|NN|_
IAI1|iai1|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
IAI1|iai1|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
IAI1|iai1|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
IAI1|iai1|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
IAI1|iai1|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
IAI1|iai1|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
Map|map|NN|_ RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ to|to|TO|_ reference|reference|VB|_ genomes|genome|NNS|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ -LRB-|-lrb-|-LRB-|_ Langmead|Langmead|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ alignment|alignment|NN|_ parameters|parameter|NNS|_ -LRB-|-lrb-|-LRB-|_ -|-|:|_ n|n|NN|_ 2-e|2-e|JJ|_ 70-l|70-l|JJ|_ 28|28|CD|_ --|--|:|_ best|best|JJS|_ -RRB-|-rrb-|-RRB-|_
MG1655|mg1655|NN|_ batch|batch|NN|_
MG1655|mg1655|NN|_ chemostat|chemostat|NN|_
MG1655|mg1655|NN|_ starvation|starvation|NN|_
MG1655|mg1655|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
Quality|quality|JJ|_ trimming|trim|VBG|_ of|of|IN|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ at|at|IN|_ Read|Read|NNP|_ Segment|Segment|NNP|_ Quality|Quality|NNP|_ Control|Control|NNP|_ Indicator|Indicator|NNP|_ .|.|.|_
Remove|remove|VBP|_ non-protein|non-protein|JJ|_ coding|code|VBG|_ counts|count|NNS|_
RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ confirmed|confirm|VBN|_ with|with|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ system|system|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ cycles|cycle|NNS|_ ,|,|,|_ pooling|pool|VBG|_ eight|eight|CD|_ bar-coded|bar-coded|JJ|_ samples|sample|NNS|_ per|per|IN|_ lane|lane|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ platform|platform|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ the|the|DT|_ Research|Research|NNP|_ Technology|Technology|NNP|_ Support|support|NN|_ Facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ RTSF|rtsf|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ Michigan|Michigan|NNP|_ State|State|NNP|_ University|University|NNP|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ IAI1|iai1|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ -LRB-|-lrb-|-LRB-|_ MG1655|mg1655|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ TW09308|tw09308|NN|_
strain|strain|NN|_ :|:|:|_ TW11588|tw11588|NN|_
Summarize|summarize|VB|_ the|the|DT|_ read|read|NN|_ count|count|NN|_ to|to|TO|_ each|each|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ All|all|DT|_ in|in|IN|_ tab-delimited|tab-delimited|JJ|_ ASCII|ASCII|NNP|_ format|format|NN|_ .|.|.|_ raw_count.txt|raw_count.txt|NN|_ -LRB-|-lrb-|-LRB-|_ pre-normalized|pre-normalized|JJ|_ read|read|NN|_ count|count|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ normalized_count.txt|normalized_count.txt|NN|_ ,|,|,|_ panGeneMap.txt|pangenemap.txt|NN|_ -LRB-|-lrb-|-LRB-|_ geneID|geneid|NN|_ map|map|NN|GEN between|between|IN|_ the|the|DT|_ strains|strain|NNS|_ and|and|CC|_ pangene|pangene|NN|_ ID|id|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Gene_annotations.txt|gene_annotations.txt|NN|_ -LRB-|-lrb-|-LRB-|_ annotation|annotation|NN|_ of|of|IN|_ genes|gene|NNS|_ -RRB-|-rrb-|-RRB-|_
treatment|treatment|NN|_ :|:|:|_ batch|batch|NN|_ growth|growth|NN|_
treatment|treatment|NN|_ :|:|:|_ chemostat|chemostat|NN|_ growth|growth|NN|_
treatment|treatment|NN|_ :|:|:|_ starvation|starvation|NN|_ growth|growth|NN|_
TW09308|tw09308|NN|_ batch|batch|NN|_
TW09308|tw09308|NN|_ chemostat|chemostat|NN|_
TW09308|tw09308|NN|_ starvation|starvation|NN|_
TW09308|tw09308|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
TW09308|tw09308|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
TW09308|tw09308|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
TW09308|tw09308|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
TW09308|tw09308|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
TW09308|tw09308|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
TW11588|tw11588|NN|_ batch|batch|NN|_
TW11588|tw11588|NN|_ chemostat|chemostat|NN|_
TW11588|tw11588|NN|_ starvation|starvation|NN|_
TW11588|tw11588|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
TW11588|tw11588|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ batch|batch|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
TW11588|tw11588|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
TW11588|tw11588|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ chemostat|chemostat|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
TW11588|tw11588|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 1|1|CD|_
TW11588|tw11588|NN|_ transcriptome|transcriptome|NN|_ from|from|IN|_ starvation|starvation|NN|_ growth|growth|NN|_ _|_|NN|_ 2|2|CD|_
All|all|DT|_ cultures|culture|NNS|_ were|be|VBD|_ based|base|VBN|_ on|on|IN|_ MOPS|mop|NNS|MED media|media|NNS|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ with|with|IN|_ full|full|JJ|_ supplement|supplement|NN|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ -RRB-|-rrb-|-RRB-|_ minus|minus|CC|_ methionine|methionine|NN|SUPP .|.|.|_ An|a|DT|_ overnight|overnight|JJ|_ liquid|liquid|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 400-fold|400-fold|JJ|_ into|into|IN|_ 200|200|CD|_ ml|ml|NN|_ fresh|fresh|JJ|_ media|media|NNS|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ kept|keep|VBN|_ in|in|IN|_ a|a|DT|_ 1|1|CD|_ liter|liter|NN|_ flask|flask|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ aeration|aeration|NN|_ until|until|IN|_ OD420|od420|NN|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_
bacteria|bacterium|NNS|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ Casava|Casava|NNP|_ versions|version|NNS|_ 1.6|1.6|CD|_ or|or|CC|_ 1.7|1.7|CD|_ .|.|.|_
Bowtie|Bowtie|NNP|_ alignments|alignment|NNS|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ wiggle|wiggle|VB|_ files|file|NNS|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ mRNA-seq|mrna-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ is|be|VBZ|_ distributed|distribute|VBN|_ into|into|IN|_ several|several|JJ|_ nucleotides|nucleotide|NNS|_ in|in|IN|_ the|the|DT|_ center|center|NN|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ .|.|.|_ For|for|IN|_ each|each|DT|_ read|read|NN|_ ,|,|,|_ the|the|DT|_ center|center|NN|_ residues|residue|NNS|_ that|that|WDT|_ are|be|VBP|_ at|at|IN|_ least|least|JJS|_ 10|10|CD|_ nucleotides|nucleotide|NNS|_ away|away|RB|_ from|from|IN|_ either|either|CC|_ ends|end|NNS|_ were|be|VBD|_ given|give|VBN|_ the|the|DT|_ same|same|JJ|_ score|score|NN|_ ,|,|,|_ which|which|WDT|_ is|be|VBZ|_ weighted|weight|VBN|_ by|by|IN|_ the|the|DT|_ length|length|NN|_ of|of|IN|_ the|the|DT|_ fragment|fragment|NN|_ -LSB-|-lsb-|-LRB-|_ Oh|oh|UH|_ et|et|FW|_ al|al|FW|_ ,|,|,|_ .|.|.|_ Cell|cell|NN|_ 147|147|CD|_ ,|,|,|_ 1295|1295|CD|_ -LRB-|-lrb-|-LRB-|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ Scores|score|NNS|_ therefore|therefore|RB|_ represent|represent|VBP|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ read|read|VBN|_ alignments|alignment|NNS|_ attributed|attribute|VBD|_ to|to|TO|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ under|under|IN|_ each|each|DT|_ scoring|score|VBG|_ scheme|scheme|NN|_ .|.|.|_ For|for|IN|_ DMS-seq|dms-seq|NN|_ ,|,|,|_ the|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ alignment|alignment|NN|_ was|be|VBD|_ the|the|DT|_ position|position|NN|_ immediately|immediately|RB|_ 5|5|CD|_ '|'|''|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ;|;|:|_ Oh|oh|UH|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ ,|,|,|_ 200|200|CD|_ mL|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ were|be|VBD|_ filtered|filter|VBN|_ rapidly|rapidly|RB|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ cell|cell|NN|_ pellet|pellet|NN|_ was|be|VBD|_ flash-frozen|flash-frozen|JJ|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ and|and|CC|_ combined|combine|VBN|_ with|with|IN|_ 650|650|CD|_ µL|µl|NN|_ of|of|IN|_ frozen|frozen|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ ,|,|,|_ 100mM|100mm|NN|_ NH4Cl|nh4cl|NN|_ ,|,|,|_ 20mM|20mm|NN|_ Tris-HCl|tris-hcl|NN|_ pH|ph|NN|_ 8.0|8.0|CD|_ ,|,|,|_ 0.1|0.1|CD|_ %|%|NN|_ Nonidet|nonidet|JJ|_ P40|p40|NN|_ ,|,|,|_ 0.4|0.4|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ ,|,|,|_ 100|100|CD|_ U|U|NNP|_
For|for|IN|_ in|in|FW|_ vivo|vivo|FW|_ DMS|dms|FW|_ modification|modification|NN|_ ,|,|,|_ 15|15|CD|_ mL|ml|NN|_ of|of|IN|_ exponentially|exponentially|RB|_ growing|grow|VBG|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ incubated|incubate|VBN|_ with|with|IN|_ 750|750|CD|_ µL|µl|NN|_ DMS|dms|NN|_ for|for|IN|_ 2|2|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ For|for|IN|_ kasugamycin|kasugamycin|NN|_ -LRB-|-lrb-|-LRB-|_ ksg|ksg|NN|_ -RRB-|-rrb-|-RRB-|_ experiments|experiment|NNS|_ ,|,|,|_ ksg|ksg|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 10|10|CD|_ mg|mg|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
mRNA-seq|mrna-seq|NN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ with|with|IN|_ control|control|NN|_ plasmid|plasmid|NN|_
mRNA-seq|mrna-seq|NN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ with|with|IN|_ plasmid|plasmid|NN|_ expressing|express|VBG|_ mini-ORF|mini-orf|NN|_ CUA|cua|NN|_
mRNA-seq|mrna-seq|NN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ WT|wt|JJ|_ with|with|IN|_ plasmid|plasmid|NN|_ expressing|express|VBG|_ mini-ORF|mini-orf|NN|_ CUG|cug|NN|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ p-CTRL|p-ctrl|NN|_ -RSB-|-rsb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ p-CUA|p-cua|NN|_ -RSB-|-rsb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_ -LSB-|-lsb-|-LRB-|_ p-CUG|p-cug|NN|_ -RSB-|-rsb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Wiggle|Wiggle|NNP|_ files|file|VBZ|_ with|with|IN|_ two|two|CD|_ columns|column|NNS|_ :|:|:|_ first|first|JJ|_ column|column|NN|_ containing|contain|VBG|_ chromosome|chromosome|NN|_ positions|position|NNS|_ and|and|CC|_ second|second|JJ|_ column|column|NN|_ containing|contain|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ position|position|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ publication|publication|NN|_ for|for|IN|_ details|detail|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ against|against|IN|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ genome|genome|NN|_ using|use|VBG|_ parameters|parameter|NNS|_ -|-|:|_ v1|v1|SYM|_ -|-|:|_ m2|m2|SYM|_ -|-|:|_ k1|k1|NN|_ .|.|.|_
The|the|DT|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ and|and|CC|_ fragmented|fragmented|JJ|_ mRNA|mrna|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ miRNA|miRNA|NNP|_ cloning|clone|VBG|_ linker-1|linker-1|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ truncated|truncate|VBN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ 2|2|CD|_ K227Q|k227q|NN|_ .|.|.|_ The|the|DT|_ ligated|ligate|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ reverse|reverse|JJ|_ transribed|transribe|VBN|_ using|use|VBG|_ the|the|DT|_ primer|primer|NN|_ 5Phos|5phos|NN|_
treatment|treatment|NN|_ :|:|:|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_
Trimmed|trim|VBD|_ reads|read|VBZ|_ were|be|VBD|_ sequentially|sequentially|RB|_ aligned|align|VBN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v0|v0|NN|_ .12.7|.12.7|CD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ and|and|CC|_ noncoding|noncoding|JJ|_ RNA|rna|NN|_ allowing|allow|VBG|_ one|one|CD|_ mismatch|mismatch|NN|_ .|.|.|_ Reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ any|any|DT|_ of|of|IN|_ these|these|DT|_ indices|index|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ .|.|.|_
5|5|CD|_ '|'|''|_ linker|linker|NN|_ and|and|CC|_ poly|poly|NN|_ A-tail|a-tail|NN|_ removal|removal|NN|_ using|use|VBG|_ READemption|reademption|NN|_
5|5|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ suspension|suspension|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ 0.625|0.625|CD|_ ml|ml|NN|_ of|of|IN|_ pre-chilled|pre-chilled|JJ|_ stop|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_
An|a|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ strain|strain|NN|_ LB226692|lb226692|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ 1:10,000|1:10,000|CD|_ in|in|IN|_ pre-warmed|pre-warmed|JJ|_ LB|lb|NN|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ g|g|NN|_
cDNA|cdna|NN|_ libraries|library|NNS|_ for|for|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ sequencing|sequencing|NN|_ platform|platform|NN|_ were|be|VBD|_ constructed|construct|VBN|_ by|by|IN|_ vertis|vertis|NN|_ Biotechnology|Biotechnology|NNP|_ AG|AG|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Berezikov|Berezikov|NNP|_ et|et|FW|_ al.|al.|FW|_ ,2006|,2006|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ without|without|IN|_ the|the|DT|_ RNA|rna|NN|_ size-fractionation|size-fractionation|NN|_ step|step|NN|_ prior|prior|RB|_ to|to|TO|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ polyA-tailed|polya-tailed|JJ|_ using|use|VBG|_ polyA|polya|NN|_ polymerase|polymerase|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ -|-|:|_ PPP|ppp|NN|_ termini|terminus|NNS|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ 5|5|CD|_ '|'|''|_ -|-|:|_ P|p|NN|_ using|use|VBG|_ tobacco|tobacco|NN|_ acid|acid|NN|_ pyrophosphatase|pyrophosphatase|NN|_ -LRB-|-lrb-|-LRB-|_ TAP|tap|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ allow|allow|VB|_ for|for|IN|_ the|the|DT|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ RNA|rna|NN|_ adapter|adapter|NN|_ .|.|.|_ First-strand|first-strand|JJ|_ cDNA|cdna|NN|_ was|be|VBD|_ synthesized|synthesize|VBN|_ by|by|IN|_ an|a|DT|_ oligo|oligo|JJ|_ -LRB-|-lrb-|-LRB-|_ dT|dt|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ adapter|adapter|NN|_ primer|primer|NN|_ and|and|CC|_ the|the|DT|_ M-MLV|m-mlv|NN|_ reverse|reverse|JJ|_ transcriptase|transcriptase|NN|_ .|.|.|_ In|in|IN|_ a|a|DT|_ PCR-based|pcr-based|JJ|_ amplification|amplification|NN|_ step|step|NN|_ using|use|VBG|_ a|a|DT|_ high|high|JJ|_ fidelity|fidelity|NN|_ DNA|dna|NN|_ polymerase|polymerase|NN|_ the|the|DT|_ cDNA|cdna|NN|_ concentration|concentration|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 20-30|20-30|CD|_ ng|ng|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O104|o104|NN|_ :|:|:|_ H4|h4|NN|_
exponentially|exponentially|RB|_ growing|grow|VBG|_ cells|cell|NNS|_
FastQ|fastq|JJ|_ quality|quality|NN|_ trimming|trim|VBG|_ using|use|VBG|_ FastX|fastx|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ a|a|DT|_ cut-off|cut-off|JJ|_ value|value|NN|_ of|of|IN|_ 20|20|CD|_
Fastq|fastq|NN|_ to|to|TO|_ fasta|fasta|NN|_ conversion|conversion|NN|_ using|use|VBG|_ FastX|fastx|NN|_ FastX|fastx|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ -RRB-|-rrb-|-RRB-|_
generation|generation|NN|_ of|of|IN|_ coverage|coverage|NN|_ graphs|graph|NNS|_ representing|represent|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ pAA|paa|NN|_ plasmid-associated|plasmid-associated|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 018658.1|018658.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018659.1|018659.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018660.1|018660.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|SYM|_ 018666.1|018666.1|CD|_
mapping|mapping|NN|_ of|of|IN|_ non-rRNA|non-rrna|JJ|_ and|and|CC|_ tRNA|trna|NN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ chromosome|chromosome|NN|_ and|and|CC|_ plasmids|plasmid|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
mapping|mapping|NN|_ of|of|IN|_ reads|read|VBZ|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_ and|and|CC|_ segemehl|segemehl|NN|_ 0.2.0|0.2.0|CD|_
normalization|normalization|NN|_ of|of|IN|_ graphs|graph|NNS|_ to|to|TO|_ the|the|DT|_ total|total|JJ|_ number|number|NN|_ of|of|IN|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ library|library|NN|_ using|use|VBG|_ READemption|reademption|NN|_ 0.3.7|0.3.7|CD|_
origin|origin|NN|_ of|of|IN|_ isolation|isolation|NN|_ :|:|:|_ patient|patient|NN|_ with|with|IN|_ hemolytic|hemolytic|JJ|_ uremic|uremic|JJ|_ syndrome|syndrome|NN|_ -LRB-|-lrb-|-LRB-|_ HUS|hus|NN|_ -RRB-|-rrb-|-RRB-|_
outbreak|outbreak|NN|_ :|:|:|_ 2011|2011|CD|_ outbreak|outbreak|NN|_ centered|center|VBN|_ in|in|IN|_ Northern|Northern|NNP|_ Germany|Germany|NNP|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ clinical|clinical|JJ|_ isolate|isolate|JJ|_ LB226692|lb226692|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ wig|wig|NN|_ files|file|NNS|_ representing|represent|VBG|_ the|the|DT|_ normalized|normalize|VBN|_ number|number|NN|_ of|of|IN|_ pAA-associated|paa-associated|JJ|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ nucleotide|nucleotide|NN|_ .|.|.|_ Files|file|NNS|_ contain|contain|VBP|_ wiggle-formatted|wiggle-formatted|JJ|_ files|file|NNS|_ data|datum|NNS|_ for|for|IN|_ accessions|accession|NNS|_ NC|NC|NNP|_ _|_|SYM|_ 018658.1|018658.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018659.1|018659.1|CD|_ ,|,|,|_ NC|NC|NNP|_ _|_|NNP|_ 018660.1|018660.1|CD|_ ,|,|,|_ and|and|CC|_ NC|NC|NNP|_ _|_|SYM|_ 018666.1|018666.1|CD|_ .|.|.|_
TEX|TEX|NNP|_ -|-|:|_ _|_|SYM|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_
TEX|tex|NN|_ +|+|CC|_ _|_|SYM|_ E.|e.|FW|_ coli|coli|FW|_ O104|o104|NN|_ :|:|:|_ H4|h4|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ Nano|Nano|NNP|_ Drop|Drop|NNP|_ .|.|.|_ RNA|rna|NN|_ integrity|integrity|NN|_ was|be|VBD|_ monitored|monitor|VBN|_ using|use|VBG|_ the|the|DT|_ R6K|r6k|NN|_ ScreenTape|screentape|NN|_ system|system|NN|_ on|on|IN|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2200|2200|CD|_ TapeStation|TapeStation|NNP|_ .|.|.|_ gDNA|gdna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 1U|1u|NN|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD600|od600|NN|_ of|of|IN|_ 0.6|0.6|CD|_ -LRB-|-lrb-|-LRB-|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ divided|divide|VBN|_ into|into|IN|_ 10|10|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ volumes|volume|NNS|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ STOP|stop|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ ,|,|,|_ 5|5|CD|_ %|%|NN|_ phenol|phenol|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 4.7|4.7|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ 20|20|CD|_ min|min|NN|_ incubation|incubation|NN|_ on|on|IN|_ ice|ice|NN|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ ˚C|˚c|NN|_ and|and|CC|_ 7000|7000|CD|_ x|x|CC|_ g|g|NN|_ in|in|IN|_ a|a|DT|_ centrifuge|centrifuge|NN|_ .|.|.|_ Pellets|pellet|NNS|_ from|from|IN|_ one|one|CD|_ aliquot|aliquot|NN|_ were|be|VBD|_ gently|gently|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ RNAProtect|rnaprotect|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ further|further|JJ|_ stabilize|stabilize|VB|_ the|the|DT|_ RNA|rna|NN|_ .|.|.|_ Remaining|remain|VBG|_ samples|sample|NNS|_ were|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ RNAlater|rnalater|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ placed|place|VBN|_ at|at|IN|_ -80|-80|CD|_ ˚C|˚c|NN|_ for|for|IN|_ archival|archival|JJ|_ storage|storage|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ on|on|IN|_ column|column|NN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ '|'|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ 23S|23s|NN|_ and|and|CC|_ 16S|16s|NN|_ rRNAs|rrna|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ subtractive|subtractive|JJ|_ hybridization|hybridization|NN|_ using|use|VBG|_ the|the|DT|_ MICROBExpress|microbexpress|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ modifications|modification|NNS|_ .|.|.|_ Compared|compare|VBN|_ with|with|IN|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ ,|,|,|_ 50|50|CD|_ %|%|NN|_ more|more|JJR|_ capture|capture|NN|_ oligonucleotides|oligonucleotide|NNS|_ and|and|CC|_ magnetic|magnetic|JJ|_ beads|bead|NNS|_ were|be|VBD|_ used|use|VBN|_ .|.|.|_ 5S|5s|NN|_ rRNAs|rrna|NNS|_ -LRB-|-lrb-|-LRB-|_ 120|120|CD|_ nt|nt|NNS|_ in|in|IN|_ length|length|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ during|during|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ on|on|IN|_ column|column|NN|_ .|.|.|_ Specifically|specifically|RB|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ depletion|depletion|NN|_ on|on|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RiboZero|RiboZero|NNP|_ -LRB-|-lrb-|-LRB-|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_
Crooks|Crooks|NNPS|_ _|_|SYM|_ aero|aero|FW|_
Crooks|Crooks|NNPS|_ _|_|SYM|_ anaero|anaero|FW|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism strains|strain|NNS|_ E.coli|e.coli|JJ|_ C|c|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 4860|4860|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ Crooks|crook|NNS|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1576|1576|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ DH5α|dh5α|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 6897|6897|CD|_ -RRB-|-rrb-|-RRB-|_ E.|e.|FW|_ coli|coli|FW|_ W|w|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 1116|1116|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ DSMZ|dsmz|NN|_ 5911|5911|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ obtained|obtain|VBN|_ from|from|IN|_ DSMZ-German|DSMZ-German|NNP|_ Collection|Collection|NNP|_ of|of|IN|_ Microorganism|Microorganism|NNP|_ and|and|CC|_ Cell|cell|NN|_ Cultures|culture|NNS|_ ;|;|:|_ E.|e.|FW|_ coli|coli|FW|_ BL21|bl21|NN|_ -LRB-|-lrb-|-LRB-|_ DE3|de3|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ purchased|purchase|VBN|_ as|as|IN|_ competent|competent|JJ|_ cells|cell|NNS|_ from|from|IN|_ Agilent|Agilent|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ ATCC|atcc|NN|_ 700926|700926|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ strains|strain|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ containing|contain|VBG|_ Na2HPO4|na2hpo4|NN|_ x|x|NN|_ 7H2O|7h2o|NN|_ -LRB-|-lrb-|-LRB-|_ 6.8|6.8|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ KH2PO4|kh2po4|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NaCl|nacl|NN|_ -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ NH4Cl|nh4cl|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ MgSO4|mgso4|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ CaCl2|cacl2|NN|_ -LRB-|-lrb-|-LRB-|_ 0.1|0.1|CD|_ mmol|mmol|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ trace|trace|NN|_ elements|element|NNS|_ ,|,|,|_ Wolf|Wolf|NNP|_ 's|'s|POS|_ vitamin|vitamin|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ g|g|NN|_ L-1|l-1|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Anoxic|anoxic|JJ|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ glucose|glucose|NN|SUPP was|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ flushing|flush|VBG|_ solution|solution|NN|_ with|with|IN|_ oxygen|oxygen|NN|_ free|free|JJ|_ nitrogen|nitrogen|NN|_ -LRB-|-lrb-|-LRB-|_ 95|95|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ from|from|IN|_ single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ each|each|DT|_ of|of|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ strains|strain|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ optical|optical|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ flasks|flask|NNS|_ or|or|CC|_ 300|300|CD|_ ml|ml|NN|_ oxygen-free|oxygen-free|JJ|_ sealed|sealed|JJ|_ bottles|bottle|NNS|_ containing|contain|VBG|_ 50|50|CD|_ ml|ml|NN|_ glucose-M9|glucose-m9|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ in|in|IN|_ a|a|DT|_ shaking|shake|VBG|_ incubator|incubator|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ .|.|.|_
Gene|Gene|NNP|_ expression|expression|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ per|per|IN|_ strain|strain|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ analyzed|analyze|VBN|_ in|in|IN|_ the|the|DT|_ statistical|statistical|JJ|_ software|software|NN|_ program|program|NN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ www.r-project.org|www.r-project.org|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ EdgeR|edger|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 3|3|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ CQN|cqn|NN|_ package|package|NN|_ ,|,|,|_ which|which|WDT|_ accounts|account|VBZ|_ for|for|IN|_ both|both|DT|_ gene|gene|NN|_ length|length|NN|_ and|and|CC|_ GC|gc|NN|_ content|content|JJ|_ effects|effect|NNS|_ -LRB-|-lrb-|-LRB-|_ 4|4|LS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ were|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ comparing|compare|VBG|_ expression|expression|NN|_ values|value|NNS|_ under|under|IN|_ anaerobic|anaerobic|JJ|_ and|and|CC|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_ Those|those|DT|_ genes|gene|NNS|_ with|with|IN|_ adjusted|adjusted|JJ|_ P|p|NN|_ values|value|NNS|_ less|less|JJR|_ than|than|IN|_ 0.01|0.01|CD|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ ,|,|,|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ less|less|JJR|_ than|than|IN|_ 1|1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ identified|identify|VBN|_ as|as|IN|_ significantly|significantly|RB|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ gene|gene|NN|_ annotations|annotation|NNS|_ were|be|VBD|_ automatically|automatically|RB|_ made|make|VBN|_ using|use|VBG|_ the|the|DT|_ biomaRt|biomart|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ together|together|RB|_ with|with|IN|_ the|the|DT|_ annotation|annotation|NN|_ files|file|VBZ|_ available|available|JJ|_ at|at|IN|_ the|the|DT|_ Ensembl|ensembl|NN|_ database|database|NN|_ -LRB-|-lrb-|-LRB-|_ www.ensembl.org|www.ensembl.org|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ gene|gene|NN|_ set|set|NN|_ enrichment|enrichment|NN|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ GSEA|gsea|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ piano|piano|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ 6|6|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ All|all|DT|_ R|r|NN|_ packages|package|NNS|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ are|be|VBP|_ available|available|JJ|_ in|in|IN|_ Bioconductor|Bioconductor|NNP|_ -LRB-|-lrb-|-LRB-|_ www.bioconductor.org|www.bioconductor.org|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ Crooks|crook|NNS|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ gene|gene|NN|_ expresion|expresion|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
The|The|NNP|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|preparation|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ with|with|IN|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ seven|seven|CD|_ E.|e.|FW|_ coli|coli|FW|_ cultures|culture|NNS|_ grown|grow|VBN|_ in|in|IN|_ triplicate|triplicate|NN|_ to|to|TO|_ an|a|DT|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase under|under|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_ RT-PCR|rt-pcr|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ SuperScript|SuperScript|NNP|_ ®|®|NNP|_ II|II|NNP|_ One-step|one-step|JJ|_ RT-PCR|rt-pcr|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ using|use|VBG|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq2000|hiseq2000|NN|_ platform|platform|NN|_ with|with|IN|_ a|a|DT|_ paired-end|paired-end|NN|_ protocol|protocol|NN|_ and|and|CC|_ read|read|VB|_ lengths|length|NNS|_ of|of|IN|_ 50|50|CD|_ nt|nt|NNS|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ a|a|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Fluorometer|Fluorometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ integrity|integrity|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ DNA|dna|NN|_ contamination|contamination|NN|_ ,|,|,|_ removal|removal|NN|_ of|of|IN|_ rRNAs|rrna|NNS|_ and|and|CC|_ cDNA|cdna|NN|_ library|library|NN|_ validation|validation|NN|_ were|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glycerol|glycerol|NN|SUPP
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glycerol|glycerol|NN|SUPP +|+|CC|_ propionate|propionate|NN|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M4|m4|NN|_ minimal|minimal|JJ|_ medium|medium|NN|_ under|under|IN|_ oxic|oxic|JJ|_ and|and|CC|_ anoxic|anoxic|JJ|_ conditions|condition|NNS|_ .|.|.|_ The|the|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ 1.27|1.27|CD|_ mM|mm|NN|KWSUPP K2HPO4|k2hpo4|NN|_ ,|,|,|_ 0.73|0.73|CD|_ mM|mm|NN|KWSUPP KH2PO4|kh2po4|NN|_ ,|,|,|_ 5|5|CD|_ mM|mm|NN|KWSUPP sodium|sodium|NN|_ HEPES|hepes|NN|_ ,|,|,|_ 150|150|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 9|9|CD|_ mM|mm|NN|KWSUPP -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ g|g|NN|_
Cluster|cluster|NN|_ detection|detection|NN|_ and|and|CC|_ base|base|NN|_ calling|calling|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RTA|RTA|NNP|_ v1|v1|NN|_ .13|.13|CD|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ quality|quality|NN|_ of|of|IN|_ the|the|DT|_ reads|read|VBZ|_ was|be|VBD|_ assessed|assess|VBN|_ with|with|IN|_ CASAVA|casava|NN|_ v1|v1|NN|_ .8.1|.8.1|CD|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
delta-rnr|delta-rnr|NN|_ mutant|mutant|JJ|_ _|_|NN|_ anoxic|anoxic|JJ|_ -LRB-|-lrb-|-LRB-|_ NO3|no3|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ glycerol|glycerol|NN|SUPP
delta-rnr|delta-rnr|JJ|_ mutant|mutant|JJ|_ _|_|NN|_ anoxic|anoxic|JJ|_ -LRB-|-lrb-|-LRB-|_ NO3|no3|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ glycerol|glycerol|NN|SUPP +|+|CC|_ propionate|propionate|NN|_
delta-rnr|delta-rnr|JJ|_ mutant|mutant|JJ|_ _|_|NN|_ oxic|oxic|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP
delta-rnr|delta-rnr|JJ|_ mutant|mutant|JJ|_ _|_|NN|_ oxic|oxic|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP +|+|CC|_ propionate|propionate|NN|_
d|d|NN|_ _|_|CD|_ rnr|rnr|NN|GEN NO3|no3|NN|_ 1|1|CD|_
d|d|NN|_ _|_|CD|_ rnr|rnr|NN|GEN NO3|no3|NN|_ 2|2|CD|_
d|d|NN|_ _|_|CD|_ rnr|rnr|NN|GEN NO3|no3|NN|_ w|w|NN|_
d|d|NN|_ _|_|CD|_ rnr|rnr|NN|GEN O2|o2|CD|_ 1|1|CD|_
d|d|NN|_ _|_|CD|_ rnr|rnr|NN|GEN O2|o2|CD|_ 2|2|CD|_
d|d|NN|_ _|_|CD|_ rnr|rnr|NN|GEN O2|o2|CD|_ w|w|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
Gene|gene|NN|_ expression|expression|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ by|by|IN|_ determining|determine|VBG|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ that|that|IN|_ overlapped|overlap|VBD|_ with|with|IN|_ the|the|DT|_ annotated|annotated|JJ|_ gene|gene|NN|_ loci|locus|NNS|_ using|use|VBG|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ Anders|Anders|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2015|2015|CD|_ ,|,|,|_ doi|doi|FW|_ :|:|:|_ 10.1093|10.1093|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ ribosome-depleted|ribosome-depleted|JJ|_ -RRB-|-rrb-|-RRB-|_
No|no|DT|_ further|further|JJ|_ treatment|treatment|NN|_ was|be|VBD|_ applied|apply|VBN|_ .|.|.|_
oxic|oxic|JJ|_
RNA-Seq|rna-seq|NN|_
Strand-specific|strand-specific|JJ|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ from|from|IN|_ 50|50|CD|_ ng|ng|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ samples|sample|NNS|_ following|follow|VBG|_ the|the|DT|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ protocol|protocol|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ ,|,|,|_ without|without|IN|_ purification|purification|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ modification|modification|NN|_ of|of|IN|_ the|the|DT|_ 2nd|2nd|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ as|as|IN|_ previously|previously|RB|_ described|describe|VBN|_ -LRB-|-lrb-|-LRB-|_ Parkhomchuk|Parkhomchuk|NNP|_ et|et|FW|_ al.|al.|FW|_ 2009|2009|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ multiplex|multiplex|JJ|_ primers|primer|NNS|_ to|to|TO|_ allow|allow|VB|_ simultaneous|simultaneous|JJ|_ sequencing|sequencing|NN|_ in|in|IN|_ a|a|DT|_ single|single|JJ|_ lane|lane|NN|_ .|.|.|_ Sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ a|a|DT|_ HiSeq1500|hiseq1500|NN|_ using|use|VBG|_ SBS|SBS|NNP|_ v3|v3|NN|_ kits|kit|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ generate|generate|VB|_ paired-end|paired-end|NN|_ reads|read|VBZ|_ of|of|IN|_ 2|2|CD|_ x|x|CC|_ 50|50|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ RPG|rpg|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ gene|gene|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ HTSeq|htseq|NN|_ ,|,|,|_ mapping|map|VBG|_ raw|raw|JJ|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ fastq|fastq|NN|_ format|format|NN|_ -RRB-|-rrb-|-RRB-|_ against|against|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ genome|genome|NN|_ and|and|CC|_ using|use|VBG|_ a|a|DT|_ GFF|gff|NN|_ file|file|NN|_ derived|derive|VBN|_ from|from|IN|_ the|the|DT|_ annotation|annotation|NN|_ of|of|IN|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ available|available|JJ|_ from|from|IN|_ NCBI|NCBI|NNP|_ .|.|.|_
The|the|DT|_ sequence|sequence|NN|_ data|datum|NNS|_ were|be|VBD|_ mapped|map|VBN|_ against|against|IN|_ the|the|DT|_ genome|genome|NN|_ sequence|sequence|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|ncbi|NN|_ accession|accession|NN|_ number|number|NN|_ NC|nc|NN|_ _|_|CD|_ 000913.3|000913.3|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ doi|doi|FW|_ :|:|:|_ 10.1038|10.1038|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Protect|Protect|NNP|_ Bacteria|bacterium|NNS|_ Mini|Mini|NNP|_ Kit|kit|NN|_ from|from|IN|_ Qiagen|Qiagen|NNP|_ -LRB-|-lrb-|-LRB-|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ isolated|isolate|VBN|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ purified|purify|VBN|_ from|from|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ contaminations|contamination|NNS|_ using|use|VBG|_ Ambion|Ambion|NNP|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ DNA-free|dna-free|NN|_ ,|,|,|_ Ambion|Ambion|NNP|_ by|by|IN|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Darmstadt|Darmstadt|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ further|further|JJ|_ subjected|subject|VBN|_ to|to|TO|_ an|a|DT|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ step|step|NN|_ using|use|VBG|_ the|the|DT|_ MICROBExpress|MICROBExpress|NNP|_ Kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ `|`|``|_ s|be|VBZ|_ instructions|instruction|NNS|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Darmstadt|Darmstadt|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
wild|wild|JJ|_ type|type|NN|_ _|_|CD|_ anoxic|anoxic|JJ|_ -LRB-|-lrb-|-LRB-|_ NO3|no3|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ glycerol|glycerol|NN|SUPP
wild|wild|JJ|_ type|type|NN|_ _|_|CD|_ anoxic|anoxic|JJ|_ -LRB-|-lrb-|-LRB-|_ NO3|no3|NN|_ -RRB-|-rrb-|-RRB-|_ _|_|SYM|_ glycerol|glycerol|NN|SUPP +|+|CC|_ propionate|propionate|NN|_
wild|wild|JJ|_ type|type|NN|_ _|_|CD|_ oxic|oxic|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP
wild|wild|JJ|_ type|type|NN|_ _|_|CD|_ oxic|oxic|JJ|_ _|_|NN|_ glycerol|glycerol|NN|SUPP +|+|CC|_ propionate|propionate|NN|_
WT|wt|JJ|_ NO3|no3|NN|_ 1|1|CD|_
WT|wt|JJ|_ NO3|no3|NN|_ 2|2|CD|_
WT|wt|JJ|_ NO3|no3|NN|_ w|w|NN|_
WT|WT|NNP|_ O2|o2|CD|_ 1|1|CD|_
WT|wt|NN|_ O2|o2|CD|_ 2|2|CD|_
WT|wt|NN|_ O2|o2|CD|_ w|w|NN|_
Control|Control|NNP|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_ ,1.5|,1.5|CD|_ h|h|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
Control|Control|NNP|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_ ,1.5|,1.5|CD|_ h|h|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
Control|Control|NNP|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_ ,1.5|,1.5|CD|_ h|h|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
Control109|control109|NN|_ _|_|CD|_ 0.8|0.8|CD|_ %|%|NN|_ Bu|bu|NN|_ _|_|CD|_ 1.5|1.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
Control109|control109|NN|_ _|_|CD|_ 0.8|0.8|CD|_ %|%|NN|_ Bu|bu|NN|_ _|_|CD|_ 1.5|1.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
Control109|control109|NN|_ _|_|CD|_ 0.8|0.8|CD|_ %|%|NN|_ Bu|bu|NN|_ _|_|CD|_ 1.5|1.5|CD|_ h|h|NN|_ _|_|CD|_ rep3|rep3|NN|_
Data|Data|NNP|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ software|software|NN|_ 10.7|10.7|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ -LRB-|-lrb-|-LRB-|_ protocol|protocol|NN|_ GE1-v1|ge1-v1|NN|_ _|_|CD|_ 91|91|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ background|background|NN|_ subtracted|subtract|VBN|_ and|and|CC|_ spatially|spatially|RB|_ detrended|detrend|VBD|_ Processed|processed|JJ|_ Signal|signal|NN|_ intensities|intensity|NNS|_ .|.|.|_ Features|feature|NNS|_ flagged|flag|VBD|_ in|in|IN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ as|as|IN|_ Feature|Feature|NNP|_ Non-uniform|non-uniform|JJ|_ outliers|outlier|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ strains|strain|NNS|_ harboring|harbor|VBG|_ σ70|σ70|NN|_ mutant|mutant|JJ|_ B8|b8|NN|_ and|and|CC|_ WT|wt|NN|_ were|be|VBD|_ cultured|culture|VBN|_ overnight|overnight|JJ|_ and|and|CC|_ inoculated|inoculate|VBN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ fresh|fresh|JJ|_ medium|medium|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_
Mutant|mutant|JJ|_ B8|b8|NN|_ _|_|NN|_ 0.8|0.8|CD|_ %|%|NN|_ Bu|bu|NN|_ _|_|CD|_ 1.5|1.5|CD|_ h|h|NN|_ _|_|CD|_ rep1|rep1|NN|_
Mutant|mutant|JJ|_ B8|b8|NN|_ _|_|NN|_ 0.8|0.8|CD|_ %|%|NN|_ Bu|bu|NN|_ _|_|CD|_ 1.5|1.5|CD|_ h|h|NN|_ _|_|CD|_ rep2|rep2|NN|_
Mutant|mutant|JJ|_ B8|b8|NN|_ _|_|NN|_ 0.8|0.8|CD|_ %|%|NN|_ Bu|bu|NN|_ _|_|CD|_ 1.5|1.5|CD|_ h|h|NN|_ _|_|CD|_ rep3|rep3|NN|_
Mutant|mutant|JJ|_ B8|b8|NN|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_ ,1.5|,1.5|CD|_ h|h|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
Mutant|mutant|JJ|_ B8|b8|NN|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_ ,1.5|,1.5|CD|_ h|h|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
Mutant|mutant|JJ|_ B8|b8|NN|_ ,|,|,|_ 0.8|0.8|CD|_ %|%|NN|_ butanol|butanol|NN|_ ,1.5|,1.5|CD|_ h|h|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
n-Butanol|n-butanol|NN|_ -LRB-|-lrb-|-LRB-|_ 0.8|0.8|CD|_ %|%|NN|_ ,|,|,|_ v|v|LS|_
phenotype|phenotype|NN|_ :|:|:|_ 0.6|0.6|CD|_ %|%|NN|_ n-butanol|n-butanol|NN|_ tolerance|tolerance|NN|_
phenotype|phenotype|NN|_ :|:|:|_ 2|2|CD|_ %|%|NN|_ n-butanol|n-butanol|NN|_ tolerance|tolerance|NN|_
strain|strain|NN|_ :|:|:|_ JM109|jm109|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Hilden|hilden|NN|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ and|and|CC|_ checked|check|VBD|_ for|for|IN|_ a|a|DT|_ RIN|rin|NN|_ number|number|NN|_ to|to|TO|_ inspect|inspect|VB|_ RNA|rna|NN|_ integration|integration|NN|_ by|by|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|JJ|_ technologies|technology|NNS|_ ,|,|,|_ Santa|Santa|NNP|_ Clara|Clara|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ US|US|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Qualified|qualify|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ further|further|JJ|_ purified|purify|VBN|_ by|by|IN|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ GmBH|GmBH|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ RNase‐Free|rnase‐free|NN|_ DNase|dnase|NN|_ Set|set|VB|_ -LRB-|-lrb-|-LRB-|_ QIAGEN|QIAGEN|NNP|_ ,|,|,|_ GmBH|GmBH|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ the|the|DT|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase at|at|IN|_ 37ºC|37ºc|NN|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ medium|medium|NN|_ .|.|.|_
Enteroheamorragic|enteroheamorragic|JJ|_ E.|e.|FW|_ coli|coli|FW|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 10828|10828|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 11109|11109|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 11117|11117|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 11128|11128|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 11619|11619|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 11711|11711|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 11788|11788|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 11845|11845|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 12009|12009|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ 13369|13369|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ ED71|ed71|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O111|o111|NN|_ strain|strain|NN|_ PMK5|pmk5|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 980551|980551|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 980706|980706|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 980938|980938|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 981456|981456|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 981795|981795|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 982243|982243|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 990281|990281|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O157|o157|NN|_ strain|strain|NN|_ 990570|990570|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ 11044|11044|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ 11368|11368|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ 11656|11656|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ 12719|12719|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ 12929|12929|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ 13065|13065|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ 13247|13247|CD|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O26|o26|NN|_ strain|strain|NN|_ ED411|ed411|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Genomic-tip|genomic-tip|NN|_ 100|100|CD|_
O103|o103|NN|_ no.|no.|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 10828|10828|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O103|o103|NN|_ no.|no.|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 10828|10828|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O103|o103|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11117|11117|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O103|o103|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11117|11117|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O103|o103|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11711|11711|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O103|o103|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11711|11711|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O103|o103|NN|_ no.|no.|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11845|11845|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O103|o103|NN|_ no.|no.|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11845|11845|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O103|o103|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 12009|12009|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O103|o103|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 12009|12009|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O103|o103|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ PMK5|pmk5|NN|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O103|o103|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ PMK5|pmk5|NN|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O111|o111|NN|_ no.|no.|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11109|11109|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O111|o111|NN|_ no.|no.|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11109|11109|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O111|o111|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11128|11128|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O111|o111|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11128|11128|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O111|o111|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11619|11619|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O111|o111|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11619|11619|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O111|o111|NN|_ no.|no.|RB|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11788|11788|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O111|o111|NN|_ no.|no.|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11788|11788|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O111|o111|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 13369|13369|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O111|o111|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 13369|13369|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O111|o111|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ ED71|ed71|NN|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O111|o111|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ ED71|ed71|NN|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 980938|980938|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 980938|980938|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 980706|980706|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 980706|980706|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 990281|990281|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 990281|990281|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 980551|980551|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 980551|980551|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 990570|990570|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 990570|990570|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 981456|981456|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 981456|981456|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 982243|982243|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 982243|982243|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ no.|no.|NN|_ 9|9|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 981795|981795|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O157|o157|NN|_ no.|no.|NN|_ 9|9|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 981795|981795|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O157|o157|NN|_ strain|strain|NN|_ Sakai|Sakai|NNP|_
O26|o26|NN|_ no.|no.|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11044|11044|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11044|11044|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O26|o26|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11368|11368|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11368|11368|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O26|o26|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11656|11656|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 11656|11656|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O26|o26|NN|_ no.|no.|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 12719|12719|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 12719|12719|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O26|o26|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 12929|12929|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 12929|12929|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O26|o26|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 13065|13065|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 13065|13065|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O26|o26|NN|_ no.|no.|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 13247|13247|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ 13247|13247|CD|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
O26|o26|NN|_ no.|no.|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ ED411|ed411|NN|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 1|1|CD|_
O26|o26|NN|_ no.|no.|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ strain|strain|NN|_ ED411|ed411|NN|_ -RRB-|-rrb-|-RRB-|_ replicate|replicate|VBP|_ 2|2|CD|_
Spots|spot|NNS|_ with|with|IN|_ reference|reference|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ lower|lower|JJR|_ than|than|IN|_ the|the|DT|_ local|local|JJ|_ background|background|NN|_ -LRB-|-lrb-|-LRB-|_ LBG|lbg|NN|_ -RRB-|-rrb-|-RRB-|_ plus|plus|CC|_ 5|5|CD|_ standard|standard|JJ|_ deviations|deviation|NNS|_ or|or|CC|_ with|with|IN|_ some|some|DT|_ spotting|spot|VBG|_ abnormalities|abnormality|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ analysis|analysis|NN|_ .|.|.|_ Signal|signal|NN|_ intensities|intensity|NNS|_ of|of|IN|_ other|other|JJ|_ spots|spot|NNS|_ were|be|VBD|_ corrected|correct|VBN|_ by|by|IN|_ subtracting|subtract|VBG|_ the|the|DT|_ LBG|LBG|NNP|_ .|.|.|_
172mM|172mm|NN|_ SCFA|scfa|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
172mM|172mm|NN|_ SCFA|scfa|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
30mM|30mm|NN|_ SCFA|scfa|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
30mM|30mm|NN|_ SCFA|scfa|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
30mM|30mm|NN|_ SCFA|scfa|NN|_ replicate|replicate|VBP|_ 3|3|CD|_
30mM|30mm|NN|_ SCFA|scfa|NN|_ replicate|replicate|VB|_ 4|4|CD|_
e.|e.|FW|_ coli|coli|FW|_ subset|subset|NN|_ :|:|:|_ enterohemorrhagic|enterohemorrhagic|JJ|_ E.coli|e.coli|JJ|_
enterohemorrhagic|enterohemorrhagic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ 172mM|172mm|NN|_ short|short|JJ|_ chain|chain|NN|_ fatty|fatty|JJ|_ acid|acid|NN|_ mix|mix|NN|_
enterohemorrhagic|enterohemorrhagic|JJ|_ E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ 30mM|30mM|NNP|_ short|short|JJ|_ chain|chain|NN|_ fatty|fatty|JJ|_ acid|acid|NN|_ mix|mix|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Images|image|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ extraction|extraction|NN|_ protocol|protocol|NN|_ GE2|ge2|NN|_ _|_|NN|_ 107|107|CD|_ _|_|SYM|_ Sept09|sept09|NN|_ and|and|CC|_ Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 10.7.3.1|10.7.3.1|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
N172-1|n172-1|NN|_
N172-2|n172-2|NN|_
N30-1|n30-1|NN|_
N30-2|n30-2|NN|_
N30-3|n30-3|NN|_
N30-4|n30-4|NN|_
overnight|overnight|JJ|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ in|in|IN|_ Luria|Luria|NNP|_ Broth|Broth|NNP|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ shaking|shake|VBG|_
overnight|overnight|JJ|_ culture|culture|NN|_ subcultured|subculture|VBN|_ in|in|IN|_ either|either|DT|_ of|of|IN|_ the|the|DT|_ SCFA|scfa|NN|_ mixes|mix|VBZ|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ the|the|DT|_ sodium|sodium|NN|SUPP chloride|chloride|NN|SUPP controls|control|NNS|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37C|37c|NN|_ ,|,|,|_ static|static|JJ|_ with|with|IN|_ 5|5|CD|_ %|%|NN|_ CO2|co2|NN|_ to|to|TO|_ OD600|od600|NN|_ of|of|IN|_ 1|1|CD|_
total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ Extraction|Extraction|NNP|_ Protocol|Protocol|NNP|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 172mM|172mm|NN|_ NaCl|nacl|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 172mM|172mm|NN|_ short|short|JJ|_ chain|chain|NN|_ fatty|fatty|JJ|_ acid|acid|NN|_ mix|mix|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 30mM|30mm|NN|_ NaCl|nacl|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ 30mM|30mm|NN|_ short|short|JJ|_ chain|chain|NN|_ fatty|fatty|JJ|_ acid|acid|NN|_ mix|mix|NN|_
Caulobacter|caulobacter|NN|_ crescentus|crescentus|NN|_ and|and|CC|_ derivatives|derivative|NNS|_ were|be|VBD|_ grown|grow|VBN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ in|in|IN|_ PYE|pye|NN|_ -LRB-|-lrb-|-LRB-|_ Peptone|peptone|NN|_ yeast|yeast|NN|SUPP extract|extract|NN|SUPP -RRB-|-rrb-|-RRB-|_ or|or|CC|_ LB|lb|NN|_
DNA|dna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ by|by|IN|_ FASTERIS|FASTERIS|NNP|_ SA|SA|NNP|_ ,|,|,|_ Switzerland|Switzerland|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ REC-Seq|rec-seq|NN|_ -LRB-|-lrb-|-LRB-|_ restriction|restriction|NN|_ enzyme|enzyme|NN|_ cleavage|cleavage|NN|_ --|--|:|_ sequencing|sequencing|NN|_ -RRB-|-rrb-|-RRB-|_ 1|1|CD|_ ug|ug|NN|_ of|of|IN|_ genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ C.|c.|FW|_ crescentus|crescentus|FW|_ NA1000|na1000|NN|_ and|and|CC|_ S.|S.|NNP|_ meliloti|melilotus|NNS|_ Rm2011|rm2011|NN|_ was|be|VBD|_ cleaved|cleave|VBN|_ with|with|IN|_ HinfI|hinfi|NN|_ ,|,|,|_ a|a|DT|_ blocked|block|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ biotinylated|biotinylate|VBN|_ -RRB-|-rrb-|-RRB-|_ specific|specific|JJ|_ adaptor|adaptor|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ ends|end|NNS|_ and|and|CC|_ the|the|DT|_ ligated|ligate|VBN|_ fragments|fragment|NNS|_ were|be|VBD|_ then|then|RB|_ sheared|shear|VBN|_ to|to|TO|_ an|a|DT|_ average|average|JJ|_ size|size|NN|_ of|of|IN|_ 150-400|150-400|CD|_ bp|bp|NN|_ -LRB-|-lrb-|-LRB-|_ Fasteris|fasteris|NN|_ SA|SA|NNP|_ ,|,|,|_ Geneva|Geneva|NNP|_ ,|,|,|_ CH|ch|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ were|be|VBD|_ then|then|RB|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ sheared|sheared|JJ|_ ends|end|NNS|_ followed|follow|VBN|_ by|by|IN|_ deep-sequencing|deep-sequencing|NN|_ using|use|VBG|_ a|a|DT|_ Hi-Seq|hi-seq|JJ|_ Illumina|Illumina|NNP|_ sequencer|sequencer|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ bp|bp|NN|_ single|single|JJ|_ end|end|NN|_ -RRB-|-rrb-|-RRB-|_ reads|read|VBZ|_ were|be|VBD|_ quality|quality|NN|_ controlled|control|VBN|_ with|with|IN|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
genome|genome|NN|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
genotype|genotype|NN|_
GHA507|gha507|NN|_
Library|Library|NNP|_ strategy|strategy|NN|_ :|:|:|_ REC-Seq|rec-seq|NN|_
OTHER|other|JJ|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab|tab|NN|_ delimited|delimit|VBD|_ text|text|NN|_ files|file|NNS|_ ,|,|,|_ with|with|IN|_ feature|feature|NN|_ annotation|annotation|NN|_ ,|,|,|_ REC|rec|NN|_ _|_|CD|_ seq|seq|NN|_ score|score|NN|_ ,|,|,|_ gene|gene|NN|_ name|name|NN|_ and|and|CC|_ description|description|NN|_
To|to|TO|_ remove|remove|VB|_ contaminating|contaminate|VBG|_ sequences|sequence|NNS|_ ,|,|,|_ the|the|DT|_ reads|read|VBZ|_ were|be|VBD|_ split|split|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ HinfI|hinfi|NN|_ consensus|consensus|NN|_ motif|motif|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ G|g|NN|_ ^|^|SYM|_ ANTC-3|antc-3|NN|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ considered|consider|VBN|_ as|as|IN|_ a|a|DT|_ barcode|barcode|NN|_ sequence|sequence|NN|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
cy|cy|NN|_ _|_|CD|_ a4|a4|NN|_
cy|cy|NN|_ _|_|CD|_ b4|b4|NN|_
cyc1|cyc1|NN|_
cyc2|cyc2|NN|_
cyc3|cyc3|NN|_
cyc4|cyc4|NN|_
cyd1|cyd1|NN|_
cyd2|cyd2|NN|_
cyd3|cyd3|NN|_
cyd4|cyd4|NN|_
dnaC|dnac|NN|GEN genomic|genomic|JJ|_ DNA|dna|NN|_ ,|,|,|_ Sau3A|sau3a|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
reference|reference|NN|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ min|min|NN|_ +.2|+.2|CD|_ %|%|NN|_ glu|glu|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ RNA|rna|NN|_
tnaA2trpA46PR9|tnaa2trpa46pr9|NN|_ vs.|vs.|CC|_ tnaA2|tnaa2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_
tnaA2trpA46PR9|tnaa2trpa46pr9|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ ,|,|,|_ 30|30|CD|_ ug|ug|NN|_ total|total|JJ|_
tnaA2trpR2|tnaa2trpr2|NN|_ vs.|vs.|CC|_ tnaA2|tnaa2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
tnaA2trpR2|tnaa2trpr2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
tnaA2|tnaa2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ ,30|,30|CD|_ ug|ug|NN|_ total|total|JJ|_
tnaA2|tnaa2|NN|_ ,|,|,|_ W3110|w3110|NN|_ minimal|minimal|JJ|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
tnaA2|tnaa2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
trpEA2trpR2|trpea2trpr2|NN|_ vs.|vs.|CC|_ trpEA2|trpea2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
trpEA2trpR2|trpea2trpr2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
trpEA2|trpea2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
trpR2|trpr2|NN|_ +50|+50|CD|_ ug|ug|NN|_
trpR2tnaA2|trpr2tnaa2|NN|_ ,|,|,|_ W3110|w3110|NN|_ minimal|minimal|JJ|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
trpR2tnaA2|trpr2tnaa2|NN|_ ,|,|,|_ W3110|w3110|NN|_ min|min|NN|_ +|+|CC|_ Trp|trp|NN|_ 50ug|50ug|JJ|_
trpR2|trpr2|NN|_ +|+|CC|_ trp|trp|NN|_ vs.|vs.|NN|_ -|-|:|_ trp|trp|NN|_ ,|,|,|_ min|min|NN|_ +.2|+.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ W3110|w3110|NN|_
trpR2|trpr2|NN|_ vs.|vs.|CC|_ wt|wt|JJ|_ ,|,|,|_ min|min|NN|_ +.2|+.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ W3110|w3110|NN|_
W3110|w3110|NN|_ trpR2|trpr2|NN|_ ,|,|,|_ min|min|NN|_ +.2|+.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 30|30|CD|_ ug|ug|NN|_ RNA|rna|NN|_
W3110|w3110|NN|_ trpR2|trpr2|NN|_ -|-|:|_ trp|trp|NN|_ ,|,|,|_ 30|30|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
W3110|w3110|NN|_ trpR2|trpr2|NN|_ +|+|CC|_ trp|trp|NN|_ ,|,|,|_ 30|30|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
W3110|w3110|NN|_ wt|wt|JJ|_ ,|,|,|_ min|min|NN|_ +.2|+.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 30|30|CD|_ ug|ug|NN|_ RNA|rna|NN|_
W3110|w3110|NN|_ wt-trp|wt-trp|NN|_ ,|,|,|_ 30|30|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
W3110|w3110|NN|_ wt|wt|JJ|_ +|+|CC|_ trp|trp|NN|_ ,|,|,|_ 30|30|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
wt|wt|JJ|_ +50|+50|CD|_ ug|ug|NN|_
wt|wt|JJ|_ +|+|CC|_ trp|trp|NN|_ vs.|vs.|NN|_ -|-|:|_ trp|trp|NN|_ ,|,|,|_ min|min|NN|_ +.2|+.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ W3110|w3110|NN|_
At|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ ,|,|,|_ 15|15|CD|_ ml|ml|NN|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ was|be|VBD|_ mixed|mix|VBN|_ with|with|IN|_ 30|30|CD|_ ml|ml|NN|_ of|of|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ vortexed|vortex|VBN|_ for|for|IN|_ 5s|5|NNS|_ ,|,|,|_ incubated|incubate|VBN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ ,|,|,|_ and|and|CC|_ centrifuged|centrifuge|VBN|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ at|at|IN|_ 5000g|5000g|CD|_ .|.|.|_ The|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Midi|Midi|NNP|_ kit|kit|NN|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ DNase|dnase|NN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ elution|elution|NN|_ of|of|IN|_ RNA|rna|NN|_ from|from|IN|_ the|the|DT|_ column|column|NN|_ was|be|VBD|_ with|with|IN|_ 160|160|CD|_ μl|μl|NN|_ RNase-free|rnase-free|NN|_ water|water|NN|_ .|.|.|_
At|at|IN|_ OD630nm|od630nm|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ ,|,|,|_ the|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ filtered|filter|VBN|_ through|through|IN|_ 47-mm|47-mm|JJ|_ diameter|diameter|NN|_ polycarbonate|polycarbonate|JJ|_ membrane|membrane|NN|_ filter|filter|NN|_ -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ µm|µm|NN|_ pore|pore|NN|_ size|size|NN|_ ;|;|:|_ Millipore|Millipore|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ washed|wash|VBN|_ with|with|IN|_ the|the|DT|_ same|same|JJ|_ medium|medium|NN|_ without|without|IN|_ hypoxanthine|hypoxanthine|NN|_ -LRB-|-lrb-|-LRB-|_ Hx|hx|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ resuspended|resuspend|VBD|_ at|at|IN|_ the|the|DT|_ same|same|JJ|_ cell|cell|NN|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ OD630|od630|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ medium|medium|NN|_ without|without|IN|_ Hx|hx|NN|_ ,|,|,|_ and|and|CC|_ growth|growth|NN|_ was|be|VBD|_ continued|continue|VBN|_ as|as|IN|_ before|before|RB|_ .|.|.|_ The|the|DT|_ OD630|od630|NN|_ was|be|VBD|_ followed|follow|VBN|_ closely|closely|RB|_ during|during|IN|_ the|the|DT|_ next|next|JJ|_ two|two|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ periodically|periodically|RB|_ diluted|dilute|VBN|_ with|with|IN|_ fresh|fresh|JJ|_ ,|,|,|_ pre-warmed|pre-warmed|JJ|_ medium|medium|NN|_ without|without|IN|_ Hx|hx|NN|_ to|to|TO|_ keep|keep|VB|_ OD|od|NN|_ between|between|IN|_ values|value|NNS|_ 0.1|0.1|CD|_ and|and|CC|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ low-dilution|low-dilution|JJ|_ protocol|protocol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ microarray|microarray|NN|_ analysis|analysis|NN|_ -LRB-|-lrb-|-LRB-|_ see|see|VB|_ below|below|IN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 0|0|CD|_ ,|,|,|_ 15|15|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 45|45|CD|_ ,|,|,|_ 60|60|CD|_ and|and|CC|_ 120|120|CD|_ minutes|minute|NNS|_ .|.|.|_ In|in|IN|_ a|a|DT|_ parallel|parallel|JJ|_ procedure|procedure|NN|_ ,|,|,|_ the|the|DT|_ optA1|opta1|NN|_ gpt|gpt|NN|GEN double|double|JJ|_ mutant|mutant|NN|_ was|be|VBD|_ also|also|RB|_ followed|follow|VBN|_ in|in|IN|_ a|a|DT|_ near-identical|near-identical|JJ|_ manner|manner|NN|_ using|use|VBG|_ a|a|DT|_ more|more|RBR|_ highly|highly|RB|_ diluted|dilute|VBN|_ culture|culture|NN|_ over|over|IN|_ a|a|DT|_ six-hour|six-hour|JJ|_ incubation|incubation|NN|_ period|period|NN|_ in|in|IN|_ the|the|DT|_ absence|absence|NN|_ of|of|IN|_ hypoxanthine|hypoxanthine|NN|_ -LRB-|-lrb-|-LRB-|_ high-dilution|high-dilution|JJ|_ protocol|protocol|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ effectiveness|effectiveness|NN|_ of|of|IN|_ the|the|DT|_ latter|latter|JJ|_ treatment|treatment|NN|_ was|be|VBD|_ followed|follow|VBN|_ microscopically|microscopically|RB|_ by|by|IN|_ observing|observe|VBG|_ the|the|DT|_ extensive|extensive|JJ|_ cellular|cellular|JJ|_ filamentation|filamentation|NN|_ associated|associate|VBN|_ with|with|IN|_ dGTP|dgtp|NN|_ starvation|starvation|NN|_ .|.|.|_
control|control|NN|_ strain|strain|NN|_ w|w|NN|_
control|control|NN|_ strain|strain|NN|_ with|with|IN|_ hypoxanthine|hypoxanthine|NN|_
Data|Data|NNP|_ was|be|VBD|_ obtained|obtain|VBN|_ using|use|VBG|_ the|the|DT|_ GeneChip|GeneChip|NNP|_ ®|®|NNP|_ Command|command|NN|_ Console|console|NN|_ and|and|CC|_ Expression|expression|NN|_ Console|Console|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ AGCC|AGCC|NNP|_ ;|;|:|_ Version|Version|NNP|_ 3.2|3.2|CD|_ and|and|CC|_ Expression|expression|NN|_ Console|console|NN|_ ;|;|:|_ Version|Version|NNP|_ 1.2|1.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ MAS5|mas5|NN|_ algorithm|algorithm|NN|_ to|to|TO|_ generate|generate|VB|_ .|.|.|_ CHP|chp|NN|_ files|file|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
gpt|gpt|NN|GEN _|_|NN|_ 0|0|CD|_ _|_|NN|_ Hx|hx|NN|_ Rep1|rep1|NN|_
gpt|gpt|NN|GEN _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep2|rep2|JJ|_
gpt|gpt|NN|GEN _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep3|rep3|JJ|_
gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
gpt|gpt|NN|GEN _|_|CD|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
gpt|gpt|NN|GEN strain|strain|NN|_ w|w|NN|_
gpt|gpt|NN|GEN strain|strain|NN|_ with|with|IN|_ hypoxanthine|hypoxanthine|NN|_
optA1|opta1|NN|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ Hx|hx|NN|_ Rep1|rep1|NN|_
optA1|opta1|NN|_ _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 0|0|CD|_ _|_|NN|_ Hx|hx|NN|_ Rep1|rep1|NN|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 180|180|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 180|180|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 180|180|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 240|240|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 240|240|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 240|240|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 300|300|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 300|300|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 300|300|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 360|360|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 360|360|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 360|360|CD|_ -LRB-|-lrb-|-LRB-|_ High|high|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 360|360|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 360|360|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|CD|_ gpt|gpt|NN|GEN _|_|NN|_ 360|360|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
optA1|opta1|NN|_ _|_|SYM|_ gpt|gpt|FW|GEN _|_|FW|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
optA1|opta1|NN|_ gpt|gpt|NN|GEN strain|strain|NN|_ w|w|NN|_
optA1|opta1|NN|_ gpt|gpt|NN|GEN strain|strain|NN|_ with|with|IN|_ hypoxanthine|hypoxanthine|NN|_
optA1|opta1|NN|_ strain|strain|NN|_ w|w|NN|_
optA1|opta1|NN|_ strain|strain|NN|_ with|with|IN|_ hypoxanthine|hypoxanthine|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
The|the|DT|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ exponentially|exponentially|RB|_ -LRB-|-lrb-|-LRB-|_ after|after|IN|_ initiation|initiation|NN|_ by|by|IN|_ a|a|DT|_ 1,000-fold|1,000-fold|JJ|_ dilution|dilution|NN|_ from|from|IN|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ ~|~|NN|_ 5|5|CD|_ generations|generation|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ Vogel-Bonner|Vogel-Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ VB|VB|NNP|_ -RRB-|-rrb-|-RRB-|_ minimal|minimal|JJ|_ medium|medium|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ pantothenic|pantothenic|JJ|_ acid|acid|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ µg|µg|NN|_
WT|wt|JJ|_ _|_|NN|_ 0|0|CD|_ _|_|NN|_ Hx|hx|NN|_ Rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep2|rep2|JJ|_
WT|wt|JJ|_ _|_|NN|_ 0|0|CD|_ _|_|SYM|_ Hx|hx|FW|_ Rep3|rep3|JJ|_
WT|wt|JJ|_ _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
WT|wt|JJ|_ _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
WT|wt|JJ|_ _|_|NN|_ 120|120|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
WT|wt|JJ|_ _|_|NN|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
WT|wt|JJ|_ _|_|NN|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
WT|wt|JJ|_ _|_|NN|_ 15|15|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
WT|wt|JJ|_ _|_|NN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
WT|wt|JJ|_ _|_|NN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
WT|wt|JJ|_ _|_|NN|_ 30|30|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
WT|wt|JJ|_ _|_|NN|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
WT|wt|JJ|_ _|_|NN|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
WT|wt|JJ|_ _|_|NN|_ 45|45|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
WT|wt|JJ|_ _|_|NN|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep1|rep1|JJ|_
WT|wt|JJ|_ _|_|NN|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep2|rep2|JJ|_
WT|wt|JJ|_ _|_|NN|_ 60|60|CD|_ -LRB-|-lrb-|-LRB-|_ Low|low|JJ|_ Dilution|dilution|NN|_ -RRB-|-rrb-|-RRB-|_ Rep3|rep3|JJ|_
Alignment|alignment|NN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ MG1655|mg1655|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ TMAP|tmap|NN|_ map4|map4|NN|_ algorithm|algorithm|NN|_ with|with|IN|_ 5|5|CD|_ '|'|''|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ soft-clipping|soft-clipping|JJ|_ and|and|CC|_ a|a|DT|_ minimum|minimum|JJ|_ seed|seed|NN|_ length|length|NN|_ of|of|IN|_ 20|20|CD|_ nt|nt|NNS|_
Basecalling|basecalling|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ Torrent|Torrent|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5|5|CD|_ software|software|NN|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ settings|setting|NNS|_ .|.|.|_
Briefly|briefly|RB|_ ,|,|,|_ hot|hot|JJ|_ phenol-chloroform|phenol-chloroform|JJ|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ mixing|mix|VBG|_ the|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ in|in|IN|_ 1/2|1/2|CD|_ volume|volume|NN|_ of|of|IN|_ 99|99|CD|_ °C|°c|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 2|2|CD|_ %|%|NN|_ SDS|sds|NN|_ ,|,|,|_ 16|16|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ made|make|VBN|_ in|in|IN|_ RNAse-free|rnase-free|JJ|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 10|10|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ suspension|suspension|NN|_ was|be|VBD|_ extracted|extract|VBN|_ twice|twice|RB|_ with|with|IN|_ 1|1|CD|_ volume|volume|NN|_ of|of|IN|_ 65|65|CD|_ °C|°c|NN|_ acid|acid|NN|_ phenol|phenol|NN|_
Clindamycin|Clindamycin|NNP|_ _|_|NNP|_ replicate|replicate|VB|_ _|_|SYM|_ 1|1|CD|_
Clindamycin|clindamycin|NN|_ _|_|NN|_ replicate|replicate|VBP|_ _|_|NN|_ 2|2|CD|_
Clindamycin|Clindamycin|NNP|_ _|_|NNP|_ replicate|replicate|VB|_ _|_|SYM|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ K12|k12|NN|_
E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ NM580|nm580|NN|_ -LRB-|-lrb-|-LRB-|_ genotype|genotype|NN|_ MG1655|mg1655|NN|_ ermBL-ermB|ermbl-ermb|NN|_ '|'|''|_ :|:|:|_ :|:|:|_ LacZ|lacz|NN|_ -RRB-|-rrb-|-RRB-|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ until|until|IN|_ OD600|od600|NN|_ of|of|IN|_ ~|~|NN|_ 0.3|0.3|CD|_ .|.|.|_
Erythromycin|Erythromycin|NNP|_ _|_|NNP|_ replicate|replicate|VB|_ _|_|SYM|_ 1|1|CD|_
Erythromycin|erythromycin|NN|_ _|_|NN|_ replicate|replicate|VBP|_ _|_|NN|_ 2|2|CD|_
Erythromycin|Erythromycin|NNP|_ _|_|NNP|_ replicate|replicate|VB|_ _|_|SYM|_ 3|3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ ,|,|,|_ NCBI|NCBI|NNP|_ Reference|Reference|NNP|_ Sequence|sequence|NN|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
Ion|Ion|NNP|_ Xpress|Xpress|NNP|_ barcoded|barcode|VBD|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ Magnatic|Magnatic|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ ,|,|,|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ IonXpress|ionxpress|NN|_ RNA-seq|rna-seq|NN|_ v2|v2|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ directions|direction|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ File|file|VB|_ with|with|IN|_ normalized|normalize|VBN|_ sequencing|sequencing|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ comparison|comparison|NN|_ of|of|IN|_ expression|expression|NN|_ in|in|IN|_ antibiotic|antibiotic|JJ|_ treated|treat|VBN|_ to|to|TO|_ untreated|untreated|JJ|_ cells|cell|NNS|_ .|.|.|_
The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ untreated|untreated|JJ|_ ,|,|,|_ or|or|CC|_ treated|treat|VBN|_ with|with|IN|_ -LRB-|-lrb-|-LRB-|_ 100µg|100µg|JJ|_
The|the|DT|_ total|total|JJ|_ sequencing|sequencing|NN|_ base|base|NN|_ pair|pair|NN|_ coverage|coverage|NN|_ for|for|IN|_ all|all|DT|_ annotated|annotated|JJ|_ genes|gene|NNS|_ was|be|VBD|_ summed|sum|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ normalized|normalize|VBD|_ to|to|TO|_ total|total|JJ|_ coverage|coverage|NN|_ using|use|VBG|_ bedtools|bedtool|NNS|_ and|and|CC|_ custom|custom|NN|_ R|r|NN|_ scripts|script|NNS|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Wu|Wu|NNP|_ et|et|FW|_ al.|al.|FW|_ 2015|2015|CD|_ PLoS|PLoS|NNP|_ Genetics|Genetics|NNP|_ Nov|Nov|NNP|_ 6|6|CD|_ ;|;|:|_ 11|11|CD|_ -LRB-|-lrb-|-LRB-|_ 11|11|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e1005655|e1005655|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ clindamycin|clindamycin|NN|_
treatment|treatment|NN|_ :|:|:|_ erythromycin|erythromycin|NN|_
treatment|treatment|NN|_ :|:|:|_ untreated|untreated|JJ|_
Untreated|untreated|JJ|_ _|_|NN|_ replicate|replicate|VB|_ _|_|SYM|_ 1|1|CD|_
Untreated|untreated|JJ|_ _|_|NN|_ replicate|replicate|VBP|_ _|_|NN|_ 2|2|CD|_
Untreated|untreated|JJ|_ _|_|NN|_ replicate|replicate|VB|_ _|_|SYM|_ 3|3|CD|_
Aerobic|aerobic|JJ|_ 1|1|CD|_
Aerobic|aerobic|JJ|_ 2|2|CD|_
Aerobic|aerobic|JJ|_ 3|3|CD|_
Aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ 600|600|CD|_ mL|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ DM25|dm25|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ an|a|DT|_ orbital|orbital|JJ|_ shaking|shake|VBG|_ of|of|IN|_ 150|150|CD|_ RPM|rpm|NN|_ and|and|CC|_ inoculated|inoculate|VBN|_ with|with|IN|_ 1|1|CD|_
Anaerobic|anaerobic|JJ|_ 1|1|CD|_
Anaerobic|anaerobic|JJ|_ 3|3|CD|_
Bowtie|bowtie|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ B|b|NN|_ &|&|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_ ,|,|,|_ to|to|TO|_ remove|remove|VB|_ any|any|DT|_ sequence|sequence|NN|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ ,|,|,|_ transfer|transfer|NN|_ RNA|rna|NN|_ and|and|CC|_ non-coding|non-coding|JJ|_ RNA|rna|NN|_ sequences|sequence|NNS|_ .|.|.|_
Cultured|culture|VBN|_ cells|cell|NNS|_
Differential|differential|JJ|_ expression|expression|NN|_ between|between|IN|_ aerobic|aerobic|JJ|_ and|and|CC|_ anaerobic|anaerobic|JJ|_ environments|environment|NNS|_ was|be|VBD|_ identified|identify|VBN|_ by|by|IN|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ Love|love|NN|_ M|m|NN|_ ,|,|,|_ Huber|Huber|NNP|_ W|W|NNP|_ and|and|CC|_ Anders|Anders|NNP|_ S|s|NN|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ str|str|NN|_ .|.|.|_ REL606|rel606|NN|_ ;|;|:|_ NC|NC|NNP|_ _|_|NNP|_ 012967.1|012967.1|CD|_
growth|growth|NN|_ environment|environment|NN|_ :|:|:|_ Aerobic|aerobic|JJ|_
growth|growth|NN|_ environment|environment|NN|_ :|:|:|_ Anaerobic|anaerobic|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Stationary|stationary|JJ|_ phase|phase|NN|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
RNA-Seq|rna-seq|NN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ EDGE-Pro|edge-pro|NN|_ -LRB-|-lrb-|-LRB-|_ Magoc|magoc|NN|_ T|t|NN|_ ,|,|,|_ Wood|Wood|NNP|_ D|D|NNP|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ SL|SL|NNP|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ default|default|NN|_ parameters|parameter|NNS|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ harvested|harvest|VBN|_ cultures|culture|NNS|_ using|use|VBG|_ a|a|DT|_ hot|hot|JJ|_ lysis|lysis|NN|_ buffer|buffer|NN|_ and|and|CC|_ acid|acid|NN|_ phenol-based|phenol-based|JJ|_ extraction|extraction|NN|_ method|method|NN|_ and|and|CC|_ isopropanol|isopropanol|NN|_ precipitation|precipitation|NN|_ .|.|.|_ Following|follow|VBG|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ treat|treat|VB|_ the|the|DT|_ samples|sample|NNS|_ as|as|IN|_ per|per|IN|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ split|split|VBN|_ into|into|IN|_ five|five|CD|_ 20|20|CD|_ μL|μl|NN|_ aliquots|aliquot|NNS|_ and|and|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ were|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ each|each|DT|_ aliquot|aliquot|NN|_ .|.|.|_ Following|follow|VBG|_ DNase|dnase|NN|_ treatment|treatment|NN|_ ,|,|,|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ For|for|IN|_ each|each|DT|_ sample|sample|NN|_ ,|,|,|_ the|the|DT|_ DNase-treated|dnase-treated|JJ|_ aliquots|aliquot|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ together|together|RB|_ before|before|IN|_ purification|purification|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ measured|measure|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ the|the|DT|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ kit|kit|NN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ while|while|IN|_ RNA|rna|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Quant-iT|quant-it|JJ|_ RNA|rna|NN|_ Assay|assay|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ measured|measure|VBN|_ on|on|IN|_ a|a|DT|_ Qubit|Qubit|NNP|_ ®|®|NNP|_ 2.0|2.0|CD|_ fluorometer|fluorometer|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ sequenced|sequence|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ HiSeq|HiSeq|NNP|_ 2000|2000|CD|_ platform|platform|NN|_ at|at|IN|_ BGI|BGI|NNP|_ -LRB-|-lrb-|-LRB-|_ Shenzen|Shenzen|NNP|_ ,|,|,|_ China|China|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Sequence|sequence|NN|_ data|datum|NNS|_ from|from|IN|_ BGI|BGI|NNP|_ had|have|VBD|_ been|be|VBN|_ filtered|filter|VBN|_ to|to|TO|_ remove|remove|VB|_ reads|read|VBZ|_ containing|contain|VBG|_ ≥|≥|SYM|_ 10|10|CD|_ %|%|NN|_ unreadable|unreadable|JJ|_ bases|basis|NNS|_ ,|,|,|_ ≥|≥|SYM|_ 20|20|CD|_ %|%|NN|_ low|low|JJ|_ quality|quality|NN|_ -LRB-|-lrb-|-LRB-|_ ≤|≤|CD|_ Q20|q20|NN|_ -RRB-|-rrb-|-RRB-|_ bases|basis|NNS|_ ,|,|,|_ adapter|adapter|NN|_ contamination|contamination|NN|_ or|or|CC|_ duplicate|duplicate|VB|_ read-pairs|read-pairs|JJ|_
strain|strain|NN|_ :|:|:|_ REL4536|rel4536|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
The|the|DT|_ quality|quality|NN|_ of|of|IN|_ reads|read|VBZ|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Andrews|Andrews|NNP|_ S|s|NN|_ ,|,|,|_ 2010|2010|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ any|any|DT|_ reads|read|VBZ|_ with|with|IN|_ a|a|DT|_ quality|quality|NN|_ score|score|NN|_ ≤|≤|CD|_ Q28|q28|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ Trim|Trim|NNP|_ Galore|Galore|NNP|_ !|!|.|_ -LRB-|-lrb-|-LRB-|_ Krueger|krueger|NN|_ F|f|NN|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
DMSO|dmso|NN|_ _|_|VBD|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
DMSO|dmso|NN|_ _|_|VBD|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
DMSO|dmso|NN|_ _|_|VBD|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
DMSO|dmso|NN|_ _|_|SYM|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
DMSO|dmso|NN|_ _|_|SYM|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
DMSO|dmso|NN|_ _|_|SYM|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
DMSO|dmso|NN|_ _|_|SYM|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep4|rep4|NN|_
DMSO|dmso|NN|_ treatment|treatment|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
DMSO|dmso|NN|_ treatment|treatment|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
DMSO|dmso|NN|_ treatment|treatment|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
DMSO|dmso|NN|_ treatment|treatment|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
DMSO|dmso|NN|_ treatment|treatment|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
DMSO|dmso|NN|_ treatment|treatment|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
DMSO|dmso|NN|_ treatment|treatment|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 4|4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Raw|raw|NN|_ Microarray|Microarray|NNP|_ data|datum|NNS|_ evaluation|evaluation|NN|_ including|include|VBG|_ preprocessing|preprocessing|NN|_ ,|,|,|_ normalization|normalization|NN|_ ,|,|,|_ grouping|group|VBG|_ the|the|DT|_ differentially|differentially|RB|_ expressed|express|VBN|_ genes|gene|NNS|_ and|and|CC|_ statistical|statistical|JJ|_ analyses|analysis|NNS|_ with|with|IN|_ Moderated|moderate|VBN|_ T-test|t-test|NN|_ and|and|CC|_ Bonferroni|Bonferroni|NNP|_ FWER|FWER|NNP|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ GeneSpring|genespring|NN|_ 13.0|13.0|CD|_ Software|Software|NNP|_ .|.|.|_
Roemerine|roemerine|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
Roemerine|roemerine|JJ|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
Roemerine|roemerine|JJ|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
Roemerine|roemerine|JJ|_ _|_|NN|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
Roemerine|roemerine|JJ|_ _|_|NN|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
Roemerine|roemerine|JJ|_ _|_|NN|_ 60|60|CD|_ min|min|NN|_ _|_|CD|_ rep3|rep3|NN|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Roemerine|roemerine|NN|_ treatment|treatment|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Roemerine|roemerine|NN|_ treatment|treatment|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Roemerine|roemerine|NN|_ treatment|treatment|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Roemerine|roemerine|NN|_ treatment|treatment|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Roemerine|roemerine|NN|_ treatment|treatment|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
-LRB-|-lrb-|-LRB-|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Roemerine|roemerine|NN|_ treatment|treatment|NN|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
strain|strain|NN|_ :|:|:|_ TB1|tb1|NN|_
The|the|DT|_ pre-culture|pre-culture|JJ|_ was|be|VBD|_ the|the|DT|_ overnight|overnight|JJ|_ propagated|propagate|VBN|_ cells|cell|NNS|_ in|in|IN|_ 5|5|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED medium|medium|NN|MED at|at|IN|_ 37ºC|37ºc|NN|_ and|and|CC|_ 180|180|CD|_ rpm|rpm|NN|_ .|.|.|_ The|the|DT|_ main|main|JJ|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ 1|1|CD|_ %|%|NN|_ inoculation|inoculation|NN|_ from|from|IN|_ pre-culture|pre-culture|JJ|_ when|when|WRB|_ optical|optical|JJ|_ densities|density|NNS|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ ,|,|,|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ reached|reach|VBD|_ 0.7|0.7|CD|_ .|.|.|_ Growth|growth|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ protocols|protocol|NNS|_ given|give|VBN|_ in|in|IN|_ the|the|DT|_ manual|manual|NN|_ of|of|IN|_ QIAGEN|QIAGEN|NNP|_ -|-|:|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|Reagent|NNP|_ Handbook|Handbook|NNP|_ ,|,|,|_ QIAGEN|QIAGEN|NNP|_ -|-|:|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ and|and|CC|_ QIAGEN|QIAGEN|NNP|_ -|-|:|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ set|set|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ of|of|IN|_ each|each|DT|_ RNA|rna|NN|_ sample|sample|NN|_ was|be|VBD|_ measured|measure|VBN|_ by|by|IN|_ Qubit|Qubit|NNP|_ ®|®|NNP|_ RNA|rna|NN|_ BR|br|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
When|when|WRB|_ OD600|od600|NN|_ of|of|IN|_ the|the|DT|_ culture|culture|NN|_ reached|reach|VBD|_ 0.54|0.54|CD|_ ±|±|SYM|_ 0.06|0.06|CD|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ µg|µg|NN|_
0|0|CD|_ min|min|NN|_ Nov0|nov0|NN|_ ug|ug|NN|_
0|0|CD|_ min|min|NN|_ Nov500|nov500|NN|_ ug|ug|NN|_
1005|1005|CD|_ fork-blocking|fork-blocking|NN|_ strain|strain|NN|_ induced|induce|VBD|_ for|for|IN|_ Tus|Tus|NNP|_
1005|1005|CD|_ fork-blocking|fork-blocking|JJ|_ strain|strain|NN|_ induced|induce|VBN|_ for|for|IN|_ Tus|Tus|NNP|_ :|:|:|_ fork5|fork5|CD|_ _|_|NN|_ 2|2|CD|_
1005|1005|CD|_ fork-blocking|fork-blocking|JJ|_ strain|strain|NN|_ induced|induce|VBN|_ for|for|IN|_ Tus|Tus|NNP|_ :|:|:|_ fork5|fork5|CD|_ _|_|SYM|_ 3|3|CD|_
1005|1005|CD|_ ,|,|,|_ LB|lb|NN|_ +|+|CC|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ tus|tus|NN|GEN repressed|repress|VBN|_ -RRB-|-rrb-|-RRB-|_
1005|1005|CD|_ ,|,|,|_ LB|lb|NN|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ arabinose|arabinose|NN|_ ,|,|,|_ 2.5|2.5|CD|_ hr|hr|NN|_ -LRB-|-lrb-|-LRB-|_ tus|tus|NN|GEN induced|induce|VBN|_ -RRB-|-rrb-|-RRB-|_
1005|1005|CD|_ ,|,|,|_ LB|lb|NN|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ arabinose|arabinose|NN|_ ,|,|,|_ 3.5|3.5|CD|_ hr|hr|NN|_ -LRB-|-lrb-|-LRB-|_ tus|tus|NN|GEN induced|induce|VBN|_ -RRB-|-rrb-|-RRB-|_
1005|1005|CD|_ ,|,|,|_ LB|lb|NN|_ +|+|CC|_ 0.4|0.4|CD|_ %|%|NN|_ arabinose|arabinose|NN|_ ,|,|,|_ 90|90|CD|_ '|'|''|_ -LRB-|-lrb-|-LRB-|_ tus|tus|FW|GEN induced|induce|VBN|_ -RRB-|-rrb-|-RRB-|_
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ the|the|DT|_ resulting|result|VBG|_ assembly|assembly|NN|_ data|datum|NNS|_ were|be|VBD|_ exported|export|VBN|_ to|to|TO|_ JMP|JMP|NNP|_ Genomics|Genomics|NNP|_ -LRB-|-lrb-|-LRB-|_ SAS|SAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ TMM|TMM|NNP|_ normalization|normalization|NN|_ and|and|CC|_ ANOVA|anova|NN|_ analysis|analysis|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ samples|sample|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ in|in|IN|_ JMP|JMP|NNP|_ Genomics|Genomics|NNPS|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ and|and|CC|_ RNA|rna|NN|_ collected|collect|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ 's|'s|POS|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ Bacteria|bacterium|NNS|_ Protect|protect|VB|_ RNA|rna|NN|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ approximately|approximately|RB|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD560|od560|NN|_ =|=|JJ|_ approximately|approximately|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ LB|lb|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
genotype|genotype|NN|_ :|:|:|_ mfd|mfd|SYM|GEN -|-|:|_
genotype|genotype|NN|_ :|:|:|_ Mfd|mfd|NN|_ +|+|CC|_ +|+|CC|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|JJ|_
genotype|genotype|NN|_ :|:|:|_ Wildtype|wildtype|NN|_ with|with|IN|_ vector|vector|NN|_
mfd|mfd|NN|GEN _|_|NN|_ 1|1|CD|_
MFD|mfd|NN|_ +|+|CC|_ +|+|CC|_ _|_|SYM|_ 1|1|CD|_
mfd|mfd|NN|GEN _|_|NN|_ 2|2|CD|_
MFD|mfd|NN|_ +|+|CC|_ +|+|CC|_ _|_|SYM|_ 2|2|CD|_
mfd|mfd|NN|GEN _|_|NN|_ 3|3|CD|_
MG1655|mg1655|NN|_
MG1655|mg1655|NN|_ _|_|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ _|_|NN|_ 2|2|CD|_
MG1655|mg1655|NN|_ _|_|CD|_ 3|3|CD|_
MG1655|mg1655|NN|_ pCA24N|pca24n|NN|_ and|and|CC|_ MG1655|mg1655|NN|_ pCA24N-Mfd|pca24n-mfd|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ an|a|DT|_ OD560|od560|NN|_ of|of|IN|_ approximately|approximately|RB|_ 0.25|0.25|CD|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ 100|100|CD|_ μM|μm|NN|_ IPTG|iptg|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
MG1655|mg1655|NN|_ _|_|NN|_ vector|vector|NN|_ _|_|NN|_ 1|1|CD|_
MG1655|mg1655|NN|_ _|_|NN|_ vector|vector|NN|_ _|_|NN|_ 2|2|CD|_
Read|read|VBP|_ coverage|coverage|NN|_ maps|map|NNS|_ and|and|CC|_ RPKM|RPKM|NNP|_ data|datum|NNS|_ was|be|VBD|_ subsequently|subsequently|RB|_ generated|generate|VBN|_ by|by|IN|_ Geneious|Geneious|NNP|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|RNA-Seq|NNP|_
Sequencing|sequencing|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ approximately|approximately|RB|_ 13|13|CD|_ to|to|TO|_ 25|25|CD|_ million|million|CD|_ per|per|IN|_ sample|sample|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ imported|import|VBN|_ into|into|IN|_ Geneious|geneious|JJ|_ Pro|pro|FW|_ -LRB-|-lrb-|-LRB-|_ Biomatters|biomatter|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ assembled|assemble|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ chromosome|chromosome|NN|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ Accession|Accession|NNP|_ Number|number|NN|_ 000913.2|000913.2|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ assembly|assembly|NN|_ process|process|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ medium|medium|NN|_
bacteria|bacterium|NNS|_ grown|grow|VBN|_ in|in|IN|_ LB|lb|NN|_ in|in|FW|_ vitro|vitro|FW|_
bacteria|bacterium|NNS|_ harvested|harvest|VBN|_ from|from|IN|_ blood|blood|NN|_ of|of|IN|_ chickens|chicken|NNS|_
condition|condition|NN|_ :|:|:|_ in|in|FW|_ vitro|vitro|FW|_
condition|condition|NN|_ :|:|:|_ in|in|FW|_ vivo|vivo|FW|_
E058|e058|NN|_ in|in|FW|_ vitro|vitro|FW|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E058|e058|NN|_ in|in|FW|_ vitro|vitro|FW|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E058|e058|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E058|e058|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E058|e058|NN|_ in|in|FW|_ vivo|vivo|FW|_ ,|,|,|_ biological|biological|JJ|_ rep3|rep3|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism APEC|apec|NN|_ O2|o2|CD|_
strain|strain|NN|_ :|:|:|_ O2|o2|CD|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ MAS|mas|NN|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ trimmed|trim|VBN|_ mean|mean|NN|_ target|target|NN|_ intensity|intensity|NN|_ of|of|IN|_ each|each|DT|_ array|array|NN|_ was|be|VBD|_ arbitrarily|arbitrarily|RB|_ set|set|VBN|_ to|to|TO|_ 100|100|CD|_ .|.|.|_
The|the|DT|_ in|in|FW|_ vitro|vitro|FW|_ bacterial|bacterial|JJ|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ -LRB-|-lrb-|-LRB-|_ 5000|5000|CD|_ ×|×|CD|_ g|g|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ until|until|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ .|.|.|_ The|the|DT|_ in|in|FW|_ vivo|vivo|FW|_ bacterial|bacterial|JJ|_ samples|sample|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ with|with|IN|_ two-step|two-step|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ We|we|PRP|_ first|first|RB|_ centrifuged|centrifuge|VBD|_ the|the|DT|_ collected|collect|VBN|_ anticoagulated|anticoagulated|JJ|_ blood|blood|NN|_ samples|sample|NNS|_ at|at|IN|_ low|low|JJ|_ speed|speed|NN|_ to|to|TO|_ remove|remove|VB|_ the|the|DT|_ abundant|abundant|JJ|_ red|red|JJ|_ and|and|CC|_ white|white|JJ|_ blood|blood|NN|_ cells|cell|NNS|_ and|and|CC|_ collected|collect|VBN|_ the|the|DT|_ upper|upper|JJ|_ serum|serum|NN|_ layer|layer|NN|_ .|.|.|_ We|we|PRP|_ then|then|RB|_ used|use|VBD|_ high-speed|high-speed|JJ|_ centrifugation|centrifugation|NN|_ to|to|TO|_ precipitate|precipitate|VB|_ the|the|DT|_ bacteria|bacterium|NNS|_ from|from|IN|_ the|the|DT|_ serum|serum|NN|_ .|.|.|_
To|to|TO|_ prepare|prepare|VB|_ the|the|DT|_ in|in|FW|_ vitro|vitro|FW|_ samples|sample|NNS|_ ,|,|,|_ APEC|APEC|NNP|_ strain|strain|NN|_ E058|e058|NN|_ was|be|VBD|_ grown|grow|VBN|_ statically|statically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 10|10|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|MED broth|broth|NN|MED until|until|IN|_ the|the|DT|_ absorbance|absorbance|NN|_ at|at|IN|_ 600|600|CD|_ nm|nm|NN|_ -LRB-|-lrb-|-LRB-|_ A600|a600|NN|_ -RRB-|-rrb-|-RRB-|_ reached|reach|VBD|_ 0.4|0.4|CD|_ .|.|.|_ To|to|TO|_ prepare|prepare|VB|_ the|the|DT|_ in|in|FW|_ vivo|vivo|FW|_ samples|sample|NNS|_ ,|,|,|_ the|the|DT|_ bacteria|bacterium|NNS|_ was|be|VBD|_ harvested|harvest|VBN|_ from|from|IN|_ cardiac|cardiac|JJ|_ blood|blood|NN|_ in|in|IN|_ 1-day-old|1-day-old|JJ|_ chickens|chicken|NNS|_ at|at|IN|_ 5|5|CD|_ hours|hour|NNS|_ post|post|NN|_ infection|infection|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ from|from|IN|_ both|both|CC|_ the|the|DT|_ in|in|FW|_ vitro|vitro|FW|_ and|and|CC|_ in|in|FW|_ vivo|vivo|FW|_ samples|sample|NNS|_ of|of|IN|_ APEC|APEC|NNP|_ E058|e058|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ the|the|DT|_ RNAiso|rnaiso|NN|_ Plus|plus|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Takara|Takara|NNP|_ ,|,|,|_ Dalian|Dalian|NNP|_ ,|,|,|_ China|China|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ with|with|IN|_ NucleoSpin|nucleospin|NN|_ RNA|rna|NN|_ Clean-up|clean-up|NN|_ -LRB-|-lrb-|-LRB-|_ Macherey-Nagel|Macherey-Nagel|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ '|'|POS|_ instructions|instruction|NNS|_ .|.|.|_
1|1|CD|_ min|min|NN|_ Nov0|nov0|NN|_ ug|ug|NN|_
1|1|CD|_ min|min|NN|_ Nov500|nov500|NN|_ ug|ug|NN|_
20|20|CD|_ min|min|NN|_ Nov0|nov0|NN|_ ug|ug|NN|_
20|20|CD|_ min|min|NN|_ Nov500|nov500|NN|_ ug|ug|NN|_
20|20|CD|_ min|min|NN|_ Nov50|nov50|NN|_ ug|ug|NN|_
1.1|1.1|CD|_ A|a|DT|_
1.1|1.1|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
1.2|1.2|CD|_ A|a|DT|_
1.2|1.2|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
1.3|1.3|CD|_ A|a|DT|_
1.3|1.3|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
1.4|1.4|CD|_ A|a|DT|_
1.4|1.4|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
1.5|1.5|CD|_ A|a|DT|_
1.5|1.5|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
1.6|1.6|CD|_ A|a|DT|_
1.6|1.6|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
17.1|17.1|CD|_ A|a|DT|_
17.1|17.1|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
17.2|17.2|CD|_ A|a|DT|_
17.2|17.2|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
17.3|17.3|CD|_ A|a|DT|_
17.3|17.3|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 25|25|CD|_
17.4|17.4|CD|_ A|a|DT|_
17.4|17.4|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 25|25|CD|_
17.5|17.5|CD|_ A|a|DT|_
17.5|17.5|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
17.6|17.6|CD|_ A|a|DT|_
17.6|17.6|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 50|50|CD|_
17.8|17.8|CD|_ A|a|DT|_
17.8|17.8|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
1.7|1.7|CD|_ A|a|DT|_
1.7|1.7|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 50|50|CD|_
18.2|18.2|CD|_ A|a|DT|_
18.2|18.2|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
18.3|18.3|CD|_ A|a|DT|_
18.3|18.3|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 75|75|CD|_
18.4|18.4|CD|_ A|a|DT|_
18.4|18.4|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
2.1|2.1|CD|_ A|a|DT|_
2.1|2.1|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
2.3|2.3|CD|_ A|a|DT|_
2.3|2.3|CD|_ A|a|DT|_ _|_|NN|_ Earth|Earth|NNP|_ _|_|SYM|_ 75|75|CD|_
2.4|2.4|CD|_ A|a|DT|_
2.4|2.4|CD|_ A|a|DT|_ _|_|NN|_ Space|space|NN|_ _|_|CD|_ 75|75|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Four|four|CD|_ ml|ml|NN|_ of|of|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ suspension|suspension|NN|_ in|in|IN|_ RNALater|rnalater|NN|_ II|ii|CD|_ and|and|CC|_ Medium|medium|NN|_ E|e|NN|_ growth|growth|NN|_ medium|medium|NN|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 200g|200g|NN|_ for|for|IN|_ 5|5|CD|_ min|min|NN|_ .|.|.|_ The|the|DT|_ supernatant|supernatant|NN|_ was|be|VBD|_ discarded|discard|VBN|_ and|and|CC|_ the|the|DT|_ pellet|pellet|NN|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200ul|200ul|JJ|_ PBS|PBS|NNP|_ and|and|CC|_ mixed|mix|VBN|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 100ul|100ul|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ taken|take|VBN|_ out|out|RP|_ for|for|IN|_ DNA|dna|NN|_ and|and|CC|_ RNA|rna|NN|_ extraction|extraction|NN|_ from|from|IN|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ .|.|.|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ digestion|digestion|NN|_ .|.|.|_ Final|final|JJ|_ elution|elution|NN|_ was|be|VBD|_ made|make|VBN|_ in|in|IN|_ 30|30|CD|_ μL|μl|NN|_ dH2O|dh2o|NN|_ .|.|.|_ The|the|DT|_ concentration|concentration|NN|_ and|and|CC|_ integrity|integrity|NN|_ of|of|IN|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ RiboGreen|RiboGreen|NNP|_ ®|®|CD|_ RNA|rna|NN|_ Assay|assay|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Applied|Applied|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_
gentamycin|gentamycin|NN|_ concentration|concentration|NN|_ -LRB-|-lrb-|-LRB-|_ ug|ug|NN|_
location|location|NN|_ :|:|:|_ Earth|Earth|NNP|_
location|location|NN|_ :|:|:|_ Space|Space|NNP|_
Nineteen|nineteen|CD|_ hours|hour|NNS|_ after|after|IN|_ experiment|experiment|NN|_ start|start|NN|_ ,|,|,|_ antibiotic|antibiotic|JJ|_ -LRB-|-lrb-|-LRB-|_ Gentamicin|gentamicin|NN|_ Sulfate|sulfate|NN|_ -LRB-|-lrb-|-LRB-|_ MP|mp|NN|_ Biomedical|biomedical|NN|_ ,|,|,|_ Cat|Cat|NNP|_ No.|No.|NNP|_ 1676045|1676045|CD|_ ,|,|,|_ Santa|Santa|NNP|_ Ana|Ana|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ introducing|introduce|VBG|_ into|into|IN|_ the|the|DT|_ cultures|culture|NNS|_ .|.|.|_ Antibiotic|antibiotic|JJ|_ concentration|concentration|NN|_ varied|vary|VBD|_ from|from|IN|_ one|one|CD|_ sample|sample|NN|_ to|to|TO|_ the|the|DT|_ next|next|JJ|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 150|150|CD|_ ug|ug|NN|_
Post-processing|post-processing|NN|_ of|of|IN|_ the|the|DT|_ sequencing|sequencing|NN|_ reads|read|VBZ|_ from|from|IN|_ RNA-seq|rna-seq|NN|_ experiments|experiment|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ HudsonAlpha|HudsonAlpha|NNP|_ 's|'s|POS|_ unique|unique|JJ|_ in-house|in-house|JJ|_ RNA-seq|rna-seq|NN|_ data|data|NN|_ analysis|analysis|NN|_ pipeline|pipeline|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ quality|quality|NN|_ control|control|NN|_ checks|check|NNS|_ on|on|IN|_ raw|raw|JJ|_ sequence|sequence|NN|_ data|datum|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ Babraham|babraham|NN|_ Bioinformatics|bioinformatic|NNS|_ ,|,|,|_ Cambridge|Cambridge|NNP|_ ,|,|,|_ UK|UK|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Data-analysis|data-analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ CLC|clc|NN|_ Genomics|genomic|NNS|_ Workbench|Workbench|NNP|_ -LRB-|-lrb-|-LRB-|_ Version|Version|NNP|_ 7.5.1|7.5.1|CD|_ ,|,|,|_ CLC|clc|NN|_ Bio|bio|NN|_ ,|,|,|_ Aarhus|Aarhus|NNP|_ ,|,|,|_ Denmark|Denmark|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism -LRB-|-lrb-|-LRB-|_ DH10B|dh10b|NN|_ -RRB-|-rrb-|-RRB-|_ sequence|sequence|NN|_ was|be|VBD|_ downloaded|download|VBN|_ from|from|IN|_ the|the|DT|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ .|.|.|_ For|for|IN|_ read|read|VBN|_ mapping|mapping|NN|_ ,|,|,|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ :|:|:|_ mismatch|mismatch|NN|_ cost|cost|NN|_ =|=|JJ|_ 2|2|CD|_ ,|,|,|_ insertion|insertion|NN|_ and|and|CC|_ deletion|deletion|NN|_ cost|cost|NN|_ =|=|JJ|_ 3|3|CD|_ ,|,|,|_ length|length|NN|_ fraction|fraction|NN|_ :|:|:|_ 0.8|0.8|CD|_ ,|,|,|_ similarity|similarity|NN|_ fraction|fraction|NN|_ =|=|JJ|_ 0.8|0.8|CD|_ ,|,|,|_ global|global|JJ|_ alignment|alignment|NN|_ =|=|JJ|_ no|no|DT|_ ,|,|,|_ auto-detect|auto-detect|JJ|_ paired|paired|JJ|_ distances|distance|NNS|_ =|=|JJ|_ yes|yes|UH|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ grouped|group|VBN|_ and|and|CC|_ differential|differential|JJ|_ expression|expression|NN|_ of|of|IN|_ genes|gene|NNS|_ was|be|VBD|_ calculated|calculate|VBN|_ on|on|IN|_ the|the|DT|_ basis|basis|NN|_ of|of|IN|_ fold|fold|JJ|_ changes|change|NNS|_ -LRB-|-lrb-|-LRB-|_ using|use|VBG|_ the|the|DT|_ default|default|NN|_ cut-off|cut-off|JJ|_ ≥|≥|NN|_ ±|±|NN|_ 2.0|2.0|CD|_ -RRB-|-rrb-|-RRB-|_ observed|observe|VBN|_ in|in|IN|_ comparisons|comparison|NNS|_ between|between|IN|_ defined|define|VBN|_ conditions|condition|NNS|_ .|.|.|_
Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ rRNA|rrna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NNP|_ Gold|Gold|NNP|_ -LRB-|-lrb-|-LRB-|_ Yeast|yeast|NN|_ -RRB-|-rrb-|-RRB-|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Epicenter|epicenter|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommended|recommend|VBN|_ protocol|protocol|NN|_ .|.|.|_ Immediately|immediately|RB|_ after|after|IN|_ the|the|DT|_ rRNA|rrna|NN|_ removal|removal|NN|_ the|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragmented|JJ|_ and|and|CC|_ primed|prime|VBN|_ for|for|IN|_ the|the|DT|_ first|first|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBnext|NEBnext|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ synthesis|synthesis|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ BioLabs|BioLabs|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Ipswich|Ipswich|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Directional|directional|JJ|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ NEBNExt|NEBNExt|NNP|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ kit|kit|NN|_ .|.|.|_ Following|follow|VBG|_ this|this|DT|_ the|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ into|into|IN|_ standard|standard|JJ|_ library|library|NN|_ preparation|preparation|NN|_ protocol|protocol|NN|_ using|use|VBG|_ NEBNext|nebnext|NN|_ ®|®|NN|_ DNA|dna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Master|Master|NNP|_ Mix|Mix|NNP|_ Set|set|VB|_ for|for|IN|_ Illumina|Illumina|NNP|_ ®|®|SYM|_ with|with|IN|_ slight|slight|JJ|_ modifications|modification|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ end-repair|end-repair|NN|_ was|be|VBD|_ done|do|VBN|_ followed|follow|VBN|_ by|by|IN|_ polyA|polya|NN|_ addition|addition|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ .|.|.|_ Post-ligated|post-ligated|JJ|_ materials|material|NNS|_ were|be|VBD|_ individually|individually|RB|_ barcoded|barcode|VBN|_ with|with|IN|_ primers|primer|NNS|_ and|and|CC|_ amplified|amplify|VBN|_ through|through|IN|_ 12|12|CD|_ cycles|cycle|NNS|_ of|of|IN|_ PCR|pcr|NN|_ .|.|.|_ Final|final|JJ|_ library|library|NN|_ quantity|quantity|NN|_ was|be|VBD|_ assessed|assess|VBN|_ by|by|IN|_ Quant-iT|quant-it|NN|_ ™|™|CD|_ PicoGreen|PicoGreen|NNP|_ ®|®|CD|_ dsDNA|dsDNA|NNP|_ Assay|assay|NN|_ Kit|kit|NN|_ and|and|CC|_ the|the|DT|_ library|library|NN|_ quality|quality|NN|_ was|be|VBD|_ estimated|estimate|VBN|_ on|on|IN|_ LabChip|LabChip|NNP|_ ®|®|NNP|_ GX|GX|NNP|_ -LRB-|-lrb-|-LRB-|_ Caliper|Caliper|NNP|_ ,|,|,|_ PerkinElmer|PerkinElmer|NNP|_ ,|,|,|_ Waltham|Waltham|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Accurate|accurate|JJ|_ quantification|quantification|NN|_ of|of|IN|_ the|the|DT|_ final|final|JJ|_ libraries|library|NNS|_ for|for|IN|_ sequencing|sequencing|NN|_ applications|application|NNS|_ was|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ the|the|DT|_ qPCR-based|qpcr-based|JJ|_ KAPA|KAPA|NNP|_ Biosystems|Biosystems|NNP|_ Library|Library|NNP|_ Quantification|Quantification|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Kapa|Kapa|NNP|_ Biosystems|Biosystems|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ ,|,|,|_ Woburn|Woburn|NNP|_ ,|,|,|_ MA|MA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Each|each|DT|_ library|library|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 12.5|12.5|CD|_ nM|nm|NN|_ and|and|CC|_ pooled|pooled|JJ|_ equimolar|equimolar|JJ|_ prior|prior|JJ|_ to|to|TO|_ clustering|clustering|NN|_ .|.|.|_ Paired-End|paired-end|NN|_ -LRB-|-lrb-|-LRB-|_ PE|pe|NN|_ -RRB-|-rrb-|-RRB-|_ sequencing|sequencing|NN|_ was|be|VBD|_ performed|perform|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ sequencer|sequencer|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Samples|sample|NNS|_ were|be|VBD|_ sent|send|VBN|_ to|to|TO|_ the|the|DT|_ International|International|NNP|_ Space|Space|NNP|_ Station|Station|NNP|_ at|at|IN|_ 4C|4c|NN|_ in|in|IN|_ FPAs|fpa|NNS|_ ,|,|,|_ as|as|IN|_ described|describe|VBN|_ above|above|IN|_ .|.|.|_ Temperature|temperature|NN|_ was|be|VBD|_ increased|increase|VBN|_ to|to|TO|_ 37C|37c|NN|_ and|and|CC|_ 23|23|CD|_ hours|hour|NNS|_ later|later|RB|_ ,|,|,|_ the|the|DT|_ experiment|experiment|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ introducing|introduce|VBG|_ the|the|DT|_ inoculum|inoculum|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 4157|4157|CD|_ -RRB-|-rrb-|-RRB-|_ into|into|IN|_ the|the|DT|_ growth|growth|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Medium|medium|NN|_ E|e|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ Vogel|Vogel|NNP|_ &|&|CC|_ Bonner|Bonner|NNP|_ -LRB-|-lrb-|-LRB-|_ 1956|1956|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 5|5|CD|_ g|g|NN|_
strain|strain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 4157|4157|CD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ excel|excel|VB|_ file|file|NN|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
2|2|CD|_ min|min|NN|_ Nov10|nov10|NN|_ ug|ug|NN|_
2|2|CD|_ min|min|NN|_ Nov2|nov2|NN|_ ug|ug|NN|_
2|2|CD|_ min|min|NN|_ Nov5|nov5|NN|_ ug|ug|NN|_
15|15|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
2003|2003|CD|_ ,|,|,|_ PNAS|PNAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ minimize|minimize|VB|_ the|the|DT|_ effect|effect|NN|_ of|of|IN|_ such|such|JJ|_ contributions|contribution|NNS|_ ,|,|,|_ microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_
25|25|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
2|2|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
55|55|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
5|5|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
5|5|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_ first|first|RB|_ replicate|replicate|VB|_
-LRB-|-lrb-|-LRB-|_ B|b|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ X|x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ row|row|NN|_ -LRB-|-lrb-|-LRB-|_ Y|y|NN|_ -RRB-|-rrb-|-RRB-|_ number|number|NN|_ ,|,|,|_ red|red|JJ|_ foreground|foreground|NN|_ -LRB-|-lrb-|-LRB-|_ f|f|FW|_ _|_|FW|_ r|r|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ background|background|NN|_ -LRB-|-lrb-|-LRB-|_ b|b|NN|_ _|_|CD|_ r|r|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ green|green|JJ|_
completely|completely|RB|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_
corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ tip|tip|NN|_ .|.|.|_ Finally|finally|RB|_ ,|,|,|_ all|all|PDT|_ the|the|DT|_ log|log|NN|_ ratios|ratio|NNS|_ of|of|IN|_ the|the|DT|_ same|same|JJ|_ gene|gene|NN|_ from|from|IN|_ each|each|DT|_ slide|slide|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 15|15|CD|_ min|min|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 25|25|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
Ecoli|ecolus|NNS|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 2|2|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 35|35|CD|_ min|min|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 35|35|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 45|45|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 55|55|CD|_ min|min|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_
Ecoli|Ecoli|NNP|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_ first|first|RB|_ replicate|replicate|VB|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 15|15|CD|_ min|min|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 25|25|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 25|25|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 2|2|CD|_ min|min|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 35|35|CD|_ min|min|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 45|45|CD|_ min|min|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 55|55|CD|_ min|min|NN|_ _|_|CD|_ rep1|rep1|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 55|55|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 5|5|CD|_ min|min|NN|_ _|_|SYM|_ Rep1|rep1|JJ|_
ecoli|ecolus|NNS|_ _|_|VBP|_ aerobicanaerobic|aerobicanaerobic|JJ|_ _|_|NN|_ 5|5|CD|_ min|min|NN|_ _|_|CD|_ rep2|rep2|NN|_
Ecoli|ecolus|NNS|_ ,|,|,|_ completely|completely|RB|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_
E|e|NN|_ coli|coli|NN|_ ,|,|,|_ immediately|immediately|RB|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
Epicentre|Epicentre|NNP|_ MasterPure|MasterPure|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ Kit|kit|NN|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
fluorescent|fluorescent|JJ|_ labeling|labeling|NN|_ and|and|CC|_ hybridization|hybridization|NN|_ and|and|CC|_ scanning|scanning|NN|_ of|of|IN|_ the|the|DT|_ microarray|microarray|NN|_ images|image|NNS|_ -LRB-|-lrb-|-LRB-|_ Balazsi|balazsus|NNS|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_
foreground|foreground|NN|_ and|and|CC|_ background|background|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ median|median|JJ|_ Cy3|cy3|NN|_ -LRB-|-lrb-|-LRB-|_ green|green|JJ|_ -RRB-|-rrb-|-RRB-|_ foreground|foreground|NN|_ and|and|CC|_ background|background|NN|_
foreground|foreground|NN|_ -LRB-|-lrb-|-LRB-|_ f|f|FW|_ _|_|FW|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ background|background|NN|_ -LRB-|-lrb-|-LRB-|_ b|b|NN|_ _|_|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ intensity|intensity|NN|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ probe|probe|NN|_ within|within|IN|_ a|a|DT|_ block|block|NN|_ ,|,|,|_
further|further|JJ|_ analysis|analysis|NN|_ if|if|IN|_ the|the|DT|_ foreground|foreground|NN|_ intensity|intensity|NN|_ of|of|IN|_ less|less|JJR|_ than|than|IN|_ 50|50|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ pixels|pixel|NNS|_ within|within|IN|_ the|the|DT|_ spot|spot|NN|_
Immediately|immediately|RB|_ after|after|IN|_ turning|turn|VBG|_ off|off|RP|_ oxygen|oxygen|NN|_
infinity|infinity|NN|_ .|.|.|_ These|these|DT|_ values|value|NNS|_ were|be|VBD|_ eliminated|eliminate|VBN|_ using|use|VBG|_ the|the|DT|_ find|find|VB|_ ,|,|,|_ imag|imag|NN|_ ,|,|,|_ and|and|CC|_ isfinite|isfinite|NN|_ functions|function|NNS|_ in|in|IN|_ Matlab|Matlab|NNP|_ .|.|.|_
in|in|IN|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ ,|,|,|_ containing|contain|VBG|_ the|the|DT|_ following|follow|VBG|_ information|information|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 14,352|14,352|CD|_ entries|entry|NNS|_ :|:|:|_ block|block|NN|_
intensities|intensity|NNS|_ ,|,|,|_ respectively|respectively|RB|_ .|.|.|_ In|in|IN|_ some|some|DT|_ cases|case|NNS|_ ,|,|,|_ when|when|WRB|_ the|the|DT|_ intensity|intensity|NN|_ of|of|IN|_ the|the|DT|_ background|background|NN|_ was|be|VBD|_ higher|higher|JJR|_
Next|Next|NNP|_ ,|,|,|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ ,|,|,|_ by|by|IN|_ averaging|average|VBG|_ the|the|DT|_ log|log|NN|_ ratios|ratio|NNS|_ resulting|result|VBG|_ from|from|IN|_ all|all|DT|_ spots|spot|NNS|_ printed|print|VBN|_ by|by|IN|_ a|a|DT|_
normalized|normalize|VBD|_ as|as|IN|_ described|describe|VBN|_ before|before|IN|_ -LRB-|-lrb-|-LRB-|_ Tong|Tong|NNP|_ et|et|FW|_ al.|al.|FW|_ 2004|2004|CD|_ BBRC|BBRC|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ spots|spot|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ from|from|IN|_
of|of|IN|_ -LRB-|-lrb-|-LRB-|_ F|f|NN|_ _|_|CD|_ r-B|r-b|NN|_ _|_|NN|_ r|r|NN|_ -RRB-|-rrb-|-RRB-|_
originate|originate|VB|_ during|during|IN|_ array|array|NN|_ printing|printing|NN|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ during|during|IN|_ the|the|DT|_ collection|collection|NN|_ and|and|CC|_ processing|processing|NN|_ of|of|IN|_ samples|sample|NNS|_ ,|,|,|_
P|p|NN|_ is|be|VBZ|_ defined|define|VBN|_ by|by|IN|_ the|the|DT|_ pair|pair|NN|_ of|of|IN|_ integers|integer|NNS|_ -LRB-|-lrb-|-LRB-|_ X|x|NN|_ ,|,|,|_ Y|y|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Log|log|VB|_ ratios|ratio|NNS|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ the|the|DT|_ base|base|NN|_ 10|10|CD|_ logarithm|logarithm|NN|_
print|print|NN|_ tip|tip|NN|_ ,|,|,|_ and|and|CC|_ subtracting|subtract|VBG|_ the|the|DT|_ resulting|result|VBG|_ average|average|NN|_ from|from|IN|_ all|all|DT|_ the|the|DT|_ individual|individual|JJ|_ log|log|NN|_ ratios|ratio|NNS|_
than|than|IN|_ or|or|CC|_ equal|equal|JJ|_ to|to|TO|_ the|the|DT|_ intensity|intensity|NN|_ of|of|IN|_ the|the|DT|_ foreground|foreground|NN|_ ,|,|,|_ the|the|DT|_ resulting|result|VBG|_ log|log|NN|_ ratios|ratio|NNS|_ became|become|VBD|_ complex|complex|NN|_ or|or|CC|_
Two|two|CD|_ color|color|NN|_ cDNA|cdna|NN|_ microarray|microarray|NN|_ data|datum|NNS|_ are|be|VBP|_ never|never|RB|_ devoid|devoid|JJ|_ of|of|IN|_ spurious|spurious|JJ|_ technical|technical|JJ|_ contributions|contribution|NNS|_ that|that|WDT|_
Two|two|CD|_ color|color|NN|_ cDNA|cdna|NN|_ microarray|microarray|NN|_ data|datum|NNS|_ are|be|VBP|_ never|never|RB|_ devoid|devoid|JJ|_ of|of|IN|_ spurious|spurious|JJ|_ technical|technical|JJ|_ contributions|contribution|NNS|_ that|that|WDT|_ originate|originate|VBP|_ during|during|IN|_ array|array|NN|_ printing|printing|NN|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ during|during|IN|_ the|the|DT|_ collection|collection|NN|_ and|and|CC|_ processing|processing|NN|_ of|of|IN|_ samples|sample|NNS|_ ,|,|,|_ fluorescent|fluorescent|JJ|_ labeling|labeling|NN|_ and|and|CC|_ hybridization|hybridization|NN|_ and|and|CC|_ scanning|scanning|NN|_ of|of|IN|_ the|the|DT|_ microarray|microarray|NN|_ images|image|NNS|_ -LRB-|-lrb-|-LRB-|_ Balazsi|balazsus|NNS|_ et|et|FW|_ al.|al.|FW|_ 2003|2003|CD|_ ,|,|,|_ PNAS|PNAS|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ To|to|TO|_ minimize|minimize|VB|_ the|the|DT|_ effect|effect|NN|_ of|of|IN|_ such|such|JJ|_ contributions|contribution|NNS|_ ,|,|,|_ microarray|microarray|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ as|as|IN|_ described|describe|VBN|_ before|before|IN|_ -LRB-|-lrb-|-LRB-|_ Tong|Tong|NNP|_ et|et|FW|_ al.|al.|FW|_ 2004|2004|CD|_ BBRC|BBRC|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ spots|spot|NNS|_ were|be|VBD|_ excluded|exclude|VBN|_ from|from|IN|_ further|further|JJ|_ analysis|analysis|NN|_ if|if|IN|_ the|the|DT|_ foreground|foreground|NN|_ intensity|intensity|NN|_ of|of|IN|_ less|less|JJR|_ than|than|IN|_ 50|50|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ pixels|pixel|NNS|_ within|within|IN|_ the|the|DT|_ spot|spot|NN|_ were|be|VBD|_ above|above|IN|_ 2|2|CD|_ standard|standard|JJ|_ deviations|deviation|NNS|_ of|of|IN|_ the|the|DT|_ background|background|NN|_ .|.|.|_ We|we|PRP|_ generated|generate|VBD|_ expression|expression|NN|_ data|datum|NNS|_ tables|table|NNS|_ in|in|IN|_ Microsoft|Microsoft|NNP|_ Excel|Excel|NNP|_ ,|,|,|_ containing|contain|VBG|_ the|the|DT|_ following|follow|VBG|_ information|information|NN|_ for|for|IN|_ each|each|DT|_ of|of|IN|_ the|the|DT|_ 14,352|14,352|CD|_ entries|entry|NNS|_ :|:|:|_ block|block|NN|_ -LRB-|-lrb-|-LRB-|_ B|b|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ X|x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ row|row|NN|_ -LRB-|-lrb-|-LRB-|_ Y|y|NN|_ -RRB-|-rrb-|-RRB-|_ number|number|NN|_ ,|,|,|_ red|red|JJ|_ foreground|foreground|NN|_ -LRB-|-lrb-|-LRB-|_ f|f|FW|_ _|_|FW|_ r|r|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ background|background|NN|_ -LRB-|-lrb-|-LRB-|_ b|b|NN|_ _|_|CD|_ r|r|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ green|green|JJ|_ foreground|foreground|NN|_ -LRB-|-lrb-|-LRB-|_ f|f|FW|_ _|_|FW|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ background|background|NN|_ -LRB-|-lrb-|-LRB-|_ b|b|NN|_ _|_|CD|_ g|g|NN|_ -RRB-|-rrb-|-RRB-|_ intensity|intensity|NN|_ .|.|.|_ The|the|DT|_ position|position|NN|_ of|of|IN|_ each|each|DT|_ probe|probe|NN|_ within|within|IN|_ a|a|DT|_ block|block|NN|_ ,|,|,|_ P|p|NN|_ is|be|VBZ|_ defined|define|VBN|_ by|by|IN|_ the|the|DT|_ pair|pair|NN|_ of|of|IN|_ integers|integer|NNS|_ -LRB-|-lrb-|-LRB-|_ X|x|NN|_ ,|,|,|_ Y|y|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Log|log|VB|_ ratios|ratio|NNS|_ were|be|VBD|_ defined|define|VBN|_ as|as|IN|_ the|the|DT|_ base|base|NN|_ 10|10|CD|_ logarithm|logarithm|NN|_ of|of|IN|_ -LRB-|-lrb-|-LRB-|_ F|f|NN|_ _|_|CD|_ r-B|r-b|NN|_ _|_|NN|_ r|r|NN|_ -RRB-|-rrb-|-RRB-|_
were|be|VBD|_ above|above|IN|_ 2|2|CD|_ standard|standard|JJ|_ deviations|deviation|NNS|_ of|of|IN|_ the|the|DT|_ background|background|NN|_ .|.|.|_ We|we|PRP|_ generated|generate|VBD|_ expression|expression|NN|_ data|datum|NNS|_ tables|table|NNS|_
were|be|VBD|_ averaged|average|VBN|_ and|and|CC|_ listed|list|VBN|_ in|in|IN|_ a|a|DT|_ new|new|JJ|_ file|file|NN|_ .|.|.|_
40|40|CD|_ min|min|NN|_ Nov10|nov10|NN|_ ug|ug|NN|_
40|40|CD|_ min|min|NN|_ Nov2|nov2|NN|_ ug|ug|NN|_
40|40|CD|_ min|min|NN|_ Nov5|nov5|NN|_ ug|ug|NN|_
CAR005|car005|NN|_
CAR005|car005|NN|_ strain|strain|NN|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
G4H14|g4h14|NN|_
G4H14|g4h14|NN|_ strain|strain|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1938v1|asm1938v1|NN|_
Illumina|Illumina|NNP|_ Casava1|Casava1|NNP|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
IspG1|ispg1|NN|_
IspG1|ispg1|NN|_ strain|strain|NN|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
Single|single|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 15x100|15x100|CD|_ mm|mm|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 4|4|CD|_ ml|ml|NN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ overnight|overnight|JJ|_ .|.|.|_ 100|100|CD|_ μl|μl|NN|_ seed|seed|NN|_ culture|culture|NN|_ was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ a|a|DT|_ 100|100|CD|_ ml|ml|NN|_ flask|flask|NN|_ containing|contain|VBG|_ 10|10|CD|_ ml|ml|NN|_ LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 30ºC|30ºc|NN|_ and|and|CC|_ 250|250|CD|_ rpm|rpm|NN|_ for|for|IN|_ 5|5|CD|_ h.|h.|NN|_
strain|strain|NN|_ :|:|:|_ CAR005|car005|NN|_
strain|strain|NN|_ :|:|:|_ G4H14|g4h14|NN|_
strain|strain|NN|_ :|:|:|_ IspG1|ispg1|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ -LSB-|-lsb-|-LRB-|_ .|.|.|_ txt|txt|NN|_ -RSB-|-rsb-|-RRB-|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ RPKM|rpkm|NN|_ values|value|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Detailed|detailed|JJ|_ parameters|parameter|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapping|mapping|NN|_ :|:|:|_ bowtie2|bowtie2|NN|_ -|-|:|_ x|x|CC|_ ATCC8739|atcc8739|NN|_ -1|-1|CD|_ X|x|NN|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fq|fq|NN|_ -2|-2|CD|_ X|x|NN|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fq|fq|NN|_ --|--|:|_ no-mixed|no-mixed|JJ|_ -|-|:|_ p|p|NN|_ 2|2|CD|_ -|-|:|_ S|s|NN|_ X.sam|x.sam|NN|_
E.coli|e.coli|NN|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 8739|8739|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ATCC8739|atcc8739|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ normal|normal|JJ|_ condtion|condtion|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ %|%|NN|_ w|w|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ osmotic|osmotic|JJ|_ stress|stress|NN|_ condtion|condtion|NN|_ -LRB-|-lrb-|-LRB-|_ 12|12|CD|_ %|%|NN|_ w|w|NN|_
Illumina|Illumina|NNP|_ Casava1|casava1|NN|_ .7|.7|CD|_ software|software|NN|_ used|use|VBN|_ for|for|IN|_ basecalling|basecalling|NN|_ .|.|.|_
NZ502|nz502|NN|_ _|_|CD|_ 12|12|CD|_ %|%|NN|_ Glu|glu|NN|_
NZ502|nz502|NN|_ _|_|CD|_ 5|5|CD|_ %|%|NN|_ Glu|Glu|NNP|_
Reads|read|VBZ|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ RPKM|rpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ a|a|DT|_ protocol|protocol|NN|_ from|from|IN|_ Chepelev|Chepelev|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Research|Research|NNP|_ ,|,|,|_ 2009|2009|CD|_ .|.|.|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC8739|atcc8739|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ CP000946|cp000946|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.2.5|2.2.5|CD|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ NZ-502|nz-502|NN|_ -LRB-|-lrb-|-LRB-|_ RpoB|rpob|NN|_ mutant|mutant|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ Suc-T110|suc-t110|NN|_ -LRB-|-lrb-|-LRB-|_ parental|parental|JJ|_ strain|strain|NN|_ -RRB-|-rrb-|-RRB-|_
SucT110|suct110|NN|_ _|_|CD|_ 12|12|CD|_ %|%|NN|_ Glu|glu|NN|_
SucT110|suct110|NN|_ _|_|CD|_ 5|5|CD|_ %|%|NN|_ Glu|Glu|NNP|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ RPKM|rpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ the|the|DT|_ Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN|_ method|method|NN|_ .|.|.|_ An|a|DT|_ additional|additional|JJ|_ clean-up|clean-up|JJ|_ including|include|VBG|_ the|the|DT|_ on-column|on-column|JJ|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
ChIP-Seq|chip-seq|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ K12|k12|SYM|_ -|-|:|_ MG1655|mg1655|NN|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Exponential|Exponential|NNP|_ +|+|CC|_ O2|o2|CD|_
growth|growth|NN|_ condition|condition|NN|_ :|:|:|_ Static|static|JJ|_ +|+|CC|_ O2|o2|CD|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ ChIP-exo|ChIP-exo|NNP|_
replicate|replicate|VB|_ :|:|:|_ 1|1|CD|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
Samples|sample|NNS|_ 931|931|CD|_ ,|,|,|_ 933|933|CD|_ ,|,|,|_ 935|935|CD|_ and|and|CC|_ 937|937|CD|_ were|be|VBD|_ aligned|align|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ V|v|NN|_ 1.1.2|1.1.2|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ parameters|parameter|NNS|_ --|--|:|_ wrapper|wrapper|NN|_ basic-0|basic-0|NN|_ -|-|:|_ q|q|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ -|-|:|_ l|l|NN|_ 55|55|CD|_ -|-|:|_ k|k|NN|_ 1|1|CD|_ -5|-5|CD|_ 3|3|CD|_ -3|-3|CD|_ 40|40|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ S|s|NN|_ -|-|:|_ p|p|NN|_ 24|24|CD|_ ,|,|,|_ and|and|CC|_ samples|sample|NNS|_ 1311|1311|CD|_ ,|,|,|_ 1314|1314|CD|_ ,|,|,|_ 1317|1317|CD|_ and|and|CC|_ 1320|1320|CD|_ were|be|VBD|_ aligned|align|VBN|_ with|with|IN|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ V|v|NN|_ 1.1.2|1.1.2|CD|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ paramters|paramter|NNS|_ --|--|:|_ wrapper|wrapper|NN|_ basic-0|basic-0|NN|_ -|-|:|_ q|q|SYM|_ -|-|:|_ m|m|NN|_ 1|1|CD|_ -|-|:|_ v|v|LS|_ 2|2|CD|_ --|--|:|_ best|best|JJS|_ -|-|:|_ p|p|NN|_ 24|24|CD|_ -|-|:|_ S|s|NN|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ _|_|IN|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ replicate|replicate|VB|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 299|299|CD|_ -RRB-|-rrb-|-RRB-|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ replicate|replicate|VB|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 423|423|CD|_ -RRB-|-rrb-|-RRB-|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ replicate|replicate|VB|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 299|299|CD|_ -RRB-|-rrb-|-RRB-|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ replicate|replicate|VB|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 423|423|CD|_ -RRB-|-rrb-|-RRB-|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ _|_|NN|_ rifampicin|rifampicin|NN|SUPP
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ ,|,|,|_ replicate|replicate|VBP|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 423|423|CD|_ -RRB-|-rrb-|-RRB-|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ exponential|exponential|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_ ,|,|,|_ replicate|replicate|VBP|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 423|423|CD|_ -RRB-|-rrb-|-RRB-|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ _|_|SYM|_ static|static|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ _|_|IN|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ static|static|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ replicate|replicate|VB|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 299|299|CD|_ -RRB-|-rrb-|-RRB-|_
Sig70|sig70|NN|_ in|in|IN|_ E.|e.|FW|_ coli|coli|FW|_ ,|,|,|_ static|static|JJ|_ aerobic|aerobic|JJ|_ growth|growth|NN|_ ,|,|,|_ no|no|DT|_ rifampicin|rifampicin|NN|SUPP applied|apply|VBD|_ replicate|replicate|VB|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ run|run|NN|_ 299|299|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Each|each|DT|_ wig|wig|NN|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ alignd|alignd|NN|_ reads|read|VBZ|_ of|of|IN|_ each|each|DT|_ ChIP-exo|ChIP-exo|NNP|_ sample|sample|NN|_ .|.|.|_
The|the|DT|_ ChIP-exo|chip-exo|JJ|_ experiments|experiment|NNS|_ were|be|VBD|_ generated|generate|VBN|_ by|by|IN|_ following|follow|VBG|_ the|the|DT|_ steps|step|NNS|_ presented|present|VBN|_ by|by|IN|_ Rhee|Rhee|NNP|_ and|and|CC|_ Pugh|Pugh|NNP|_ ,|,|,|_ 2011|2011|CD|_ .|.|.|_
The|the|DT|_ samples|sample|NNS|_ were|be|VBD|_ sonicated|sonicate|VBN|_ for|for|IN|_ a|a|DT|_ total|total|NN|_ of|of|IN|_ 16|16|CD|_ minutes|minute|NNS|_ and|and|CC|_ 50|50|CD|_ uL|ul|NN|_ protein|protein|NN|_ A|a|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ none|none|NN|_
treated|treat|VBN|_ with|with|IN|_ :|:|:|_ Rifampicin|Rifampicin|NNP|_ for|for|IN|_ 20|20|CD|_ minutes|minute|NNS|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ expressing|express|VBG|_ PCK|pck|NN|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ expressing|express|VBG|_ ppc|ppc|NN|GEN
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ expressing|express|VBG|_ ppc|ppc|NN|GEN at|at|IN|_ LB-GlC|lb-glc|JJ|_ medium|medium|NN|_ ,|,|,|_ D|d|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ h-1|h-1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ W3110|w3110|NN|_ grown|grow|VBN|_ at|at|IN|_ glucose-minimal|glucose-minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ induction|induction|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ early|early|JJ|_ log|log|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ u|u|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ h-1|h-1|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ grown|grow|VBN|_ at|at|IN|_ LB-glucose|lb-glucose|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ induction|induction|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ chemostat|chemostat|NN|_ -LRB-|-lrb-|-LRB-|_ D|d|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ h-1|h-1|NN|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ KCTC|kctc|NN|_ 2223|2223|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ KCTC|kctc|NN|_ 2223|2223|CD|_ -RRB-|-rrb-|-RRB-|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ KCTC|kctc|NN|_ 2223|2223|CD|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ LB-GlC|lb-glc|JJ|_ medium|medium|NN|_ ,|,|,|_ D|d|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ h-1|h-1|NN|_
E.|e.|FW|_ coli|coli|FW|_ W3110|w3110|NN|_ with|with|IN|_ glucose-minimal|glucose-minimal|JJ|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ induced|induce|VBN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ early|early|JJ|_ log|log|NN|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ u|u|NN|_ =|=|JJ|_ 0.25|0.25|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
PCK|pck|NN|_ _|_|CD|_ glucose-minimal|glucose-minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ early|early|JJ|_ log|log|NN|_ phase|phase|NN|_
PCK|pck|NN|_ _|_|CD|_ LB-GlC|lb-glc|JJ|_ medium|medium|NN|_ _|_|NN|_ D|d|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ h-1|h-1|NN|_
PPC|PPC|NNP|_ _|_|SYM|_ glucose-minimal|glucose-minimal|JJ|_ medium|medium|NN|_ _|_|NN|_ early|early|JJ|_ log|log|NN|_ phase|phase|NN|_
PPC|PPC|NNP|_ _|_|SYM|_ LB-GlC|lb-glc|JJ|_ medium|medium|NN|_ _|_|NN|_ D|d|NN|_ =|=|JJ|_ 0.1|0.1|CD|_ h-1|h-1|NN|_
Scanned|scan|VBD|_ images|image|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 3.0|3.0|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Axon|Axon|NNP|_ Instruments|Instruments|NNP|_ ,|,|,|_ Union|Union|NNP|_ City|City|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ gene|gene|NN|_ expression|expression|NN|_ ratios|ratio|NNS|_ .|.|.|_
Scanned|scan|VBD|_ images|image|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ GenePix|GenePix|NNP|_ Pro|pro|FW|_ 3.0|3.0|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Axon|Axon|NNP|_ Instruments|Instruments|NNP|_ ,|,|,|_ Union|Union|NNP|_ City|City|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ obtain|obtain|VB|_ gene|gene|NN|_ expression|expression|NN|_ ratios|ratio|NNS|_ .|.|.|_ Logged|log|VBN|_ gene|gene|NN|_ expression|expression|NN|_ ratios|ratio|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ by|by|IN|_ LOWESS|lowess|NN|_ regression|regression|NN|_ -LRB-|-lrb-|-LRB-|_ Yang|Yang|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2002|2002|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ GeneSpring|GeneSpring|NNP|_ GX|GX|NNP|_ 7.3|7.3|CD|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ medium|medium|NN|_ for|for|IN|_ batch|batch|NN|_ culture|culture|NN|_ was|be|VBD|_ consisted|consist|VBN|_ of|of|IN|_ 11.3|11.3|CD|_ g|g|NN|_ M9|m9|NN|_ medium|medium|NN|_ ,|,|,|_ 0.2|0.2|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ •|•|SYM|_ 7H2O|7H2O|NNP|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ,|,|,|_ 1|1|CD|_ mg|mg|NN|_ thiamine|thiamine|NN|SUPP ,|,|,|_ 10|10|CD|_ g|g|NN|_ NaHCO3|nahco3|NN|_ and|and|CC|_ 9|9|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ampicillin|ampicillin|NN|_ and|and|CC|_ 0.1|0.1|CD|_ mmole|mmole|NN|_ IPTG|iptg|NN|_ per|per|IN|_ liter|liter|NN|_ .|.|.|_
The|the|DT|_ medium|medium|NN|_ for|for|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ contained|contain|VBD|_ 20|20|CD|_ g|g|NN|_ LB|lb|NN|_ ,|,|,|_ 9|9|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 10|10|CD|_ g|g|NN|_ NaHCO3|nahco3|NN|_ ,|,|,|_ 50|50|CD|_ mg|mg|NN|_ ampicillin|ampicillin|NN|_ per|per|IN|_ liter|liter|NN|_ and|and|CC|_ isopropyl|isopropyl|NN|_ -|-|:|_ -|-|:|_ D-thiogalactopyranoside|d-thiogalactopyranoside|NN|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ supplemented|supplement|VBN|_ to|to|TO|_ be|be|VB|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP .|.|.|_ The|the|DT|_ initial|initial|JJ|_ pH|ph|NN|_ of|of|IN|_ the|the|DT|_ medium|medium|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ be|be|VB|_ pH|ph|NN|_ 7.3|7.3|CD|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ N|n|NN|_ HCl|hcl|NN|_ solution|solution|NN|_ .|.|.|_ The|the|DT|_ inoculation|inoculation|NN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ 250|250|CD|_ mL-fermentor|ml-fermentor|NN|_ containing|contain|VBG|_ 100|100|CD|_ mL|ml|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Small|small|JJ|_ scale|scale|NN|_ multi-chemostat|multi-chemostat|JJ|_ fermentor|fermentor|NN|_ ;|;|:|_ Biotron|Biotron|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Bucheon|Bucheon|NNP|_ ,|,|,|_ Korea|Korea|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ culture|culture|NN|_ was|be|VBD|_ performed|perform|VBN|_ at|at|IN|_ 37|37|CD|_ C|c|NN|_ ,|,|,|_ 350|350|CD|_ rpm|rpm|NN|_ with|with|IN|_ flushing|flushing|NN|_ CO2|co2|NN|_ gas|gas|NN|_ at|at|IN|_ 20|20|CD|_ mL|ml|NN|_
Transcriptome|transcriptome|NN|_ of|of|IN|_ cells|cell|NNS|_ was|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ a|a|DT|_ RNA|rna|NN|_ extraction|extraction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ;|;|:|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_
W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ KCTC|kctc|NN|_ 2223|2223|CD|_ -RRB-|-rrb-|-RRB-|_
W3110|w3110|NN|_ overexpressing|overexpress|VBG|_ pck|pck|NN|GEN
BnTR1|bntr1|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
BnTR1|bntr1|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
BnTR1|bntr1|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
BnTR1|bntr1|NN|_ _|_|NN|_ 37|37|CD|_ _|_|CD|_ rep1|rep1|NN|_
BnTR1|bntr1|NN|_ _|_|NN|_ 37|37|CD|_ _|_|CD|_ rep2|rep2|NN|_
BnTR1|bntr1|NN|_ _|_|NN|_ 37|37|CD|_ _|_|CD|_ rep3|rep3|NN|_
BnTR1|bntr1|NN|_ ,|,|,|_ 42|42|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
BnTR1|bntr1|NN|_ ,|,|,|_ 42|42|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
BnTR1|bntr1|NN|_ ,|,|,|_ 42|42|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
BnTR1|bntr1|NN|_ _|_|CD|_ 42|42|CD|_ _|_|NN|_ rep1|rep1|NN|_
BnTR1|bntr1|NN|_ _|_|CD|_ 42|42|CD|_ _|_|NN|_ rep2|rep2|NN|_
BnTR1|bntr1|NN|_ _|_|CD|_ 42|42|CD|_ _|_|SYM|_ rep3|rep3|CD|_
Collected|collect|VBN|_ cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ phenol-chloroform|phenol-chloroform|JJ|_ and|and|CC|_ precipitated|precipitated|JJ|_ with|with|IN|_ ice|ice|NN|_ cold|cold|JJ|_ isopropanol|isopropanol|NN|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ precipitations|precipitation|NNS|_ were|be|VBD|_ further|further|JJ|_ washed|wash|VBN|_ with|with|IN|_ 70|70|CD|_ %|%|NN|_ ethanol|ethanol|NN|_ and|and|CC|_ dissolved|dissolve|VBN|_ in|in|IN|_ RNase-free|rnase-free|JJ|_ water|water|NN|_ .|.|.|_ Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ RNase-free|rnase-free|JJ|_ DNase|dnase|NN|_ I.|i.|NN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ further|further|JJ|_ purified|purify|VBN|_ using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kits|Kits|NNP|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ concentration|concentration|NN|_ and|and|CC|_ quality|quality|NN|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ A|a|DT|_ Nanodrop|nanodrop|JJ|_ ND|nd|NN|_ 1000|1000|CD|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ ,|,|,|_ Pittsburgh|Pittsburgh|NNP|_ ,|,|,|_ PA|pa|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ agarose|agarose|NN|_ gel|gel|NN|_ electrophoresis|electrophoresis|NN|_ .|.|.|_ The|the|DT|_ isolated|isolate|VBN|_ RNA|rna|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 80|80|CD|_ °C|°c|NN|_ before|before|IN|_ use|use|NN|_ .|.|.|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ 37|37|CD|_ °C|°c|NN|_
culture|culture|NN|_ temperature|temperature|NN|_ :|:|:|_ 42|42|CD|_ °C|°c|NN|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ with|with|IN|_ or|or|CC|_ without|without|IN|_ BnTR1|bntr1|NN|_ were|be|VBD|_ transferred|transfer|VBN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ and|and|CC|_ 42|42|CD|_ °C|°c|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ respectively|respectively|RB|_
E.|E.|NNP|_ coli|coli|NN|_ Rosetta|rosetta|NN|_ cells|cell|NNS|_ transformed|transform|VBN|_ with|with|IN|_ pET-28a|pet-28a|NN|_ or|or|CC|_ pET-28a-BnTR1|pet-28a-bntr1|NN|_ -LRB-|-lrb-|-LRB-|_ OD600nm|od600nm|NN|_ =|=|JJ|_ 0.6|0.6|CD|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP IPTG|iptg|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_
Emplty|Emplty|NNP|_ Vector|Vector|NNP|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
Emplty|Emplty|NNP|_ Vector|Vector|NNP|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
Emplty|Emplty|NNP|_ Vector|Vector|NNP|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
Emplty|Emplty|NNP|_ Vector|Vector|NNP|_ ,|,|,|_ 42|42|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 1|1|CD|_
Emplty|Emplty|NNP|_ Vector|Vector|NNP|_ ,|,|,|_ 42|42|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 2|2|CD|_
Emplty|Emplty|NNP|_ Vector|Vector|NNP|_ ,|,|,|_ 42|42|CD|_ °C|°c|NN|_ ,|,|,|_ replicate|replicate|VB|_ 3|3|CD|_
EmptyVector|EmptyVector|NNP|_ _|_|SYM|_ 37|37|CD|_ _|_|CD|_ rep1|rep1|NN|_
EmptyVector|EmptyVector|NNP|_ _|_|SYM|_ 37|37|CD|_ _|_|CD|_ rep2|rep2|NN|_
EmptyVector|EmptyVector|NNP|_ _|_|SYM|_ 37|37|CD|_ _|_|CD|_ rep3|rep3|NN|_
EmptyVector|EmptyVector|NNP|_ _|_|SYM|_ 42|42|CD|_ _|_|CD|_ rep1|rep1|NN|_
EmptyVector|EmptyVector|NNP|_ _|_|SYM|_ 42|42|CD|_ _|_|CD|_ rep2|rep2|NN|_
EmptyVector|EmptyVector|NNP|_ _|_|SYM|_ 42|42|CD|_ _|_|SYM|_ rep3|rep3|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Raw|raw|NN|_ data|datum|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ -LRB-|-lrb-|-LRB-|_ quantile|quantile|JJ|_ method|method|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ merged|merged|JJ|_ and|and|CC|_ filtered|filter|VBN|_ by|by|IN|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ the|the|DT|_ sibiling|sibiling|NN|_ probes|probe|NNS|_ -LRB-|-lrb-|-LRB-|_ multiple|multiple|JJ|_ probes|probe|NNS|_ to|to|TO|_ one|one|CD|_ gene|gene|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ we|we|PRP|_ used|use|VBD|_ the|the|DT|_ median|median|JJ|_ indensity|indensity|NN|_ for|for|IN|_ representation|representation|NN|_ .|.|.|_
vector|vector|NN|_ :|:|:|_ pET-28a|pet-28a|NN|_
vector|vector|NN|_ :|:|:|_ pET-28a-BnTR1|pet-28a-bntr1|NN|_
base|base|NN|_ calls|call|VBZ|_ with|with|IN|_ quality|quality|NN|_ metrics|metric|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ HiSeq|HiSeq|NNP|_ 2500|2500|CD|_ Control|Control|NNP|_ software|software|NN|_
cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|_ glucose|glucose|NN|SUPP -LRB-|-lrb-|-LRB-|_ 0.4|0.4|CD|_ %|%|NN|_ w|w|NN|_
∆|∆|CD|_ dapF|dapf|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 28|28|CD|_
∆|∆|CD|_ dapF|dapf|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 47|47|CD|_
∆|∆|CD|_ dapF|dapf|NN|GEN parent|parent|NN|_ Sample|Sample|NNP|_ 9|9|CD|_
dapF|dapf|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 10|10|CD|_
dapF|dapf|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 29|29|CD|_
dapF|dapf|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 48|48|CD|_
dapF|dapf|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|Sample|NNP|_ 11|11|CD|_
dapF|dapf|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|Sample|NNP|_ 30|30|CD|_
dapF|dapf|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 49|49|CD|_
∆|∆|CD|_ dgk|dgk|NN|_ parent|parent|NN|_ Sample|sample|NN|_ 16|16|CD|_
∆|∆|CD|_ dgk|dgk|NN|_ parent|parent|NN|_ Sample|sample|NN|_ 35|35|CD|_
∆|∆|CD|_ dgk|dgk|NN|_ parent|parent|NN|_ Sample|sample|NN|_ 54|54|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 17|17|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 36|36|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 55|55|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 18|18|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 37|37|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 56|56|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 19|19|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 38|38|CD|_
dgk|dgk|NN|_ suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 57|57|CD|_
∆|∆|CD|_ entC|entc|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 12|12|CD|_
∆|∆|CD|_ entC|entc|NN|GEN parent|parent|NN|_ Sample|Sample|NNP|_ 31|31|CD|_
∆|∆|CD|_ entC|entc|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 50|50|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|Sample|NNP|_ 13|13|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 32|32|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 51|51|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 14|14|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 33|33|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 52|52|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|Sample|NNP|_ 15|15|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 34|34|CD|_
entC|entc|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|Sample|NNP|_ 53|53|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism cell|cell|NN|_ lysate|lysate|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ BW25113|bw25113|NN|_
library|library|NN|_ construction|construction|NN|_ followed|follow|VBD|_ Illumina|Illumina|NNP|_ manufacturer|manufacturer|NN|_ protocol|protocol|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ using|use|VBG|_ the|the|DT|_ Nextera|Nextera|NNP|_ XT|XT|NNP|_ DNA|DNA|NNP|_ Library|Library|NNP|_ Preparation|Preparation|NNP|_ Kit|kit|NN|_
∆|∆|CD|_ ppk|ppk|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 24|24|CD|_
∆|∆|CD|_ ppk|ppk|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 43|43|CD|_
∆|∆|CD|_ ppk|ppk|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 5|5|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 25|25|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 44|44|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 6|6|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 26|26|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 45|45|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 2-1|2-1|CD|_ Sample|sample|NN|_ 7|7|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 27|27|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 46|46|CD|_
ppk|ppk|NN|GEN suppressor|suppressor|NN|_ 3-1|3-1|CD|_ Sample|sample|NN|_ 8|8|CD|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Trizol|trizol|NN|_ lysis|lysis|NN|_ and|and|CC|_ aqueous|aqueous|JJ|_ extraction|extraction|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ further|further|JJ|_ purification|purification|NN|_ using|use|VBG|_ a|a|DT|_ Qiagen|Qiagen|NNP|_ RNAeasy|RNAeasy|NNP|_ kit|kit|NN|_ .|.|.|_
sequences|sequence|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ parent|parent|NN|_ E.|e.|FW|_ coli|coli|FW|_ strain|strain|NN|_ genome|genome|NN|_ template|template|NN|_ and|and|CC|_ transcript|transcript|NN|_ levels|level|NNS|_ were|be|VBD|_ quantified|quantify|VBN|_ for|for|IN|_ triplicate|triplicate|NN|_ groups|group|NNS|_ of|of|IN|_ each|each|DT|_ primary|primary|JJ|_ deletion|deletion|NN|_ strain|strain|NN|_ and|and|CC|_ synthetic|synthetic|JJ|_ rescue|rescue|NN|_ -LRB-|-lrb-|-LRB-|_ i.e.|i.e.|FW|_ sup|sup|FW|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.3|2.0.3|CD|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
transcript|transcript|NN|_ abundance|abundance|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ rockhopper|rockhopper|NN|_
WT|wt|SYM|_ -|-|:|_ Keio|Keio|NNP|_ Sample|Sample|NNP|_ 1|1|CD|_
WT|wt|SYM|_ -|-|:|_ Keio|Keio|NNP|_ Sample|Sample|NNP|_ 20|20|CD|_
WT|wt|SYM|_ -|-|:|_ Keio|Keio|NNP|_ Sample|Sample|NNP|_ 39|39|CD|_
∆|∆|CD|_ zwf|zwf|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 2|2|CD|_
∆|∆|CD|_ zwf|zwf|NN|GEN parent|parent|NN|_ Sample|sample|NN|_ 21|21|CD|_
∆|∆|CD|_ zwf|zwf|NN|GEN parent|parent|NN|_ Sample|Sample|NNP|_ 40|40|CD|_
zwf|zwf|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 22|22|CD|_
zwf|zwf|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 3|3|CD|_
zwf|zwf|NN|GEN suppressor|suppressor|NN|_ 1-1|1-1|CD|_ Sample|sample|NN|_ 41|41|CD|_
zwf|zwf|NN|GEN suppressor|suppressor|NN|_ 1-2|1-2|CD|_ Sample|sample|NN|_ 23|23|CD|_
zwf|zwf|NN|GEN suppressor|suppressor|NN|_ 1-2|1-2|CD|_ Sample|sample|NN|_ 4|4|CD|_
zwf|zwf|NN|GEN suppressor|suppressor|NN|_ 1-2|1-2|CD|_ Sample|sample|NN|_ 42|42|CD|_
conducted|conduct|VBN|_ by|by|IN|_ CeGaT|cegat|NN|_ -LRB-|-lrb-|-LRB-|_ Tübingen|tübingen|NN|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ SOLiD|solid|JJ|_ standard|standard|JJ|_ protocols|protocol|NNS|_ for|for|IN|_ RNA-seq|rna-seq|JJ|_
conversion|conversion|NN|_ :|:|:|_ Convert|convert|VB|_ SOLiD|solid|JJ|_ output|output|NN|_ to|to|TO|_ fastq|fastq|NN|_ -LRB-|-lrb-|-LRB-|_ Galaxy|galaxy|NN|_ Version|version|NN|_ 1.0.0|1.0.0|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_
counting|counting|NN|_ :|:|:|_ countOverlaps|countoverlap|NNS|_ of|of|IN|_ Iranges|irange|NNS|_ ;|;|:|_ default|default|NN|_ parameters|parameter|NNS|_
culture|culture|NN|_ :|:|:|_ 18|18|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_
differential|differential|JJ|_ expression|expression|NN|_ :|:|:|_ Bioconductor|Bioconductor|NNP|_ package|package|NN|_ edgeR|edger|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.2.3|3.2.3|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ default|default|NN|_ parameters|parameter|NNS|_
EHEC|ehec|NN|_
EHEC|ehec|NN|_ either|either|CC|_ grown|grow|VBN|_ on|on|IN|_ plain|plain|JJ|_ LB|lb|NN|_ plates|plate|NNS|_ or|or|CC|_ LB|lb|NN|_ plates|plate|NNS|_ containing|contain|VBG|_ Symbioflor|symbioflor|NN|_ within|within|IN|_ the|the|DT|_ agar|agar|NN|_
EHEC|ehec|NN|_ plus|plus|CC|_ Symbioflor|Symbioflor|NNP|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655|002655|CD|_
LB|LB|NNP|_ agar|agar|NN|_ plates|plate|NNS|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 18|18|CD|_ h|h|NN|_
mapping|mapping|NN|_ :|:|:|_ bowtie|bowtie|NN|_ -LRB-|-lrb-|-LRB-|_ Galaxy|galaxy|NN|_ Version|version|NN|_ 1.1.2|1.1.2|CD|_ -RRB-|-rrb-|-RRB-|_ ;|;|:|_ 28|28|CD|_ nt|nt|NNS|_ seed|seed|NN|_ length|length|NN|_ ,|,|,|_ maximal|maximal|JJ|_ two|two|CD|_ mismatches|mismatch|NNS|_ in|in|IN|_ the|the|DT|_ seed|seed|NN|_ ,|,|,|_ a|a|DT|_ maximal|maximal|JJ|_ threshold|threshold|NN|_ of|of|IN|_ 70|70|CD|_ for|for|IN|_ the|the|DT|_ sum|sum|NN|_ of|of|IN|_ the|the|DT|_ quality|quality|NN|_ values|value|NNS|_ at|at|IN|_ mismatched|mismatched|JJ|_ positions|position|NNS|_ .|.|.|_
medium|medium|NN|_ :|:|:|_ LB|lb|NN|_
normalizing|normalizing|NN|_ :|:|:|_ convert|convert|VB|_ counts|count|NNS|_ in|in|IN|_ RPKM|rpkm|NN|_ using|use|VBG|_ Excel|Excel|NNP|_
plus|plus|CC|_ Symbioflor|Symbioflor|NNP|_
RNA-Seq|rna-seq|NN|_
scraping|scrape|VBG|_ bacteria|bacterium|NNS|_ ,|,|,|_ opening|open|VBG|_ with|with|IN|_ bead|bead|NN|_ beating|beating|NN|_ ,|,|,|_ Trizol-based|trizol-based|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depletion|depletion|NN|_ with|with|IN|_ RiboZero|RiboZero|NNP|_ ,|,|,|_ DNA|DNA|NNP|_ digest|digest|VB|_ ,|,|,|_ SoLiD|solid|JJ|_ seq|seq|NN|_ by|by|IN|_ CeGaT|cegat|NN|_ -LRB-|-lrb-|-LRB-|_ Tübingen|tübingen|NN|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ :|:|:|_ logFC|logfc|NN|_ and|and|CC|_ p-value|p-value|JJ|_
symbioflor|symbioflor|NN|_ status|status|NN|_ :|:|:|_ without|without|IN|_ Symbioflor|Symbioflor|NNP|_
symbioflor|symbioflor|NN|_ status|status|NN|_ :|:|:|_ with|with|IN|_ Symbioflor|Symbioflor|NNP|_
without|without|IN|_ Symbioflor|Symbioflor|NNP|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ G|g|NN|_ 1|1|CD|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ G|g|NN|_ 3|3|CD|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ G|g|NN|_ 4|4|CD|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ G5|g5|NN|_ isolate|isolate|NN|_ with|with|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ G5|g5|NN|_ isolate|isolate|NN|_ with|with|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ isolate|isolate|NN|_ G|g|NN|_ 3|3|CD|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ isolate|isolate|NN|_ G|g|NN|_ 4|4|CD|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ with|with|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ M1655|m1655|NN|_ #|#|#|_ 1|1|CD|_
Co-hybridization|co-hybridization|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ with|with|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ M1655|m1655|NN|_ #|#|#|_ 2|2|CD|_
control|control|NN|_ strain|strain|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
control|control|NN|_ strain|strain|NN|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_
E.|e.|FW|_ coli|coli|FW|_ G|g|NN|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ G4|g4|NN|_
E.|e.|FW|_ coli|coli|FW|_ G5|g5|NN|_
E.|e.|FW|_ coli|coli|FW|_ isolate|isolate|NN|_ G|g|NN|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ isolate|isolate|NN|_ G3|g3|NN|_
E.|E.|NNP|_ coli|coli|NN|_ isolate|isolate|NN|_ G|g|NN|_ 3|3|CD|_
E.|E.|NNP|_ coli|coli|NN|_ isolate|isolate|NN|_ G4|g4|NN|_
E.|E.|NNP|_ coli|coli|NN|_ isolate|isolate|NN|_ G5|g5|NN|_
E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
E.|e.|FW|_ coli|coli|FW|_ O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ DNA|dna|NN|_ isolation|isolation|NN|_ according|accord|VBG|_ to|to|TO|_ Grimberg|Grimberg|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nucleic|nucleic|JJ|_ acids|acid|NNS|_ research|research|NN|_ 1989|1989|CD|_ ,|,|,|_ 17|17|CD|_ -LRB-|-lrb-|-LRB-|_ 21|21|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 8893|8893|CD|_
Isolate|isolate|VB|_ G|g|NN|_ 1|1|CD|_
Isolate|isolate|VB|_ G|g|NN|_ 3|3|CD|_
Isolate|isolate|VB|_ G|g|NN|_ 4|4|CD|_
Isolate|isolate|VB|_ G5|g5|NN|_ of|of|IN|_ Symbioflor2|symbioflor2|NN|_ probiotic|probiotic|JJ|_ product|product|NN|_ from|from|IN|_ Symbiopharm|Symbiopharm|NNP|_
log2|log2|NN|_ ratio|ratio|NN|_ of|of|IN|_ isolate|isolate|JJ|_
overnight|overnight|JJ|_ in|in|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ with|with|IN|_ continuous|continuous|JJ|_ agitation|agitation|NN|_
overnight|overnight|JJ|_ in|in|IN|_ Lurie-Bertani|Lurie-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ with|with|IN|_ continuous|continuous|JJ|_ agitation|agitation|NN|_
Agilent|Agilent|NNP|_ Feature|Feature|NNP|_ Extraction|Extraction|NNP|_ Software|Software|NNP|_ -LRB-|-lrb-|-LRB-|_ v|v|LS|_ 8.5.1.1|8.5.1.1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ background|background|NN|_ subtraction|subtraction|NN|_ and|and|CC|_ LOWESS|lowess|NN|_ normalization|normalization|NN|_ .|.|.|_
Biological|Biological|NNP|_ replicates|replicate|VBZ|_ per|per|IN|_ genotype|genotype|NN|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 1|1|CD|_ mg|mg|NN|_
E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 25922|25922|CD|_ marR|marr|NN|GEN deletion|deletion|NN|_ +|+|CC|_ QnrS|qnrs|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ATCC|atcc|NN|_ 25922|25922|CD|_ marR|marr|NN|GEN deletion|deletion|NN|_ +|+|CC|_ QnrS|qnrs|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ATCC|atcc|NN|_ 25922|25922|CD|_ QnrS|qnrs|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ATCC|atcc|NN|_ 25922|25922|CD|_ QnrS|qnrs|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ATCC|atcc|NN|_ 25922|25922|CD|_ Ser83Leu|ser83leu|NN|_ +|+|CC|_ QnrS|qnrs|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ATCC|atcc|NN|_ 25922|25922|CD|_ Ser83Leu|ser83leu|NN|_ +|+|CC|_ QnrS|qnrs|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
E.|E.|NNP|_ coli|coli|NN|_ ATCC|atcc|NN|_ 25922|25922|CD|_ -LRB-|-lrb-|-LRB-|_ wild-type|wild-type|JJ|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ EC14|ec14|NN|_ ,|,|,|_ EC19|ec19|NN|_ ,|,|,|_ EC24|ec24|NN|_ -LRB-|-lrb-|-LRB-|_ LLQR|llqr|NN|_ -RRB-|-rrb-|-RRB-|_ isogenic|isogenic|JJ|_ strains|strain|NNS|_ were|be|VBD|_ tested|test|VBN|_ to|to|TO|_ evaluate|evaluate|VB|_ the|the|DT|_ global|global|JJ|_ response|response|NN|_ to|to|TO|_ relevant|relevant|JJ|_ fix|fix|NN|_ concentration|concentration|NN|_ of|of|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 1|1|CD|_ mg|mg|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism ATCC|atcc|NN|_ 25922|25922|CD|_
Exponential|exponential|JJ|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ DO600|do600|NN|_ =|=|JJ|_ 0,4|0,4|CD|_ -RRB-|-rrb-|-RRB-|_
genotype|genotype|NN|_
RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
substrain|substrain|NN|_ :|:|:|_ ATCC|atcc|NN|_ 25922|25922|CD|_
substrain|substrain|NN|_ :|:|:|_ EC14|ec14|NN|_
substrain|substrain|NN|_ :|:|:|_ EC19|ec19|NN|_
substrain|substrain|NN|_ :|:|:|_ EC24|ec24|NN|_
Wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 25922|25922|CD|_ replicate|replicate|VBP|_ 1|1|CD|_
Wild-type|wild-type|JJ|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 25922|25922|CD|_ replicate|replicate|VBP|_ 2|2|CD|_
Bacterial|bacterial|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ samples|sample|NNS|_ with|with|IN|_ RNA|rna|NN|_ Integrity|integrity|NN|_ Number|number|NN|_ -LRB-|-lrb-|-LRB-|_ RIN|rin|NN|_ -RRB-|-rrb-|-RRB-|_ >|>|JJR|_ 9|9|CD|_ were|be|VBD|_ used|use|VBN|_ for|for|IN|_ labeling|label|VBG|_
culture|culture|NN|_ media|media|NNS|_ :|:|:|_ LB|lb|NN|_
culture|culture|NN|_ media|media|NNS|_ :|:|:|_ LB|lb|NN|_ with|with|IN|_ 2.5|2.5|CD|_ mM|mm|NN|KWSUPP Fumaric|fumaric|JJ|_ acid|acid|NN|_
EDL933|edl933|NN|_ _|_|CD|_ LB|lb|NN|_ _|_|NN|_ I|I|PRP|_
EDL933|edl933|NN|_ _|_|CD|_ LB|lb|NN|_ _|_|NN|_ II|ii|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_
GeneSpring|genespr|VBG|_ GX|GX|NNP|_ v.|v.|CC|_ 13.1|13.1|CD|_
genotype|genotype|NN|_
O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ in|in|IN|_ LB|LB|NNP|_
O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ sdhA|sdha|NN|GEN in|in|IN|_ LB|LB|NNP|_
O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ EDL933|edl933|NN|_ sdhA|sdha|NN|GEN in|in|IN|_ LB|lb|NN|_ with|with|IN|_ FA|fa|NN|_
sdhA|sdha|NN|GEN _|_|CD|_ FA|FA|NNP|_ _|_|SYM|_ I|I|PRP|_
sdhA|sdha|NN|GEN _|_|CD|_ FA|FA|NNP|_ _|_|NNP|_ II|II|NNP|_
sdhA|sdhA|NNP|GEN _|_|NNP|_ FA|FA|NNP|_ _|_|VBD|_ III|iii|CD|_
sdhA|sdha|NN|GEN _|_|CD|_ LB|lb|NN|_ _|_|NN|_ I|I|PRP|_
sdhA|sdha|NN|GEN _|_|CD|_ LB|lb|NN|_ _|_|NN|_ II|ii|CD|_
sdhA|sdha|NN|GEN _|_|CD|_ LB|lb|NN|_ _|_|NN|_ III|iii|CD|_
strain|strain|NN|_ background|background|NN|_ :|:|:|_ EDL933|edl933|NN|_
The|the|DT|_ overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ bacteria|bacterium|NNS|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED were|be|VBD|_ refreshed|refresh|VBN|_ with|with|IN|_ the|the|DT|_ ratio|ratio|NN|_ of|of|IN|_ 1:100|1:100|CD|_ into|into|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED broth|broth|NN|MED ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 30|30|CD|_ ℃|℃|NN|_ with|with|IN|_ continuous|continuous|JJ|_ shaking|shake|VBG|_ until|until|IN|_ the|the|DT|_ absorbance|absorbance|NN|_ at|at|IN|_ 590|590|CD|_ nm|nm|NN|_ reached|reach|VBD|_ 0.5|0.5|CD|_ to|to|TO|_ 0.6|0.6|CD|_ .|.|.|_
The|the|DT|_ values|value|NNS|_ below|below|IN|_ 0.01|0.01|CD|_ were|be|VBD|_ set|set|VBN|_ to|to|TO|_ 0.01|0.01|CD|_ .|.|.|_ The|the|DT|_ log2|log2|NN|_ ratio|ratio|NN|_ of|of|IN|_ the|the|DT|_ intensity|intensity|NN|_ of|of|IN|_ signal|signal|NN|_ channel|channel|NN|_ to|to|TO|_ that|that|DT|_ of|of|IN|_ control|control|NN|_ channel|channel|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ and|and|CC|_ was|be|VBD|_ then|then|RB|_ normalized|normalize|VBN|_ to|to|TO|_ each|each|DT|_ slide|slide|NN|_ 's|'s|POS|_ median|median|JJ|_ intensity|intensity|NN|_ ratio|ratio|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ interpretation|interpretation|NN|_ mode|mode|NN|_ was|be|VBD|_ set|set|VBN|_ to|to|TO|_ `|`|``|_ log|log|NN|_ of|of|IN|_ ratio|ratio|NN|_ '|'|''|_ .|.|.|_ Each|each|DT|_ time|time|NN|_ point|point|NN|_ was|be|VBD|_ then|then|RB|_ tested|test|VBN|_ separately|separately|RB|_ for|for|IN|_ statistical|statistical|JJ|_ differences|difference|NNS|_ using|use|VBG|_ ANOVA|ANOVA|NNP|_ at|at|IN|_ 5|5|CD|_ %|%|NN|_ confidence|confidence|NN|_ level|level|NN|_ ,|,|,|_ in|in|IN|_ conjunction|conjunction|NN|_ with|with|IN|_ Benjamini-Hochberg|Benjamini-Hochberg|NNP|_ multiple|multiple|JJ|_ testing|testing|NN|_ correction|correction|NN|_ .|.|.|_
with|with|IN|_
10J|10j|NN|_ .0|.0|CD|_
11K|11k|CD|_ .60|.60|CD|_
12L|12l|NN|_ .120|.120|CD|_
200|200|CD|_ bp|bp|NN|_ insert|insert|NN|_ ,|,|,|_ rRNA|rrna|NN|_ depletion|depletion|NN|_
7G|7g|NN|_ .0|.0|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ Replicate|replicate|VB|_ 1|1|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ Replicate|replicate|NN|_ 1|1|CD|_
biological|biological|JJ|_ replicate|replicate|VB|_ :|:|:|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_ replicate|replicate|VBP|_ 2|2|CD|_
Dividing|divide|VBG|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_ hours|hour|NNS|_
E.|E.|NNP|_ coli|coli|NNS|_ were|be|VBD|_ sampled|sample|VBN|_ at|at|IN|_ times|time|NNS|_ =|=|JJ|_ 0|0|CD|_ ,|,|,|_ 1|1|CD|_ hour|hour|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ hours|hour|NNS|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ NC|nc|NN|_ _|_|CD|_ 00091313-Feb-2011|00091313-feb-2011|NN|_
Growing|grow|VBG|_ t|t|NN|_ =|=|JJ|_ 1|1|CD|_ hour|hour|NN|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ quality|quality|JJ|_ assessed|assess|VBN|_ and|and|CC|_ trimmed|trim|VBN|_ using|use|VBG|_ FastQC|fastqc|NN|_ version|version|NN|_ 0.10.1|0.10.1|NN|_ -LRB-|-lrb-|-LRB-|_ www.bioinformatics.babraham.ac.uk|www.bioinformatics.babraham.ac.uk|JJ|_
RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ mL|ml|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ each|each|DT|_ bacterial|bacterial|JJ|_ culture|culture|NN|_ isolated|isolate|VBN|_ at|at|IN|_ each|each|DT|_ time|time|NN|_ point|point|NN|_ .|.|.|_ The|the|DT|_ 30|30|CD|_ mL|ml|NN|_ culture|culture|NN|_ was|be|VBD|_ aliquoted|aliquote|VBN|_ into|into|IN|_ three|three|CD|_ 15|15|CD|_ mL|ml|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ EtOH|etoh|NN|_
RNA|rna|NN|_ was|be|VBD|_ pelleted|pelleted|JJ|_ -LRB-|-lrb-|-LRB-|_ 14,000|14,000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ air|air|NN|_ dried|dry|VBD|_ before|before|IN|_ suspension|suspension|NN|_ in|in|IN|_ 80|80|CD|_ µL|µl|NN|_ RNAse|rnase|NN|_ free|free|JJ|_ water|water|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ 10|10|CD|_ X|x|NN|_ Turbo|Turbo|NNP|_ DNAse|dnase|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ RNA|rna|NN|_ solution|solution|NN|_ .|.|.|_ 1|1|CD|_ µL|µl|NN|_ of|of|IN|_ TURBO|TURBO|NNP|_ DNAse|dnase|NN|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ solution|solution|NN|_ ,|,|,|_ which|which|WDT|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 30|30|CD|_ min|min|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Following|follow|VBG|_ incubation|incubation|NN|_ ,|,|,|_ 0.1|0.1|CD|_ V|v|NN|_ of|of|IN|_ DNase|dnase|NN|_ Inactivation|inactivation|NN|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ then|then|RB|_ incubated|incubate|VBN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ RT|rt|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ occasional|occasional|JJ|_ mixing|mix|VBG|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ transferred|transfer|VBN|_ into|into|IN|_ a|a|DT|_ fresh|fresh|JJ|_ microfuge|microfuge|NN|_ tube|tube|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ tested|test|VBN|_ using|use|VBG|_ the|the|DT|_ the|the|DT|_ Agilent|Agilent|NNP|_ RNA|rna|NN|_ 6000|6000|CD|_ Nano|Nano|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ analysed|analyse|VBN|_ using|use|VBG|_ the|the|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
Synchronization|synchronization|NN|_ was|be|VBD|_ achieved|achieve|VBN|_ by|by|IN|_ passaging|passaging|NN|_ cells|cell|NNS|_ through|through|IN|_ one|one|CD|_ or|or|CC|_ two|two|CD|_ rounds|round|NNS|_ of|of|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase according|accord|VBG|_ to|to|TO|_ Cutler|Cutler|NNP|_ and|and|CC|_ Evans|Evans|NNP|_ 1966|1966|CD|_ .|.|.|_ Briefly|briefly|RB|_ :|:|:|_ Individual|individual|JJ|_ colonies|colony|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|_ plate|plate|NN|_ ,|,|,|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 24|24|CD|_ h|h|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ M9|m9|NN|_ media|media|NNS|_ and|and|CC|_ grown|grow|VBN|_ O|o|NN|_
time|time|NN|_ post|post|NN|_ release|release|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ 1|1|CD|_ hour|hour|NN|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ Stationary|stationary|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ post|post|NN|_ release|release|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ 2|2|CD|_ hour2|hour2|NN|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ Stationary|stationary|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ t|t|NN|_ =|=|JJ|_ 2|2|CD|_ -RRB-|-rrb-|-RRB-|_
time|time|NN|_ post|post|NN|_ release|release|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ cells|cell|NNS|_ immediately|immediately|RB|_ following|follow|VBG|_ release|release|NN|_ from|from|IN|_ Stationary|stationary|JJ|_ phase|phase|NN|_ t|t|NN|_ =|=|JJ|_ 0|0|CD|_
BW25113|bw25113|NN|_ hha|hha|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_ LB|lb|NN|_ 4|4|CD|_ hr|hr|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
BW25113|bw25113|NN|_ hha|hha|NN|GEN mutant|mutant|JJ|_ LB|lb|NN|_ glu|glu|NN|_ 15|15|CD|_ hr|hr|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
BW25113|bw25113|NN|_ hha|hha|NN|GEN mutant|mutant|JJ|_ LB|lb|NN|_ glu|glu|NN|_ 24|24|CD|_ hr|hr|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
BW25113|bw25113|NN|_ hha|hha|NN|GEN mutant|mutant|JJ|_ LB|lb|NN|_ glu|glu|NN|_ 4|4|CD|_ hr|hr|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_
BW25113|bw25113|NN|_ w|w|NN|_
Channel|Channel|NNP|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|set|VBG|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ hha|hha|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 15|15|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|LB|NNP|_ glu|glu|NN|_ with|with|IN|_ glasswool|glasswool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ hha|hha|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 24|24|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|LB|NNP|_ glu|glu|NN|_ with|with|IN|_ glasswool|glasswool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ hha|hha|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 4|4|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|LB|NNP|_ glu|glu|NN|_ with|with|IN|_ glasswool|glasswool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ hha|hha|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 4|4|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 15|15|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|LB|NNP|_ glu|glu|NN|_ with|with|IN|_ glasswool|glasswool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 24|24|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|LB|NNP|_ glu|glu|NN|_ with|with|IN|_ glasswool|glasswool|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 4|4|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|LB|NNP|_ glu|glu|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ wild|wild|JJ|_ type|type|NN|_ after|after|IN|_ 4|4|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ at|at|IN|_ 37C|37c|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|_ glu|glu|NN|_ medium|medium|NN|_ with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 15|15|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|_ glu|glu|NN|_ medium|medium|NN|_ with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 15|15|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
``|``|``|_ The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 15|15|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 15|15|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
75th|75th|JJ|_ percentile|percentile|NN|_ shift|shift|NN|_ normalisation|normalisation|NN|_ and|and|CC|_ baseline|baseline|NN|_ adjusted|adjusted|JJ|_
agent|agent|NN|_ :|:|:|_ 1x|1x|NN|_ CORM2|corm2|NN|_
agent|agent|NN|_ :|:|:|_ 1x|1x|NN|_ vehicle|vehicle|NN|_
agent|agent|NN|_ :|:|:|_ 20x|20x|CD|_ CORM2|corm2|NN|_
agent|agent|NN|_ :|:|:|_ 20x|20x|CD|_ vehicle|vehicle|NN|_
Cultures|culture|NNS|_ were|be|VBD|_ maintained|maintain|VBN|_ on|on|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ TSA|tsa|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Becton|Becton|NNP|_ Dickinson|Dickinson|NNP|_ ,|,|,|_ Le|Le|NNP|_ Pont|Pont|NNP|_ Claix|Claix|NNP|_ ,|,|,|_ France|France|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Difco|Difco|NNP|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ broth|broth|NN|_ -LRB-|-lrb-|-LRB-|_ Lennox|lennox|NN|_ ;|;|:|_ Franklin|Franklin|NNP|_ Lakes|Lakes|NNP|_ ,|,|,|_ NJ|NJ|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ aerobically|aerobically|RB|_ on|on|IN|_ a|a|DT|_ shaker|shaker|NN|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ Bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ picked|pick|VBN|_ from|from|IN|_ 5-10|5-10|CD|_ colonies|colony|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ suspended|suspend|VBN|_ in|in|IN|_ 1|1|CD|_ ml|ml|NN|_ of|of|IN|_ PBS|PBS|NNP|_ ,|,|,|_ yielding|yield|VBG|_ a|a|DT|_ suspension|suspension|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ turbidity|turbidity|NN|_ of|of|IN|_ McFarland|McFarland|NNP|_ 0.5|0.5|CD|_ ,|,|,|_ and|and|CC|_ diluted|dilute|VBN|_ 1:100|1:100|CD|_ in|in|IN|_ minimal|minimal|JJ|_ salt|salt|NN|_ -LRB-|-lrb-|-LRB-|_ MS|ms|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 106|106|CD|_ CFU|CFU|NNP|_
E.coli-1x|e.coli-1x|NN|_ CORM2-rep1|corm2-rep1|NN|_
E.coli-1x|e.coli-1x|NN|_ CORM2-rep2|corm2-rep2|NN|_
E.coli-1x|e.coli-1x|NN|_ CORM2-rep3|corm2-rep3|NN|_
E.coli-1x|e.coli-1x|NN|_ CORM2-rep4|corm2-rep4|NN|_
E.coli-1x|e.coli-1x|NN|_ vehicle-rep1|vehicle-rep1|NN|_
E.coli-1x|e.coli-1x|NN|_ vehicle-rep2|vehicle-rep2|NN|_
E.coli-1x|e.coli-1x|NN|_ vehicle-rep3|vehicle-rep3|NN|_
E.coli-1x|e.coli-1x|NN|_ vehicle-rep4|vehicle-rep4|NN|_
E.coli-20x|e.coli-20x|NN|_ CORM2-rep1|corm2-rep1|NN|_
E.coli-20x|e.coli-20x|NN|_ CORM2-rep2|corm2-rep2|NN|_
E.coli-20x|e.coli-20x|NN|_ CORM2-rep3|corm2-rep3|NN|_
E.coli-20x|e.coli-20x|NN|_ CORM2-rep4|corm2-rep4|NN|_
E.coli-20x|e.coli-20x|NN|_ vehicle-rep1|vehicle-rep1|NN|_
E.coli-20x|e.coli-20x|NN|_ vehicle-rep2|vehicle-rep2|NN|_
E.coli-20x|e.coli-20x|NN|_ vehicle-rep3|vehicle-rep3|NN|_
E.coli-20x|e.coli-20x|NN|_ vehicle-rep4|vehicle-rep4|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Overnight|overnight|JJ|_ cultures|culture|NNS|_ of|of|IN|_ ESBL7|esbl7|NN|_ from|from|IN|_ the|the|DT|_ original|original|JJ|_ isolate|isolate|NN|_ ,|,|,|_ or|or|CC|_ isolates|isolate|NNS|_ pre-exposed|pre-expose|VBN|_ 20|20|CD|_ times|time|NNS|_ to|to|TO|_ CORM-2|corm-2|NN|_ or|or|CC|_ vehicle|vehicle|NN|_ ,|,|,|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ MS-medium|ms-medium|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ OD620|od620|NN|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.1|0.1|CD|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ exposure|exposure|NN|_ to|to|TO|_ CORM-2|corm-2|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ µM|µm|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ vehicle|vehicle|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_
RNA|rna|NN|_ isolation|isolation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ DNA|dna|NN|_ decontamination|decontamination|NN|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ quantity|quantity|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ a|a|DT|_ spectrophotometer|spectrophotometer|NN|_ Nanodrop-1000|nanodrop-1000|NN|_ -LRB-|-lrb-|-LRB-|_ Nanodrop|Nanodrop|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ measuring|measure|VBG|_ the|the|DT|_ absorbance|absorbance|NN|_ -LRB-|-lrb-|-LRB-|_ A260|a260|NN|_ ,|,|,|_ 230|230|CD|_ ,|,|,|_ 280|280|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ calculating|calculate|VBG|_ absorbance|absorbance|NN|_ ratios|ratio|NNS|_ -LRB-|-lrb-|-LRB-|_ A260|a260|NN|_
0|0|CD|_ %|%|NN|_ rep1|rep1|NN|_
0|0|CD|_ %|%|NN|_ rep2|rep2|NN|_
100|100|CD|_ %|%|NN|_ rep1|rep1|NN|_
100|100|CD|_ %|%|NN|_ rep2|rep2|NN|_
26|26|CD|_ %|%|NN|_ rep1|rep1|NN|_
26|26|CD|_ %|%|NN|_ rep2|rep2|NN|_
Base|base|NN|_ calls|call|VBZ|_ performed|perform|VBN|_ with|with|IN|_ RTA|rta|NN|_ v1|v1|NN|_ .18.5|.18.5|CD|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ frozen|frozen|JJ|_ cultures|culture|NNS|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ .|.|.|_ 5|5|CD|_ µL|µl|NN|_ of|of|IN|_ this|this|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ was|be|VBD|_ diluted|dilute|VBN|_ into|into|IN|_ 5|5|CD|_ mL|ml|NN|_ of|of|IN|_ LB|lb|NN|_ with|with|IN|_ the|the|DT|_ appropriate|appropriate|JJ|_ concentration|concentration|NN|_ of|of|IN|_ arabinose|arabinose|NN|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 20h|20h|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ culture|culture|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ using|use|VBG|_ BWA|BWA|NNP|_ 0.7.5|0.7.5|CD|_ a|a|DT|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ 200|200|CD|_ µL|µl|NN|_ of|of|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ by|by|IN|_ pelleting|pelleting|NN|_ and|and|CC|_ resuspeding|resuspeding|NN|_ in|in|IN|_ 500|500|CD|_ µL|µl|NN|_ of|of|IN|_ Trizol|trizol|NN|_ at|at|IN|_ 65|65|CD|_ °C|°c|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ Direct-Zol|Direct-Zol|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Samples|sample|NNS|_ received|receive|VBD|_ two|two|CD|_ 30-minute|30-minute|JJ|_ DNase|dnase|NN|_ treatments|treatment|NNS|_ using|use|VBG|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ then|then|RB|_ purified|purify|VBN|_ on|on|IN|_ a|a|DT|_ column|column|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ,|,|,|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Three|three|CD|_ samples|sample|NNS|_ were|be|VBD|_ prepped|prep|VBN|_ from|from|IN|_ each|each|DT|_ culture|culture|NN|_ and|and|CC|_ pooled|pool|VBD|_ to|to|TO|_ generate|generate|VB|_ sufficient|sufficient|JJ|_ RNA|rna|NN|_ .|.|.|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 0|0|CD|_ %|%|NN|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 100|100|CD|_ %|%|NN|_
rpos|rpo|NNS|_ level|level|NN|_ :|:|:|_ 26|26|CD|_ %|%|NN|_
strain|strain|NN|_ :|:|:|_ BW27786|bw27786|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ DMS2545|dms2545|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ DMS2564|dms2564|NN|_ -LRB-|-lrb-|-LRB-|_ K-12|k-12|NN|_ derivative|derivative|NN|_ -RRB-|-rrb-|-RRB-|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ A|a|DT|_ tab|tab|NN|_ deliminited|deliminit|VBN|_ file|file|NN|_ with|with|IN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ .|.|.|_
the|the|DT|_ first|first|JJ|_ ten|ten|CD|_ base|base|NN|_ pairs|pair|NNS|_ of|of|IN|_ each|each|DT|_ read|read|NN|_ were|be|VBD|_ trimmed|trim|VBN|_ using|use|VBG|_ FASTXToolkit|fastxtoolkit|NN|_ 0.0.13|0.0.13|CD|_ .|.|.|_
The|the|DT|_ number|number|NN|_ read|read|VBD|_ pairs|pair|NNS|_ mapped|map|VBN|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ with|with|IN|_ HTSeq|htseq|NN|_ 0.6.1|0.6.1|CD|_
7|7|CD|_ min|min|NN|_ Nov0|nov0|NN|_ ug|ug|NN|_
7|7|CD|_ min|min|NN|_ Nov500|nov500|NN|_ ug|ug|NN|_
80|80|CD|_ min|min|NN|_ Nov10|nov10|NN|_ ug|ug|NN|_
80|80|CD|_ min|min|NN|_ Nov5|nov5|NN|_ ug|ug|NN|_
A|a|NN|_ Linker-1|linker-1|NN|_ adapter|adapter|NN|_ -LRB-|-lrb-|-LRB-|_ IDT|idt|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ ligated|ligate|VBN|_ onto|onto|IN|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ of|of|IN|_ size|size|NN|_ selected|select|VBN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ ,|,|,|_ either|either|CC|_ ribosome|ribosome|NN|_ footprints|footprint|NNS|_ or|or|CC|_ fragmented|fragmented|JJ|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_ A|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ was|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Superscript|Superscript|NNP|_ III|III|NNP|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|ThermoFisher|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ After|after|IN|_ gel|gel|NN|_ purification|purification|NN|_ of|of|IN|_ the|the|DT|_ cDNA|cdna|NN|_ library|library|NN|_ all|all|DT|_ ssDNA|ssdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ circularized|circularize|VBN|_ using|use|VBG|_ CircLigase|CircLigase|NNP|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ For|for|IN|_ ribosome|ribosome|NN|_ profiling|profiling|NN|_ samples|sample|NNS|_ rRNA|rrna|NN|_ containing|contain|VBG|_ circles|circle|NNS|_ were|be|VBD|_ depleted|deplete|VBN|_ using|use|VBG|_ oligo-biotin|oligo-biotin|JJ|_ and|and|CC|_ streptavidin|streptavidin|JJ|_ coupled|couple|VBN|_ Dynabeads|dynabead|NNS|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ subtraction|subtraction|NN|_ .|.|.|_ A|a|DT|_ PCR|pcr|NN|_ amplification|amplification|NN|_ off|off|IN|_ the|the|DT|_ circles|circle|NNS|_ using|use|VBG|_ HF|hf|NN|_ Phusion|phusion|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ -RRB-|-rrb-|-RRB-|_ completed|complete|VBD|_ the|the|DT|_ libraries|library|NNS|_ by|by|IN|_ adding|add|VBG|_ Illumina|Illumina|NNP|_ Tru-Seq|Tru-Seq|NNP|_ adapters|adapter|NNS|_ and|and|CC|_ a|a|DT|_ unique|unique|JJ|_ index|index|NN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_
All|All|NNP|_ strains|strain|NNS|_ were|be|VBD|_ grown|grow|VBN|_ shaking|shake|VBG|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ 200mL|200ml|NN|_ cultures|culture|NNS|_ of|of|IN|_ MOPS|mop|NNS|MED complete-glucose|complete-glucose|JJ|_ liquid|liquid|JJ|_ media|media|NNS|_ -LRB-|-lrb-|-LRB-|_ unless|unless|IN|_ otherwise|otherwise|RB|_ annotated|annotated|JJ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 1L|1l|NN|_ flasks|flask|NNS|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ OD|od|NN|_ -LRB-|-lrb-|-LRB-|_ 420nm|420nm|NN|_ -RRB-|-rrb-|-RRB-|_ between|between|IN|_ 0.4|0.4|CD|_ -|-|:|_ 0.6|0.6|CD|_
Cells|cell|NNS|_ from|from|IN|_ each|each|DT|_ strain|strain|NN|_ were|be|VBD|_ rapidly|rapidly|RB|_ harvested|harvest|VBN|_ by|by|IN|_ filtration|filtration|NN|_ and|and|CC|_ lysate|lysate|NN|_ was|be|VBD|_ produced|produce|VBN|_ by|by|IN|_ pulverization|pulverization|NN|_ of|of|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ cooled|cool|VBN|_ samples|sample|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
OTHER|OTHER|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ E.coli|e.coli|VB|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ to|to|TO|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ randomly|randomly|RB|_ assigned|assign|VBN|_ to|to|TO|_ one|one|CD|_ of|of|IN|_ those|those|DT|_ positions|position|NNS|_
Remaining|remain|VBG|_ linker-1|linker-1|NN|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ fastq|fastq|NN|_ files|file|NNS|_ using|use|VBG|_ fastx|fastx|NN|_ _|_|NN|_ clipper|clipper|NN|_
RF2|rf2|NN|_ *|*|SYM|_ _|_|SYM|_ exp1|exp1|NN|_ _|_|NN|_ mRNA|mrna|NN|_
RF2|rf2|NN|_ *|*|SYM|_ _|_|SYM|_ exp1|exp1|FW|_ _|_|FW|_ ribosome|ribosome|NN|_
RF2|rf2|NN|_ *|*|SYM|_ _|_|SYM|_ exp3|exp3|FW|_ _|_|FW|_ mRNA|mrna|NN|_
RF2|rf2|NN|_ *|*|SYM|_ _|_|SYM|_ exp3|exp3|FW|_ _|_|FW|_ ribosome|ribosome|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|SYM|_ exp2|exp2|FW|_ _|_|FW|_ repA|repa|NN|_ _|_|NN|_ mRNA|mrna|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|SYM|_ exp2|exp2|FW|_ _|_|FW|_ repA|repa|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|CD|_ exp2|exp2|NN|_ _|_|CD|_ repB|repb|NN|_ _|_|NN|_ mRNA|mrna|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|CD|_ exp2|exp2|NN|_ _|_|CD|_ repB|repb|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|CD|_ exp3|exp3|NN|_ _|_|NN|_ mRNA|mrna|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|CD|_ exp3|exp3|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|SYM|_ exp4|exp4|FW|_ _|_|FW|_ repA|repa|NN|_ _|_|NN|_ mRNA|mrna|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|SYM|_ exp4|exp4|FW|_ _|_|FW|_ repA|repa|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|CD|_ exp4|exp4|NN|_ _|_|CD|_ repB|repb|NN|_ _|_|NN|_ mRNA|mrna|NN|_
RF2|rf2|NN|_ *|*|SYM|_ ∆|∆|SYM|_ RF3|rf3|NN|_ _|_|CD|_ exp4|exp4|NN|_ _|_|CD|_ repB|repb|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
∆|∆|CD|_ RF3|rf3|NN|_ _|_|CD|_ exp1|exp1|NN|_ _|_|NN|_ mRNA|mrna|NN|_
∆|∆|CD|_ RF3|rf3|NN|_ _|_|CD|_ exp1|exp1|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
∆|∆|CD|_ RF3|rf3|NN|_ _|_|CD|_ exp3|exp3|NN|_ _|_|NN|_ mRNA|mrna|NN|_
∆|∆|CD|_ RF3|rf3|NN|_ _|_|CD|_ exp3|exp3|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
∆|∆|CD|_ RF3|rf3|NN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ mRNA|mrna|NN|_
∆|∆|CD|_ RF3|rf3|NN|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ ribosome|ribosome|NN|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ deltaprfC|deltaprfc|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_ prfB-Bstrain|prfb-bstrain|JJ|_ allele|allele|NN|_ deltaprfC|deltaprfc|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Bedgraph|Bedgraph|NNP|_ wiggle|wiggle|NN|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ and|and|CC|_ replicate|replicate|VB|_ for|for|IN|_ all|all|DT|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ after|after|IN|_ computational|computational|JJ|_ rRNA|rrna|NN|_ and|and|CC|_ tRNA|trna|NN|_ subtraction|subtraction|NN|_
The|the|DT|_ aligned|align|VBN|_ reads|read|VBZ|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ and|and|CC|_ sorted|sort|VBN|_ and|and|CC|_ indexed|index|VBN|_ using|use|VBG|_ SAMtools|samtool|NNS|_
The|the|DT|_ remaining|remain|VBG|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v.|v.|CC|_ 0.12.0|0.12.0|CD|_ allowing|allow|VBG|_ for|for|IN|_ one|one|CD|_ mismatch|mismatch|NN|_ and|and|CC|_ reads|read|VBZ|_ aligning|align|VBG|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ one|one|CD|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ were|be|VBD|_ discarded|discard|VBN|_
whole|whole|JJ|_ cell|cell|NN|_ lysate|lysate|NN|_
Whole|whole|JJ|_ cell|cell|NN|_ lysates|lysate|NNS|_ were|be|VBD|_ clarified|clarify|VBN|_ by|by|IN|_ brief|brief|JJ|_ centrifugation|centrifugation|NN|_ .|.|.|_ Ribosome|ribosome|NN|_ footprints|footprint|NNS|_ were|be|VBD|_ created|create|VBN|_ using|use|VBG|_ Mnase|Mnase|NNP|_ digestion|digestion|NN|_ -LRB-|-lrb-|-LRB-|_ 45|45|CD|_ enzyme|enzyme|NN|_ units|unit|NNS|_ per|per|IN|_ absorbance|absorbance|NN|_ unit|unit|NN|_ of|of|IN|_ lysate|lysate|NN|_ at|at|IN|_ 260nm|260nm|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Using|use|VBG|_ sucrose|sucrose|NN|_ gradients|gradient|NNS|_ the|the|DT|_ monosome|monosome|JJ|_ fraction|fraction|NN|_ of|of|IN|_ lysate|lysate|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ footprints|footprint|NNS|_ were|be|VBD|_ size|size|NN|_ selected|select|VBN|_ and|and|CC|_ converted|convert|VBN|_ to|to|TO|_ a|a|DT|_ cDNA|cdna|NN|_ library|library|NN|_ .|.|.|_ Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ purified|purify|VBN|_ lysate|lysate|NN|_ for|for|IN|_ a|a|DT|_ simultaneous|simultaneous|JJ|_ RNA-seq|rna-seq|NN|_ library|library|NN|_ production|production|NN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ .|.|.|_ Small|small|JJ|_ RNA|rna|NN|_ and|and|CC|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ subtraction|subtraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ total|total|JJ|_ RNA|rna|NN|_ samples|sample|NNS|_ using|use|VBG|_ MEGAClear|megaclear|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ MicrobExpress|microbexpress|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoFisher|thermofisher|NN|_ -RRB-|-rrb-|-RRB-|_ kits|kit|NNS|_ .|.|.|_ Subtracted|subtract|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ subjected|subject|VBN|_ to|to|TO|_ alkaline|alkaline|NN|_ fragmentation|fragmentation|NN|_ prior|prior|RB|_ to|to|TO|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_
Wiggle|Wiggle|NNP|_ files|file|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ center|center|NN|_ mapping|map|VBG|_ the|the|DT|_ reads|read|VBZ|_ between|between|IN|_ 20-40bps|20-40bp|NNS|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ 10bp|10bp|JJ|_ trim|trim|JJ|_ on|on|IN|_ either|either|DT|_ side|side|NN|_ of|of|IN|_ the|the|DT|_ read|read|NN|_ then|then|RB|_ mapping|map|VBG|_ the|the|DT|_ read|read|NN|_ across|across|IN|_ the|the|DT|_ remaining|remain|VBG|_ location|location|NN|_ using|use|VBG|_ Plastid|Plastid|NNP|_ .|.|.|_
WT|wt|VBD|_ _|_|CD|_ exp1|exp1|NN|_ _|_|NN|_ mRNA|mrna|NN|_
WT|wt|JJ|_ _|_|NN|_ exp1|exp1|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
WT|wt|JJ|_ _|_|NN|_ exp2|exp2|NN|_ _|_|NN|_ mRNA|mrna|NN|_
WT|wt|JJ|_ _|_|NN|_ exp2|exp2|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
WT|wt|JJ|_ _|_|NN|_ exp3|exp3|NN|_ _|_|NN|_ mRNA|mrna|NN|_
WT|wt|JJ|_ _|_|NN|_ exp3|exp3|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
WT|wt|JJ|_ _|_|NN|_ exp4|exp4|NN|_ _|_|NN|_ mRNA|mrna|NN|_
WT|wt|JJ|_ _|_|NN|_ exp4|exp4|NN|_ _|_|NN|_ ribosome|ribosome|NN|_
WT|wt|JJ|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ mRNA|mrna|NN|_
WT|wt|JJ|_ _|_|NN|_ minimal|minimal|JJ|_ _|_|NN|_ ribosome|ribosome|NN|_
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flask|flask|NN|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Flask|flask|NN|_ state|state|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Flask|flask|NN|_ state|state|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Flask|flask|NN|_ state|state|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Flask|flask|NN|_ state|state|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Flask|flask|NN|_ state|state|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Flask|flask|NN|_ state|state|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Flask|flask|NN|_ state|state|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Flask|flask|NN|_ state|state|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg|μg|NN|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ '|'|POS|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ '|'|''|_ .|.|.|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
Tube|Tube|NNP|_ state|state|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Tube|Tube|NNP|_ state|state|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Tube|Tube|NNP|_ state|state|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Tube|Tube|NNP|_ state|state|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Tube|Tube|NNP|_ state|state|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Tube|Tube|NNP|_ state|state|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Tube|Tube|NNP|_ state|state|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Tube|Tube|NNP|_ state|state|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ the|the|DT|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase at|at|IN|_ 37ºC|37ºc|NN|_ in|in|IN|_ Luria-Bertani|luria-bertani|JJ|_ medium|medium|NN|_ .|.|.|_
Enteroheamorragic|enteroheamorragic|JJ|_ E.|e.|FW|_ coli|coli|FW|_
Enteropathogenic|enteropathogenic|JJ|_ E.|e.|FW|_ coli|coli|FW|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ strain|strain|NN|_ ICC219|icc219|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ strain|strain|NN|_ ICC221|icc221|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ strain|strain|NN|_ ICC222|icc222|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ st58|st58|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ st957|st957|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ TB182A|tb182a|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ WC211|wc211|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ strain|strain|NN|_ WC416|wc416|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ the|the|DT|_ Genomic-tip|genomic-tip|NN|_ 100|100|CD|_
O157|o157|NN|_ strain|strain|NN|_ Sakai|Sakai|NNP|_
O55|O55|NNP|_ :|:|:|_ H6|h6|NN|_ ICC219|icc219|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ ICC219|icc219|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ ICC221|icc221|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ ICC221|icc221|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ ICC222|icc222|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H6|h6|NN|_ ICC222|icc222|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ st58|st58|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ st58|st58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ st957|st957|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ st957|st957|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ TB182A|tb182a|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ TB182A|tb182a|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ WC211|wc211|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ WC211|wc211|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ WC416|wc416|NN|_ replicate|replicate|VBP|_ 1|1|CD|_
O55|o55|NN|_ :|:|:|_ H7|h7|NN|_ WC416|wc416|NN|_ replicate|replicate|VBP|_ 2|2|CD|_
Spots|spot|NNS|_ with|with|IN|_ reference|reference|NN|_ signal|signal|NN|_ intensities|intensity|NNS|_ lower|lower|JJR|_ than|than|IN|_ the|the|DT|_ local|local|JJ|_ background|background|NN|_ -LRB-|-lrb-|-LRB-|_ LBG|lbg|NN|_ -RRB-|-rrb-|-RRB-|_ plus|plus|CC|_ 5|5|CD|_ standard|standard|JJ|_ deviations|deviation|NNS|_ or|or|CC|_ with|with|IN|_ some|some|DT|_ spotting|spot|VBG|_ abnormalities|abnormality|NNS|_ were|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ analysis|analysis|NN|_ .|.|.|_ Signal|signal|NN|_ intensities|intensity|NNS|_ of|of|IN|_ other|other|JJ|_ spots|spot|NNS|_ were|be|VBD|_ corrected|correct|VBN|_ by|by|IN|_ subtracting|subtract|VBG|_ the|the|DT|_ LBG|LBG|NNP|_ .|.|.|_
A|a|NN|_ total|total|NN|_ of|of|IN|_ two|two|CD|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ .|.|.|_ ompR-8myc|ompr-8myc|NN|_ tagged|tag|VBD|_ cells|cell|NNS|_ were|be|VBD|_ cultured|culture|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
chip|chip|NN|_ antibody|antibody|NN|_ :|:|:|_ anti-myc|anti-myc|JJ|_ -LRB-|-lrb-|-LRB-|_ Santa|Santa|NNP|_ Cruz|Cruz|NNP|_ Biotech|Biotech|NNP|_ ,|,|,|_ sc-28207|sc-28207|NN|_ -RRB-|-rrb-|-RRB-|_
ChIP-exo|chip-exo|NN|_ reads|read|VBZ|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ ASM584v2|asm584v2|NN|_ genome|genome|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ using|use|VBG|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ S|s|NN|_
ChIP-Seq|chip-seq|JJ|_
ChIP-seq|chip-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
Crosslinked|crosslink|VBN|_ cells|cell|NNS|_ were|be|VBD|_ then|then|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ ul|ul|NN|_ of|of|IN|_ lysis|lysis|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 40|40|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ inhibitor|inhibitor|NN|_ cocktail|cocktail|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mg|mg|NN|_ in|in|IN|_ 0.25|0.25|CD|_ ml|ml|NN|_ of|of|IN|_ DMSO|dmso|NN|_ and|and|CC|_ 0.75|0.75|CD|_ ml|ml|NN|_ of|of|IN|_ TDW|tdw|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lyzed|lyze|VBN|_ with|with|IN|_ 1|1|CD|_ ul|ul|NN|_ of|of|IN|_ lysozyme|lysozyme|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ 37oC|37oc|NN|_ on|on|IN|_ a|a|DT|_ rocker|rocker|NN|_ .|.|.|_ 0.55|0.55|CD|_ ml|ml|NN|_ of|of|IN|_ 2X|2x|NN|_ IP|IP|NNP|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 100|100|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 200|200|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 2|2|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ was|be|VBD|_ sonicated|sonicate|VBN|_ to|to|TO|_ fragmentize|fragmentize|VB|_ genomic|genomic|JJ|_ DNA|dna|NN|_ .|.|.|_ 0.3|0.3|CD|_ ml|ml|NN|_ of|of|IN|_ Wash|Wash|NNP|_ buffer|buffer|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 140|140|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ added|add|VBN|_ to|to|TO|_ make|make|VB|_ the|the|DT|_ volume|volume|NN|_ up|up|IN|_ to|to|TO|_ 1.4|1.4|CD|_ ml|ml|NN|_ .|.|.|_ Only|only|RB|_ 0.7|0.7|CD|_ ml|ml|NN|_ was|be|VBD|_ taken|take|VBN|_ and|and|CC|_ transfered|transfer|VBN|_ to|to|TO|_ a|a|DT|_ new|new|JJ|_ tube|tube|NN|_ ,|,|,|_ and|and|CC|_ 15|15|CD|_ ul|ul|NN|_ of|of|IN|_ Anti-c-myc|anti-c-myc|JJ|_ mouse|mouse|NN|_ antibody|antibody|NN|_ was|be|VBD|_ added|add|VBN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ sample|sample|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ overnight|overnight|RB|_ at|at|IN|_ 4|4|CD|_ oC|oc|NN|_ to|to|TO|_ make|make|VB|_ Antibody-TF|antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ 50|50|CD|_ ul|ul|NN|_ of|of|IN|_ Dynabeads|Dynabeads|NNP|_ Pan|Pan|NNP|_ mouse|mouse|NN|_ IgG|igg|NN|_ were|be|VBD|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ bead|bead|NN|_ washing|wash|VBG|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ mg|mg|NN|_ BSA|bsa|NN|_ in|in|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ PBS|PBS|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ the|the|DT|_ sample|sample|NN|_ .|.|.|_ Cell|cell|NN|_ lysate|lysate|NN|_ with|with|IN|_ beads|bead|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ or|or|CC|_ overnight|overnight|JJ|_ at|at|IN|_ 4oC|4oc|NN|_ to|to|TO|_ make|make|VB|_ Dynabead-antibody-TF|dynabead-antibody-tf|NN|_ complex|complex|NN|_ .|.|.|_ The|the|DT|_ beads|bead|NNS|_ were|be|VBD|_ pulled|pull|VBN|_ down|down|RP|_ on|on|IN|_ a|a|DT|_ magnet|magnet|NN|_ stand|stand|NN|_ ,|,|,|_ and|and|CC|_ washed|wash|VBN|_ 2|2|CD|_ times|time|NNS|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ I|i|NN|_ and|and|CC|_ with|with|IN|_ wash|wash|NN|_ buffer|buffer|NN|_ II|ii|CD|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 7.5|7.5|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 500|500|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ wash|wash|NN|_ buffer|buffer|NN|_ III|iii|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 250|250|CD|_ mM|mm|NN|KWSUPP LiCl|licl|NN|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ Triton|Triton|NNP|_ X-100|x-100|NN|_ and|and|CC|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ wash|wash|NN|_ buffer|buffer|NN|_ IV|iv|CD|_ -LRB-|-lrb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1mM|1mm|NN|_ EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ bead-bound|bead-bound|JJ|_ TF-DNA|tf-dna|NN|_ complex|complex|NN|_ was|be|VBD|_ then|then|RB|_ end-repaired|end-repaired|JJ|_ ,|,|,|_ dA-tailed|da-tailed|JJ|_ ,|,|,|_ and|and|CC|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ first|first|JJ|_ adapter|adapter|NN|_ .|.|.|_ Adapter-ligated|adapter-ligated|JJ|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ treated|treat|VBN|_ with|with|IN|_ nick-repair|nick-repair|JJ|_ reagent|reagent|NN|_ ,|,|,|_ and|and|CC|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ lambda|lambda|NN|_ exonuclease|exonuclease|NN|_ and|and|CC|_ RecJ|recj|NN|_ exonuclease|exonuclease|NN|_ .|.|.|_ Then|then|RB|_ DNA|dna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ away|away|RB|_ from|from|IN|_ Dynabeads|Dynabeads|NNPS|_ by|by|IN|_ incubating|incubate|VBG|_ in|in|IN|_ 200|200|CD|_ ul|ul|NN|_ of|of|IN|_ elution|elution|NN|_ buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ %|%|NN|_ SDS|sds|NN|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RRB-|-rrb-|-RRB-|_ at|at|IN|_ 65oC|65oc|NN|_ overnight|overnight|JJ|_ .|.|.|_ Protein|protein|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ treating|treat|VBG|_ 4|4|CD|_ ul|ul|NN|_ of|of|IN|_ protease|protease|NN|_ K|k|NN|_ and|and|CC|_ being|be|VBG|_ incubated|incubate|VBN|_ at|at|IN|_ 55|55|CD|_ oC|oc|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ ,|,|,|_ and|and|CC|_ by|by|IN|_ Phenol-Chloroform-IAA|phenol-chloroform-iaa|NN|_ extraction|extraction|NN|_ .|.|.|_ Purified|purify|VBN|_ DNA|dna|NN|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ bulid|bulid|VB|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ another|another|DT|_ dA-tailing|da-tailing|NN|_ ,|,|,|_ second|second|JJ|_ strand|strand|NN|_ ligation|ligation|NN|_ ,|,|,|_ and|and|CC|_ 3|3|CD|_ '|'|''|_ overhang|overhang|NN|_ removal|removal|NN|_ stpes|stpe|NNS|_ .|.|.|_ Then|then|RB|_ the|the|DT|_ sequencing|sequencing|NN|_ library|library|NN|_ was|be|VBD|_ amplified|amplify|VBN|_ with|with|IN|_ PCR|pcr|NN|_ enrichment|enrichment|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cells|cell|NNS|_ were|be|VBD|_ crosslinked|crosslink|VBN|_ in|in|IN|_ 1|1|CD|_ %|%|NN|_ formaldehyde|formaldehyde|NN|_ for|for|IN|_ 25|25|CD|_ minutes|minute|NNS|_ at|at|IN|_ RT|rt|NN|_ on|on|IN|_ a|a|DT|_ rocker|rocker|NN|_ ,|,|,|_ then|then|RB|_ washed|wash|VBN|_ 3|3|CD|_ times|time|NNS|_ with|with|IN|_ 50|50|CD|_ ml|ml|NN|_ of|of|IN|_ ice-cold|ice-cold|JJ|_ TBS|tbs|NN|_ -LRB-|-lrb-|-LRB-|_ Tris|tris|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ -RRB-|-rrb-|-RRB-|_ each|each|DT|_ time|time|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ each|each|DT|_ peak|peak|NN|_ detected|detect|VBN|_ with|with|IN|_ MACE|MACE|NNP|_ ,|,|,|_ binding|bind|VBG|_ intensity|intensity|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ by|by|IN|_ averaging|average|VBG|_ read|read|VBN|_ counts|count|NNS|_ from|from|IN|_ two|two|CD|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ and|and|CC|_ dividing|divide|VBG|_ by|by|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
genotype|genotype|NN|_ :|:|:|_ ompR-8myc|ompr-8myc|NN|_
MACE|mace|VBP|_ software|software|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
OmpR|ompr|NN|TF NaCl|nacl|NN|_ 1|1|CD|_
OmpR|ompr|NN|TF NaCl|nacl|NN|_ 2|2|CD|_
Read|Read|NNP|_ count|count|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ for|for|IN|_ each|each|DT|_ genomic|genomic|JJ|_ position|position|NN|_ from|from|IN|_ sequence|sequence|NN|_ alignment|alignment|NN|_ ,|,|,|_ and|and|CC|_ 95|95|CD|_ %|%|NN|_ strongest|strongest|JJS|_ intensity|intensity|NN|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ background|background|NN|_ intensity|intensity|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ in|in|IN|_ gff|gff|NN|_ format|format|NN|_ which|which|WDT|_ has|have|VBZ|_ 8|8|CD|_ columns|column|NNS|_ :|:|:|_ sequence|sequence|NN|_ id|id|NN|_ ,|,|,|_ source|source|NN|_ -LRB-|-lrb-|-LRB-|_ empty|empty|JJ|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ feature|feature|NN|_ -LRB-|-lrb-|-LRB-|_ +|+|CC|_
E.|E.|NNP|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ WT|wt|NN|_ and|and|CC|_ ΔompR|δompr|NN|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid-log|mid-log|JJ|_ phase|phase|NN|_ aerobically|aerobically|RB|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED media|media|NNS|MED supplemented|supplement|VBN|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP .|.|.|_ Then|then|RB|_ cells|cell|NNS|_ were|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ 0.3|0.3|CD|_ M|m|NN|_ of|of|IN|_ NaCl|nacl|NN|_ at|at|IN|_ mid-log|mid-log|JJ|_ pahse|pahse|NN|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ with|with|IN|_ agitation|agitation|NN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Fragments|fragment|NNS|_ Per|per|IN|_ Kilobase|kilobase|NN|_ of|of|IN|_ exon|exon|NN|_ per|per|IN|_ Megabase|megabase|NN|_ of|of|IN|_ library|library|NN|_ size|size|NN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ calculated|calculate|VBN|_ using|use|VBG|_ cufflinks|cufflink|NNS|_ v.|v.|CC|_ 1.3.0|1.3.0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
genotype|genotype|NN|_ :|:|:|_ ompR|ompr|NN|GEN deletion|deletion|NN|_ mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ WT|wt|JJ|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|rna-seq|JJ|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ onto|onto|IN|_ NC|nc|NN|_ _|_|CD|_ 000913|000913|CD|_ reference|reference|NN|_ genome|genome|NN|_ sequence|sequence|NN|_ using|use|VBG|_ bowtie|bowtie|NN|_ v1|v1|NN|_ .0.0|.0.0|CD|_ with|with|IN|_ parameters|parameter|NNS|_ -|-|:|_ X|x|NN|_ 1000|1000|CD|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -3|-3|CD|_ 3|3|LS|_ -|-|:|_ S|s|NN|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ comma-delimited|comma-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_ .|.|.|_
The|the|DT|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ the|the|DT|_ RNAprotect|rnaprotect|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ isolated|isolate|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Valencia|Valencia|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ gDNA|gdna|NN|_ Eliminator|eliminator|NN|_ spin|spin|NN|_ column|column|NN|_ in|in|IN|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ and|and|CC|_ concentration|concentration|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ analysis|analysis|NN|_ with|with|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ 1000|1000|CD|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
WT|WT|NNP|_ NaCl|nacl|NN|_ 1|1|CD|_
WT|wt|JJ|_ NaCl|nacl|NN|_ 2|2|CD|_
ΔompR|δompr|NN|_ NaCl|nacl|NN|_ 1|1|CD|_
ΔompR|δompr|NN|_ NaCl|nacl|NN|_ 2|2|CD|_
0|0|CD|_ min|min|NN|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_
0|0|CD|_ min|min|NN|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_
30|30|CD|_ min|min|NN|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_
30|30|CD|_ min|min|NN|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_
90|90|CD|_ min|min|NN|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_
90|90|CD|_ min|min|NN|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_
All|all|DT|_ data|datum|NNS|_ was|be|VBD|_ processed|process|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ Ver|Ver|NNP|_ .2.03|.2.03|CD|_ .|.|.|_ Rockhopper|Rockhopper|NNP|_ is|be|VBZ|_ an|a|DT|_ utomatic|utomatic|JJ|_ \|\|NN|_ bacterial|bacterial|JJ|_ RNA-seq|rna-seq|NN|_ analysis|analysis|NN|_ tool|tool|NN|_ ;|;|:|_ for|for|IN|_ additional|additional|JJ|_ information|information|NN|_ see|see|VB|_ :|:|:|_ McClure|McClure|NNP|_ ,|,|,|_ R.|R.|NNP|_ ,|,|,|_ et|et|FW|_ al.|al.|FW|_ -LRB-|-lrb-|-LRB-|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ \|\|SYM|_ Computational|computational|JJ|_ analysis|analysis|NN|_ of|of|IN|_ bacterial|bacterial|JJ|_ RNA-Seq|rna-seq|NN|_ data|datum|NNS|_ .|.|.|_ \|\|SYM|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ 41|41|CD|_ -LRB-|-lrb-|-LRB-|_ 14|14|CD|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ e140|e140|NN|_ .|.|.|_ The|the|DT|_ default|default|NN|_ general|general|JJ|_ parameters|parameter|NNS|_ were|be|VBD|_ used|use|VBN|_ with|with|IN|_ the|the|DT|_ erbose|erbose|JJ|_ output|output|NN|_ \|\|CD|_ tab|tab|NN|_ ticked|tick|VBN|_ and|and|CC|_ the|the|DT|_ \|\|JJ|_ orientation|orientation|NN|_ of|of|IN|_ mate-pair|mate-pair|JJ|_ reads|read|VBZ|_ \|\|RB|_ changed|change|VBN|_ to|to|TO|_ f|f|FW|_ \|\|FW|_ .|.|.|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ minus|minus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 0|0|CD|_ min|min|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 30|30|CD|_ min|min|NN|_
Clinical|clinical|JJ|_ isolate|isolate|NN|_ ,|,|,|_ plus|plus|CC|_ ciprofloxacin|ciprofloxacin|NN|_ ,|,|,|_ 90|90|CD|_ min|min|NN|_
E.|E.|NNP|_ coli|coli|NN|_ ST131|st131|NN|_ UR40|ur40|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ ciprofloxacin|ciprofloxacin|NN|_ -LRB-|-lrb-|-LRB-|_ 2µg|2µg|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O25b|o25b|NN|_ :|:|:|_ H4-ST131|h4-st131|NN|_
Extraction|extraction|NN|_ followed|follow|VBN|_ by|by|IN|_ DNase|dnase|NN|_ treatment|treatment|NN|_ with|with|IN|_ TURBO|TURBO|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ from|from|IN|_ Ambion|Ambion|NNP|_ .|.|.|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ Ribo-zero|ribo-zero|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ .|.|.|_ Followed|follow|VBN|_ by|by|IN|_ RNA-seq|rna-seq|JJ|_ library|library|NN|_ prep|prep|NN|_ using|use|VBG|_ an|a|DT|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ Stranded|Stranded|NNP|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 017644.1|017644.1|CD|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism NA114|na114|NN|_ -RRB-|-rrb-|-RRB-|_
isolate|isolate|NN|_ :|:|:|_ UR40|ur40|NN|_
RNA-Seq|rna-seq|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ *|*|SYM|_ txt|txt|NN|_ ,|,|,|_ *|*|SYM|_ xml|xml|NN|_ :|:|:|_ These|these|DT|_ files|file|NNS|_ contain|contain|VBP|_ the|the|DT|_ raw|raw|JJ|_ counts|count|NNS|_ ,|,|,|_ normalized|normalize|VBD|_ counts|count|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ values|value|NNS|_ ,|,|,|_ expression|expression|NN|_ values|value|NNS|_ ,|,|,|_ P-values|p-value|NNS|_ and|and|CC|_ Q-values|q-value|NNS|_ .|.|.|_ Each|each|DT|_ file|file|NN|_ contains|contain|VBZ|_ the|the|DT|_ values|value|NNS|_ for|for|IN|_ both|both|DT|_ samples|sample|NNS|_ at|at|IN|_ the|the|DT|_ indicated|indicate|VBN|_ timepoint|timepoint|NN|_ .|.|.|_
The|the|DT|_ cultures|culture|NNS|_ were|be|VBD|_ balanced|balanced|JJ|_ and|and|CC|_ grown|grow|VBN|_ in|in|IN|_ CAMHB|CAMHB|NNP|_ media|media|NNS|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ Celsius|Celsius|NNP|_ .|.|.|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 30|30|CD|_ min|min|NN|_
time|time|NN|_ point|point|NN|_ :|:|:|_ 90|90|CD|_ min|min|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ a|a|DT|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ GeneJET|GeneJET|NNP|_ RNA|rna|NN|_ isolation|isolation|NN|_ kit|kit|NN|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ ciprofloxacin|ciprofloxacin|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
Ancestral|ancestral|JJ|_ E.|e.|FW|_ coli|coli|FW|_ B|b|NN|_ REL606|rel606|NN|_ strain|strain|NN|_
A|a|NN|_ pool|pool|NN|_ of|of|IN|_ 3|3|CD|_ E.|e.|FW|_ coli|coli|FW|_ clones|clone|NNS|_ forming|form|VBG|_ large|large|JJ|_ colonies|colony|NNS|_ when|when|WRB|_ plated|plate|VBN|_ on|on|IN|_ TTagar|ttagar|NN|_ and|and|CC|_ derived|derive|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ B|b|NN|_ REL606|rel606|NN|_ after|after|IN|_ 150|150|CD|_ days|day|NNS|_ of|of|IN|_ seasonal|seasonal|JJ|_ evolution|evolution|NN|_ experiment|experiment|NN|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ in|in|IN|_ DMga|dmga|JJ|_ medium|medium|NN|_ .|.|.|_
A|a|NN|_ pool|pool|NN|_ of|of|IN|_ 3|3|CD|_ E.|e.|FW|_ coli|coli|FW|_ clones|clone|NNS|_ forming|form|VBG|_ small|small|JJ|_ colonies|colony|NNS|_ when|when|WRB|_ plated|plate|VBN|_ on|on|IN|_ TTagar|ttagar|NN|_ and|and|CC|_ derived|derive|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ B|b|NN|_ REL606|rel606|NN|_ after|after|IN|_ 150|150|CD|_ days|day|NNS|_ of|of|IN|_ seasonal|seasonal|JJ|_ evolution|evolution|NN|_ experiment|experiment|NN|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ in|in|IN|_ DMga|dmga|JJ|_ medium|medium|NN|_ .|.|.|_
A|a|NN|_ pool|pool|NN|_ of|of|IN|_ 3|3|CD|_ E.|e.|FW|_ coli|coli|FW|_ clones|clone|NNS|_ forming|form|VBG|_ small|small|JJ|_ colonies|colony|NNS|_ when|when|WRB|_ plated|plate|VBN|_ on|on|IN|_ TTagar|ttagar|NN|_ and|and|CC|_ derived|derive|VBN|_ from|from|IN|_ E.|e.|FW|_ coli|coli|FW|_ B|b|NN|_ REL606|rel606|NN|_ after|after|IN|_ 150|150|CD|_ days|day|NNS|_ of|of|IN|_ seasonal|seasonal|JJ|_ evolution|evolution|NN|_ experiment|experiment|NN|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ in|in|IN|_ DMga|dmga|JJ|_ medium|medium|NN|_ .|.|.|_
A|a|NN|_ ,|,|,|_ TP1|tp1|NN|_
A|a|NN|_ ,|,|,|_ TP2|tp2|NN|_
A|a|NN|_ ,|,|,|_ TP3|tp3|NN|_
A|a|NN|_ ,|,|,|_ TP4|tp4|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12|12|CD|_ hours|hour|NNS|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 12hours|12hours|CD|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 18|18|CD|_ hours|hour|NNS|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 18hours|18hours|CD|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 3.5|3.5|CD|_ hours|hour|NNS|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 4|4|CD|_ hours|hour|NNS|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 4hours|4hours|CD|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
Frozen|frozen|JJ|_ bacteria|bacterium|NNS|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ 18|18|CD|_ mm|mm|NN|_ test|test|NN|_ tubes|tube|NNS|_ containing|contain|VBG|_ DMga|dmga|JJ|_ medium|medium|NN|_ ,|,|,|_ 500µL|500µl|NN|_ of|of|IN|_ culture|culture|NN|_ was|be|VBD|_ transferred|transfer|VBN|_ to|to|TO|_ 50mL|50ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ DMga|dmga|NN|_ in|in|IN|_ 500mL|500ml|NN|_ flasks|flask|NNS|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 7hours|7hours|CD|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ 250rpm|250rpm|NN|_ .|.|.|_ Extraction|extraction|NN|_ was|be|VBD|_ performed|perform|VBN|_ just|just|RB|_ after|after|IN|_ .|.|.|_
LA|LA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl1|repl1|NN|_
LA|LA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl2|repl2|NN|_
LA|LA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl3|repl3|NN|_
LA|LA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl4|repl4|NN|_
LA|LA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl5|repl5|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl1|repl1|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl2|repl2|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl3|repl3|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl4|repl4|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl5|repl5|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl1|repl1|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl2|repl2|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl3|repl3|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl4|repl4|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl5|repl5|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl1|repl1|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl2|repl2|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl3|repl3|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl4|repl4|NN|_
LA|LA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl5|repl5|NN|_
L|l|NN|_ ,|,|,|_ TP1|tp1|NN|_
L|l|NN|_ ,|,|,|_ TP2|tp2|NN|_
L|l|NN|_ ,|,|,|_ TP3|tp3|NN|_
L|l|NN|_ ,|,|,|_ TP4|tp4|NN|_
SA|SA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl1|repl1|NN|_
SA|SA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl2|repl2|NN|_
SA|SA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl3|repl3|NN|_
SA|SA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl4|repl4|NN|_
SA|SA|NNP|_ _|_|NNP|_ TP1|tp1|NN|_ _|_|CD|_ repl5|repl5|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl1|repl1|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl2|repl2|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl3|repl3|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl4|repl4|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP2|tp2|NN|_ _|_|CD|_ repl5|repl5|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl1|repl1|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl2|repl2|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl3|repl3|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl4|repl4|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP3|tp3|NN|_ _|_|CD|_ repl5|repl5|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl1|repl1|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl2|repl2|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl3|repl3|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|CD|_ repl4|repl4|NN|_
SA|SA|NNP|_ _|_|SYM|_ TP4|tp4|NN|_ _|_|SYM|_ repl5|repl5|CD|_
Statistical|statistical|JJ|_ preprocessing|preprocess|VBG|_ steps|step|NNS|_ were|be|VBD|_ conducted|conduct|VBN|_ with|with|IN|_ ArrayPipe|arraypipe|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1.7|1.7|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ a|a|DT|_ web-based|web-based|JJ|_ software|software|NN|_ designed|design|VBN|_ for|for|IN|_ processing|processing|NN|_ of|of|IN|_ microarray|microarray|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ www.pathogenomics.ca|www.pathogenomics.ca|JJ|_
S|s|NN|_ ,|,|,|_ TP1|tp1|NN|_
S|s|NN|_ ,|,|,|_ TP2|tp2|NN|_
S|s|NN|_ ,|,|,|_ TP3|tp3|NN|_
S|s|NN|_ ,|,|,|_ TP4|tp4|NN|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ removed|remove|VBN|_ using|use|VBG|_ Ambion|Ambion|NNP|_ DNA-free|dna-free|JJ|_ kit|kit|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ 2|2|CD|_ %|%|NN|_ agarose|agarose|NN|_ gels|gel|NNS|_ and|and|CC|_ OD260|od260|NN|_
VALUEs|value|NNS|_ are|be|VBP|_ calculated|calculate|VBN|_ as|as|IN|_ log2-transformed|log2-transformed|JJ|_ -LRB-|-lrb-|-LRB-|_ test|test|NN|_
dnaC2|dnac2|NN|_ 30|30|CD|_ '|'|''|_ at|at|IN|_ 30|30|CD|_ deg|deg|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ gen|gen|NN|_ DNA|dna|NN|_ ,|,|,|_ pdN6|pdn6|NN|_ RT|rt|NN|_
dnaC2|dnac2|NN|_ 90|90|CD|_ '|'|''|_ at|at|IN|_ 42|42|CD|_ deg|deg|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ gen|gen|NN|_ DNA|dna|NN|_ ,|,|,|_ pdN6|pdn6|NN|_ RT|rt|NN|_
dnaC2|dnac2|NN|_ synchrony|synchrony|NN|_ 30|30|CD|_ '|'|''|_ after|after|IN|_ shift|shift|NN|_ ,|,|,|_ print|print|NN|_ 7|7|CD|_ array|array|NN|_
dnaC|dnac|NN|GEN fully|fully|RB|_ replicated|replicate|VBN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ Sau3AI|sau3ai|NN|_ ,|,|,|_ pdN6|pdn6|NN|_ RT|rt|NN|_
dnaC|dnac|NN|GEN fully|fully|RB|_ replicated|replicate|VBN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ Say3AI|say3ai|NN|_ ,|,|,|_ pdN6|pdn6|NN|_ RT|rt|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ Illumina|Illumina|NNP|_ CASAVA|CASAVA|NNP|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ induced|induce|VBN|_ with|with|IN|_ arabinose|arabinose|NN|_ or|or|CC|_ heat|heat|NN|_ shocked|shocked|JJ|_ ,|,|,|_ then|then|RB|_ harvested|harvest|VBN|_ and|and|CC|_ flash|flash|VB|_ frozen|frozen|JJ|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ ribosome|ribosome|NN|_ footprint|footprint|NN|_ extraction|extraction|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ ,|,|,|_ then|then|RB|_ samples|sample|NNS|_ were|be|VBD|_ taken|take|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ cultures|culture|NNS|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_ _|_|NN|_ f|f|FW|_ _|_|FW|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_ _|_|NN|_ f|f|FW|_ _|_|FW|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_ _|_|NN|_ f|f|FW|_ _|_|FW|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 10|10|CD|_ min|min|NN|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 20|20|CD|_ min|min|NN|_ _|_|NN|_ f|f|FW|_ _|_|FW|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 20|20|CD|_ min|min|NN|_ _|_|NN|_ f|f|FW|_ _|_|FW|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 20|20|CD|_ min|min|NN|_ _|_|NN|_ f|f|FW|_ _|_|FW|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 20|20|CD|_ min|min|NN|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 20|20|CD|_ min|min|NN|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ 42C|42c|CD|_ _|_|SYM|_ 20|20|CD|_ min|min|NN|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ pBAD|pbad|FW|_ _|_|FW|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ pBad|pbad|FW|_ _|_|FW|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ pBAD|pbad|FW|_ _|_|FW|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|SYM|_ pBAD|pbad|FW|_ _|_|FW|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 4|4|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBAD|pbad|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBAD|pbad|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBAD|pbad|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBAD|pbad|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 4|4|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32I54N|pbadsigma32i54n|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32I54N|pbadsigma32i54n|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32I54N|pbadsigma32i54n|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32I54N|pbadsigma32i54n|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32wt|pbadsigma32wt|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32wt|pbadsigma32wt|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32wt|pbadsigma32wt|NN|_ _|_|SYM|_ 30C|30c|FW|_ _|_|FW|_ f|f|FW|_ _|_|SYM|_ 3|3|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32wt|pbadsigma32wt|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 1|1|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32wt|pbadsigma32wt|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|NN|_ 2|2|CD|_
ecoli|ecolus|NNS|_ _|_|VBP|_ k12|k12|NN|_ _|_|CD|_ pBADsigma32wt|pbadsigma32wt|NN|_ _|_|SYM|_ 30C|30c|CD|_ _|_|NN|_ m|m|NN|_ _|_|SYM|_ 3|3|CD|_
E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ defined|define|VBN|_ rich|rich|JJ|MED media|media|NNS|MED at|at|IN|_ 30C|30C|NNP|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.2|000913.2|CD|_
growth|growth|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30C|NNP|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 0|0|CD|_ min|min|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ 20|20|CD|_ min|min|NN|_
heat|heat|NN|_ shock|shock|NN|_ time|time|NN|_ :|:|:|_ None|none|NN|_
induction|induction|NN|_ :|:|:|_ 0.2|0.2|CD|_ %|%|NN|_ arabinose|arabinose|NN|_
induction|induction|NN|_ :|:|:|_ None|none|NN|_
Library|Library|NNP|_ strategy|strategy|NN|_ :|:|:|_ Ribo-Seq|Ribo-Seq|NNP|_
OTHER|OTHER|NNP|_
plasmid|plasmid|NN|_ :|:|:|_ None|none|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBAD|pbad|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBADsigma32I54N|pbadsigma32i54n|NN|_
plasmid|plasmid|NN|_ :|:|:|_ pBADsigma32wt|pbadsigma32wt|NN|_
Polysomes|polysome|NNS|_ were|be|VBD|_ digested|digest|VBN|_ with|with|IN|_ MNase|mnase|NN|_ ,|,|,|_ monosomes|monosome|NNS|_ were|be|VBD|_ purified|purify|VBN|_ by|by|IN|_ sucrose|sucrose|NN|_ gradient|gradient|NN|_ ultracentrifugation|ultracentrifugation|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ resulting|result|VBG|_ mRNA|mrna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ gel-purified|gel-purified|JJ|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ MG1655|mg1655|NN|_ genome|genome|NN|_ with|with|IN|_ Bowtie|Bowtie|NNP|_ .|.|.|_
Reads|Reads|NNPS|_ were|be|VBD|_ trimmed|trim|VBN|_ and|and|CC|_ adaptors|adaptor|NNS|_ removed|remove|VBN|_ using|use|VBG|_ the|the|DT|_ fastx|fastx|NN|_ _|_|NN|_ toolkit|toolkit|NN|_ .|.|.|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
replicate|replicate|VBP|_ :|:|:|_ 3|3|CD|_
replicate|replicate|VB|_ :|:|:|_ 4|4|CD|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ dephosphorylated|dephosphorylate|VBN|_ ,|,|,|_ ligated|ligate|VBN|_ to|to|TO|_ an|a|DT|_ adaptor|adaptor|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcribed|transcribe|VBN|_ ,|,|,|_ circularized|circularize|VBN|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ Illumina|Illumina|NNP|_ adaptors|adaptor|NNS|_ and|and|CC|_ barcodes|barcode|NNS|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ normalizedcounts.txt|normalizedcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ EdgeR-normalized|edger-normalize|VBN|_ counts|count|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ ecoli|ecolus|NNS|_ _|_|VBP|_ heatshock|heatshock|NN|_ _|_|NN|_ rawcounts.txt|rawcounts.txt|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ has|have|VBZ|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ per|per|FW|_ kilobase|kilobase|NN|_ million|million|CD|_ for|for|IN|_ each|each|DT|_ E.|e.|FW|_ coli|coli|FW|_ gene|gene|NN|_ -LRB-|-lrb-|-LRB-|_ EcoCyc|ecocyc|NN|_ gene|gene|NN|_ names|name|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ at|at|IN|_ each|each|DT|_ position|position|NN|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ was|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ in-house|in-house|JJ|_ Python|Python|NNP|_ scripts|script|NNS|_ .|.|.|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ reads|read|VBZ|_ mapping|map|VBG|_ to|to|TO|_ each|each|DT|_ gene|gene|NN|_ was|be|VBD|_ counted|count|VBN|_ and|and|CC|_ normalized|normalize|VBN|_ using|use|VBG|_ EdgeR|edger|NN|_ .|.|.|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ phenol|phenol|NN|_ chloroform|chloroform|NN|_ and|and|CC|_ alkaline|alkaline|NN|_ fragmented|fragmented|JJ|_ ,|,|,|_ then|then|RB|_ fragments|fragment|NNS|_ -LRB-|-lrb-|-LRB-|_ 20-40|20-40|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ gel-purified|gel-purified|JJ|_ .|.|.|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 30C|30c|CD|_
treatment|treatment|NN|_ temperature|temperature|NN|_ :|:|:|_ 42C|42c|NN|_
All|all|DT|_ data|datum|NNS|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ McClure|McClure|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ as|as|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ .|.|.|_
Blue|blue|JJ|_ _|_|NN|_ 1|1|CD|_
Blue|blue|JJ|_ _|_|NN|_ 2|2|CD|_
Data|datum|NNS|_ were|be|VBD|_ visualized|visualize|VBN|_ in|in|IN|_ the|the|DT|_ Rockhopper|Rockhopper|NNP|_ IGV|igv|NN|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ McClure|McClure|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ TreeView|TreeView|NNP|_ 3.0|3.0|CD|_ -LRB-|-lrb-|-LRB-|_ Saldana|Saldana|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2004|2004|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Log-phase|log-phase|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|MED broth|broth|NN|MED ,|,|,|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ inoculated|inoculate|VBN|_ with|with|IN|_ one|one|CD|_ blue|blue|JJ|_ colony|colony|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 5|5|CD|_ hr|hr|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_
growth|growth|NN|_ protocol|protocol|NN|_ :|:|:|_ Log-phase|log-phase|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|MED broth|broth|NN|MED ,|,|,|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ inoculated|inoculate|VBN|_ with|with|IN|_ one|one|CD|_ pale|pale|JJ|_ colony|colony|NN|_ and|and|CC|_ grown|grow|VBN|_ for|for|IN|_ 5|5|CD|_ hr|hr|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_
Log-phase|log-phase|NN|_ cultures|culture|NNS|_ -LRB-|-lrb-|-LRB-|_ LB|lb|NN|MED broth|broth|NN|MED ,|,|,|_ Miller|Miller|NNP|_ formulation|formulation|NN|_ -RRB-|-rrb-|-RRB-|_ inoculated|inoculate|VBN|_ with|with|IN|_ either|either|CC|_ blue|blue|JJ|_ or|or|CC|_ pale|pale|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ grown|grow|VBN|_ for|for|IN|_ 5|5|CD|_ hr|hr|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ celsius|celsius|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ flash|flash|NN|_ frozen|freeze|VBN|_ on|on|IN|_ dry|dry|JJ|_ ice|ice|NN|_ .|.|.|_
Pale|Pale|NNP|_ _|_|SYM|_ 1|1|CD|_
Pale|Pale|NNP|_ _|_|SYM|_ 3|3|CD|_
parent|parent|NN|_ strain|strain|NN|_ :|:|:|_ BW27785|bw27785|NN|_
phenotype|phenotype|NN|_ :|:|:|_ Blue|Blue|NNP|_ colony-color|colony-color|NN|_ -LRB-|-lrb-|-LRB-|_ prion-containing|prion-containing|JJ|_ -RRB-|-rrb-|-RRB-|_
phenotype|phenotype|NN|_ :|:|:|_ Pale|Pale|NNP|_ colony-color|colony-color|NN|_ -LRB-|-lrb-|-LRB-|_ prion-lacking|prion-lacking|NN|_ -RRB-|-rrb-|-RRB-|_
Purified|purify|VBN|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ rRNA|rrna|NN|_ using|use|VBG|_ a|a|DT|_ Ribo-Zero|ribo-zero|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ and|and|CC|_ sequenced|sequence|VBN|_ on|on|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ NextSeq|NextSeq|NNP|_ 500|500|CD|_ sequencer|sequencer|NN|_ at|at|IN|_ the|the|DT|_ Harvard|Harvard|NNP|_ Biopolymers|Biopolymers|NNP|_ Facility|Facility|NNP|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Specifically|specifically|RB|_ ,|,|,|_ data|datum|NNS|_ were|be|VBD|_ treated|treat|VBN|_ as|as|IN|_ two|two|CD|_ experiments|experiment|NNS|_ constituting|constitute|VBG|_ either|either|CC|_ two|two|CD|_ -LRB-|-lrb-|-LRB-|_ lue|lue|NN|_ \|\|NN|_ cell|cell|NN|_ transcriptomes|transcriptome|NNS|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ three|three|CD|_ -LRB-|-lrb-|-LRB-|_ \|\|CD|_ pale|pale|JJ|_ \|\|NN|_ cell|cell|NN|_ transcriptomes|transcriptome|NNS|_ -RRB-|-rrb-|-RRB-|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Tab-delimited|tab-delimited|JJ|_ text|text|NN|_ file|file|NN|_ includes|include|VBZ|_ Rockhopper|Rockhopper|NNP|_ -LRB-|-lrb-|-LRB-|_ McClure|McClure|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2013|2013|CD|_ -RRB-|-rrb-|-RRB-|_ normalized|normalize|VBD|_ transcript|transcript|NN|_ abundance|abundance|NN|_ measurements|measurement|NNS|_ -LRB-|-lrb-|-LRB-|_ Expression|expression|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ transcript|transcript|NN|_ abundance|abundance|NN|_ ratios|ratio|NNS|_ -LRB-|-lrb-|-LRB-|_ Expression|expression|NN|_ Ratio|ratio|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ qValues|qvalue|NNS|_ -LRB-|-lrb-|-LRB-|_ qValue|qvalue|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ raw|raw|JJ|_ data|datum|NNS|_ that|that|WDT|_ were|be|VBD|_ treated|treat|VBN|_ as|as|IN|_ two|two|CD|_ experiments|experiment|NNS|_ constituting|constitute|VBG|_ either|either|CC|_ two|two|CD|_ -LRB-|-lrb-|-LRB-|_ lue|lue|NN|_ \|\|NN|_ cell|cell|NN|_ transcriptomes|transcriptome|NNS|_ ;|;|:|_ Blue|blue|JJ|_ _|_|NN|_ 1|1|CD|_ .|.|.|_ fastq|fastq|NN|_ ,|,|,|_ Blue|blue|JJ|_ _|_|NN|_ 2|2|CD|_ .|.|.|_ fastq|fastq|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ three|three|CD|_ -LRB-|-lrb-|-LRB-|_ \|\|CD|_ pale|pale|JJ|_ \|\|NN|_ cell|cell|NN|_ transcriptomes|transcriptome|NNS|_ ;|;|:|_ Pale|Pale|NNP|_ _|_|SYM|_ 1|1|LS|_ .|.|.|_ fastq|fastq|NN|_ ,|,|,|_ Pale|Pale|NNP|_ _|_|SYM|_ 2|2|LS|_ .|.|.|_ fastq|fastq|NN|_ ,|,|,|_ Pale|Pale|NNP|_ _|_|SYM|_ 3|3|LS|_ .|.|.|_ fastq|fastq|NN|_ -RRB-|-rrb-|-RRB-|_ biological|biological|JJ|_ replicates|replicate|VBZ|_ .|.|.|_ Gene|Gene|NNP|_ annotation|annotation|NN|_ ,|,|,|_ gene|gene|NN|_ product|product|NN|_ description|description|NN|_ ,|,|,|_ and|and|CC|_ strand|strand|NN|_ information|information|NN|_ is|be|VBZ|_ also|also|RB|_ included|include|VBN|_ .|.|.|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ Rho|rho|NN|_ prion-containing|prion-containing|JJ|_ cells|cell|NNS|_
Total|total|JJ|_ RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ Rho|rho|NN|_ prion-lacking|prion-lacking|JJ|_ cells|cell|NNS|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ cell|cell|NN|_ pellets|pellet|NNS|_ with|with|IN|_ TRI|TRI|NNP|_ Reagent|Reagent|NNP|_ -LRB-|-lrb-|-LRB-|_ MRC|MRC|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ precipitated|precipitated|JJ|_ ,|,|,|_ resuspended|resuspended|JJ|_ in|in|IN|_ DNase|dnase|NN|_ Reaction|reaction|NN|_ Buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|invitrogen|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 30|30|CD|_ min|min|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ DNase-treated|dnase-treated|JJ|_ samples|sample|NNS|_ were|be|VBD|_ subsequently|subsequently|RB|_ purified|purify|VBN|_ with|with|IN|_ an|a|DT|_ Rneasy|Rneasy|NNP|_ Plus|Plus|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_ STR|str|NN|_ reference|reference|NN|_ 1|1|CD|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_ STR|str|NN|_ reference|reference|NN|_ 1|1|CD|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_ STR|str|NN|_ reference|reference|NN|_ 2|2|CD|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_ STR|str|NN|_ reference|reference|NN|_ 2|2|CD|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_ STR|str|NN|_ reference|reference|NN|_ 3|3|CD|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR|str|NN|_ culture|culture|NN|_ STR|str|NN|_ reference|reference|NN|_ 3|3|CD|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P1|p1|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P1|p1|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P1|p1|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P1|p1|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P1|p1|NN|_ 28h|28h|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P1|p1|NN|_ 28h|28h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P3|p3|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P3|p3|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P3|p3|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P3|p3|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P3|p3|NN|_ 28h|28h|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P3|p3|NN|_ 28h|28h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 210|210|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 210|210|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 25h|25h|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 25h|25h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 26h|26h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 28h|28h|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 28h|28h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 330|330|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 45|45|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 45|45|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ PFR|pfr|NN|_ P5|p5|NN|_ 75|75|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 10|10|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 120|120|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 210|210|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 210|210|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 25h|25h|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 25h|25h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 25|25|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 26h|26h|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 26h|26h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 28h|28h|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 28h|28h|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 330|330|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 330|330|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 45|45|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 45|45|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 5|5|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 75|75|CD|_ min|min|NN|_ ,|,|,|_ rep1|rep1|NN|_
chemostat|chemostat|NN|_ STR-PFR|str-pfr|NN|_ culture|culture|NN|_ STR|str|NN|_ 75|75|CD|_ min|min|NN|_ ,|,|,|_ rep2|rep2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ substrain|substrain|NN|_ W3110|w3110|NN|_ was|be|VBD|_ used|use|VBN|_ in|in|IN|_ this|this|DT|_ study|study|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ two-compartment|two-compartment|JJ|_ bioreactor|bioreactor|NN|_ system|system|NN|_ consisting|consist|VBG|_ of|of|IN|_ an|a|DT|_ STR|str|NN|_ -LRB-|-lrb-|-LRB-|_ 3L|3l|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ a|a|DT|_ recycle|recycle|VB|_ loop|loop|NN|_ -LRB-|-lrb-|-LRB-|_ PFR|pfr|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ defined|define|VBN|_ medium|medium|NN|_ at|at|IN|_ pH7|ph7|NN|_ and|and|CC|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ Bioreactor|Bioreactor|NNP|_ cultivations|cultivation|NNS|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ a|a|DT|_ minimal|minimal|JJ|_ medium|medium|NN|_ containing|contain|VBG|_ -LRB-|-lrb-|-LRB-|_ per|per|IN|_ liter|liter|NN|_ -RRB-|-rrb-|-RRB-|_ 19.0|19.0|CD|_ g|g|NN|_ glucose|glucose|NN|SUPP ,|,|,|_ 1.0|1.0|CD|_ g|g|NN|_ NaH2PO4|nah2po4|NN|_ .|.|.|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 2.6|2.6|CD|_ g|g|NN|_ K2HPO4|k2hpo4|NN|_ ,|,|,|_ 3.8|3.8|CD|_ g|g|NN|_ -LRB-|-lrb-|-LRB-|_ NH4|nh4|NN|_ -RRB-|-rrb-|-RRB-|_ 2SO4|2so4|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ trace|trace|NN|_ element|element|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ 0.11|0.11|CD|_ g|g|NN|_ Na3C6H5O7|na3c6h5o7|NN|_ ,|,|,|_ 0.00835|0.00835|CD|_ g|g|NN|_ FeCl3|fecl3|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ ZnSO4|znso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00005|0.00005|CD|_ g|g|NN|_ MnSO4|mnso4|NN|_ ·|·|NN|_ H2O|h2o|NN|_ ,|,|,|_ 0.0008|0.0008|CD|_ g|g|NN|_ CuSO4|cuso4|NN|_ ·|·|NN|_ 5|5|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.00009|0.00009|CD|_ g|g|NN|_ CoCl2|cocl2|NN|_ ·|·|NN|_ 6|6|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.0044|0.0044|CD|_ g|g|NN|_ CaCl2|cacl2|NN|_ ·|·|NN|_ 2|2|CD|_ H2O|h2o|NN|_ ,|,|,|_ 0.1|0.1|CD|_ g|g|NN|_ MgSO4|mgso4|NN|_ ·|·|NN|_ 7|7|CD|_ H2O|h2o|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ STR-PFR|str-pfr|NN|_ was|be|VBD|_ operated|operate|VBN|_ as|as|IN|_ a|a|DT|_ chemostat|chemostat|NN|_ with|with|IN|_ ammonia|ammonia|NN|_ as|as|IN|_ the|the|DT|_ growth-limiting|growth-limiting|JJ|_ substrate|substrate|NN|_ .|.|.|_ First|first|RB|_ ,|,|,|_ a|a|DT|_ reference|reference|NN|_ steady|steady|JJ|_ state|state|NN|_ -LRB-|-lrb-|-LRB-|_ µ|µ|NN|_ =|=|JJ|_ 0.2|0.2|CD|_ h|h|NN|_ −|−|NN|_ 1|1|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ established|establish|VBN|_ in|in|IN|_ the|the|DT|_ STR|str|NN|_ and|and|CC|_ sampled|sample|VBD|_ three|three|CD|_ times|time|NNS|_ during|during|IN|_ a|a|DT|_ 16|16|CD|_ h|h|NN|_ period|period|NN|_ following|follow|VBG|_ establishment|establishment|NN|_ of|of|IN|_ the|the|DT|_ steady|steady|JJ|_ state|state|NN|_ .|.|.|_ Then|then|RB|_ ,|,|,|_ the|the|DT|_ PFR|pfr|NN|_ was|be|VBD|_ added|add|VBN|_ and|and|CC|_ samples|sample|NNS|_ for|for|IN|_ RNA-sequencing|rna-sequencing|NN|_ were|be|VBD|_ aquired|aquire|VBN|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
First|First|NNP|_ ,|,|,|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ from|from|IN|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-ZeroTM|Ribo-ZeroTM|NNP|_ Magnetic|magnetic|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Bacteria|bacterium|NNS|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ Madison|Madison|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Next|next|RB|_ ,|,|,|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ TruSeq|truseq|NN|_ mRNA|mrna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ San|San|NNP|_ Diego|Diego|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM1024v1|asm1024v1|NN|_ -LRB-|-lrb-|-LRB-|_ NCBI|NCBI|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ K12|k12|NN|_ subst|subst|NN|_ .|.|.|_ W3110|w3110|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_
HTseq-derived|htseq-derived|JJ|_ raw|raw|JJ|_ count|count|NN|_ data|datum|NNS|_ were|be|VBD|_ used|use|VBN|_ as|as|IN|_ input|input|NN|_ after|after|IN|_ a|a|DT|_ non-specific|non-specific|JJ|_ filtering|filter|VBG|_ step|step|NN|_ that|that|WDT|_ removed|remove|VBD|_ residual|residual|JJ|_ rRNAs|rrna|NNS|_ and|and|CC|_ tRNAs|trna|NNS|_ and|and|CC|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_ with|with|IN|_ fewer|fewer|JJR|_ than|than|IN|_ 2|2|CD|_ counts|count|NNS|_ per|per|IN|_ million|million|CD|_ -LRB-|-lrb-|-LRB-|_ 16-20|16-20|CD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ more|more|JJR|_ than|than|IN|_ 25|25|CD|_ %|%|NN|_ of|of|IN|_ the|the|DT|_ dataset|dataset|NN|_ .|.|.|_
Raw|raw|NN|_ counts|count|NNS|_ were|be|VBD|_ derived|derive|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ respective|respective|JJ|_ annotations|annotation|NNS|_ available|available|JJ|_ from|from|IN|_ UCSC|UCSC|NNP|_ genome|genome|NN|_ browser|browser|NN|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
replicate|replicate|VBP|_ :|:|:|_ 1|1|CD|_
replicate|replicate|VB|_ :|:|:|_ 2|2|CD|_
RNA-Seq|rna-seq|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P1|p1|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P3|p3|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ PFR|pfr|NN|_ P5|p5|NN|_
sample|sample|NN|_ port|port|NN|_ :|:|:|_ STR|str|NN|_
Sampling|sample|VBG|_ by|by|IN|_ directly|directly|RB|_ placing|place|VBG|_ the|the|DT|_ culture|culture|NN|_ sample|sample|NN|_ into|into|IN|_ RNAprotect|rnaprotect|NN|_ Bacteria|bacterium|NNS|_ Reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ following|follow|VBG|_ short|short|JJ|_ centrifugation|centrifugation|NN|_ the|the|DT|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ −|−|CD|_ 70|70|CD|_ °C|°c|NN|_ .|.|.|_
Sequenced|sequence|VBD|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ using|use|VBG|_ Cutadapt|Cutadapt|NNP|_ v.|v.|CC|_ 1.8.3|1.8.3|CD|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ substr|substr|NN|_ .|.|.|_ W3110|w3110|CD|_ whole|whole|JJ|_ genome|genome|NN|_ from|from|IN|_ NCBI|ncbi|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ AP009048|ap009048|NN|_ .1|.1|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ RNA-seq|rna-seq|NN|_ aligner|aligner|NN|_ STAR|star|NN|_ v.|v.|CC|_ 2.4.2|2.4.2|CD|_ a.|a.|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ W3110|w3110|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xlsx|xlsx|NN|_ file|file|NN|_ format|format|NN|_ includes|include|VBZ|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_ before|before|IN|_ and|and|CC|_ after|after|IN|_ filtering|filter|VBG|_ for|for|IN|_ low|low|JJ|_ coverage|coverage|NN|_ genes|gene|NNS|_
The|the|DT|_ bcl2fastq|bcl2fastq|NN|_ Conversion|conversion|NN|_ Software|Software|NNP|_ v.|v.|CC|_ 1.8.4|1.8.4|CD|_ from|from|IN|_ Illumina|Illumina|NNP|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
The|the|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ ,|,|,|_ with|with|IN|_ on|on|IN|_ column|column|NN|_ RNase-Free|rnase-free|NN|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ ,|,|,|_ -LRB-|-lrb-|-LRB-|_ both|both|CC|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ isolation|isolation|NN|_ -LRB-|-lrb-|-LRB-|_ RNA|rna|NN|_ ≥|≥|NN|_ 200|200|CD|_ bases|basis|NNS|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ was|be|VBD|_ determined|determine|VBN|_ by|by|IN|_ a|a|DT|_ Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ ,|,|,|_ Boeblingen|Boeblingen|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
time|time|NN|_ :|:|:|_ 0-15h|0-15h|JJ|_
time|time|NN|_ :|:|:|_ 0-16h|0-16h|JJ|_
time|time|NN|_ :|:|:|_ 0-2h|0-2h|JJ|_
time|time|NN|_ :|:|:|_ 10|10|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 120|120|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 210|210|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 25h|25h|JJ|_
time|time|NN|_ :|:|:|_ 25|25|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 26h|26h|JJ|_
time|time|NN|_ :|:|:|_ 28h|28h|JJ|_
time|time|NN|_ :|:|:|_ 330|330|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 45|45|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_
time|time|NN|_ :|:|:|_ 75|75|CD|_ min|min|NN|_
0|0|CD|_ '|'|''|_ ,|,|,|_ before|before|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
0|0|CD|_ '|'|''|_ lexA|lexA|NNP|GEN ,|,|,|_ before|before|IN|_ UV|uv|NN|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
0|0|CD|_ '|'|''|_ wt|wt|JJ|_ ,|,|,|_ before|before|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
ATCACG-D1|atcacg-d1|NN|_
CGATGT-D2|cgatgt-d2|NN|_
DGE|dge|NN|_ analysis|analysis|NN|_ used|use|VBD|_ a|a|DT|_ false-discovery|false-discovery|JJ|_ rate|rate|NN|_ -LRB-|-lrb-|-LRB-|_ FDR|FDR|NNP|_ -RRB-|-rrb-|-RRB-|_ of|of|IN|_ 0.10|0.10|CD|_ .|.|.|_
Differential|differential|JJ|_ gene|gene|NN|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ DGE|dge|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ then|then|RB|_ performed|perform|VBN|_ on|on|IN|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ '|'|POS|_ Cuffdiff|cuffdiff|JJ|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.0.7|0.0.7|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
For|for|IN|_ the|the|DT|_ whole-transcriptome|whole-transcriptome|JJ|_ analysis|analysis|NN|_ ,|,|,|_ sequencing|sequencing|NN|_ was|be|VBD|_ verified|verify|VBN|_ using|use|VBG|_ FASTQC|fastqc|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.11.2|0.11.2|CD|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ confirm|confirm|VB|_ base-call|base-call|JJ|_ quality|quality|NN|_ in|in|IN|_ each|each|DT|_ indexed|index|VBN|_ file|file|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180568|fm180568|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180569|fm180569|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ FM180570|fm180570|NN|_
genotype|genotype|NN|_
Incubation|incubation|NN|_ and|and|CC|_ RNA|rna|NN|_ harvesting|harvesting|NN|_ were|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ all|all|DT|_ samples|sample|NNS|_ simultaneously|simultaneously|RB|_ and|and|CC|_ under|under|IN|_ RNase-free|rnase-free|JJ|_ conditions|condition|NNS|_ to|to|TO|_ minimize|minimize|VB|_ biological|biological|JJ|_ variability|variability|NN|_ in|in|IN|_ gene|gene|NN|_ expression|expression|NN|_ between|between|IN|_ each|each|DT|_ sample|sample|NN|_ .|.|.|_ Bacterial|bacterial|JJ|_ concentrations|concentration|NNS|_ were|be|VBD|_ equalized|equalize|VBN|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ density|density|NN|_ -LRB-|-lrb-|-LRB-|_ by|by|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Indices|Indices|NNPS|_ corresponding|correspond|VBG|_ to|to|TO|_ the|the|DT|_ same|same|JJ|_ sample|sample|NN|_ were|be|VBD|_ merged|merge|VBN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ uploaded|upload|VBD|_ to|to|TO|_ a|a|DT|_ cloud-based|cloud-based|JJ|_ variant|variant|NN|_ of|of|IN|_ Galaxy|Galaxy|NNP|_ named|name|VBD|_ RNA23|RNA23|NNP|_ Rocket|Rocket|NNP|_
LB|lb|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ inoculated|inoculate|VBN|_ by|by|IN|_ a|a|DT|_ frozen|frozen|JJ|_ stock|stock|NN|_ of|of|IN|_ WT|WT|NNP|_ or|or|CC|_ perC-mutant|perc-mutant|JJ|_ strain|strain|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ .|.|.|_ Flasks|flask|NNS|_ containing|contain|VBG|_ low-glucose|low-glucose|JJ|_ DMEM|dmem|NN|_ were|be|VBD|_ inoculated|inoculate|VBN|_ 1:100|1:100|CD|_ with|with|IN|_ the|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ 225|225|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ to|to|TO|_ mid-exponential|mid-exponential|JJ|_ phase|phase|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ 0.3-0.5|0.3-0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ quality|quality|JJ|_ checked|check|VBN|_ with|with|IN|_ SAMstat|samstat|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 1.08|1.08|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ transcripts|transcript|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ in|in|IN|_ Cufflinks|Cufflinks|NNP|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_
Resulting|result|VBG|_ mRNA|mrna|NN|_ was|be|VBD|_ reverse-transcribed|reverse-transcribed|JJ|_ to|to|TO|_ cDNA|cdna|NN|_ libraries|library|NNS|_ via|via|IN|_ SuperScript|SuperScript|NNP|_ III|III|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ reverse|reverse|VB|_ transcription|transcription|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ 18080051|18080051|CD|_ -RRB-|-rrb-|-RRB-|_ as|as|IN|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cDNA|cdna|NN|_ libraries|library|NNS|_ were|be|VBD|_ multiplexed|multiplex|VBN|_ to|to|TO|_ distinguish|distinguish|VB|_ replicates|replicate|VBZ|_ from|from|IN|_ one|one|CD|_ another|another|DT|_ ,|,|,|_ barcoded|barcode|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ ,|,|,|_ and|and|CC|_ then|then|RB|_ amplified|amplify|VBN|_ with|with|IN|_ random|random|JJ|_ hexamers|hexamer|NNS|_ for|for|IN|_ 15|15|CD|_ PCR|pcr|NN|_ cycles|cycle|NNS|_ .|.|.|_ Transcripts|transcript|NNS|_ were|be|VBD|_ sequenced|sequence|VBN|_ for|for|IN|_ 50|50|CD|_ bases|basis|NNS|_ in|in|IN|_ single-end|single-end|JJ|_ fashion|fashion|NN|_ within|within|IN|_ one|one|CD|_ lane|lane|NN|_ of|of|IN|_ an|a|DT|_ Illumina|Illumina|NNP|_ Hiseq|Hiseq|NNP|_ 2000|2000|CD|_ flow|flow|NN|_ cell|cell|NN|_ .|.|.|_ This|this|DT|_ yielded|yield|VBD|_ roughly|roughly|RB|_ 30|30|CD|_ million|million|CD|_ reads|read|VBZ|_ per|per|IN|_ sample|sample|NN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Samples|sample|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ 1:1|1:1|CD|_ in|in|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ ,|,|,|_ Carlsbad|Carlsbad|NNP|_ ,|,|,|_ CA|CA|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ inhibit|inhibit|VB|_ RNase|rnase|NN|_ activity|activity|NN|_ and|and|CC|_ then|then|RB|_ centrifuged|centrifuge|VBD|_ -LRB-|-lrb-|-LRB-|_ 5000|5000|CD|_ x|x|CC|_ g|g|NN|_ ,|,|,|_ 10|10|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Pellets|pellet|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ TE|TE|NNP|_
source|source|NN|_ :|:|:|_ Bustamante|Bustamante|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2011|2011|CD|_
strain|strain|NN|_ :|:|:|_ JPEP22|jpep22|NN|_
Subsequent|subsequent|JJ|_ data|datum|NNS|_ visualizations|visualization|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.1.2|3.1.2|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 3.0|3.0|CD|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ bedgraph|bedgraph|NN|_ :|:|:|_ Data|datum|NNS|_ presented|present|VBN|_ in|in|IN|_ a|a|DT|_ 4|4|CD|_ column|column|NN|_ BED|bed|NN|_ format|format|NN|_ ,|,|,|_ of|of|IN|_ which|which|WDT|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ start|start|NN|_ position|position|NN|_ of|of|IN|_ the|the|DT|_ chromosome|chromosome|NN|_ ,|,|,|_ the|the|DT|_ third|third|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ end|end|NN|_ position|position|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ fourth|fourth|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ that|that|DT|_ sample|sample|NN|_ .|.|.|_ Chromosome|chromosome|NN|_ positions|position|NNS|_ are|be|VBP|_ specified|specify|VBN|_ as|as|IN|_ 0-relative|0-relative|JJ|_ .|.|.|_ The|the|DT|_ first|first|JJ|_ chromosome|chromosome|NN|_ position|position|NN|_ is|be|VBZ|_ 0|0|CD|_ .|.|.|_ The|the|DT|_ last|last|JJ|_ position|position|NN|_ in|in|IN|_ a|a|DT|_ chromosome|chromosome|NN|_ of|of|IN|_ length|length|NN|_ N|n|NN|_ would|would|MD|_ be|be|VB|_ N|n|NN|_ -|-|:|_ 1|1|CD|_ .|.|.|_ Only|only|RB|_ positions|position|NNS|_ specified|specify|VBN|_ have|have|VBP|_ data|datum|NNS|_ .|.|.|_ Positions|position|NNS|_ not|not|RB|_ specified|specify|VBN|_ do|do|VBP|_ not|not|RB|_ have|have|VB|_ data|datum|NNS|_ and|and|CC|_ will|will|MD|_ not|not|RB|_ be|be|VB|_ graphed|graph|VBN|_ .|.|.|_ All|all|DT|_ positions|position|NNS|_ specified|specify|VBN|_ in|in|IN|_ the|the|DT|_ input|input|NN|_ data|datum|NNS|_ are|be|VBP|_ in|in|IN|_ numerical|numerical|JJ|_ order|order|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tabular|tabular|JJ|_ :|:|:|_ Tabular|tabular|JJ|_ data|datum|NNS|_ that|that|WDT|_ informs|inform|VBZ|_ the|the|DT|_ excel|excel|VB|_ spreadsheet|spreadsheet|NN|_ .|.|.|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Data|datum|NNS|_ contain|contain|VBP|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ xls|xl|NNS|_ :|:|:|_ The|the|DT|_ data|datum|NNS|_ are|be|VBP|_ averaged|average|VBN|_ across|across|IN|_ the|the|DT|_ three|three|CD|_ samples|sample|NNS|_ per|per|IN|_ strain|strain|NN|_ .|.|.|_ Both|both|DT|_ averaged|average|VBD|_ strain|strain|NN|_ data|datum|NNS|_ are|be|VBP|_ presented|present|VBN|_ for|for|IN|_ each|each|DT|_ gene|gene|NN|_ on|on|IN|_ the|the|DT|_ same|same|JJ|_ line|line|NN|_ .|.|.|_ Excel|Excel|NNP|_ spreadsheet|spreadsheet|NN|_ containing|contain|VBG|_ gene|gene|NN|_ ID|id|NN|_ ,|,|,|_ gene|gene|NN|_ number|number|NN|_ ,|,|,|_ locus|locus|NN|_ ,|,|,|_ fragments|fragment|NNS|_ per|per|IN|_ kilobase|kilobase|NN|_ mapped|map|VBN|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ WT|WT|NNP|_ and|and|CC|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ log2|log2|NN|_ -LRB-|-lrb-|-LRB-|_ fold-change|fold-change|NN|_ -RRB-|-rrb-|-RRB-|_ relative|relative|JJ|_ epxression|epxression|NN|_ of|of|IN|_ WT|WT|NNP|_ over|over|IN|_ mutant|mutant|JJ|_ strains|strain|NNS|_ ,|,|,|_ test-statistic|test-statistic|JJ|_ ,|,|,|_ p-value|p-value|NN|_ ,|,|,|_ q-value|q-value|NN|_ ,|,|,|_ and|and|CC|_ significance|significance|NN|_ analyzed|analyze|VBD|_ via|via|IN|_ the|the|DT|_ cummeRbund|cummerbund|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ whereby|whereby|WRB|_ a|a|DT|_ q-value|q-value|NN|_ of|of|IN|_ <|<|JJR|_ 0.05|0.05|CD|_ is|be|VBZ|_ considered|consider|VBN|_ significant|significant|JJ|_ .|.|.|_
TTAGGC-D3|ttaggc-d3|NN|_
Using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.0.2|2.0.2|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ an|a|DT|_ EPEC|epec|NN|_ O127|o127|NN|_ :|:|:|_ H6|h6|NN|_ reference|reference|NN|_ genome|genome|NN|_ -LRB-|-lrb-|-LRB-|_ EMBL|embl|NN|_
Whole|whole|JJ|_ bacterial|bacterial|JJ|_ cell|cell|NN|_ RNA|rna|NN|_ transcriptome|transcriptome|NN|_
10|10|CD|_ min|min|NN|_ after|after|IN|_ UVtreatment|uvtreatment|NN|_ 1|1|CD|_ '|'|''|_ ,|,|,|_ 40J|40j|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ in|in|IN|_ Davis|Davis|NNP|_ +0.4|+0.4|CD|_ %|%|NN|_ glu|glu|NN|_
10|10|CD|_ min|min|NN|_ UV|uv|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
Cells|cell|NNS|_ treated|treat|VBN|_ with|with|IN|_ bacterial|bacterial|JJ|_ protect|protect|VBP|_ reagent|reagent|NN|_ and|and|CC|_ freeze|freeze|NN|_ at|at|IN|_ -70|-70|CD|_ C|c|NN|_
E.|e.|FW|_ coli|coli|FW|_ grow|grow|VB|_ in|in|IN|_ LB|lb|NN|_ rich|rich|JJ|MED medium|medium|NN|MED to|to|TO|_ OD600|od600|NN|_ =|=|JJ|_ 2.4|2.4|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genotype|genotype|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_
RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ via|via|IN|_ Invitrogen|Invitrogen|NNP|_ RNAeasy|RNAeasy|NNP|_ Kit|kit|NN|_ and|and|CC|_ treated|treat|VBN|_ with|with|IN|_ DNaseI|dnasei|NN|_ to|to|TO|_ remove|remove|VB|_ all|all|DT|_ DNA|dna|NN|_
The|the|DT|_ data|datum|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ version|version|NN|_ 5.0|5.0|CD|_ -LRB-|-lrb-|-LRB-|_ MAS|mas|NN|_ 5.0|5.0|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ trimmed|trim|VBN|_ mean|mean|NN|_ target|target|NN|_ intensity|intensity|NN|_ of|of|IN|_ each|each|DT|_ array|array|NN|_ was|be|VBD|_ arbitrarily|arbitrarily|RB|_ set|set|VBN|_ to|to|TO|_ 100|100|CD|_ .|.|.|_
W3110|w3110|NN|_ lsrK|lsrk|NN|GEN mutants|mutant|NNS|_
W3110|w3110|NN|_ lsrK|lsrk|NN|GEN mutants|mutant|NNS|_
W3110|w3110|NN|_ lsrK|lsrk|NN|GEN mutants|mutant|NNS|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
W3110|w3110|NN|_ lsrK|lsrk|NN|GEN mutants|mutant|NNS|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
W3110|w3110|NN|_ lsrR|lsrr|NN|GEN mutants|mutant|NNS|_
W3110|w3110|NN|_ lsrR|lsrr|NN|GEN mutants|mutant|NNS|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
W3110|w3110|NN|_ lsrR|lsrr|NN|GEN mutants|mutant|NNS|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
W3110|w3110|NN|_ wild|wild|JJ|_ type|type|NN|_
W3110|w3110|NN|_ wild|wild|JJ|_ type|type|NN|_ ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
W3110|w3110|NN|_ wild|wild|JJ|_ type|type|NN|_ ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
20|20|CD|_ min|min|NN|_ after|after|IN|_ UVtreatment|uvtreatment|NN|_ 1|1|CD|_ '|'|''|_ ,|,|,|_ 40J|40j|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ in|in|IN|_ Davis|Davis|NNP|_ +0.4|+0.4|CD|_ %|%|NN|_ glu|glu|NN|_
20|20|CD|_ min|min|NN|_ untreatedcells|untreatedcell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
20|20|CD|_ min|min|NN|_ UV|uv|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
20|20|CD|_ min|min|NN|_ UVtreatment|uvtreatment|NN|_ control|control|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ in|in|IN|_ Davis|Davis|NNP|_ +0.4|+0.4|CD|_ %|%|NN|_ glu|glu|NN|_
antibody|antibody|NN|_ :|:|:|_ Monoclonal|monoclonal|JJ|_ ANTI-FLAG|anti-flag|NN|_ M2|m2|NN|_ antibody|antibody|NN|_ -LRB-|-lrb-|-LRB-|_ F3165|f3165|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ Sigma|Sigma|NNP|_
background|background|NN|_ :|:|:|_ crp|crp|NN|GEN mutant|mutant|JJ|_ background|background|NN|_ ,|,|,|_ fis|fi|VBZ|GEN flag|flag|NN|_ tag|tag|NN|GEN
background|background|NN|_ :|:|:|_ fis|fis|NN|GEN mutant|mutant|JJ|_ background|background|NN|_ ,|,|,|_ crp|crp|NN|GEN flag|flag|NN|_ tag|tag|NN|GEN
background|background|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ,|,|,|_ crp|crp|NN|GEN flag|flag|NN|_ tag|tag|NN|GEN
background|background|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_ ,|,|,|_ fis|fi|VBZ|GEN flag|flag|NN|_ tag|tag|NN|GEN
BAM|bam|NN|_ files|file|NNS|_ of|of|IN|_ each|each|DT|_ ChIP|chip|NN|_ biological|biological|JJ|_ replicate|replicate|VB|_ and|and|CC|_ the|the|DT|_ input|input|NN|_ replicate|replicate|VB|_ samples|sample|NNS|_ were|be|VBD|_ used|use|VBN|_ in|in|IN|_ the|the|DT|_ MACS|macs|NN|_ peak|peak|NN|_ calling|call|VBG|_ program|program|NN|_ with|with|IN|_ the|the|DT|_ -|-|:|_ f|f|FW|_ BAMPE|bampe|FW|_ parameter|parameter|NN|_
Cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ in|in|IN|_ the|the|DT|_ required|require|VBN|_ growth|growth|NN|_ phase|phase|NN|_ in|in|IN|_ formaldehyde|formaldehyde|NN|_ ,|,|,|_ quenched|quench|VBN|_ ,|,|,|_ washed|wash|VBN|_ and|and|CC|_ lysed|lyse|VBN|_ .|.|.|_ Fragmented|fragmented|JJ|_ DNA|dna|NN|_ -|-|:|_ protein|protein|NN|_ complex|complex|NN|_ were|be|VBD|_ pulled|pull|VBN|_ using|use|VBG|_ the|the|DT|_ monoclonal|monoclonal|JJ|_ flag|flag|NN|_ tag|tag|NN|GEN antibody|antibody|NN|_ .|.|.|_ The|the|DT|_ complex|complex|NN|_ was|be|VBD|_ then|then|RB|_ washed|wash|VBN|_ ,|,|,|_ reverse|reverse|VB|_ cross-linked|cross-linked|JJ|_ and|and|CC|_ obtained|obtain|VBN|_ DNA|dna|NN|_ purified|purify|VBN|_ using|use|VBG|_ Qiagen|Qiagen|NNP|_ min|min|NN|_ elute|elute|NN|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ from|from|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ rich|rich|JJ|_ Lysogeny|lysogeny|JJ|_ broth|broth|NN|_ at|at|IN|_ 37|37|CD|_ degrees|degree|NNS|_ in|in|IN|_ aerobic|aerobic|JJ|_ conditions|condition|NNS|_ .|.|.|_
ChIP-Seq|chip-seq|NN|_
crp.ee.chipseq|crp.ee.chipseq|NN|_
crp.ee.input|crp.ee.input|JJ|_
crp.me.chipseq|crp.me.chipseq|NN|_
crp.me|crp.me|NN|_ ,|,|,|_ input|input|NN|_
crp.me.input|crp.me.input|JJ|_
crpmutant.fis.ee.chipseq|crpmutant.fis.ee.chipseq|NN|_
crpmutant.fis.ee.input|crpmutant.fis.ee.input|JJ|_
crpmutant.fis.me.chipseq|crpmutant.fis.me.chipseq|NN|_
crpmutant.fis.me.input|crpmutant.fis.me.input|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
fis.ee.chipseq|fis.ee.chipseq|JJ|_
fis.ee.input|fis.ee.input|JJ|_
fis.me.chipseq|fis.me.chipseq|NN|_
fis.me.input|fis.me.input|JJ|_
fismutant.crp.ee.chipseq|fismutant.crp.ee.chipseq|NN|_
fismutant.crp.ee.input|fismutant.crp.ee.input|JJ|_
fismutant.crp.me.chipseq|fismutant.crp.me.chipseq|NN|_
fismutant.crp.me.input|fismutant.crp.me.input|JJ|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC000913|nc000913|NN|_ .2|.2|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Early|early|JJ|_ exponential|exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Mid|Mid|NNP|_ exponential|exponential|JJ|_
SAM|SAM|NNP|_ files|file|VBZ|_ thus|thus|RB|_ obtained|obtain|VBN|_ were|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ BAM|BAM|NNP|_ files|file|NNS|_ using|use|VBG|_ samtools|samtool|NNS|_ view|view|VBP|_ command|command|NN|_
Samples|sample|NNS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ K|k|NN|_ 12|12|CD|_ MG1655|mg1655|NN|_ reference|reference|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ NC000913|nc000913|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ using|use|VBG|_ BWA|bwa|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ WITH|with|IN|_ -|-|:|_ q|q|NN|_ 30|30|CD|_ parameter|parameter|NN|_ for|for|IN|_ trimming|trim|VBG|_ of|of|IN|_ reads|read|VBZ|_ below|below|IN|_ PHRED|PHRED|NNP|_ quality|quality|NN|_ score|score|NN|_ of|of|IN|_ 30|30|CD|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ peaks.bed|peaks.bed|VBN|_
Truseq|truseq|NN|_ ChIP|chip|NN|_ kit|kit|NN|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ library|library|NN|_ preparation|preparation|NN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ end|end|NN|_ repaired|repair|VBN|_ and|and|CC|_ adapters|adapter|NNS|_ were|be|VBD|_ ligated|ligate|VBN|_ .|.|.|_ After|after|IN|_ ligation|ligation|NN|_ ,|,|,|_ purify|purify|VB|_ ligation|ligation|NN|_ products|product|NNS|_ and|and|CC|_ then|then|RB|_ amplify|amplify|VB|_ .|.|.|_
BGI|BGI|NNP|_ inhouse|inhouse|NNP|_ software|software|NN|_ ``|``|``|_ filter|filter|NN|_ _|_|NN|_ fq|fq|NN|_ ''|''|''|_ for|for|IN|_ basecalling|basecalling|NN|_ and|and|CC|_ trimming|trim|VBG|_
Duplicate|duplicate|VB|_ O|o|NN|_
E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913|000913|CD|_
induction|induction|NN|_ :|:|:|_ induced|induce|VBN|_ 50|50|CD|_ µM|µm|NN|_ IPTG|iptg|NN|_
ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_
ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_
ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_
ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_
Read-mapping|read-mapping|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ soap2|soap2|NN|_ .21|.21|CD|_ .|.|.|_ Mapping|mapping|NN|_ towards|towards|IN|_ genes|gene|NNS|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ -|-|:|_ m|m|NN|_ 0|0|CD|_ -|-|:|_ x|x|CC|_ 1000|1000|CD|_ -|-|:|_ s|s|NNS|_ 28|28|CD|_ -|-|:|_ l|l|NN|_ 32|32|CD|_ -|-|:|_ v|v|LS|_ 5|5|LS|_ -|-|:|_ r|r|NN|_ 2|2|CD|_ -|-|:|_ p|p|NN|_ 3|3|CD|_
replicates|replicate|VBZ|_ :|:|:|_ ORF1|orf1|NN|_ replicate|replicate|VB|_ 1|1|CD|_
replicates|replicate|VBZ|_ :|:|:|_ ORF1|orf1|NN|_ replicate|replicate|VB|_ 2|2|CD|_
replicates|replicate|VBZ|_ :|:|:|_ Svi3-3|svi3-3|NN|_ replicate|replicate|VB|_ 1|1|CD|_
replicates|replicate|VBZ|_ :|:|:|_ Svi3-3|svi3-3|NN|_ replicate|replicate|VB|_ 2|2|CD|_
replicates|replicate|VBZ|_ :|:|:|_ WT|WT|NNP|_ replicate|replicate|VB|_ 1|1|CD|_
replicates|replicate|VBZ|_ :|:|:|_ WT|WT|NNP|_ replicate|replicate|VB|_ 2|2|CD|_
RNA-Seq|rna-seq|JJ|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ columns|column|NNS|_ in|in|IN|_ the|the|DT|_ processed|process|VBN|_ files|file|NNS|_ are|be|VBP|_ the|the|DT|_ following|follow|VBG|_ in|in|IN|_ order|order|NN|_ :|:|:|_ GeneID|geneid|NN|_ ,|,|,|_ Length|length|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7655775|7655775|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7178582|7178582|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7706927|7706927|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7070827|7070827|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8018710|8018710|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8299205|8299205|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 7313736|7313736|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8344539|8344539|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8074159|8074159|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ mapped|map|VBD|_ _|_|CD|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ 8103887|8103887|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|SYM|_ IPTG|iptg|SYM|_ _|_|SYM|_ coverage|coverage|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|IPTG|NNP|_ _|_|CD|_ coverage|coverage|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ ORF1|orf1|NN|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ rpkm|rpkm|NN|_ ,|,|,|_ Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_ _|_|NN|_ rpkm|rpkm|NN|_ ,|,|,|_ Symbol|symbol|NN|_ -LRB-|-lrb-|-LRB-|_ gene|gene|NN|_ name|name|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Description|description|NN|_ ,|,|,|_ KEGG|KEGG|NNP|_ Orthology|Orthology|NNP|_ ,|,|,|_ GO|GO|NNP|_ Component|Component|NNP|_ ,|,|,|_ GO|GO|NNP|_ Function|function|NN|_ ,|,|,|_ and|and|CC|_ GO|GO|NNP|_ Process|process|VBP|_
Svi3|svi3|NN|_ _|_|NN|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_
Svi3|svi3|NN|_ _|_|CD|_ 3|3|CD|_ _|_|NN|_ 1|1|CD|_ _|_|CD|_ IPTG|iptg|NN|_
Svi3|svi3|NN|_ _|_|CD|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_
Svi3|svi3|NN|_ _|_|CD|_ 3|3|CD|_ _|_|NN|_ 2|2|CD|_ _|_|CD|_ IPTG|iptg|NN|_
The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ immediately|immediately|RB|_ mixed|mix|VBN|_ with|with|IN|_ RNA|rna|NN|_ Protect|protect|VB|_ Bacterial|bacterial|JJ|_ reagent|reagent|NN|_ ®|®|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ processed|process|VBN|_ by|by|IN|_ the|the|DT|_ RNAeasy|RNAeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ instructions|instruction|NNS|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ for|for|IN|_ whole|whole|JJ|_ cell|cell|NN|_ proteomics|proteomic|NNS|_ were|be|VBD|_ chilled|chill|VBN|_ in|in|IN|_ ice-slush|ice-slush|JJ|_ ,|,|,|_ pelleted|pelleted|JJ|_ at|at|IN|_ 14000|14000|CD|_ rpm|rpm|NN|_ ,|,|,|_ 4|4|CD|_ °C|°c|NN|_ and|and|CC|_ the|the|DT|_ media|media|NNS|_ was|be|VBD|_ aspirated|aspirate|VBN|_ .|.|.|_ The|the|DT|_ cells|cell|NNS|_ were|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ 3|3|CD|_ ×|×|NN|_ 1.5|1.5|CD|_ mL|ml|NN|_ PBS|PBS|NNP|_ with|with|IN|_ pelleting|pelleting|NN|_ at|at|IN|_ as|as|IN|_ above|above|IN|_ in|in|IN|_ between|between|IN|_ .|.|.|_ The|the|DT|_ final|final|JJ|_ pellet|pellet|NN|_ was|be|VBD|_ stored|store|VBN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ until|until|IN|_ being|be|VBG|_ shipped|ship|VBN|_ to|to|TO|_ the|the|DT|_ Proteomics|Proteomics|NNP|_ Core|Core|NNP|_ Facility|Facility|NNP|_ at|at|IN|_ University|University|NNP|_ of|of|IN|_ Gothenburg|Gothenburg|NNP|_ for|for|IN|_ processing|processing|NN|_ .|.|.|_ The|the|DT|_ RNA|rna|NN|_ was|be|VBD|_ shipped|ship|VBN|_ to|to|TO|_ BGI|BGI|NNP|_ for|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ sequencing|sequencing|NN|_ .|.|.|_
The|the|DT|_ gene|gene|NN|_ expression|expression|NN|_ values|value|NNS|_ were|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ RPKM|rpkm|NN|_ -LRB-|-lrb-|-LRB-|_ reads|read|VBZ|_ per|per|IN|_ kilobase|kilobase|NN|_ transcriptome|transcriptome|NN|_ per|per|IN|_ million|million|CD|_ mapped|map|VBD|_ reads|read|VBZ|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ the|the|DT|_ inhouse|inhouse|NNP|_ BGI|BGI|NNP|_ pipeline|pipeline|NN|_ .|.|.|_
The|the|DT|_ pCA24N,-gfp|pca24n,-gfp|NN|_
TruSeq|truseq|NN|_
WT1|wt1|NN|_ _|_|CD|_ IPTG|iptg|NN|_
WT2|wt2|NN|_ _|_|CD|_ IPTG|iptg|NN|_
An|a|DT|_ o|o|NN|_
E.|E.|NNP|_ coli|coli|NN|_ TolC|tolc|NN|_ cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ o|o|NN|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_ _|_|NN|_ A|a|NN|_
Eco|eco|NN|_ _|_|CD|_ TolC|tolc|NN|_ _|_|NN|_ 0|0|CD|_ min|min|NN|_ _|_|NN|_ B|b|NN|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ Carolacton|Carolacton|NNP|_ _|_|NNP|_ A|A|NNP|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_ _|_|CD|_ Carolacton|Carolacton|NNP|_ _|_|NN|_ B|b|NN|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ A|a|DT|_
Eco|eco|NN|_ _|_|CD|_ TolC|tolc|NN|_ _|_|CD|_ 15|15|CD|_ min|min|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ B|b|NN|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ Carolacton|Carolacton|NNP|_ _|_|NNP|_ A|A|NNP|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|CD|_ Carolacton|Carolacton|NNP|_ _|_|NN|_ B|b|NN|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ A|a|DT|_
Eco|eco|NN|_ _|_|CD|_ TolC|tolc|NN|_ _|_|CD|_ 30|30|CD|_ min|min|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ B|b|NN|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 5|5|CD|_ min|min|NN|_ _|_|CD|_ Carolacton|Carolacton|NNP|_ _|_|NNP|_ A|A|NNP|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 5|5|CD|_ min|min|NN|_ _|_|CD|_ Carolacton|Carolacton|NNP|_ _|_|NN|_ B|b|NN|_
Eco|Eco|NNP|_ _|_|SYM|_ TolC|tolc|NN|_ _|_|CD|_ 5|5|CD|_ min|min|NN|_ _|_|NN|_ control|control|NN|_ _|_|CD|_ A|a|DT|_
Eco|eco|NN|_ _|_|CD|_ TolC|tolc|NN|_ _|_|CD|_ 5|5|CD|_ min|min|NN|_ _|_|NN|_ control|control|NN|_ _|_|NN|_ B|b|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP018801|cp018801|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
genotype|genotype|NN|_ :|:|:|_ TolC|tolc|NN|_ defective|defective|JJ|_ -LRB-|-lrb-|-LRB-|_ TolC|tolc|NN|_ -|-|:|_ -RRB-|-rrb-|-RRB-|_
Libraries|library|NNS|_ of|of|IN|_ RNA|rna|NN|_ fractions|fraction|NNS|_ were|be|VBD|_ constructed|construct|VBN|_ with|with|IN|_ the|the|DT|_ ScriptSeq|ScriptSeq|NNP|_ V2|v2|NN|_ RNA-Seq|rna-seq|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ guidelines|guideline|NNS|_ .|.|.|_
planktonic|planktonic|JJ|_ cells|cell|NNS|_
Raw|raw|NN|_ read|read|VBD|_ counts|count|NNS|_ of|of|IN|_ transcripts|transcript|NNS|_ were|be|VBD|_ obtained|obtain|VBN|_ by|by|IN|_ aligning|align|VBG|_ samples|sample|NNS|_ 1-14|1-14|CD|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ and|and|CC|_ counting|count|VBG|_ mapped|map|VBN|_ reads|read|VBZ|_ per|per|IN|_ feature|feature|NN|_ using|use|VBG|_ Rockhopper|Rockhopper|NNP|_ v2|v2|NN|_ .0.3|.0.3|CD|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ FastQC|fastqc|NN|_ v0|v0|NN|_ .11.2|.11.2|CD|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ The|the|DT|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ raw|raw|JJ|_ read|read|NN|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ time-point|time-point|NN|_ for|for|IN|_ both|both|DT|_ biol|biol|NN|_ .|.|.|_ replicates|replicate|VBZ|_ of|of|IN|_ control|control|NN|_ and|and|CC|_ Carolacton-treated|carolacton-treated|JJ|_ samples|sample|NNS|_ as|as|IN|_ obtained|obtain|VBN|_ from|from|IN|_ Rockhopper|Rockhopper|NNP|_ .|.|.|_ A|a|DT|_ FASTA|fasta|NN|_ file|file|NN|_ on|on|IN|_ the|the|DT|_ series|series|NN|_ record|record|NN|_ contains|contain|VBZ|_ the|the|DT|_ transcript|transcript|NN|_ sequences|sequence|NNS|_ .|.|.|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0|0|CD|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 15|15|CD|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 30|30|CD|_
time|time|NN|_ point|point|NN|_ -LRB-|-lrb-|-LRB-|_ minutes|minute|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_
Total|total|JJ|_ cellular|cellular|JJ|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturers|manufacturer|NNS|_ protocol|protocol|NN|_ .|.|.|_ Residual|residual|JJ|_ DNA|dna|NN|_ in|in|IN|_ the|the|DT|_ fractions|fraction|NNS|_ was|be|VBD|_ digested|digest|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 27|27|CD|_ Kunitz|Kunitz|NNP|_ units|unit|NNS|_ Dnase|Dnase|NNP|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ absence|absence|NN|_ of|of|IN|_ DNA|dna|NN|_ verified|verify|VBN|_ by|by|IN|_ Polymerase|polymerase|NN|_ chain|chain|NN|_ reaction|reaction|NN|_ -LRB-|-lrb-|-LRB-|_ PCR|pcr|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ was|be|VBD|_ conducted|conduct|VBN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ epicentre|epicentre|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ quality|quality|NN|_ control|control|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ extracts|extract|NNS|_ ,|,|,|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ the|the|DT|_ successful|successful|JJ|_ mRNA|mrna|NN|_ enrichment|enrichment|NN|_ ,|,|,|_ was|be|VBD|_ conducted|conduct|VBN|_ by|by|IN|_ using|use|VBG|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ 0.5|0.5|CD|_ µg|µg|NN|_
treatment|treatment|NN|_ :|:|:|_ none|none|NN|_
antibody|antibody|NN|_ :|:|:|_ anti-FLAG|anti-flag|JJ|_ mAb|mab|NN|_
antibody|antibody|NN|_ vendor|vendor|NN|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8|1.8|CD|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ LB|LB|NNP|MED media|media|NNS|MED with|with|IN|_ 1mM|1mm|NN|_ IPTG|iptg|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_
ChIP-Seq|chip-seq|JJ|_
CsiR|csir|NN|TF _|_|CD|_ ChIPSeq|chipseq|NN|_
CsiR|csir|NN|TF _|_|CD|_ RNASeq|rnaseq|NN|_
Culture|culture|NN|_ cells|cell|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
For|for|IN|_ chromatin|chromatin|NN|_ immunoprecipitation|immunoprecipitation|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ fixed|fix|VBN|_ with|with|IN|_ formaldehyde|formaldehyde|NN|_ and|and|CC|_ glycine|glycine|NN|_ and|and|CC|_ sheared|shear|VBD|_ via|via|IN|_ sonication|sonication|NN|_ .|.|.|_ Sheared|shear|VBN|_ DNA|dna|NN|_ from|from|IN|_ lysate|lysate|NN|_ was|be|VBD|_ immunoprecipitated|immunoprecipitate|VBN|_ -LRB-|-lrb-|-LRB-|_ IP|IP|NNP|_ -RRB-|-rrb-|-RRB-|_ out|out|IN|_ using|use|VBG|_ an|a|DT|_ anti-FLAG|anti-flag|JJ|_ mAb|mab|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ washed|wash|VBN|_ with|with|IN|_ IPP150|ipp150|NN|_ buffer|buffer|NN|_ and|and|CC|_ purified|purify|VBN|_ via|via|IN|_ ProteinaseK|ProteinaseK|NNP|_ digestion|digestion|NN|_ and|and|CC|_ Qiaquick|qiaquick|NN|_ PCR|pcr|NN|_ purification|purification|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -|-|:|_ Cat|cat|NN|_ .|.|.|_ No.|no.|NN|_ 28106|28106|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
For|for|IN|_ total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pellete|VBN|_ in|in|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ -RRB-|-rrb-|-RRB-|_
Nac|Nac|NNP|TF _|_|NNP|_ ChIPSeq|ChIPSeq|NNP|_
Nac|Nac|NNP|TF _|_|SYM|_ RNASeq|rnaseq|NN|_
NtrC|ntrc|NN|TF _|_|CD|_ ChIPSeq|chipseq|NN|_
OmpR|ompr|NN|TF _|_|CD|_ ChIPSeq|chipseq|NN|_
Peak|peak|JJ|_ calling|calling|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ SPAT|SPAT|NNP|_
Reads|Reads|NNPS|_ were|be|VBD|_ aligned|align|VBN|_ to|to|TO|_ GenBank|genbank|NN|_ ID|id|NN|_ U00096|u00096|NN|_ .2|.2|NN|_
RNA-Seq|rna-seq|NN|_
R|r|NN|_ scripts|script|NNS|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ GenomicRanges|genomicrange|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ custom|custom|NN|_ scripts|script|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ calculate|calculate|VB|_ RPKMs|rpkm|NNS|_ .|.|.|_ Fold-change|fold-change|NN|_ was|be|VBD|_ calculated|calculate|VBN|_ as|as|IN|_ ratio|ratio|NN|_ of|of|IN|_ RPKMs|rpkm|NNS|_ after|after|IN|_ TF|tf|NN|_ induction|induction|NN|_ to|to|TO|_ control|control|VB|_ experiment|experiment|NN|_ .|.|.|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ .|.|.|_ xlsx|xlsx|NN|_ files|file|NNS|_ contain|contain|VBP|_ peak|peak|JJ|_ region|region|NN|_ locations|location|NNS|_ and|and|CC|_ gene|gene|NN|_ expression|expression|NN|_ value|value|NN|_ for|for|IN|_ ChIP-Seq|chip-seq|NN|_ and|and|CC|_ RNA-Seq|rna-seq|NN|_ respectively|respectively|RB|_
The|the|DT|_ appropriate|appropriate|JJ|_ protocols|protocol|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ procedures|procedure|NNS|_
Total|Total|NNP|_ RNA|rna|NN|_ extraction|extraction|NN|_ was|be|VBD|_ done|do|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ and|and|CC|_ DNAse|dnase|NN|_ digested|digest|VBN|_ .|.|.|_ RNA|rna|NN|_ purfication|purfication|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ Rneasy|Rneasy|NNP|_ spin|spin|VB|_ columns|column|NNS|_
transcription|transcription|NN|_ factor|factor|NN|_ :|:|:|_ CsiR|csir|NN|TF
transcription|transcription|NN|_ factor|factor|NN|_ :|:|:|_ Nac|Nac|NNP|TF
transcription|transcription|NN|_ factor|factor|NN|_ :|:|:|_ NtrC|ntrc|NN|TF
transcription|transcription|NN|_ factor|factor|NN|_ :|:|:|_ OmpR|ompr|NN|TF
40|40|CD|_ min|min|NN|_ after|after|IN|_ UVtreatment|uvtreatment|NN|_ 1|1|CD|_ ,|,|,|_ 40J|40j|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ in|in|IN|_ Davis|Davis|NNP|_ +0.4|+0.4|CD|_ %|%|NN|_ glu|glu|NN|_
40|40|CD|_ min|min|NN|_ untreatedcells|untreatedcell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
batch|batch|NN|_ :|:|:|_ 10|10|CD|_
batch|batch|NN|_ :|:|:|_ 11|11|CD|_
batch|batch|NN|_ :|:|:|_ 12|12|CD|_
batch|batch|NN|_ :|:|:|_ 13|13|CD|_
batch|batch|NN|_ :|:|:|_ 14|14|CD|_
batch|batch|NN|_ :|:|:|_ 15|15|CD|_
batch|batch|NN|_ :|:|:|_ 16|16|CD|_
batch|batch|NN|_ :|:|:|_ 17|17|CD|_
batch|batch|NN|_ :|:|:|_ 18|18|CD|_
batch|batch|NN|_ :|:|:|_ 19|19|CD|_
batch|batch|NN|_ :|:|:|_ 20|20|CD|_
batch|batch|NN|_ :|:|:|_ 21|21|CD|_
batch|batch|NN|_ :|:|:|_ 22|22|CD|_
batch|batch|NN|_ :|:|:|_ 23|23|CD|_
batch|batch|NN|_ :|:|:|_ 24|24|CD|_
batch|batch|NN|_ :|:|:|_ 25|25|CD|_
batch|batch|NN|_ :|:|:|_ 26|26|CD|_
batch|batch|NN|_ :|:|:|_ 27|27|CD|_
batch|batch|NN|_ :|:|:|_ 7|7|CD|_
batch|batch|NN|_ :|:|:|_ 8|8|CD|_
batch|batch|NN|_ :|:|:|_ 9|9|CD|_
bowtie2-build|bowtie2-build|JJ|_ final|final|JJ|_ _|_|NN|_ reference|reference|NN|_ _|_|CD|_ seqs|seq|NNS|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ gluconate|gluconate|NN|_
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glucose|glucose|NN|SUPP
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ glycerol|glycerol|NN|SUPP
carbon|carbon|NN|_ source|source|NN|_ :|:|:|_ lactate|lactate|NN|_
convert|convert|VBP|_ back|back|RB|_ to|to|TO|_ sorted.sam|sorted.sam|NN|_ with|with|IN|_ samtools|samtool|NNS|_
convert|convert|VBP|_ bowtie|bowtie|NN|_ output|output|NN|_ .|.|.|_ sam|sam|NN|_ to|to|TO|_ .|.|.|_ bam|bam|NN|_ with|with|IN|_ samtools|samtool|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism B|b|NN|_ str|str|NN|_ .|.|.|_ REL606|rel606|NN|_
exponential|exponential|JJ|_ culture|culture|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ reference|reference|NN|_ sequence|sequence|NN|_ is|be|VBZ|_ REL606|REL606|NNP|_
get|get|VB|_ raw|raw|JJ|_ counts|count|NNS|_ for|for|IN|_ reads|read|VBZ|_ mapped|map|VBN|_ with|with|IN|_ htseq-count|htseq-count|JJ|_
gluconate|gluconate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 091|091|CD|_
gluconate|gluconate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 092|092|CD|_
gluconate|gluconate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 093|093|CD|_
gluconate|gluconate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 094|094|CD|_
gluconate|gluconate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 095|095|CD|_
gluconate|gluconate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 096|096|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 016|016|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 017|017|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 018|018|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 019|019|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 020|020|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 021|021|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 022|022|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 023|023|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 024|024|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 025|025|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 026|026|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 027|027|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 028|028|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 029|029|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 030|030|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 031|031|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 032|032|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 033|033|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 097|097|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 098|098|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 099|099|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 100|100|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 101|101|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 102|102|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|NN|_ 103|103|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 104|104|CD|_
glucose|glucose|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 105|105|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 034|034|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 035|035|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 036|036|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 037|037|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 038|038|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 039|039|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 040|040|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 041|041|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 042|042|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 043|043|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 044|044|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 045|045|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 046|046|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 047|047|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 048|048|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 049|049|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 050|050|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 052|052|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 053|053|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 054|054|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 055|055|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 056|056|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 057|057|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 058|058|CD|_
glycerol|glycerol|NN|SUPP _|_|CD|_ time|time|NN|_ _|_|NN|_ course|course|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 059|059|CD|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ exponential|exponential|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ late|late|JJ|_ _|_|NN|_ stationary|stationary|JJ|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ stationary|stationary|JJ|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 10|10|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 14|14|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 168|168|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 24|24|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 26|26|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 27|27|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 28|28|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 29|29|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 3|3|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 336|336|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 4|4|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 48|48|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5.5|5.5|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 6|6|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 6.5|6.5|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 7|7|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 8|8|CD|_
growth|growth|NN|_ time|time|NN|_ -LRB-|-lrb-|-LRB-|_ hours|hour|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 9|9|CD|_
Illumina|Illumina|NNP|_ Ribozero|Ribozero|NNP|_ rRNA|rrna|NN|_ removal|removal|NN|_ followed|follow|VBN|_ by|by|IN|_ NEB|NEB|NNP|_ Next|next|JJ|_ RNA|rna|NN|_ library|library|NN|_ Prep|Prep|NNP|_ set|set|VBD|_ .|.|.|_
lactate|lactate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 085|085|CD|_
lactate|lactate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 086|086|CD|_
lactate|lactate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 087|087|CD|_
lactate|lactate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 088|088|CD|_
lactate|lactate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 089|089|CD|_
lactate|lactate|NN|_ _|_|NN|_ growth|growth|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 090|090|CD|_
late|late|JJ|_ stationary|stationary|JJ|_ culture|culture|NN|_
map|map|NN|GEN trimmed|trim|VBD|_ reads|read|VBZ|_ to|to|TO|_ reference|reference|NN|_ sequence|sequence|NN|_ in|in|IN|_ indexes|index|NNS|_ file|file|VBP|_ with|with|IN|_ bowtie2|bowtie2|NN|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ levels|level|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ baseMg|basemg|NN|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ levels|level|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ highMg|highmg|NN|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ levels|level|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ lowMg|lowmg|NN|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0.005|0.005|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0.01|0.01|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0.02|0.02|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0.04|0.04|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0.08|0.08|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 0.8|0.8|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 200|200|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 400|400|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 50|50|CD|_
mg|mg|NN|_ +2|+2|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 8|8|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 106|106|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 107|107|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 108|108|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 109|109|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 110|110|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 111|111|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 112|112|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 113|113|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 114|114|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 115|115|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 116|116|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 117|117|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 118|118|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 119|119|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 120|120|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 121|121|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 122|122|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 123|123|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 124|124|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 125|125|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 126|126|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 127|127|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 128|128|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 129|129|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 130|130|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 131|131|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 132|132|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 133|133|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 134|134|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 135|135|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 136|136|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 137|137|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 138|138|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 139|139|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 140|140|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ high|high|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 141|141|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 142|142|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 143|143|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 144|144|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 145|145|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 146|146|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 147|147|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 148|148|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 149|149|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 150|150|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 151|151|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 152|152|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 153|153|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 154|154|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 155|155|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 156|156|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 157|157|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 158|158|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 159|159|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 160|160|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 161|161|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 162|162|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 163|163|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 164|164|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 165|165|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|VBD|_ 166|166|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 167|167|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 168|168|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 169|169|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 170|170|CD|_
MgSO4|mgso4|NN|_ _|_|CD|_ stress|stress|NN|_ _|_|RB|_ low|low|JJ|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 171|171|CD|_
na|na|TO|_ +1|+1|NN|_ -LRB-|-lrb-|-LRB-|_ levels|level|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ baseNa|basena|NN|_
na|na|TO|_ +1|+1|NN|_ -LRB-|-lrb-|-LRB-|_ levels|level|NNS|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ highNa|highna|NN|_
na|na|TO|_ +1|+1|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 100|100|CD|_
na|na|TO|_ +1|+1|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 200|200|CD|_
na|na|TO|_ +1|+1|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 300|300|CD|_
na|na|TO|_ +1|+1|NN|_ -LRB-|-lrb-|-LRB-|_ mm|mm|NN|_ -RRB-|-rrb-|-RRB-|_ :|:|:|_ 5|5|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 061|061|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 063|063|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 064|064|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 065|065|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 066|066|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 067|067|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 068|068|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 069|069|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 070|070|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 071|071|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 072|072|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 073|073|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 074|074|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 075|075|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 076|076|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 077|077|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 079|079|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 080|080|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 081|081|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 082|082|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 083|083|CD|_
NaCl|nacl|NN|_ _|_|CD|_ stress|stress|NN|_ :|:|:|_ MURI|MURI|NNP|_ _|_|SYM|_ 084|084|CD|_
RNA-Seq|rna-seq|NN|_
RNAsnap|rnasnap|NN|_ followed|follow|VBN|_ by|by|IN|_ purification|purification|NN|_ through|through|IN|_ Zymo|Zymo|NNP|_ RNA|rna|NN|_ clean|clean|JJ|_ and|and|CC|_ concentrator|concentrator|NN|_ .|.|.|_
stationary|stationary|JJ|_ culture|culture|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ txt|txt|NN|_ files|file|NNS|_ including|include|VBG|_ count|count|NN|_ numbers|number|NNS|_ of|of|IN|_ RNA|rna|NN|_ 's|'s|POS|_ and|and|CC|_ quality|quality|NN|_ control|control|NN|_ were|be|VBD|_ generated|generate|VBN|_
trim|trim|JJ|_ adaptors|adaptor|NNS|_ on|on|IN|_ raw|raw|JJ|_ reads|read|VBZ|_ and|and|CC|_ moved|move|VBD|_ trimmed|trimmed|RBR|_ reads|read|VBZ|_ to|to|TO|_ trimmed|trimmed|RBR|_ _|_|SYM|_ reads|read|VBZ|_ with|with|IN|_ flexbar|flexbar|JJ|_
BW25113|bw25113|NN|_
Data|Data|NNP|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ LOWESS|LOWESS|NNP|_ algorithm|algorithm|NN|_ and|and|CC|_ analyzed|analyze|VBN|_ for|for|IN|_ statistical|statistical|JJ|_ significance|significance|NN|_ using|use|VBG|_ the|the|DT|_ MeV|mev|NN|_ package|package|NN|_
EJW3|ejw3|NN|_ ,|,|,|_ BW25113|bw25113|NN|_ rpoC|rpoc|NN|GEN K370|k370|NN|_ _|_|CD|_ A396dup|a396dup|NN|_
EJW3|ejw3|NN|_ in|in|IN|_ M9|m9|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
EJW3|ejw3|NN|_ in|in|IN|_ M9|m9|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
EJW3|ejw3|NN|_ in|in|IN|_ M9|m9|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.6|0.6|CD|_ M|m|NN|_ NaCl|nacl|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
EJW3|ejw3|NN|_ in|in|IN|_ M9|m9|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.6|0.6|CD|_ M|m|NN|_ NaCl|nacl|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
EYG1|eyg1|NN|_ in|in|IN|_ M9|m9|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
EYG1|eyg1|NN|_ in|in|IN|_ M9|m9|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
EYG1|eyg1|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ rpoC|rpoc|NN|GEN K370|k370|NN|_ _|_|CD|_ A396dup|a396dup|NN|_
EYG|eyg|NN|_ in|in|IN|_ M9|m9|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.6|0.6|CD|_ M|m|NN|_ NaCl|nacl|NN|_ Replicate|replicate|VB|_ 1|1|CD|_
EYG|eyg|NN|_ in|in|IN|_ M9|m9|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.6|0.6|CD|_ M|m|NN|_ NaCl|nacl|NN|_ Replicate|replicate|VB|_ 2|2|CD|_
genotype|genotype|NN|_ :|:|:|_ rpoC|rpoc|NN|GEN K370|k370|NN|_ _|_|CD|_ A396dup|a396dup|NN|_ mutant|mutant|JJ|_
genotype|genotype|NN|_ :|:|:|_ Wild-type|wild-type|JJ|_ strain|strain|NN|_
Grown|Grown|NNP|_ in|in|IN|_ glucose|glucose|NN|SUPP M9|m9|NN|_ media|media|NNS|_ with|with|IN|_ or|or|CC|_ without|without|IN|_ supplementation|supplementation|NN|_ of|of|IN|_ 0.6|0.6|CD|_ M|m|NN|_ NaCl|nacl|NN|_
MG1655|mg1655|NN|_
protocol|protocol|NN|_ :|:|:|_ M9|m9|NN|_
protocol|protocol|NN|_ :|:|:|_ M9|m9|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.6|0.6|CD|_ M|m|NN|_ NaCl|nacl|NN|_
Samples|sample|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ mid|mid|JJ|GrowthPhase exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD|od|NN|_ approx|approx|RB|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Cultures|culture|NNS|_ were|be|VBD|_ then|then|RB|_ quickly|quickly|RB|_ chilled|chill|VBN|_ to|to|TO|_ ≤|≤|VB|_ 4|4|CD|_ ºC|ºc|NN|_ on|on|IN|_ dry|dry|JJ|_ ice|ice|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
control|control|NN|_ strain|strain|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
L-threonine|l-threonine|NN|_ producing|produce|VBG|_ strain|strain|NN|_
L-threonine|l-threonine|NN|_ producing|produce|VBG|_ strain|strain|NN|_ vs|vs|CC|_ control|control|NN|_ strain|strain|NN|_
The|the|DT|_ mean|mean|JJ|_ signal|signal|NN|_ intensity|intensity|NN|_ values|value|NNS|_ of|of|IN|_ the|the|DT|_ duplicate|duplicate|VB|_ spots|spot|NNS|_ were|be|VBD|_ averaged|average|VBN|_ and|and|CC|_ then|then|RB|_ normalized|normalize|VBN|_ by|by|IN|_ the|the|DT|_ global|global|JJ|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_ The|the|DT|_ genes|gene|NNS|_ showing|show|VBG|_ the|the|DT|_ p-values|p-value|NNS|_ lower|lower|JJR|_ than|than|IN|_ 0.05|0.05|CD|_ were|be|VBD|_ considered|consider|VBN|_ to|to|TO|_ be|be|VB|_ significant|significant|JJ|_ .|.|.|_
using|use|VBG|_ RNeasy|RNeasy|NNP|_ Mini|Mini|NNP|_ Kit|kit|NN|_
W3110|w3110|NN|_ -LRB-|-lrb-|-LRB-|_ lacI-deleted|laci-deleted|JJ|_ -RRB-|-rrb-|-RRB-|_ strain|strain|NN|_ harboring|harbor|VBG|_ pKK223-3|pkk223-3|NN|_
ATCC2|atcc2|NN|_
ATCC3|atcc3|NN|_
Broiler|broiler|NN|_ Fecal|fecal|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
first|first|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ the|the|DT|_ use|use|NN|_ of|of|IN|_ SuperScriptII|superscriptii|NN|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ strand|strand|NN|_ cDNA|cdna|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ done|do|VBN|_ before|before|IN|_ end-pair|end-pair|JJ|_ and|and|CC|_ dA-tailing|da-tailing|JJ|_
Following|follow|VBG|_ \|\|SYM|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Preparation|Preparation|NNP|_ Guide|Guide|NNP|_ \|\|NNP|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ UCSC|UCSC|NNP|_ mm10|mm10|CD|_
Human|Human|NNP|_
No|No|NNP|_ treatment|treatment|NN|_
Reads|read|VBZ|_ longer|longer|JJR|_ than|than|IN|_ 25|25|CD|_ nt|nt|NNS|_ and|and|CC|_ ≤|≤|NN|_ 2|2|CD|_ N|n|NN|_ -LRB-|-lrb-|-LRB-|_ ambiguous|ambiguous|JJ|_ nucleotides|nucleotide|NNS|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ preserved|preserve|VBN|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
RNA-Seq|rna-seq|NN|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ were|be|VBD|_ done|do|VBN|_ using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ using|use|VBG|_ FASTX-Toolkit|fastx-toolkit|NN|_ version|version|NN|_ 0.0.13|0.0.13|CD|_ and|and|CC|_ Perl|Perl|NNP|_ version|version|NN|_ 5.8.8|5.8.8|CD|_
strain|strain|NN|_ :|:|:|_ E.|e.|FW|_ coli|coli|FW|_ ATCC|atcc|NN|_ 25922|25922|CD|_
strain|strain|NN|_ :|:|:|_ Poultry|Poultry|NNP|_ E.|E.|NNP|_ coli|coli|NN|_ Virulent|virulent|JJ|_ and|and|CC|_ multidrug|multidrug|JJ|_ resistant|resistant|JJ|_
Strains|strain|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ in|in|IN|_ MH|mh|NN|_ broth|broth|NN|_ at|at|IN|_ log|log|NN|_ phase|phase|NN|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ and|and|CC|_ raw|raw|JJ|_ fragment|fragment|NN|_ counts|count|NNS|_ for|for|IN|_ each|each|DT|_ Sample|Sample|NNP|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ extracted|extract|VBN|_ from|from|IN|_ the|the|DT|_ bacterial|bacterial|JJ|_ isolates|isolate|NNS|_ using|use|VBG|_ TRIzol|trizol|NN|_
Using|use|VBG|_ blind|blind|JJ|_ and|and|CC|_ fit-only|fit-only|JJ|_ parameter|parameter|NN|_ in|in|IN|_ DE-Seq|de-seq|NN|_ pakage|pakage|NN|_ ,|,|,|_ expressions|expression|NNS|_ of|of|IN|_ genes|gene|NNS|_ in|in|IN|_ all|all|DT|_ samples|sample|NNS|_ were|be|VBD|_ changed|change|VBN|_ to|to|TO|_ count|count|VB|_ per|per|IN|_ gene|gene|NN|_ ,|,|,|_ using|use|VBG|_ RNA-Seq|rna-seq|NN|_ protocol|protocol|NN|_ on|on|IN|_ Illumina|Illumina|NNP|_ HiSeq2500|hiseq2500|NN|_ platform|platform|NN|_
biomass|biomass|NN|_ collected|collect|VBN|_ in|in|IN|_ the|the|DT|_ transition|transition|NN|_ between|between|IN|_ exponential|exponential|JJ|_ to|to|TO|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
EHEC|ehec|NN|_ in|in|IN|_ LB|LB|NNP|_ Experiment|Experiment|NNP|_ 1|1|CD|_ -LSB-|-lsb-|-LRB-|_ RIBO-Seq|ribo-seq|NN|_ -RSB-|-rsb-|-RRB-|_
EHEC|ehec|NN|_ in|in|IN|_ LB|LB|NNP|_ Experiment|Experiment|NNP|_ 1|1|CD|_ -LSB-|-lsb-|-LRB-|_ RNA-Seq|rna-seq|NN|_ -RSB-|-rsb-|-RRB-|_
EHEC|ehec|NN|_ in|in|IN|_ LB|LB|NNP|_ Experiment|Experiment|NNP|_ 2|2|CD|_ -LSB-|-lsb-|-LRB-|_ RIBO-Seq|ribo-seq|NN|_ -RSB-|-rsb-|-RRB-|_
EHEC|ehec|NN|_ in|in|IN|_ LB|LB|NNP|_ Experiment|Experiment|NNP|_ 2|2|CD|_ -LSB-|-lsb-|-LRB-|_ RNA-Seq|rna-seq|NN|_ -RSB-|-rsb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism O157|o157|NN|_ :|:|:|_ H7|h7|NN|_ str|str|NN|_ .|.|.|_ EDL933|edl933|NN|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 002655|002655|CD|_
growth|growth|NN|_ media|media|NNS|_ :|:|:|_ LB|lb|NN|MED medium|medium|NN|MED
Illumina|Illumina|NNP|_ fastq|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ submitted|submit|VBN|_ to|to|TO|_ the|the|DT|_ galaxy|galaxy|NN|_ pipeline|pipeline|NN|_ =|=|JJ|_ >|>|JJR|_ grooming|grooming|NN|_ =|=|JJ|_ >|>|JJR|_ mapping|mapping|NN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 002655|002655|CD|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ default|default|NN|_ but|but|CC|_ seed|seed|NN|_ 19|19|CD|_ nt|nt|NNS|_ &|&|CC|_ zero|zero|CD|_ mismatches|mismatch|NNS|_ within|within|IN|_ seed|seed|NN|_ -RRB-|-rrb-|-RRB-|_
LB|lb|NN|MED medium|medium|NN|MED ,|,|,|_ 180|180|CD|_ rpm|rpm|NN|_ shaking|shake|VBG|_ ,|,|,|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ ,|,|,|_ between|between|IN|_ exponential|exponential|JJ|_ and|and|CC|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase
Library|Library|NNP|_ strategy|strategy|NN|_ :|:|:|_ RIBO-seq|ribo-seq|JJ|_
ligation|ligation|NN|_ ,|,|,|_ rt-PCR|rt-pcr|NN|_ ,|,|,|_ PCR|pcr|NN|_
OTHER|other|JJ|_
RNA-Seq|rna-seq|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Reads|read|NNS|_ ,|,|,|_ RPKM|rpkm|NN|_ ,|,|,|_ and|and|CC|_ RCV|RCV|NNP|_ mapped|map|VBD|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 002655|002655|CD|_ -LRB-|-lrb-|-LRB-|_ RCV|rcv|NN|_ =|=|JJ|_ Ribosomal|ribosomal|JJ|_ Coverage|Coverage|NNP|_ Value|value|NN|_ =|=|JJ|_ RPKM-footprint|rpkm-footprint|NN|_ over|over|IN|_ RPKM-transcription|rpkm-transcription|NN|_ -RRB-|-rrb-|-RRB-|_
Trizol|trizol|NN|_ for|for|IN|_ RNAseq|rnaseq|NN|_ ,|,|,|_ gradient|gradient|NN|_ centrifugation|centrifugation|NN|_ =|=|JJ|_ >|>|JJR|_ RNase|rnase|NN|_ digestions|digestion|NNS|_ =|=|JJ|_ >|>|JJR|_ Trizol|trizol|NN|_ =|=|JJ|_ >|>|JJR|_ gel|gel|NN|_ extraction|extraction|NN|_ for|for|IN|_ RIBOseq|riboseq|NN|_
Truseq|truseq|NN|_ Small|small|JJ|_ RNA|rna|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 018220|018220|CD|_ and|and|CC|_ NC|NC|NNP|_ _|_|SYM|_ 000913|000913|CD|_
MG1655|mg1655|NN|_ _|_|CD|_ LB|lb|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ LB1|lb1|NN|_
MG1655|mg1655|NN|_ _|_|CD|_ LB2|lb2|NN|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_
RNA-Seq|RNA-Seq|NNP|_
Single|single|JJ|_ colonies|colony|NNS|_ of|of|IN|_ P.|P.|NNP|_ putida|putida|NN|_ strain|strain|NN|_ DOT-T1E|dot-t1e|NN|_ and|and|CC|_ E.|e.|FW|_ coli|coli|FW|_ MG1655|mg1655|NN|_ were|be|VBD|_ grown|grow|VBN|_ overnight|overnight|RB|_ in|in|IN|_ Luria|Luria|NNP|_ --|--|:|_ Bertani|Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ medium|medium|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ .|.|.|_ Overnight|overnight|JJ|_ cultures|culture|NNS|_ were|be|VBD|_ diluted|dilute|VBN|_ to|to|TO|_ a|a|DT|_ starting|start|VBG|_ OD600|od600|NN|_ of|of|IN|_ 0.01|0.01|CD|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ medium|medium|NN|_ and|and|CC|_ 50|50|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ were|be|VBD|_ disposed|dispose|VBN|_ in|in|RP|_ separate|separate|JJ|_ 250|250|CD|_ ml|ml|NN|_ Erlenmeyer|erlenmeyer|NN|_ flasks|flask|NNS|_ and|and|CC|_ incubated|incubate|VBN|_ with|with|IN|_ shaking|shake|VBG|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ .|.|.|_ When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ 0.5|0.5|CD|_ at|at|IN|_ OD600|od600|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ antibiotics|antibiotic|NNS|_ were|be|VBD|_ added|add|VBN|_ at|at|IN|_ sub-lethal|sub-lethal|JJ|_ concentrations|concentration|NNS|_ to|to|TO|_ the|the|DT|_ culture|culture|NN|_ medium|medium|NN|_ to|to|TO|_ reach|reach|VB|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ µg|µg|NN|_
strain|strain|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CoK12|cok12|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|JJ|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ reads|read|VBZ|_ related|related|JJ|_ with|with|IN|_ MG1655|mg1655|NN|_ strain|strain|NN|_ in|in|IN|_ samples|sample|NNS|_ Co-culture|co-culture|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CoT1E|cot1e|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|JJ|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ reads|read|VBZ|_ related|related|JJ|_ with|with|IN|_ DOT-T1E|dot-t1e|NN|_ strain|strain|NN|_ in|in|IN|_ samples|sample|NNS|_ Co-culture|co-culture|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ K12|k12|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|NN|_ of|of|IN|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ samples|sample|NNS|_ MG1655|mg1655|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ T1E|t1e|NN|_ _|_|CD|_ LB.xlsx|lb.xlsx|NN|_ :|:|:|_ Average|average|NN|_ of|of|IN|_ expression|expression|NN|_ values|value|NNS|_ of|of|IN|_ samples|sample|NNS|_ DOT-T1E|dot-t1e|NN|_ _|_|CD|_ LB1|lb1|NN|_ and|and|CC|_ LB2|lb2|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimited|tab-delimited|JJ|_ text|text|NN|_ files|file|NNS|_ include|include|VBP|_ the|the|DT|_ average|average|NN|_ of|of|IN|_ the|the|DT|_ expression|expression|NN|_ values|value|NNS|_ obtained|obtain|VBN|_ in|in|IN|_ Rockhopper|Rockhopper|NNP|_ for|for|IN|_ the|the|DT|_ replicates|replicate|VBZ|_ of|of|IN|_ each|each|DT|_ condition|condition|NN|_
We|we|PRP|_ use|use|VBP|_ Rockhopper|Rockhopper|NNP|_ for|for|IN|_ alignment|alignment|NN|_ and|and|CC|_ the|the|DT|_ complete|complete|JJ|_ analysis|analysis|NN|_ of|of|IN|_ data|datum|NNS|_
Adapters|adapter|NNS|_ trimmed|trim|VBD|_ with|with|IN|_ Cutadapt|cutadapt|NN|_ -LRB-|-lrb-|-LRB-|_ v1|v1|NN|_ .12|.12|CD|_ -RRB-|-rrb-|-RRB-|_
Aligned|align|VBN|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ with|with|IN|_ bwa|bwa|NN|_ version|version|NN|_ 0.7.7|0.7.7|CD|_
bacterial|bacterial|JJ|_ cells|cell|NNS|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ to|to|TO|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase in|in|IN|_ Lysogeny|Lysogeny|NNP|_ broth|broth|NN|_ ,|,|,|_ 37oC|37oc|NN|_ with|with|IN|_ shaking|shake|VBG|_
Cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ after|after|IN|_ the|the|DT|_ addition|addition|NN|_ of|of|IN|_ rifampicin|rifampicin|NN|SUPP -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ μg|μg|NN|_
Count|count|NN|_ reads|read|VBZ|_ aligned|align|VBN|_ to|to|TO|_ each|each|DT|_ base|base|NN|_ IGVtools|igvtools|NN|_ -LRB-|-lrb-|-LRB-|_ version|version|NN|_ 2.3.71|2.3.71|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ window|window|NN|_ size|size|NN|_ =|=|JJ|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Gave|give|VBD|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ to|to|TO|_ all|all|DT|_ values|value|NNS|_ of|of|IN|_ 0|0|CD|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
genotype|genotype|NN|_
Index|Index|NNP|_ and|and|CC|_ sort|sort|NN|_ alignments|alignment|NNS|_ with|with|IN|_ samtools|samtool|NNS|_ version|version|NN|_ 1.2|1.2|CD|_
Normalized|normalize|VBN|_ decay|decay|NN|_ values|value|NNS|_ with|with|IN|_ average|average|NN|_ of|of|IN|_ stable|stable|JJ|_ genes|gene|NNS|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN
RNA-Seq|rna-seq|NN|_
rnc|rnc|SYM|GEN -|-|:|_ _|_|SYM|_ time0|time0|CD|_
rnc|rnc|SYM|GEN -|-|:|_ _|_|SYM|_ time10|time10|CD|_
rnc|rnc|SYM|GEN -|-|:|_ _|_|SYM|_ time20|time20|CD|_
rnc|rnc|SYM|GEN -|-|:|_ _|_|SYM|_ time2|time2|CD|_ .5|.5|CD|_
rnc|rnc|SYM|GEN -|-|:|_ _|_|SYM|_ time5|time5|CD|_
rnc|rnc|SYM|GEN -|-|:|_ _|_|SYM|_ time7|time7|CD|_ .5|.5|CD|_
rRNA|rrna|NN|_ reduction|reduction|NN|_ with|with|IN|_ EpiCentre|EpiCentre|NNP|_ Ribo-Zero|Ribo-Zero|NNP|_ Gram|Gram|NNP|_ Negative|negative|JJ|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ reduction|reduction|NN|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ug|ug|NN|_ -RRB-|-rrb-|-RRB-|_ &|&|CC|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Library|Library|NNP|_ Prep|Prep|NNP|_
strain|strain|NN|_ :|:|:|_ MG1693|mg1693|NN|_
strain|strain|NN|_ :|:|:|_ SK4455|sk4455|NNS|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ In|in|IN|_ the|the|DT|_ .|.|.|_ txt|txt|NN|_ files|file|VBZ|_ the|the|DT|_ first|first|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ coordinate|coordinate|NN|_ of|of|IN|_ the|the|DT|_ base|base|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ NC|NC|NNP|_ _|_|SYM|_ 000913.3|000913.3|CD|_ and|and|CC|_ the|the|DT|_ second|second|JJ|_ column|column|NN|_ is|be|VBZ|_ the|the|DT|_ number|number|NN|_ of|of|IN|_ normalized|normalize|VBN|_ reads|read|VBZ|_ at|at|IN|_ that|that|DT|_ position|position|NN|_ .|.|.|_ All|all|DT|_ 0|0|CD|_ values|value|NNS|_ were|be|VBD|_ given|give|VBN|_ a|a|DT|_ pseudocount|pseudocount|NN|_ of|of|IN|_ 0.01|0.01|CD|_ .|.|.|_ Counts|count|NNS|_ are|be|VBP|_ normalized|normalize|VBN|_ so|so|IN|_ that|that|IN|_ the|the|DT|_ averages|average|NNS|_ of|of|IN|_ ssrA|ssra|NN|GEN ,|,|,|_ ssrS|ssrs|NN|GEN ,|,|,|_ and|and|CC|_ rnpB|rnpb|NN|GEN are|be|VBP|_ stable|stable|JJ|_ throughout|throughout|IN|_ the|the|DT|_ decay|decay|NN|_ from|from|IN|_ 0|0|CD|_ to|to|TO|_ 20|20|CD|_ minutes|minute|NNS|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time0|time0|CD|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time10|time10|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time20|time20|JJ|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time2|time2|CD|_ .5|.5|CD|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time5|time5|CD|_
time|time|NN|_ point|point|NN|_ :|:|:|_ time7|time7|CD|_ .5|.5|CD|_
Total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ and|and|CC|_ DNase-treated|dnase-treated|JJ|_ according|accord|VBG|_ to|to|TO|_ published|publish|VBN|_ protocols|protocol|NNS|_ -LRB-|-lrb-|-LRB-|_ Khodurksy|khodurksy|NN|_ A|a|NN|_ ,|,|,|_ Bernstein|Bernstein|NNP|_ J|J|NNP|_ ,|,|,|_ Peter|Peter|NNP|_ B|B|NNP|_ ,|,|,|_ Rhodius|Rhodius|NNP|_ V|V|NNP|_ ,|,|,|_ Wendisch|Wendisch|NNP|_ V|V|NNP|_ ,|,|,|_ Zimmer|Zimmer|NNP|_ D.|D.|NNP|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism Spotted|spot|VBN|_ Double-Strand|Double-Strand|NNP|_ DNA|DNA|NNP|_ Microarrays|Microarrays|NNPS|_ -RRB-|-rrb-|-RRB-|_
WTA|WTA|NNP|_ _|_|SYM|_ time0|time0|CD|_
WTA|WTA|NNP|_ _|_|SYM|_ time10|time10|CD|_
WTA|WTA|NNP|_ _|_|SYM|_ time20|time20|CD|_
WTA|WTA|NNP|_ _|_|SYM|_ time2|time2|CD|_ .5|.5|CD|_
WTA|WTA|NNP|_ _|_|SYM|_ time5|time5|CD|_
WTA|WTA|NNP|_ _|_|SYM|_ time7|time7|CD|_ .5|.5|CD|_
WTB|wtb|NN|_ _|_|CD|_ time0|time0|NN|_
WTB|wtb|NN|_ _|_|CD|_ time2|time2|NN|_ .5|.5|CD|_
WTB|wtb|NN|_ _|_|SYM|_ time7|time7|CD|_ .5|.5|CD|_
10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ pre-adenylated|pre-adenylated|JJ|_ -LRB-|-lrb-|-LRB-|_ rApp|rapp|NN|_ -RRB-|-rrb-|-RRB-|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ nascent|nascent|JJ|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ mature|mature|JJ|_ -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_ in|in|IN|_ a|a|DT|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ using|use|VBG|_ 400|400|CD|_ U|U|NNP|_ T4|t4|NN|_ RNA|rna|NN|_ Ligase|ligase|NN|_ 2|2|CD|_ ,|,|,|_ Deletion|deletion|NN|_ Mutant|mutant|JJ|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ LR2D11310K|lr2d11310k|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ PEG-8000|peg-8000|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ Fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 65|65|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.3|8.3|CD|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP KCl|kcl|NN|_ ;|;|:|_ 5|5|CD|_ mM|mm|NN|KWSUPP MgCl2|mgcl2|NN|_ -RSB-|-rsb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ fragmented|fragment|VBN|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 8|8|CD|_ minutes|minute|NNS|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ in|in|IN|_ 5.5|5.5|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heat-denatured|heat-denatured|JJ|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 10|10|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 5|5|CD|_ pmol|pmol|NN|_ of|of|IN|_ RT|rt|NN|_ primer|primer|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_ RNaseOUT|RNaseOUT|NNP|_ ™|™|NNP|_ Recombinant|recombinant|JJ|_ Ribonuclease|ribonuclease|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 10777-019|10777-019|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ SuperScript|SuperScript|NNP|_ ®|®|SYM|_ III|iii|CD|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ -LRB-|-lrb-|-LRB-|_ Invitrogen|Invitrogen|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ 18080-044|18080-044|CD|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ minutes|minute|NNS|_ .|.|.|_ Template|template|NN|_ RNA|rna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ μl|μl|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ 40-150|40-150|CD|_ nt|nt|NN|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ passive|passive|NN|_ diffusion|diffusion|NN|_ in|in|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ moderate|moderate|JJ|_ shaking|shake|VBG|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg|μg|NN|_
10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ pre-adenylated|pre-adenylated|JJ|_ -LRB-|-lrb-|-LRB-|_ rApp|rapp|NN|_ -RRB-|-rrb-|-RRB-|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ 1|1|CD|_ μg|μg|NN|_ of|of|IN|_ nascent|nascent|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ either|either|CC|_ total|total|NN|_ ,|,|,|_ or|or|CC|_ rRNA-depleted|rrna-depleted|JJ|_ using|use|VBG|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ MRZB12424|mrzb12424|NN|_ -RRB-|-rrb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ using|use|VBG|_ 400|400|CD|_ U|U|NNP|_ T4|t4|NN|_ RNA|rna|NN|_ Ligase|ligase|NN|_ 2|2|CD|_ ,|,|,|_ Deletion|deletion|NN|_ Mutant|mutant|JJ|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ PEG-8000|peg-8000|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 5.5|5.5|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heat-denatured|heat-denatured|JJ|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 10|10|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 5|5|CD|_ pmol|pmol|NN|_ of|of|IN|_ RT|rt|NN|_ primer|primer|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_ RNaseOUT|RNaseOUT|NNP|_ ™|™|NNP|_ Recombinant|recombinant|JJ|_ Ribonuclease|ribonuclease|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ SuperScript|SuperScript|NNP|_ ®|®|SYM|_ III|iii|CD|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ minutes|minute|NNS|_ .|.|.|_ Template|template|NN|_ RNA|rna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ μl|μl|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ three|three|CD|_ gel|gel|NN|_ slices|slice|NNS|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ ranges|range|NNS|_ of|of|IN|_ 40-200|40-200|CD|_ nt|nt|NNS|_ ,|,|,|_ 200-400|200-400|CD|_ nt|nt|NNS|_ ,|,|,|_ and|and|CC|_ 400-600|400-600|CD|_ nt|nt|NNS|_ were|be|VBD|_ cut|cut|VBN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ passive|passive|NN|_ diffusion|diffusion|NN|_ in|in|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ moderate|moderate|JJ|_ shaking|shake|VBG|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg|μg|NN|_
10|10|CD|_ pmol|pmol|NN|_ of|of|IN|_ a|a|DT|_ pre-adenylated|pre-adenylated|JJ|_ -LRB-|-lrb-|-LRB-|_ rApp|rapp|NN|_ -RRB-|-rrb-|-RRB-|_ adapter|adapter|NN|_ were|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ rnpB|rnpb|NN|GEN nascent|nascent|JJ|_ RNA|rna|NN|_ in|in|IN|_ a|a|DT|_ reaction|reaction|NN|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ using|use|VBG|_ 400|400|CD|_ U|U|NNP|_ T4|t4|NN|_ RNA|rna|NN|_ Ligase|ligase|NN|_ 2|2|CD|_ ,|,|,|_ Deletion|deletion|NN|_ Mutant|mutant|JJ|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ %|%|NN|_ PEG-8000|peg-8000|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 25|25|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ hours|hour|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ RNA|rna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 5.5|5.5|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heat-denatured|heat-denatured|JJ|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 10|10|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 0.5|0.5|CD|_ mM|mm|NN|KWSUPP dNTPs|dntp|NNS|_ ,|,|,|_ 5|5|CD|_ pmol|pmol|NN|_ of|of|IN|_ RT|rt|NN|_ primer|primer|NN|_ ,|,|,|_ 20|20|CD|_ U|U|NNP|_ RNaseOUT|RNaseOUT|NNP|_ ™|™|NNP|_ Recombinant|recombinant|JJ|_ Ribonuclease|ribonuclease|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ and|and|CC|_ 100|100|CD|_ U|U|NNP|_ SuperScript|SuperScript|NNP|_ ®|®|SYM|_ III|iii|CD|_ Reverse|reverse|JJ|_ Transcriptase|transcriptase|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 50|50|CD|_ °C|°c|NN|_ for|for|IN|_ 50|50|CD|_ minutes|minute|NNS|_ .|.|.|_ Template|template|NN|_ RNA|rna|NN|_ was|be|VBD|_ degraded|degrade|VBN|_ by|by|IN|_ adding|add|VBG|_ 1|1|CD|_ μl|μl|NN|_ of|of|IN|_ 1|1|CD|_ M|m|NN|_ NaOH|naoh|NN|_ ,|,|,|_ and|and|CC|_ incubating|incubate|VBG|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Reaction|reaction|NN|_ clean-up|clean-up|JJ|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ cDNA|cdna|NN|_ was|be|VBD|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ cDNA|cdna|NN|_ fragments|fragment|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ in|in|IN|_ the|the|DT|_ range|range|NN|_ of|of|IN|_ 40-300|40-300|CD|_ nt|nt|NNS|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ DNA|dna|NN|_ was|be|VBD|_ recovered|recover|VBN|_ by|by|IN|_ passive|passive|NN|_ diffusion|diffusion|NN|_ in|in|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ moderate|moderate|JJ|_ shaking|shake|VBG|_ .|.|.|_ cDNA|cdna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg|μg|NN|_
2|2|CD|_ μg|μg|NN|_ of|of|IN|_ RNA|rna|NN|_ from|from|IN|_ the|the|DT|_ cytoplasmic|cytoplasmic|JJ|_ fraction|fraction|NN|_ were|be|VBD|_ diluted|dilute|VBN|_ in|in|IN|_ 20|20|CD|_ μl|μl|NN|_ of|of|IN|_ Fragmentation|fragmentation|NN|_ buffer|buffer|NN|_ ,|,|,|_ and|and|CC|_ fragmented|fragmented|JJ|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Fragmented|fragmented|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ .|.|.|_ End|end|NN|_ repair|repair|NN|_ of|of|IN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 20|20|CD|_ μl|μl|NN|_ ,|,|,|_ in|in|IN|_ the|the|DT|_ presence|presence|NN|_ of|of|IN|_ 20|20|CD|_ U|U|NNP|_ T4|t4|NN|_ Polynucleotide|Polynucleotide|NNP|_ Kinase|kinase|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ M0201L|m0201l|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 20|20|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ by|by|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 1|1|CD|_ hour|hour|NN|_ .|.|.|_ End-repaired|end-repaired|JJ|_ RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ again|again|RB|_ using|use|VBG|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ 2X|2x|NN|_ RNA|rna|NN|_ Loading|load|VBG|_ Dye|dye|NN|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ end-repaired|end-repaired|JJ|_ RNA|rna|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ heated|heat|VBN|_ to|to|TO|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ placed|place|VBN|_ on|on|IN|_ ice|ice|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ corresponding|correspond|VBG|_ to|to|TO|_ fragments|fragment|NNS|_ above|above|IN|_ 200|200|CD|_ nt|nt|NNS|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ The|the|DT|_ gel|gel|NN|_ slice|slice|NN|_ was|be|VBD|_ crushed|crush|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ through|through|IN|_ a|a|DT|_ punctured|punctured|JJ|_ 0.5|0.5|CD|_ ml|ml|NN|_ tube|tube|NN|_ ,|,|,|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ μl|μl|NN|_ of|of|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 60|60|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ then|then|RB|_ rotated|rotate|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ to|to|TO|_ allow|allow|VB|_ passive|passive|JJ|_ diffusion|diffusion|NN|_ of|of|IN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ into|into|IN|_ buffer|buffer|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg|μg|NN|_
3|3|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_
3|3|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ ,|,|,|_ Replicate|replicate|VB|_ #|#|#|_ 1|1|CD|_
3|3|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ ,|,|,|_ Replicate|replicate|VB|_ #|#|#|_ 2|2|CD|_
3|3|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_
3|3|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_ ,|,|,|_ Replicate|replicate|VB|_ #|#|#|_ 1|1|CD|_
3|3|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_ ,|,|,|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_ ,|,|,|_ Replicate|replicate|VB|_ #|#|#|_ 2|2|CD|_
A|a|DT|_ single|single|JJ|_ colony|colony|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism was|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ LB|lb|NN|MED medium|medium|NN|MED without|without|IN|_ antibiotics|antibiotic|NNS|_ ,|,|,|_ and|and|CC|_ grown|grow|VBN|_ at|at|IN|_ 37C|37c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 150|150|CD|_ RPM|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ approximately|approximately|RB|_ 4|4|CD|_ hours|hour|NNS|_ ,|,|,|_ until|until|IN|_ OD600|od600|NN|_ was|be|VBD|_ ~|~|CD|_ 0.3|0.3|CD|_ -LRB-|-lrb-|-LRB-|_ log|log|NN|_ phase|phase|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ EDTA|edta|NN|_ was|be|VBD|_ then|then|RB|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ for|for|IN|_ additional|additional|JJ|_ 5|5|CD|_ minutes|minute|NNS|_ to|to|TO|_ make|make|VB|_ bacteria|bacterium|NNS|_ permeable|permeable|JJ|_ to|to|TO|_ Actinomycin|Actinomycin|NNP|_ D.|D.|NNP|_ Actinomycin|Actinomycin|NNP|_ D|D|NNP|_ was|be|VBD|_ then|then|RB|_ added|add|VBN|_ to|to|TO|_ a|a|DT|_ final|final|JJ|_ concentration|concentration|NN|_ of|of|IN|_ 5|5|CD|_ g|g|NN|_
DMS-seq|dms-seq|NN|_ -LRB-|-lrb-|-LRB-|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_
DMS-seq|dms-seq|NN|_ -LRB-|-lrb-|-LRB-|_ Total|total|JJ|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_
Each|each|DT|_ bacteria|bacterium|NNS|_ pellet|pellet|NN|_ from|from|IN|_ a|a|DT|_ 25|25|CD|_ ml|ml|NN|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ~|~|NN|_ 0.3|0.3|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ homogeneously|homogeneously|RB|_ resuspended|resuspend|VBN|_ in|in|IN|_ 200|200|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|Buffer|NNP|_ A|A|NNP|_ -LSB-|-lsb-|-LRB-|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ ;|;|:|_ 20|20|CD|_ %|%|NN|_ Sucrose|sucrose|NN|_ ;|;|:|_ 100|100|CD|_ mM|mm|NN|KWSUPP NaCl|nacl|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 200|200|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ by|by|IN|_ pipetting|pipetting|NN|_ .|.|.|_ 50|50|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ B|b|NN|_ -LSB-|-lsb-|-LRB-|_ 50|50|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ ;|;|:|_ 120|120|CD|_ mM|mm|NN|KWSUPP Tris|Tris|NNP|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 1|1|CD|_ µl|µl|NN|_ Ready-Lyse|ready-lyse|NN|_ ™|™|CD|_ Lysozyme|Lysozyme|NNP|_ Solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ R1810M|r1810m|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ dropwise|dropwise|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ vial|vial|NN|_ was|be|VBD|_ gently|gently|RB|_ tilted|tilted|JJ|_ 5|5|CD|_ times|time|NNS|_ to|to|TO|_ ensure|ensure|VB|_ homogenous|homogenous|JJ|_ mixing|mix|VBG|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 1|1|CD|_ minute|minute|NN|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ 250|250|CD|_ µl|µl|NN|_ of|of|IN|_ Buffer|buffer|NN|_ C|c|NN|_ -LSB-|-lsb-|-LRB-|_ 0.5|0.5|CD|_ %|%|NN|_ Tween-20|tween-20|NN|_ :|:|:|_ 0.4|0.4|CD|_ %|%|NN|_ NaDOC|nadoc|NN|_ ;|;|:|_ 2|2|CD|_ M|m|NN|_ NaCl|nacl|NN|_ ;|;|:|_ 10|10|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -RSB-|-rsb-|-RRB-|_ were|be|VBD|_ immediately|immediately|RB|_ added|add|VBN|_ dropwise|dropwise|NN|_ .|.|.|_ The|the|DT|_ sample|sample|NN|_ was|be|VBD|_ then|then|RB|_ incubated|incubate|VBN|_ 5|5|CD|_ minutes|minute|NNS|_ at|at|IN|_ room|room|NN|_ temperature|temperature|NN|_ .|.|.|_ At|at|IN|_ this|this|DT|_ stage|stage|NN|_ the|the|DT|_ solution|solution|NN|_ clears|clear|VBZ|_ considerably|considerably|RB|_ without|without|IN|_ increasing|increase|VBG|_ its|its|PRP$|_ viscosity|viscosity|NN|_ ,|,|,|_ and|and|CC|_ nucleoid|nucleoid|JJ|_ becomes|become|VBZ|_ visible|visible|JJ|_ .|.|.|_ Using|use|VBG|_ a|a|DT|_ cut|cut|NN|_ P1000|p1000|NN|_ pipette|pipette|NN|_ tip|tip|NN|_ ,|,|,|_ the|the|DT|_ whole|whole|JJ|_ sample|sample|NN|_ was|be|VBD|_ gently|gently|RB|_ layered|layer|VBN|_ on|on|IN|_ the|the|DT|_ top|top|NN|_ of|of|IN|_ a|a|DT|_ 5-30|5-30|CD|_ %|%|NN|_ w|w|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
FastQ|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ examined|examine|VBN|_ using|use|VBG|_ the|the|DT|_ FastQC|fastqc|NN|_ tool|tool|NN|_ .|.|.|_ All|all|PDT|_ the|the|DT|_ relevant|relevant|JJ|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ nascent|nascent|JJ|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ analysis|analysis|NN|_ and|and|CC|_ normalization|normalization|NN|_ steps|step|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ custom|custom|NN|_ wrapper|wrapper|NN|_ built|build|VBN|_ on|on|IN|_ top|top|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ Framework13|framework13|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ reads|read|VBZ|_ were|be|VBD|_ clipped|clip|VBN|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Cutadapt|cutadapt|JJ|_ v1|v1|NN|_ .10|.10|CD|_ ,|,|,|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 15|15|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ to|to|TO|_ extract|extract|NN|_ transcripts|transcript|NNS|_ '|'|POS|_ sequences|sequence|NNS|_ .|.|.|_ Forward|forward|RB|_ and|and|CC|_ reverse|reverse|RB|_ reads|read|VBZ|_ were|be|VBD|_ independently|independently|RB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ transcriptome|transcriptome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v1|v1|NN|_ .1.2|.1.2|CD|_ ,|,|,|_ by|by|IN|_ allowing|allow|VBG|_ up|up|RP|_ to|to|TO|_ 7|7|CD|_ mapping|mapping|NN|_ positions|position|NNS|_ to|to|TO|_ enable|enable|VB|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ 7|7|CD|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -|-|:|_ m|m|NN|_ 7|7|CD|_ -|-|:|_ a|a|DT|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ -5|-5|CD|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ --|--|:|_ norc|norc|NN|_ for|for|IN|_ forward|forward|RB|_ reads|read|VBZ|_ ,|,|,|_ --|--|:|_ nofw|nofw|NN|_ for|for|IN|_ reverse|reverse|JJ|_ reads|read|VBZ|_ -RSB-|-rsb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Forward|forward|RB|_ and|and|CC|_ reverse|reverse|VB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ re-paired|re-paired|JJ|_ .|.|.|_ Using|use|VBG|_ reverse|reverse|JJ|_ read|read|NN|_ mapping|mapping|NN|_ positions|position|NNS|_ -LRB-|-lrb-|-LRB-|_ corresponding|correspond|VBG|_ to|to|TO|_ RNA|rna|NN|_ Polymerase|polymerase|NN|_ positions|position|NNS|_ along|along|IN|_ gene|gene|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ forward|forward|RB|_ reads|read|VBZ|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ separate|separate|JJ|_ SAM|SAM|NNP|_ files|file|NNS|_ for|for|IN|_ each|each|DT|_ transcription|transcription|NN|_ intermediate|intermediate|NN|_ .|.|.|_ When|when|WRB|_ analysis|analysis|NN|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ deciles|decile|NNS|_ of|of|IN|_ transcription|transcription|NN|_ ,|,|,|_ genes|gene|NNS|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ 10|10|CD|_ equally|equally|RB|_ sized|size|VBN|_ deciles|decile|NNS|_ ,|,|,|_ and|and|CC|_ reads|read|VBZ|_ belonging|belong|VBG|_ to|to|TO|_ transcription|transcription|NN|_ intermediates|intermediate|NNS|_ falling|fall|VBG|_ in|in|IN|_ the|the|DT|_ same|same|JJ|_ decile|decile|NN|_ were|be|VBD|_ pooled|pool|VBN|_ .|.|.|_ SAM|SAM|NNP|_ files|file|NNS|_ were|be|VBD|_ then|then|RB|_ passed|pass|VBN|_ to|to|TO|_ the|the|DT|_ rf-count|rf-count|JJ|_ tool|tool|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ Framework|framework|NN|_ to|to|TO|_ generate|generate|VB|_ RT-stop|rt-stop|JJ|_ counts|count|NNS|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ .|.|.|_ Resulting|result|VBG|_ RC|rc|NN|_ files|file|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ rf-norm|rf-norm|NN|_ tool|tool|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ Framework|framework|NN|_ in|in|IN|_ 50|50|CD|_ nt|nt|NNS|_ sliding|slide|VBG|_ windows|window|NNS|_ ,|,|,|_ with|with|IN|_ a|a|DT|_ 25|25|CD|_ nt|nt|NNS|_ offset|offset|VBP|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ sm|sm|NN|_ 2|2|CD|_ -|-|:|_ nm|nm|NN|_ 2|2|CD|_ -|-|:|_ ec|ec|NN|_ 0|0|CD|_ -|-|:|_ mc|mc|NN|_ 0|0|CD|_ -|-|:|_ n|n|NN|_ 50|50|CD|_ -|-|:|_ nw|nw|NN|_ 50|50|CD|_ -|-|:|_ wo|will|MD|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Mapping|mapping|NN|_ of|of|IN|_ DMS-seq|dms-seq|JJ|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ mature|mature|JJ|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ by|by|IN|_ using|use|VBG|_ the|the|DT|_ rf-count|rf-count|JJ|_ tool|tool|NN|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ cl|cl|NN|_ 15|15|CD|_ -|-|:|_ bm|bm|NN|_ 7|7|CD|_ -|-|:|_ ba|ba|SYM|_ -|-|:|_ b5|b5|NN|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Resulting|result|VBG|_ RC|rc|NN|_ files|file|NNS|_ were|be|VBD|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ rf-norm|rf-norm|NN|_ tool|tool|NN|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ sm|sm|NN|_ 2|2|CD|_ -|-|:|_ nm|nm|NN|_ 2|2|CD|_ -|-|:|_ ec|ec|NN|_ 50|50|CD|_ -|-|:|_ mc|mc|NN|_ 50|50|CD|_ -|-|:|_ n|n|NN|_ 50|50|CD|_ -|-|:|_ nw|nw|NN|_ 50|50|CD|_ -|-|:|_ wo|will|MD|_ 25|25|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ The|the|DT|_ rf-norm|rf-norm|JJ|_ tool|tool|NN|_ generates|generate|VBZ|_ a|a|DT|_ XML|xml|NN|_ file|file|NN|_ for|for|IN|_ each|each|DT|_ transcript|transcript|NN|_ -LRB-|-lrb-|-LRB-|_ or|or|CC|_ for|for|IN|_ each|each|DT|_ transcription|transcription|NN|_ intermediate|intermediate|JJ|_
FastQ|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ examined|examine|VBN|_ using|use|VBG|_ the|the|DT|_ FastQC|fastqc|NN|_ tool|tool|NN|_ .|.|.|_ All|all|PDT|_ the|the|DT|_ relevant|relevant|JJ|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ nascent|nascent|JJ|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ analysis|analysis|NN|_ and|and|CC|_ normalization|normalization|NN|_ steps|step|NNS|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ a|a|DT|_ custom|custom|NN|_ wrapper|wrapper|NN|_ built|build|VBN|_ on|on|IN|_ top|top|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ Framework13|framework13|NN|_ .|.|.|_ Briefly|briefly|RB|_ ,|,|,|_ reads|read|VBZ|_ were|be|VBD|_ clipped|clip|VBN|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Cutadapt|cutadapt|JJ|_ v1|v1|NN|_ .10|.10|CD|_ ,|,|,|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 15|15|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_ Forward|forward|RB|_ and|and|CC|_ reverse|reverse|RB|_ reads|read|VBZ|_ were|be|VBD|_ independently|independently|RB|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ RNase|rnase|NN|_ P|p|NN|_ -LRB-|-lrb-|-LRB-|_ rnpB|rnpb|NN|GEN -RRB-|-rrb-|-RRB-|_ gene|gene|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v1|v1|NN|_ .1.2|.1.2|CD|_ ,|,|,|_ by|by|IN|_ allowing|allow|VBG|_ up|up|RP|_ to|to|TO|_ 7|7|CD|_ mapping|mapping|NN|_ positions|position|NNS|_ to|to|TO|_ enable|enable|VB|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ 7|7|CD|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -|-|:|_ m|m|NN|_ 7|7|CD|_ -|-|:|_ a|a|DT|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ -5|-5|CD|_ 5|5|CD|_ -LSB-|-lsb-|-LRB-|_ --|--|:|_ norc|norc|NN|_ for|for|IN|_ forward|forward|RB|_ reads|read|VBZ|_ ,|,|,|_ --|--|:|_ nofw|nofw|NN|_ for|for|IN|_ reverse|reverse|JJ|_ reads|read|VBZ|_ -RSB-|-rsb-|-RRB-|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Forward|forward|RB|_ and|and|CC|_ reverse|reverse|VB|_ mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ then|then|RB|_ re-paired|re-paired|JJ|_ .|.|.|_ Using|use|VBG|_ reverse|reverse|JJ|_ read|read|NN|_ mapping|mapping|NN|_ positions|position|NNS|_ -LRB-|-lrb-|-LRB-|_ corresponding|correspond|VBG|_ to|to|TO|_ RNA|rna|NN|_ Polymerase|polymerase|NN|_ positions|position|NNS|_ along|along|IN|_ gene|gene|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ forward|forward|RB|_ reads|read|VBZ|_ were|be|VBD|_ split|split|VBN|_ into|into|IN|_ separate|separate|JJ|_ SAM|SAM|NNP|_ files|file|NNS|_ for|for|IN|_ each|each|DT|_ transcription|transcription|NN|_ intermediate|intermediate|NN|_ .|.|.|_ SAM|SAM|NNP|_ files|file|NNS|_ were|be|VBD|_ then|then|RB|_ passed|pass|VBN|_ to|to|TO|_ the|the|DT|_ rf-count|rf-count|JJ|_ tool|tool|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ Framework|framework|NN|_ to|to|TO|_ generate|generate|VB|_ RT-stop|rt-stop|JJ|_ counts|count|NNS|_ -LRB-|-lrb-|-LRB-|_ RC|rc|NN|_ -RRB-|-rrb-|-RRB-|_ files|file|NNS|_ ,|,|,|_ that|that|WDT|_ were|be|VBD|_ then|then|RB|_ normalized|normalize|VBN|_ using|use|VBG|_ the|the|DT|_ rf-norm|rf-norm|NN|_ tool|tool|NN|_ .|.|.|_
FastQ|fastq|NN|_ files|file|NNS|_ were|be|VBD|_ examined|examine|VBN|_ using|use|VBG|_ the|the|DT|_ FastQC|fastqc|NN|_ tool|tool|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ adapter|adapter|NN|_ sequences|sequence|NNS|_ using|use|VBG|_ Cutadapt|cutadapt|JJ|_ v1|v1|NN|_ .10|.10|CD|_ ,|,|,|_ discarding|discard|VBG|_ reads|read|VBZ|_ shorter|shorter|JJR|_ than|than|IN|_ 15|15|CD|_ nucleotides|nucleotide|NNS|_ .|.|.|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ -LRB-|-lrb-|-LRB-|_ GenBank|genbank|NN|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ as|as|IN|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ .|.|.|_ Reads|read|NNS|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie|Bowtie|NNP|_ v1|v1|NN|_ .1.2|.1.2|CD|_ ,|,|,|_ by|by|IN|_ allowing|allow|VBG|_ up|up|RP|_ to|to|TO|_ 7|7|CD|_ mapping|mapping|NN|_ positions|position|NNS|_ to|to|TO|_ enable|enable|VB|_ mapping|map|VBG|_ to|to|TO|_ the|the|DT|_ 7|7|CD|_ E.|e.|FW|_ coli|coli|FW|_ rRNA|rrna|NN|_ genes|gene|NNS|_ -LRB-|-lrb-|-LRB-|_ parameters|parameter|NNS|_ :|:|:|_ -|-|:|_ n|n|NN|_ 2|2|CD|_ -|-|:|_ m|m|NN|_ 7|7|CD|_ -|-|:|_ a|a|DT|_ --|--|:|_ best|best|JJS|_ --|--|:|_ strata|strata|NN|_ -5|-5|CD|_ 5|5|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .2|.2|NN|_
In|in|FW|_ vitro|vitro|FW|_ transcription|transcription|NN|_ reactions|reaction|NNS|_ were|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ a|a|DT|_ final|final|JJ|_ volume|volume|NN|_ of|of|IN|_ 50|50|CD|_ µl|µl|NN|_ .|.|.|_ Each|each|DT|_ reaction|reaction|NN|_ contained|contain|VBD|_ 2|2|CD|_ µl|µl|NN|_ E.|e.|FW|_ coli|coli|FW|_ RNA|rna|NN|_ Polymerase|polymerase|NN|_ Holoenzyme|holoenzyme|NN|_ -LRB-|-lrb-|-LRB-|_ NEB|neb|NN|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ M0551S|m0551s|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 5|5|CD|_ µl|µl|NN|_ E.|e.|FW|_ coli|coli|FW|_ RNA|rna|NN|_ Polymerase|polymerase|NN|_ Buffer|buffer|NN|_ -LRB-|-lrb-|-LRB-|_ 10X|10x|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 1|1|CD|_ µl|µl|NN|_ SUPERase|superase|NN|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ AM2696|am2696|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ 500|500|CD|_ ng|ng|NN|_ template|template|NN|_ DNA|dna|NN|_ .|.|.|_ Reactions|reaction|NNS|_ were|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ to|to|TO|_ allow|allow|VB|_ formation|formation|NN|_ of|of|IN|_ the|the|DT|_ RNA|rna|NN|_ Polymerase-DNA|polymerase-dna|JJ|_ binary|binary|JJ|_ complex|complex|NN|_ .|.|.|_ Transcription|transcription|NN|_ was|be|VBD|_ started|start|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ µl|µl|NN|_ NTPs|ntp|NNS|_ -LRB-|-lrb-|-LRB-|_ 25|25|CD|_ mM|mm|NN|KWSUPP each|each|DT|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ and|and|CC|_ incubated|incubate|VBN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ for|for|IN|_ 5|5|CD|_ minutes|minute|NNS|_ .|.|.|_ Transcription|transcription|NN|_ was|be|VBD|_ stopped|stop|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ µl|µl|NN|_ DNase|dnase|NN|_ I|i|CD|_ -LRB-|-lrb-|-LRB-|_ 50|50|CD|_ U|U|NNP|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ 3|3|CD|_ '|'|''|_ -|-|:|_ end|end|NN|_ RNA-seq|rna-seq|NN|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ DMS-seq|dms-seq|NN|_
library|library|NN|_ strategy|strategy|NN|_ :|:|:|_ SPET-seq|spet-seq|JJ|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ In|in|FW|_ vitro|vitro|FW|_ synthesized|synthesize|VBN|_ RNase|rnase|NN|_ P|p|NN|_ -LRB-|-lrb-|-LRB-|_ rnpB|rnpb|NN|GEN -RRB-|-rrb-|-RRB-|_ RNA|rna|NN|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ Cytosolic|cytosolic|JJ|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_
molecule|molecule|NN|_ subtype|subtype|NN|_ :|:|:|_ Total|total|JJ|_ RNA|rna|NN|_ -LRB-|-lrb-|-LRB-|_ Nucleoid|nucleoid|NN|_ fraction|fraction|NN|_ -RRB-|-rrb-|-RRB-|_
OTHER|other|NN|_
RNA-Seq|rna-seq|NN|_
RNA|rna|NN|_ was|be|VBD|_ purified|purify|VBN|_ on|on|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ following|follow|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ ,|,|,|_ and|and|CC|_ eluted|elute|VBN|_ in|in|IN|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ nuclease-free|nuclease-free|JJ|_ water|water|NN|_ .|.|.|_ 6|6|CD|_ μl|μl|NN|_ of|of|IN|_ 2X|2x|NN|_ RNA|rna|NN|_ Loading|load|VBG|_ Dye|dye|NN|_ -LRB-|-lrb-|-LRB-|_ ThermoScientific|ThermoScientific|NNP|_ ,|,|,|_ cat|cat|NN|_ .|.|.|_ R0641|r0641|NN|_ -RRB-|-rrb-|-RRB-|_ were|be|VBD|_ added|add|VBN|_ to|to|TO|_ purified|purify|VBN|_ RNA|rna|NN|_ .|.|.|_ Both|both|DT|_ DMS|dms|NN|_ treated|treat|VBN|_ and|and|CC|_ untreated|untreated|JJ|_ samples|sample|NNS|_ were|be|VBD|_ heated|heat|VBN|_ at|at|IN|_ 95|95|CD|_ °C|°c|NN|_ for|for|IN|_ 2|2|CD|_ minutes|minute|NNS|_ ,|,|,|_ and|and|CC|_ immediately|immediately|RB|_ placed|place|VBN|_ on|on|IN|_ ice|ice|NN|_ .|.|.|_ Samples|sample|NNS|_ were|be|VBD|_ resolved|resolve|VBN|_ on|on|IN|_ a|a|DT|_ 10|10|CD|_ %|%|NN|_ TBE-Urea|tbe-urea|NN|_ polyacrylamide|polyacrylamide|NN|_ gel|gel|NN|_ ,|,|,|_ and|and|CC|_ a|a|DT|_ gel|gel|NN|_ slice|slice|NN|_ ranging|range|VBG|_ from|from|IN|_ 50|50|CD|_ nt|nt|NNS|_ to|to|TO|_ the|the|DT|_ full-length|full-length|JJ|_ product|product|NN|_ was|be|VBD|_ cut|cut|VBN|_ .|.|.|_ Gel|gel|NN|_ slices|slice|NNS|_ were|be|VBD|_ crushed|crush|VBN|_ by|by|IN|_ centrifugation|centrifugation|NN|_ through|through|IN|_ a|a|DT|_ punctured|punctured|JJ|_ 0.5|0.5|CD|_ ml|ml|NN|_ tube|tube|NN|_ ,|,|,|_ and|and|CC|_ resuspended|resuspend|VBN|_ in|in|IN|_ 500|500|CD|_ μl|μl|NN|_ of|of|IN|_ Diffusion|Diffusion|NNP|_ buffer|buffer|NN|_ -LSB-|-lsb-|-LRB-|_ 500|500|CD|_ mM|mm|NN|KWSUPP Ammonium|ammonium|NN|_ acetate|acetate|NN|SUPP ;|;|:|_ 0.05|0.05|CD|_ %|%|NN|_ SDS|sds|NN|_ -RSB-|-rsb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 60|60|CD|_ U|U|NNP|_ SUPERase|SUPERase|NNP|_ •|•|SYM|_ In|in|IN|_ ™|™|CD|_ RNase|rnase|NN|_ Inhibitor|inhibitor|NN|_ ,|,|,|_ then|then|RB|_ rotated|rotate|VBD|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ for|for|IN|_ 16|16|CD|_ hours|hour|NNS|_ to|to|TO|_ allow|allow|VB|_ passive|passive|JJ|_ diffusion|diffusion|NN|_ of|of|IN|_ RNA|rna|NN|_ fragments|fragment|NNS|_ into|into|IN|_ buffer|buffer|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ precipitated|precipitate|VBN|_ by|by|IN|_ addition|addition|NN|_ of|of|IN|_ 1|1|CD|_ ml|ml|NN|_ Isopropanol|isopropanol|NN|_ ,|,|,|_ and|and|CC|_ 2|2|CD|_ μl|μl|NN|_ Glycogen|glycogen|NN|_ -LRB-|-lrb-|-LRB-|_ 20|20|CD|_ μg|μg|NN|_
rnpB|rnpb|NN|GEN SPET-seq|spet-seq|NN|_ -LRB-|-lrb-|-LRB-|_ in|in|FW|_ vitro|vitro|FW|_ -RRB-|-rrb-|-RRB-|_
SPET-seq|spet-seq|NN|_ -LRB-|-lrb-|-LRB-|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_
SPET-seq|spet-seq|NN|_ -LRB-|-lrb-|-LRB-|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Replicate|replicate|VB|_ #|#|#|_ 1|1|CD|_
SPET-seq|spet-seq|NN|_ -LRB-|-lrb-|-LRB-|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ Replicate|replicate|VB|_ #|#|#|_ 2|2|CD|_
SPET-seq|spet-seq|NN|_ -LRB-|-lrb-|-LRB-|_ Total|total|JJ|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
substr|substr|NN|_ :|:|:|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ DMS-seq|dms-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ 's|'s|POS|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Mapped|map|VBN|_ reads|read|VBZ|_ were|be|VBD|_ rescaled|rescale|VBN|_ to|to|TO|_ a|a|DT|_ size|size|NN|_ of|of|IN|_ 10|10|CD|_ bp|bp|NN|_ ,|,|,|_ and|and|CC|_ BEDGraph|bedgraph|NN|_ files|file|NNS|_ were|be|VBD|_ generated|generate|VBN|_ using|use|VBG|_ the|the|DT|_ genomeCoverageBed|genomecoveragebed|JJ|_ utility|utility|NN|_ of|of|IN|_ the|the|DT|_ BEDTools|bedtool|NNS|_ suite|suite|NN|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ 's|'s|POS|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ SPET-seq|spet-seq|NN|_ data|datum|NNS|_ -LRB-|-lrb-|-LRB-|_ pooled|pooled|JJ|_ Total|total|JJ|_ and|and|CC|_ Ribo|Ribo|NNP|_ -|-|:|_ RNA|rna|NN|_ from|from|IN|_ both|both|DT|_ replicates|replicate|VBZ|_ -RRB-|-rrb-|-RRB-|_ is|be|VBZ|_ provided|provide|VBN|_ in|in|IN|_ the|the|DT|_ form|form|NN|_ of|of|IN|_ RNA|rna|NN|_ Framework|framework|NN|_ 's|'s|POS|_ -LRB-|-lrb-|-LRB-|_ http|http|NN|_ :|:|:|_
10A|10a|NN|_ _|_|CD|_ MG+PMA|MG+PMA|NNP|_ _|_|CD|_ t60|t60|NN|_
10B|10b|NN|_ _|_|CD|_ MG+PMA|MG+PMA|NNP|_ _|_|CD|_ t60|t60|NN|_
10C|10c|CD|_ _|_|NN|_ MG+PMA|mg+pma|NN|_ _|_|CD|_ t60|t60|NN|_
1A|1a|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t0|t0|NN|_
1B|1b|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t0|t0|NN|_
1C|1c|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t0|t0|NN|_
2A|2a|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t10|t10|NN|_
2B|2b|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t10|t10|NN|_
2C|2c|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t10|t10|NN|_
3A|3a|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t30|t30|NN|_
3B|3b|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t30|t30|NN|_
3C|3c|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t30|t30|NN|_
4A|4a|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t60|t60|NN|_
4B|4b|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t60|t60|NN|_
4C|4c|NN|_ _|_|CD|_ MG|mg|NN|_ _|_|NN|_ t60|t60|NN|_
5A|5a|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t10|t10|NN|_
5B|5b|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t10|t10|NN|_
5C|5c|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t10|t10|NN|_
6A|6a|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t30|t30|NN|_
6B|6b|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t30|t30|NN|_
6C|6c|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t30|t30|NN|_
7A|7a|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t60|t60|NN|_
7B|7b|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t60|t60|NN|_
7C|7c|NN|_ _|_|CD|_ MG+H|mg+h|NN|_ g|g|NN|_ _|_|CD|_ t60|t60|NN|_
8A|8a|NN|_ _|_|CD|_ MG+PMA|MG+PMA|NNP|_ _|_|CD|_ t10|t10|NN|_
8B|8b|NN|_ _|_|CD|_ MG+PMA|MG+PMA|NNP|_ _|_|CD|_ t10|t10|NN|_
8C|8c|NN|_ _|_|CD|_ MG+PMA|MG+PMA|NNP|_ _|_|CD|_ t10|t10|NN|_
9A|9a|NN|_ _|_|CD|_ MG+PMA|MG+PMA|NNP|_ _|_|SYM|_ t30|t30|CD|_
9B|9b|NN|_ _|_|SYM|_ MG+PMA|mg+pma|JJS|_ _|_|SYM|_ t30|t30|CD|_
9C|9c|NN|_ _|_|NN|_ MG+PMA|mg+pma|NN|_ _|_|CD|_ t30|t30|NN|_
E.|E.|NNP|_ coli|coli|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
For|for|IN|_ each|each|DT|_ biological|biological|JJ|_ RNA-Seq|rna-seq|NN|_ replicate|replicate|VB|_ E|e|NN|_ coli|coli|NN|_ K-12|k-12|NN|_ MG1655|mg1655|NN|_ was|be|VBD|_ subcultured|subculture|VBN|_ from|from|IN|_ cyrostorage|cyrostorage|NN|_ on|on|IN|_ Luria-Bertani|Luria-Bertani|NNP|_ -LRB-|-lrb-|-LRB-|_ LB|LB|NNP|_ -RRB-|-rrb-|-RRB-|_ agar|agar|NN|_ overnight|overnight|JJ|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ .|.|.|_ A|a|DT|_ half-dozen|half-dozen|JJ|_ well-isolated|well-isolated|JJ|_ colonies|colony|NNS|_ were|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ starter|starter|JJ|_ culture|culture|NN|_ in|in|IN|_ Neidhardt|Neidhardt|NNP|_ MOPS|MOPS|NNP|MED Minimal|minimal|JJ|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ NM3|nm3|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Neidhardt|Neidhardt|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 1974|1974|CD|_ ,|,|,|_ J|J|NNP|_ Bacteriol|Bacteriol|NNP|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ 0.2|0.2|CD|_ %|%|NN|_ final|final|JJ|_ glucose|glucose|NN|SUPP concentration|concentration|NN|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 20|20|CD|_ mg|mg|NN|_
Forward|forward|RB|_ -|-|:|_ and|and|CC|_ reverse-read|reverse-read|JJ|_ mate-pairs|mate-pair|NNS|_ were|be|VBD|_ assembled|assemble|VBN|_ and|and|CC|_ aligned|align|VBN|_ to|to|TO|_ the|the|DT|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism MG1655|mg1655|NN|_ K-12|k-12|NN|_ genome|genome|NN|_ using|use|VBG|_ Bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nat|Nat|NNP|_ Methods|method|NNS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ SAMtools|samtool|NNS|_ -LRB-|-lrb-|-LRB-|_ Li|Li|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2009|2009|CD|_ ,|,|,|_ Bioinformatics|bioinformatic|NNS|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ convert|convert|VB|_ Bowtie2|bowtie2|NN|_ output|output|NN|_ -LRB-|-lrb-|-LRB-|_ .|.|.|_ bam|bam|NN|_ file|file|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ SAM|SAM|NNP|_ format|format|NN|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ ASM584v2|asm584v2|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ -RRB-|-rrb-|-RRB-|_
Mapped|map|VBD|_ read|read|VBN|_ counts|count|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ for|for|IN|_ differential|differential|JJ|_ expression|expression|NN|_ -LRB-|-lrb-|-LRB-|_ false|false|JJ|_ discovery|discovery|NN|_ rate|rate|NN|_ of|of|IN|_ <|<|JJR|_ 0.01|0.01|CD|_ ,|,|,|_ fold-change|fold-change|JJ|_ >|>|RBR|_ 2|2|LS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ baySeq|bayseq|NN|_ package|package|NN|_ in|in|IN|_ R|r|NN|_ -LRB-|-lrb-|-LRB-|_ Hardcastle|hardcastle|NN|_ and|and|CC|_ Kelly|Kelly|NNP|_ ,|,|,|_ 2010|2010|CD|_ ,|,|,|_ BMC|BMC|NNP|_ Bioinformatics|Bioinformatics|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Within|within|IN|_ baySeq|bayseq|NN|_ ,|,|,|_ two-way|two-way|JJ|_ comparisons|comparison|NNS|_ using|use|VBG|_ quantile|quantile|JJ|_ normalization|normalization|NN|_ were|be|VBD|_ made|make|VBN|_ for|for|IN|_ all|all|DT|_ three|three|CD|_ biological|biological|JJ|_ replicate|replicate|VBP|_ transcriptomes|transcriptome|NNS|_ over|over|IN|_ time|time|NN|_ for|for|IN|_ HgCl2|hgcl2|NN|_ exposure|exposure|NN|_ or|or|CC|_ PMA|pma|NN|_ exposure|exposure|NN|_ versus|versus|CC|_ the|the|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_
One|one|CD|_ cell|cell|NN|_ pellet|pellet|NN|_ from|from|IN|_ each|each|DT|_ condition|condition|NN|_ and|and|CC|_ sampling|sampling|NN|_ time|time|NN|_ was|be|VBD|_ thawed|thaw|VBN|_ on|on|IN|_ ice|ice|NN|_ ;|;|:|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ by|by|IN|_ RNAsnap|rnasnap|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Stead|stead|NN|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ Nucleic|Nucleic|NNP|_ Acids|Acids|NNP|_ Res|Res|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ contamination|contamination|NN|_ was|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ two|two|CD|_ treatments|treatment|NNS|_ with|with|IN|_ Turbo-DNase|turbo-dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ;|;|:|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ depletion|depletion|NN|_ was|be|VBD|_ performed|perform|VBN|_ with|with|IN|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ rRNA|rrna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ concentrated|concentrate|VBD|_ using|use|VBG|_ RNA|rna|NN|_ Clean|clean|JJ|_ and|and|CC|_ Concentrator|Concentrator|NNP|_ ™|™|SYM|_ -5|-5|CD|_ columns|column|NNS|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ following|follow|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_
Quality|Quality|NNP|_ control|control|NN|_ processing|processing|NN|_ of|of|IN|_ sequence|sequence|NN|_ data|datum|NNS|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Galaxy|galaxy|NN|_ -LRB-|-lrb-|-LRB-|_ https|http|NNS|_ :|:|:|_
RNA-Seq|rna-seq|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ raw|raw|JJ|_ read|read|NN|_ counts|count|VBZ|_ as|as|RB|_ determined|determine|VBN|_ by|by|IN|_ HTseq-Count|htseq-count|NN|_ ,|,|,|_ provided|provide|VBN|_ in|in|IN|_ .|.|.|_ csv|csv|NN|_ format|format|NN|_
The|the|DT|_ number|number|NN|_ of|of|IN|_ sequence|sequence|NN|_ reads|read|VBZ|_ that|that|IN|_ aligned|align|VBN|_ to|to|TO|_ features|feature|NNS|_ in|in|IN|_ annotation|annotation|NN|_ file|file|NN|_ -LRB-|-lrb-|-LRB-|_ Escherichia|escherichia|FW|_ _|_|FW|_ coli|coli|FW|_ _|_|SYM|_ str|str|FW|_ _|_|FW|_ k|k|NN|_ _|_|SYM|_ 12|12|CD|_ _|_|SYM|_ substr|substr|FW|_ _|_|FW|_ mg1655.GCA|mg1655.gca|NN|_ _|_|SYM|_ 000005845.2.24|000005845.2.24|CD|_ .|.|.|_ gtf|gtf|NN|_ from|from|IN|_ http|http|NN|_ :|:|:|_
The|the|DT|_ quality|quality|NN|_ and|and|CC|_ quantity|quantity|NN|_ of|of|IN|_ rRNA-depleted|rrna-depleted|JJ|_ RNA|rna|NN|_ was|be|VBD|_ assessed|assess|VBN|_ on|on|IN|_ a|a|DT|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ RNA|rna|NN|_ pico|pico|NN|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ recommendations|recommendation|NNS|_ .|.|.|_ Next|next|JJ|_ generation|generation|NN|_ sequencing|sequencing|NN|_ -LRB-|-lrb-|-LRB-|_ NGS|ngs|NN|_ -RRB-|-rrb-|-RRB-|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ using|use|VBG|_ the|the|DT|_ Kapa|Kapa|NNP|_ biosystems|biosystem|NNS|_ NGS|NGS|NNP|_ stranded|strand|VBD|_ library|library|NN|_ prep|prep|JJ|_ kit|kit|NN|_ for|for|IN|_ RNA-Seq|rna-seq|NN|_ with|with|IN|_ dual|dual|JJ|_ indexed|index|VBN|_ Illumina|Illumina|NNP|_ adapters|adapter|NNS|_ .|.|.|_ The|the|DT|_ mode|mode|NN|_ library|library|NN|_ insert|insert|NN|_ size|size|NN|_ was|be|VBD|_ ~|~|CD|_ 150|150|CD|_ bp|bp|NN|_ ,|,|,|_ as|as|IN|_ determined|determine|VBN|_ by|by|IN|_ high|high|JJ|_ sensitivity|sensitivity|NN|_ NGS|ngs|NN|_ fragment|fragment|NN|_ analysis|analysis|NN|_ kit|kit|NN|_ for|for|IN|_ Fragment|fragment|NN|_ Analyzer|analyzer|NN|_ ™|™|NN|_ -LRB-|-lrb-|-LRB-|_ Advanced|Advanced|NNP|_ Analytical|Analytical|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ instructions|instruction|NNS|_ .|.|.|_ Quantification|quantification|NN|_ of|of|IN|_ each|each|DT|_ library|library|NN|_ was|be|VBD|_ done|do|VBN|_ by|by|IN|_ qPCR|qpcr|NN|_ and|and|CC|_ all|all|DT|_ 30|30|CD|_ libraries|library|NNS|_ were|be|VBD|_ pooled|pool|VBN|_ in|in|IN|_ equal|equal|JJ|_ concentrations|concentration|NNS|_ .|.|.|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t10|t10|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t30|t30|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ HgCl2|hgcl2|NN|_ at|at|IN|_ t60|t60|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t10|t10|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t30|t30|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|NN|_ +|+|CC|_ 3µM|3µm|NN|_ PMA|pma|NN|_ at|at|IN|_ t60|t60|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t0|t0|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t10|t10|NN|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t30|t30|CD|_
treatment|treatment|NN|_ :|:|:|_ MG1655|mg1655|SYM|_ -|-|:|_ unexposed|unexposed|JJ|_ at|at|IN|_ t60|t60|CD|_
When|when|WRB|_ cultures|culture|NNS|_ reached|reach|VBD|_ OD595|od595|NN|_ ≈|≈|CD|_ 0.470|0.470|CD|_ -LRB-|-lrb-|-LRB-|_ ~|~|NN|_ 200|200|CD|_ min|min|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ two|two|CD|_ cultures|culture|NNS|_ were|be|VBD|_ made|make|VBN|_ 3|3|CD|_ µM|µm|NN|_ mercuric|mercuric|NN|_ chloride|chloride|NN|_ -LRB-|-lrb-|-LRB-|_ HgCl2|hgcl2|NN|_ -RRB-|-rrb-|-RRB-|_ or|or|CC|_ 3|3|CD|_ µM|µm|NN|_ phenylmercuric-acetate|phenylmercuric-acetate|NN|_ -LRB-|-lrb-|-LRB-|_ PMA|pma|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ third|third|JJ|_ was|be|VBD|_ left|leave|VBN|_ as|as|IN|_ an|a|DT|_ unexposed|unexposed|JJ|_ control|control|NN|_ .|.|.|_ Duplicate|duplicate|VB|_ 1|1|CD|_ ml|ml|NN|_ aliquots|aliquot|NNS|_ of|of|IN|_ each|each|DT|_ culture|culture|NN|_ were|be|VBD|_ collected|collect|VBN|_ at|at|IN|_ 0|0|CD|_ -LRB-|-lrb-|-LRB-|_ unexposed|unexposed|JJ|_ control|control|NN|_ only|only|RB|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ 10|10|CD|_ ,|,|,|_ 30|30|CD|_ ,|,|,|_ 60|60|CD|_ min|min|NN|_ after|after|IN|_ mercurial|mercurial|JJ|_ exposure|exposure|NN|_ and|and|CC|_ immediately|immediately|RB|_ centrifuged|centrifuge|VBN|_ at|at|IN|_ 21|21|CD|_ krpm|krpm|NN|_ ,|,|,|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ .|.|.|_ Spent|spent|JJ|_ medium|medium|NN|_ was|be|VBD|_ aspirated|aspirate|VBN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ frozen|freeze|VBN|_ at|at|IN|_ -70|-70|CD|_ °C|°c|NN|_ within|within|IN|_ 5|5|CD|_ min|min|NN|_ after|after|IN|_ collection|collection|NN|_ .|.|.|_
5|5|CD|_ min|min|NN|_ after|after|IN|_ UVtreatment|uvtreatment|NN|_ 1|1|CD|_ ,|,|,|_ 40J|40j|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ in|in|IN|_ Davis|Davis|NNP|_ +0.4|+0.4|CD|_ %|%|NN|_ glu|glu|NN|_
5|5|CD|_ min|min|NN|_ untreatedcells|untreatedcell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
60|60|CD|_ min|min|NN|_ after|after|IN|_ UVtreatment|uvtreatment|NN|_ 1|1|CD|_ ,|,|,|_ 40J|40j|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ in|in|IN|_ Davis|Davis|NNP|_ +0.4|+0.4|CD|_ %|%|NN|_ glu|glu|NN|_
60|60|CD|_ min|min|NN|_ untreatedcells|untreatedcell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
60|60|CD|_ min|min|NN|_ UV|uv|NN|_ treated|treat|VBN|_ cells|cell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_
60|60|CD|_ min|min|NN|_ UVtreatment|uvtreatment|NN|_ control|control|NN|_ ,|,|,|_ MG1655|mg1655|NN|_ in|in|IN|_ Davis|Davis|NNP|_ +0.4|+0.4|CD|_ %|%|NN|_ glu|glu|NN|_
Bacteria|bacterium|NNS|_ cells|cell|NNS|_
Basecalls|basecall|NNS|_ performed|perform|VBN|_ using|use|VBG|_ CASAVA|CASAVA|NNP|_ version|version|NN|_ 1.8.2|1.8.2|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ CP009273|cp009273|NN|_ .1|.1|CD|_
MT|mt|NNS|_ _|_|VBP|_ 12h|12h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
MT|mt|NNS|_ _|_|VBP|_ 12h|12h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
MT|mt|NNS|_ _|_|VBP|_ 24h|24h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
MT|mt|NNS|_ _|_|VBP|_ 24h|24h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
MT|mt|NNS|_ _|_|VBP|_ 48h|48h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
MT|mt|NNS|_ _|_|VBP|_ 48h|48h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
MT|mt|NNS|_ _|_|VBP|_ 6h|6h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
MT|mt|NNS|_ _|_|VBP|_ 6h|6h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
product|product|NN|_ :|:|:|_ Butanol|Butanol|NNP|_
Quantification|quantification|NN|_ of|of|IN|_ gene|gene|NN|_ expression|expression|NN|_ and|and|CC|_ analysis|analysis|NN|_ of|of|IN|_ gene|gene|NN|_ differential|differential|JJ|_ expression|expression|NN|_ were|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Fragment|fragment|NN|_ Per|per|IN|_ Kilo|Kilo|NNP|_ bases|basis|NNS|_ per|per|IN|_ Million|Million|NNP|_ reads|read|VBZ|_ -LRB-|-lrb-|-LRB-|_ FPKM|fpkm|NN|_ -RRB-|-rrb-|-RRB-|_ value|value|NN|_ based|base|VBN|_ rsem|rsem|NN|_ software|software|NN|_ version|version|NN|_ 1.2.4|1.2.4|CD|_ and|and|CC|_ edgeR|edger|NN|_ version|version|NN|_ 3.4.2|3.4.2|CD|_ -LRB-|-lrb-|-LRB-|_ Bioconductor|bioconductor|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ respectively|respectively|RB|_
RNA|rna|NN|_ libraries|library|NNS|_ were|be|VBD|_ prepared|prepare|VBN|_ for|for|IN|_ sequencing|sequencing|NN|_ using|use|VBG|_ standard|standard|JJ|_ Illumina|Illumina|NNP|_ protocols|protocol|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
Sequenced|sequence|VBN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ for|for|IN|_ adaptor|adaptor|NN|_ sequence|sequence|NN|_ ,|,|,|_ and|and|CC|_ masked|mask|VBN|_ for|for|IN|_ low-complexity|low-complexity|NN|_ or|or|CC|_ low-quality|low-quality|JJ|_ sequence|sequence|NN|_ ,|,|,|_ then|then|RB|_ mapped|map|VBD|_ to|to|TO|_ CP009273|CP009273|NNP|_ .1|.1|CD|_ whole|whole|JJ|_ genome|genome|NN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_
strain|strain|NN|_ :|:|:|_ BW25113|bw25113|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Excel|Excel|NNP|_ file|file|NN|_ include|include|VBP|_ FPKM|fpkm|NN|_ values|value|NNS|_ of|of|IN|_ different|different|JJ|_ genes|gene|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
Total|Total|NNP|_ RNAs|rna|NNS|_ were|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ TRIzol|trizol|NN|_ reagent|reagent|NN|_ ,|,|,|_ followed|follow|VBN|_ by|by|IN|_ clean-up|clean-up|JJ|_ and|and|CC|_ DNase|dnase|NN|_ I|i|CD|_ treatment|treatment|NN|_ with|with|IN|_ QIAGEN|QIAGEN|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_ .|.|.|_ Illumina|Illumina|NNP|_ TruSeq|TruSeq|NNP|_ RNA|rna|NN|_ Sample|sample|NN|_ Prep|Prep|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #FC|#fc|NN|_ -122-1001|-122-1001|CD|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ for|for|IN|_ the|the|DT|_ construction|construction|NN|_ of|of|IN|_ sequencing|sequencing|NN|_ libraries|library|NNS|_ .|.|.|_
WT|WT|NNP|_ _|_|SYM|_ 12h|12h|CD|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 12h|12h|NN|_ _|_|CD|_ rep2|rep2|NN|_
WT|wt|VBD|_ _|_|CD|_ 24h|24h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
WT|wt|VBD|_ _|_|CD|_ 24h|24h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
WT|wt|JJ|_ _|_|NN|_ 48h|48h|NN|_ _|_|CD|_ rep1|rep1|NN|_
WT|wt|JJ|_ _|_|NN|_ 48h|48h|NN|_ _|_|CD|_ rep2|rep2|NN|_
WT|wt|VBD|_ _|_|CD|_ 6h|6h|JJ|_ _|_|NN|_ rep1|rep1|NN|_
WT|wt|VBD|_ _|_|CD|_ 6h|6h|JJ|_ _|_|NN|_ rep2|rep2|NN|_
cell|cell|NN|_ culture|culture|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
evolved|evolve|VBD|_ 1|1|CD|_ min|min|NN|_ rep6|rep6|NN|_
evolved|evolve|VBD|_ 1|1|CD|_ min|min|NN|_ rep8|rep8|NN|_
evolved|evolve|VBD|_ 5|5|CD|_ min|min|NN|_ rep6|rep6|NN|_
evolved|evolve|VBD|_ 5|5|CD|_ min|min|NN|_ rep8|rep8|NN|_
evolved|evolve|VBD|_ 9|9|CD|_ min|min|NN|_ rep6|rep6|NN|_
evolved|evolve|VBD|_ 9|9|CD|_ min|min|NN|_ rep7|rep7|NN|_
Fragmentation|fragmentation|NN|_ and|and|CC|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ of|of|IN|_ RNA|rna|NN|_ with|with|IN|_ random|random|JJ|_ primers|primer|NNS|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ NEB|NEB|NNP|_ First|First|NNP|_ Strand|Strand|NNP|_ Synthesis|synthesis|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Second|second|JJ|_ strand|strand|NN|_ synthesis|synthesis|NN|_ was|be|VBD|_ done|do|VBN|_ with|with|IN|_ the|the|DT|_ NEBNext|nebnext|NN|_ Ultra|Ultra|NNP|_ Directional|Directional|NNP|_ RNA|rna|NN|_ Second|second|JJ|_ Strand|strand|NN|_ Synthesis|synthesis|NN|_ Module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ then|then|RB|_ purified|purify|VBN|_ with|with|IN|_ 1.7|1.7|CD|_ x|x|CC|_ AMPURE|AMPURE|NNP|_ Bead|Bead|NNP|_ XP|xp|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ DNA|dna|NN|_ end|end|NN|_ repair|repair|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ with|with|IN|_ the|the|DT|_ NEBNext|nebnext|NN|_ end|end|NN|_ repair|repair|NN|_ module|module|NN|_ ,|,|,|_ dA-tailing|da-tailing|NN|_ used|use|VBD|_ the|the|DT|_ NEBNext|nebnext|NN|_ dA-Tailing|da-tailing|NN|_ Module|module|NN|_ and|and|CC|_ adapter|adapter|NN|_ ligation|ligation|NN|_ used|use|VBD|_ the|the|DT|_ NEBNext|NEBNext|NNP|_ Quick|Quick|NNP|_ Ligation|ligation|NN|_ module|module|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ PCR|pcr|NN|_ amplification|amplification|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ for|for|IN|_ 10|10|CD|_ rounds|round|NNS|_ of|of|IN|_ synthesis|synthesis|NN|_ using|use|VBG|_ the|the|DT|_ NEBNext|nebnext|NN|_ High-Fidelity|high-fidelity|NN|_ PCR|pcr|NN|_ Master|master|NN|_ Mix|mix|VB|_ with|with|IN|_ NEBNext|nebnext|NN|_ USER|user|NN|_ Enzyme|enzyme|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ samples|sample|NNS|_ were|be|VBD|_ purified|purify|VBN|_ with|with|IN|_ 1.0|1.0|CD|_ x|x|CC|_ AMPURE|AMPURE|NNP|_ Bead|Bead|NNP|_ XP|xp|NN|_ -LRB-|-lrb-|-LRB-|_ Beckman|Beckman|NNP|_ Coulter|Coulter|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Library|Library|NNP|_ quality|quality|NN|_ was|be|VBD|_ verified|verify|VBN|_ on|on|IN|_ a|a|DT|_ Bio-Analyzer|Bio-Analyzer|NNP|_ DNA|DNA|NNP|_ chip|chip|NN|_ -LRB-|-lrb-|-LRB-|_ Agilent|agilent|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ U00096|u00096|NN|_ .3|.3|NN|_ -LRB-|-lrb-|-LRB-|_ E.|e.|FW|_ coli|coli|FW|_ K12|k12|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ NC|nc|NN|_ _|_|VBP|_ 001604.1|001604.1|CD|_ -LRB-|-lrb-|-LRB-|_ T7|t7|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ excluding|exclude|VBG|_ ribosomal|ribosomal|JJ|_ genes|gene|NNS|_ ,|,|,|_ and|and|CC|_ with|with|IN|_ recoded|recode|VBN|_ gene|gene|NN|_ 10|10|CD|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Bull|bull|NN|_ ,|,|,|_ 2012|2012|CD|_ ,|,|,|_ PMCID|pmcid|NN|_ :|:|:|_ PMC3457771|pmc3457771|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ place|place|NN|_ of|of|IN|_ wild-type|wild-type|JJ|_ sequence|sequence|NN|_ for|for|IN|_ analysis|analysis|NN|_ of|of|IN|_ recoded|recode|VBN|_ and|and|CC|_ evolved|evolve|VBD|_ strains|strain|NNS|_
infection|infection|NN|_ :|:|:|_ T7|t7|NN|_
pseudoalignment|pseudoalignment|NN|_ and|and|CC|_ quantitation|quantitation|NN|_ with|with|IN|_ kallisto|kallisto|FW|_ v0|v0|FW|_ .42.5|.42.5|CD|_ with|with|IN|_ parameters|parameter|NNS|_ --|--|:|_ single|single|JJ|_ -|-|:|_ l|l|NN|_ 450|450|CD|_ -|-|:|_ s|s|NNS|_ 250|250|CD|_
RNA-Seq|rna-seq|JJ|_
RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ Trizol|Trizol|NNP|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Fisher|Fisher|NNP|_ Scientific|Scientific|NNP|_ -RRB-|-rrb-|-RRB-|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ tab-delimitted|tab-delimitted|JJ|_ text|text|NN|_ files|file|NNS|_ contain|contain|VBP|_ TPM|tpm|NN|_ -LRB-|-lrb-|-LRB-|_ transcripts|transcript|NNS|_ per|per|IN|_ million|million|CD|_ -RRB-|-rrb-|-RRB-|_ values|value|NNS|_ for|for|IN|_ each|each|DT|_ sample|sample|NN|_
t7|t7|NN|_ genotype|genotype|NN|_ :|:|:|_ evolved|evolve|VBD|_ ,|,|,|_ codon-deoptimized|codon-deoptimized|JJ|_ gene|gene|NN|_ 10|10|CD|_
t7|t7|NN|_ genotype|genotype|NN|_ :|:|:|_ wild-type|wild-type|JJ|_ gene|gene|NN|_ 10|10|CD|_
t7|t7|NN|_ strain|strain|NN|_ :|:|:|_ evolved|evolve|VBD|_
t7|t7|NN|_ strain|strain|NN|_ :|:|:|_ wild|wild|JJ|_ type|type|NN|_
time|time|NN|_ :|:|:|_ 1|1|CD|_ min|min|NN|_ post-infection|post-infection|JJ|_
time|time|NN|_ :|:|:|_ 5|5|CD|_ min|min|NN|_ post-infection|post-infection|JJ|_
time|time|NN|_ :|:|:|_ 9|9|CD|_ min|min|NN|_ post-infection|post-infection|JJ|_
WT|wt|NN|_ 1|1|CD|_ min|min|NN|_ rep7|rep7|NN|_
WT|wt|VBD|_ 9|9|CD|_ min|min|NN|_ rep7|rep7|NN|_
WT|wt|VBD|_ 9|9|CD|_ min|min|NN|_ rep8|rep8|NN|_
3XSCOTS|3xscots|CD|_ cDNA|cdna|NN|_ 24|24|CD|_ h|h|NN|_ post-infection|post-infection|JJ|_
3XSCOTS|3xscot|NNS|_ cDNA|cdna|NN|_ in|in|IN|_ RPMI|rpmi|NN|_ medium|medium|NN|_
3XSCOTS|3xscots|CD|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ 24|24|CD|_ h|h|NN|_ post-infection|post-infection|JJ|_
3XSCOTS|3xscot|NNS|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ 2h|2h|JJ|_ post-infection|post-infection|JJ|_
3XSCOTS|3xscot|NNS|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ 8h|8h|JJ|_ post-infection|post-infection|JJ|_
3XSCOTS|3xscot|NNS|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ 8h|8h|JJ|_ post-infection|post-infection|JJ|_
3XSCOTS|3xscot|NNS|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ after|after|IN|_ 8h|8h|JJ|_ post-infection|post-infection|JJ|_
3XSCOTS|3xscot|NNS|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ in|in|IN|_ RPMI|rpmi|NN|_
3XSCOTS|3xscots|CD|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ in|in|IN|_ RPMI|rpmi|NN|_ medium|medium|NN|_
After|after|IN|_ backgroud|backgroud|NN|_ correction|correction|NN|_ and|and|CC|_ total|total|JJ|_ intensity|intensity|NN|_ normalization|normalization|NN|_ ,|,|,|_ ratio|ratio|NN|_ to|to|TO|_ reference|reference|NN|_ were|be|VBD|_ calculated|calculate|VBN|_ and|and|CC|_ log|log|NN|_ base|base|NN|_ 2|2|CD|_ transformed|transform|VBN|_
EDL933|edl933|NN|_ 24|24|CD|_ h|h|NN|_ post|post|NN|_ infection|infection|NN|_ in|in|IN|_ THP-1|thp-1|NN|_ humans|human|NNS|_ cells|cell|NNS|_
EDL933|edl933|NN|_ 8h|8h|NN|_ post-infection|post-infection|NN|_ in|in|IN|_ THP-1|thp-1|NN|_ human|human|JJ|_ cells|cell|NNS|_
EDL933|edl933|NN|_ 8h|8h|NN|_ post|post|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_
EDL933|edl933|NN|_ cDNA|cdna|NN|_ 24|24|CD|_ h|h|NN|_ post-infcetion|post-infcetion|NN|_ of|of|IN|_ THP-1|thp-1|NN|_ human|human|JJ|_ cells|cell|NNS|_
EDL933|edl933|NN|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ 24|24|CD|_ h|h|NN|_ post|post|NN|_ -|-|:|_ infection|infection|NN|_ of|of|IN|_ THP-1|thp-1|NN|_ human|human|JJ|_ cells|cell|NNS|_
EDL933|edl933|NN|_ cDNA|cdna|NN|_ obtained|obtain|VBN|_ 24h|24h|JJ|_ post-infection|post-infection|NN|_ of|of|IN|_ THP-1|thp-1|NN|_ human|human|JJ|_ cells|cell|NNS|_
EDL933|edl933|NN|_ from|from|IN|_ overnight|overnight|JJ|_ culture|culture|NN|_ in|in|IN|_ LB|lb|NN|MED broth|broth|NN|MED
EDL933|edl933|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
EDL933|edl933|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
EDL933|edl933|NN|_ genommic|genommic|JJ|_ DNA|dna|NN|_
EDL933|edl933|NN|_ infection|infection|NN|_ of|of|IN|_ THP-1|thp-1|NN|_ cells|cell|NNS|_ ,|,|,|_ recovered|recover|VBD|_ 2|2|CD|_ h|h|NN|_ post-infection|post-infection|JJ|_
EDL933|edl933|NN|_ infection|infection|NN|_ of|of|IN|_ THP-1|thp-1|NN|_ cells|cell|NNS|_ ,|,|,|_ recovered|recover|VBD|_ 2h|2h|JJ|_ post-infection|post-infection|JJ|_
EDL933|edl933|NN|_ in|in|IN|_ humans|human|NNS|_ macrophages|macrophage|NNS|_ 8h|8h|VBP|_ post-infection|post-infection|JJ|_
EDL933|edl933|NN|_ in|in|IN|_ RPMI|rpmi|NN|_ medium|medium|NN|_
EDL933|edl933|NN|_ in|in|IN|_ THP-1|thp-1|NN|_ cells|cell|NNS|_ 8h|8h|VBP|_ post-infection|post-infection|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genomic|genomic|JJ|_ DNA|dna|NN|_ E.|e.|FW|_ coli|coli|FW|_ EDL933|edl933|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ from|from|IN|_ EDL933|edl933|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ of|of|IN|_ EDL933|edl933|NN|_
Genomic|genomic|JJ|_ DNA|dna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ by|by|IN|_ standard|standard|JJ|_ phenol-chloroform|phenol-chloroform|NN|_ method|method|NN|_ -LRB-|-lrb-|-LRB-|_ Sambrook|Sambrook|NNP|_ ,|,|,|_ J|J|NNP|_ ,|,|,|_ Molecular|molecular|JJ|_ Cloning|cloning|NN|_ ,|,|,|_ 3rd|3rd|JJ|_ Edition|edition|NN|_ -RRB-|-rrb-|-RRB-|_
Reference|Reference|NNP|_ DNA|DNA|NNP|_ genomic|genomic|JJ|_ DNA|dna|NN|_
Reference|Reference|NNP|_ genomic|genomic|JJ|_ DNA|dna|NN|_
REference|reference|NN|_ genomic|genomic|JJ|_ DNA|dna|NN|_
RPMI|rpmi|NN|_ 1A|1a|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ first|first|JJ|_ duplicate|duplicate|VB|_
RPMI|rpmi|NN|_ 1B|1b|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
RPMI|rpmi|NN|_ 2A|2a|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ ,|,|,|_ first|first|RB|_ replicate|replicate|VB|_
RPMI|rpmi|NN|_ 2B|2b|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
T24|t24|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ first|first|JJ|_ replicate|replicate|VB|_
T24|t24|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
T24|t24|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ first|first|JJ|_ replicate|replicate|VB|_
T24|t24|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
T2|t2|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ first|first|RB|_ replicate|replicate|VB|_
T2|t2|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
T2|t2|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ first|first|JJ|_ replicate|replicate|VB|_
T2|t2|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
T8|t8|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ first|first|RB|_ replicate|replicate|VB|_
T8|t8|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 1|1|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
T8|t8|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ first|first|JJ|_ replicate|replicate|VB|_
T8|t8|NN|_ THP-1|thp-1|NN|_ infection|infection|NN|_ ,|,|,|_ Microarray|Microarray|NNP|_ #|#|#|_ 2|2|CD|_ second|second|JJ|_ replicate|replicate|VBP|_
TRIzol|trizol|NN|_ reagent|reagent|NN|_ -LRB-|-lrb-|-LRB-|_ Gibco|Gibco|NNP|_ BRL|brl|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ instruction|instruction|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ treated|treat|VBN|_ with|with|IN|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Ambion|ambion|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ sample|sample|NN|_ was|be|VBD|_ converted|convert|VBN|_ to|to|TO|_ cDNA|cdna|NN|_ in|in|IN|_ 5|5|CD|_ independent|independent|JJ|_ reverse-transcription|reverse-transcription|JJ|_ reactions|reaction|NNS|_ as|as|IN|_ described|describe|VBN|_ previously|previously|RB|_ -LRB-|-lrb-|-LRB-|_ Graham|Graham|NNP|_ ,|,|,|_ J.|J.|NNP|_ 1999|1999|CD|_ .|.|.|_ PNAS|PNAS|NNP|_ 96:11554-559|96:11554-559|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Bacterial|bacterial|JJ|_ transcript|transcript|NN|_ were|be|VBD|_ purified|purify|VBN|_ from|from|IN|_ host|host|NN|_ transcript|transcript|NN|_ by|by|IN|_ using|use|VBG|_ 3|3|CD|_ round|round|NN|_ of|of|IN|_ the|the|DT|_ SCOTS|SCOTS|NNP|_ procedure|procedure|NN|_ -LRB-|-lrb-|-LRB-|_ Daigle|daigle|NN|_ ,|,|,|_ F.|F.|NNP|_ 2002|2002|CD|_ .|.|.|_ Methods|method|NNS|_ Enzymol|Enzymol|NNP|_ .|.|.|_ 358:108-122|358:108-122|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Data|Data|NNP|_ were|be|VBD|_ analyzed|analyze|VBN|_ with|with|IN|_ RMA|rma|NN|_ -LRB-|-lrb-|-LRB-|_ Robust|robust|JJ|_ Multiarray|Multiarray|NNP|_ Analysis|analysis|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ Affymetrix|Affymetrix|NNP|_ default|default|NN|_ analysis|analysis|NN|_ settings|setting|NNS|_ and|and|CC|_ global|global|JJ|_ scaling|scaling|NN|_ as|as|IN|_ normalization|normalization|NN|_ method|method|NN|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF N|n|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF Q|Q|NNP|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ _|_|NN|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ CRP|crp|NN|TF R|r|NN|_ strain|strain|NN|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ acetate|acetate|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ acetate|acetate|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ and|and|CC|_ its|its|PRP$|_ mutants|mutant|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ M9|m9|NN|MED minimal|minimal|JJ|MED medium|medium|NN|MED with|with|IN|_ 10mM|10mm|NN|_ glucose|glucose|NN|SUPP or|or|CC|_ 30mM|30mm|NN|_ acetate|acetate|NN|SUPP as|as|IN|_ sole|sole|JJ|_ carbon|carbon|NN|_ source|source|NN|_ .|.|.|_ Samples|sample|NNS|_ for|for|IN|_ RNA|rna|NN|_ extraction|extraction|NN|_ were|be|VBD|_ taken|take|VBN|_ in|in|IN|_ middle|middle|JJ|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 0.5|0.5|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ in|in|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase -LRB-|-lrb-|-LRB-|_ OD600|od600|NN|_ ≈|≈|CD|_ 1.5|1.5|CD|_ -RRB-|-rrb-|-RRB-|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ glucose|glucose|NN|SUPP _|_|NN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl1|repl1|NN|_
E.|E.|NNP|_ coli|coli|NN|_ Wild|Wild|NNP|_ type|type|NN|_ _|_|CD|_ glucose|glucose|NN|SUPP _|_|NN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase _|_|NN|_ repl2|repl2|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ acetate|acetate|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ exponential|exponential|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep1|rep1|NN|_
E.|e.|FW|_ coli|coli|FW|_ wt|wt|JJ|_ grown|grow|VBN|_ in|in|IN|_ glucose|glucose|NN|SUPP batch|batch|NN|_ minimal|minimal|JJ|_ media|media|NNS|_ ,|,|,|_ cells|cell|NNS|_ were|be|VBD|_ harvested|harvest|VBN|_ at|at|IN|_ stationary|stationary|JJ|GrowthPhase phase|phase|NN|GrowthPhase ,|,|,|_ biological|biological|JJ|_ rep2|rep2|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism K-12|k-12|NN|_
genotyp|genotyp|NN|_
Total|total|JJ|_ RNA|rna|NN|_ extraction|extraction|NN|_ using|use|VBG|_ Vantage|Vantage|NNP|_ ™|™|CD|_ RNA|rna|NN|_ Purification|purification|NN|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Origene|Origene|NNP|_ ,|,|,|_ Rockville|Rockville|NNP|_ ,|,|,|_ MD|MD|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ performed|perform|VBN|_ according|accord|VBG|_ with|with|IN|_ the|the|DT|_ manufacter|manufacter|NN|_ instructions|instruction|NNS|_ .|.|.|_ Purity|purity|NN|_ and|and|CC|_ concentration|concentration|NN|_ of|of|IN|_ isolated|isolate|VBN|_ RNA|rna|NN|_ were|be|VBD|_ assessed|assess|VBN|_ in|in|IN|_ a|a|DT|_ NanoDrop|NanoDrop|NNP|_ One|one|CD|_ spectrophotometer|spectrophotometer|NN|_ -LRB-|-lrb-|-LRB-|_ Thermo|Thermo|NNP|_ Scientific|Scientific|NNP|_ Incorporated|Incorporated|NNP|_ ,|,|,|_ WI|WI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ Quality|Quality|NNP|_ was|be|VBD|_ evaluated|evaluate|VBN|_ by|by|IN|_ microfluidic|microfluidic|JJ|_ capillary|capillary|JJ|_ electrophoresis|electrophoresis|NN|_ on|on|IN|_ an|a|DT|_ Agilent|Agilent|NNP|_ 2100|2100|CD|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Inc|Inc|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Adpater|adpater|NN|_ sequences|sequence|NNS|_ were|be|VBD|_ clipped|clip|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
AR1|ar1|NN|_ -|-|:|_
Base|base|NN|_ calls|call|NNS|_ were|be|VBD|_ made|make|VBN|_ using|use|VBG|_ MiSeq|MiSeq|NNP|_ Reporter|reporter|NN|_ v.|v.|CC|_ 2.6.2.1|2.6.2.1|CD|_
Cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ in|in|IN|_ Tissue|tissue|NN|_ and|and|CC|_ Cell|cell|NN|_ lysis|lysis|NN|_ solution|solution|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ proteinase|proteinase|NN|_ K.|K.|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ and|and|CC|_ DNase|dnase|NN|_ treated|treat|VBN|_ using|use|VBG|_ the|the|DT|_ RNeasy|RNeasy|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ amount|amount|NN|_ of|of|IN|_ total|total|JJ|_ RNA|rna|NN|_ in|in|IN|_ each|each|DT|_ sample|sample|NN|_ was|be|VBD|_ quantified|quantify|VBN|_ using|use|VBG|_ the|the|DT|_ Qubit|Qubit|NNP|_ 2.0|2.0|CD|_ Flurometer|Flurometer|NNP|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ quality|quality|NN|_ was|be|VBD|_ assessed|assess|VBN|_ using|use|VBG|_ the|the|DT|_ RNA6000|rna6000|NN|_ Nano|Nano|NNP|_ Chip|Chip|NNP|_ on|on|IN|_ the|the|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ 2100|2100|CD|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
Cells|cell|NNS|_ were|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ TB7|tb7|NN|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP until|until|IN|_ OD600|od600|NN|_ ~|~|NN|_ 1.8|1.8|CD|_ .|.|.|_
Differential|differential|JJ|_ expression|expression|NN|_ testing|testing|NN|_ between|between|IN|_ sample|sample|NN|_ groups|group|NNS|_ was|be|VBD|_ performed|perform|VBN|_ in|in|IN|_ Rstudio|Rstudio|NNP|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.0.36|1.0.36|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ DESeq2|deseq2|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 1.14.1|1.14.1|CD|_ -RRB-|-rrb-|-RRB-|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_
genotype|genotype|NN|_
growth|growth|NN|_ phase|phase|NN|_ :|:|:|_ Late|late|JJ|_ exponential|exponential|JJ|_
K100Q|k100q|NN|_
K100Q|k100q|NN|_ rep|rep|NN|GEN 1|1|CD|_
K100Q|k100q|NN|_ rep|rep|NN|GEN 2|2|CD|_
K100Q|k100q|NN|_ rep|rep|NN|GEN 3|3|CD|_
K100R|k100r|NN|_
K100R|k100r|NN|_ rep|rep|NN|GEN 1|1|CD|_
K100R|k100r|NN|_ rep|rep|NN|GEN 2|2|CD|_
K100R|k100r|NN|_ rep|rep|NN|GEN 3|3|CD|_
Low|low|JJ|_ quality|quality|NN|_ reads|read|VBZ|_ were|be|VBD|_ trimmed|trim|VBN|_ with|with|IN|_ CutAdapt|cutadapt|JJ|_
Mapped|map|VBD|_ reads|read|VBZ|_ were|be|VBD|_ counted|count|VBN|_ using|use|VBG|_ the|the|DT|_ Python|Python|NNP|_ package|package|NN|_ HTSeq|htseq|NN|_ -LRB-|-lrb-|-LRB-|_ v.|v.|CC|_ 0.6.1|0.6.1|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ;|;|:|_ htseq-count|htseq-count|NN|_ -|-|:|_ m|m|NN|_ union|union|NN|_ -|-|:|_ r|r|NN|_ pos|pos|SYM|_ -|-|:|_ i|i|FW|_ gene|gene|NN|_ _|_|NN|_ name|name|NN|_ -|-|:|_ a|a|DT|_ 10|10|CD|_
media|media|NNS|_ :|:|:|_ Tryptone|tryptone|NN|_ broth|broth|NN|_ buffered|buffer|VBD|_ to|to|TO|_ pH|ph|NN|_ 7|7|CD|_ supplemented|supplement|VBN|_ with|with|IN|_ 22|22|CD|_ mM|mm|NN|KWSUPP glucose|glucose|NN|SUPP
RNA-Seq|rna-seq|NN|_
rRNA|rrna|NN|_ depletion|depletion|NN|_ ,|,|,|_ fragmentation|fragmentation|NN|_ ,|,|,|_ reverse|reverse|JJ|_ transcription|transcription|NN|_ ,|,|,|_ tagging|tagging|NN|_ ,|,|,|_ barcoding|barcoding|NN|_ ,|,|,|_ limited|limited|JJ|_ cycle|cycle|NN|_ PCR|pcr|NN|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_
ScriptSeq|scriptseq|NN|_ v2|v2|NN|_ Complete|complete|JJ|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ EpiCentre|EpiCentre|NNP|_ -RRB-|-rrb-|-RRB-|_
strain|strain|NN|_ :|:|:|_ K-12|k-12|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ Comma|comma|NN|_ separated|separated|JJ|_ value|value|NN|_ files|file|NNS|_ include|include|VBP|_ log-fold|log-fold|JJ|_ changes|change|NNS|_ and|and|CC|_ associated|associate|VBN|_ p-values|p-value|NNS|_ for|for|IN|_ each|each|DT|_ comparison|comparison|NN|_ made|make|VBD|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ text|text|NN|_ files|file|NNS|_ containing|contain|VBG|_ gene|gene|NN|_ counts|count|VBZ|_ output|output|NN|_ by|by|IN|_ htseq-count|htseq-count|JJ|_
The|the|DT|_ resulting|result|VBG|_ reads|read|VBZ|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ reference|reference|NN|_ genome|genome|NN|_ of|of|IN|_ Escherichia|escherichia|FW|Organism coli|coli|FW|Organism str|str|FW|_ .|.|.|_ K-12|k-12|NN|_ substr|substr|NN|_ .|.|.|_ MG1655|mg1655|NN|_ using|use|VBG|_ Tophat2|tophat2|NN|_ using|use|VBG|_ the|the|DT|_ following|follow|VBG|_ parameters|parameter|NNS|_ ,|,|,|_ --|--|:|_ GTF|gtf|NN|_ --|--|:|_ library|library|NN|_ type|type|NN|_ fr-secondstrand|fr-secondstrand|JJ|_
WT|wt|JJ|_ rep|rep|NN|GEN 1|1|CD|_
WT|wt|JJ|_ rep|rep|NN|GEN 2|2|CD|_
WT|wt|JJ|_ rep|rep|NN|GEN 3|3|CD|_
Affymetrix|Affymetrix|NNP|_ Microarray|Microarray|NNP|_ Suite|Suite|NNP|_ 5.0|5.0|CD|_
Dilution|Dilution|NNP|_ rate|rate|NN|_ =|=|JJ|_ 0.14|0.14|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 0|0|CD|_ %|%|NN|_ tannin|tannin|NN|_ _|_|NN|_ #|#|#|_ 2|2|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 0|0|CD|_ %|%|NN|_ tannin|tannin|NN|_ _|_|NN|_ #|#|#|_ 8|8|CD|_
E.coli|e.coli|NNS|_ _|_|VBP|_ 1|1|CD|_ %|%|NN|_ tannin|tannin|NN|_ _|_|NN|_ #|#|#|_ 3|3|CD|_
e.coli|e.coli|NNS|_ _|_|VBP|_ 1|1|CD|_ %|%|NN|_ tannin|tannin|NN|_ _|_|NN|_ #|#|#|_ 5|5|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW13711|bw13711|NN|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ plus|plus|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP with|with|IN|_ 1|1|CD|_ %|%|NN|_ Acacia|Acacia|NNP|_ mearnsii|mearnsii|NN|_ condensed|condensed|JJ|_ tannins|tannin|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW13711|bw13711|NN|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ plus|plus|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP without|without|IN|_ Acacia|Acacia|NNP|_ mearnsii|mearnsii|NN|_ condensed|condensed|JJ|_ tannins|tannin|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism BW13711|bw13711|NN|_ grown|grow|VBN|_ anaerobically|anaerobically|RB|_ in|in|IN|_ continuous|continuous|JJ|_ culture|culture|NN|_ in|in|IN|_ MOPS|MOPS|NNP|MED medium|medium|NN|_ plus|plus|CC|_ 0.4|0.4|CD|_ %|%|NN|_ glucose|glucose|NN|SUPP without|without|IN|_ Acacia|Acacia|NNP|_ mearnsii|mearnsii|NN|_ condensed|condensed|JJ|_ tannins|tannin|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism continous|continous|JJ|_ culture|culture|NN|_ without|without|IN|_ tannins|tannin|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism continuous|continuous|JJ|_ culture|culture|NN|_ with|with|IN|_ 1|1|CD|_ %|%|NN|_ tannins|tannin|NNS|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism with|with|IN|_ 1|1|CD|_ %|%|NN|_ tannins|tannin|NNS|_
Incubation|incubation|NN|_ temperature|temperature|NN|_ =|=|JJ|_ 37C|37c|NN|_
pH|ph|NN|_ =|=|JJ|_ 5.3|5.3|CD|_
pH|ph|NN|_ =|=|JJ|_ 5.7|5.7|CD|_
Promega|Promega|NNP|_ RNase-free|RNase-free|NNP|_ DNase|dnase|NN|_
Qiagen|Qiagen|NNP|_ Rneasy|Rneasy|NNP|_ mini|minus|NNS|_ kit|kit|NN|_
50|50|CD|_ bp|bp|NN|_ single-end|single-end|JJ|_ reads|read|VBZ|_ ,|,|,|_ were|be|VBD|_ mapped|map|VBN|_ to|to|TO|_ the|the|DT|_ genome|genome|NN|_ with|with|IN|_ using|use|VBG|_ bowtie2|bowtie2|NN|_ -LRB-|-lrb-|-LRB-|_ Langmead|langmead|NN|_ and|and|CC|_ Salzberg|Salzberg|NNP|_ ,|,|,|_ 2012|2012|CD|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ default|default|NN|_ parameters|parameter|NNS|_ .|.|.|_ Alignments|alignment|NNS|_ with|with|IN|_ bowtie2|bowtie2|NN|_ mapping|map|VBG|_ quality|quality|NN|_ values|value|NNS|_ lower|lower|JJR|_ than|than|IN|_ 40|40|CD|_ were|be|VBD|_ not|not|RB|_ retained|retain|VBN|_ for|for|IN|_ further|further|JJ|_ analysis|analysis|NN|_ ,|,|,|_ leaving|leave|VBG|_ 128,413,654|128,413,654|CD|_ and|and|CC|_ 76,508,335|76,508,335|CD|_ reads|read|VBZ|_ .|.|.|_
E.|E.|NNP|_ coli|coli|NN|_ 3|3|CD|_ '|'|''|_ RACE|race|NN|_ Rep1|rep1|JJ|_
E.|e.|FW|_ coli|coli|FW|_ 3|3|CD|_ '|'|''|_ RACE|race|NN|_ Rep2|rep2|JJ|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 000913.3|000913.3|CD|_
In|in|IN|_ order|order|NN|_ to|to|TO|_ distinguish|distinguish|VB|_ between|between|IN|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ of|of|IN|_ transient|transient|JJ|_ products|product|NNS|_ of|of|IN|_ RNA|rna|NN|_ metabolism|metabolism|NN|_ and|and|CC|_ stable|stable|JJ|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ ,|,|,|_ we|we|PRP|_ developed|develop|VBD|_ an|a|DT|_ algorithm|algorithm|NN|_ to|to|TO|_ call|call|VB|_ coverage|coverage|NN|_ peaks|peak|NNS|_ .|.|.|_ The|the|DT|_ algorithm|algorithm|NN|_ will|will|MD|_ be|be|VB|_ discussed|discuss|VBN|_ in|in|IN|_ detail|detail|NN|_ in|in|IN|_ an|a|DT|_ upcoming|upcoming|JJ|_ manuscript|manuscript|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ scripts|script|NNS|_ used|use|VBN|_ are|be|VBP|_ available|available|JJ|_ upon|upon|IN|_ request|request|NN|_ from|from|IN|_ the|the|DT|_ authors|author|NNS|_ .|.|.|_ In|in|IN|_ short|short|RB|_ ,|,|,|_ positions|position|NNS|_ in|in|IN|_ the|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ genome|genome|NN|_ were|be|VBD|_ considered|consider|VBN|_ in|in|IN|_ descending|descend|VBG|_ order|order|NN|_ of|of|IN|_ coverage|coverage|NN|_ and|and|CC|_ assigned|assign|VBN|_ a|a|DT|_ p-value|p-value|NN|_ based|base|VBN|_ on|on|IN|_ a|a|DT|_ Poisson|Poisson|NNP|_ distribution|distribution|NN|_ parameterized|parameterize|VBN|_ by|by|IN|_ the|the|DT|_ mean|mean|NN|_ coverage|coverage|NN|_ of|of|IN|_ all|all|DT|_ covered|cover|VBN|_ bases|basis|NNS|_ in|in|IN|_ the|the|DT|_ genome|genome|NN|_ .|.|.|_ Peaks|peak|NNS|_ were|be|VBD|_ rejected|reject|VBN|_ if|if|IN|_ their|they|PRP$|_ p-values|p-value|NNS|_ exceeded|exceed|VBD|_ 1e-4|1e-4|NN|_ or|or|CC|_ if|if|IN|_ there|there|EX|_ existed|exist|VBD|_ a|a|DT|_ >|>|JJR|_ 10-bp|10-bp|JJ|_ window|window|NN|_ containing|contain|VBG|_ the|the|DT|_ peak|peak|NN|_ in|in|IN|_ which|which|WDT|_ all|all|DT|_ positions|position|NNS|_ were|be|VBD|_ within|within|IN|_ 2-fold|2-fold|JJ|_ coverage|coverage|NN|_ of|of|IN|_ the|the|DT|_ peak|peak|JJ|_ position|position|NN|_ .|.|.|_ Parameters|parameter|NNS|_ were|be|VBD|_ chosen|choose|VBN|_ based|base|VBN|_ on|on|IN|_ analysis|analysis|NN|_ of|of|IN|_ annotated|annotated|JJ|_ 3|3|CD|_ '|'|''|_ ends|end|VBZ|_ as|as|RB|_ well|well|RB|_ as|as|IN|_ qualitative|qualitative|JJ|_ analysis|analysis|NN|_ of|of|IN|_ peaks|peak|NNS|_ .|.|.|_ This|this|DT|_ resulted|result|VBD|_ in|in|IN|_ 20,019|20,019|CD|_ peaks|peak|NNS|_ .|.|.|_
RNA-Seq|rna-seq|NN|_
strain|strain|NN|_ :|:|:|_ K12|k12|NN|_ MG1655|mg1655|NN|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ BIGWIG|bigwig|NN|_ file|file|NN|_ containing|contain|VBG|_ coverage|coverage|NN|_ tracks|track|NNS|_ from|from|IN|_ 3|3|CD|_ '|'|''|_ RACE|race|NN|_ data|datum|NNS|_
Supplementary|supplementary|JJ|_ _|_|NN|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ GFF|gff|NN|_ file|file|NN|_ containing|contain|VBG|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ annotations|annotation|NNS|_
total|total|JJ|_ DNaseI|dnasei|NN|_ treated|treat|VBN|_ RNA|rna|NN|_ was|be|VBD|_ depleted|deplete|VBN|_ of|of|IN|_ ribosomal|ribosomal|JJ|_ RNA|rna|NN|_ using|use|VBG|_ the|the|DT|_ Ribo-Zero|Ribo-Zero|NNP|_ ™|™|NN|_ RNA|rna|NN|_ removal|removal|NN|_ kit|kit|NN|_ for|for|IN|_ Gram-negative|gram-negative|JJ|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Epicentre|Epicentre|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ adapter|adapter|NN|_ ,|,|,|_ based|base|VBN|_ on|on|IN|_ the|the|DT|_ Illumina|Illumina|NNP|_ multiplexing|multiplex|VBG|_ adapter|adapter|NN|_ sequence|sequence|NN|_ -LRB-|-lrb-|-LRB-|_ Oligonucleotide|oligonucleotide|NN|_ sequences|sequence|NNS|_ ©|©|SYM|_ 2007-2014|2007-2014|CD|_ Illumina|Illumina|NNP|_ ,|,|,|_ Inc.|Inc.|NNP|_ .|.|.|_ All|all|DT|_ rights|rights|NNS|_ reserved|reserve|VBN|_ -RRB-|-rrb-|-RRB-|_ blocked|block|VBD|_ at|at|IN|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ end|end|NN|_ with|with|IN|_ an|a|DT|_ inverted|inverted|JJ|_ dT|dt|NN|_ -LRB-|-lrb-|-LRB-|_ 5|5|CD|_ '|'|''|_ -|-|:|_ GAUCGGAAGAGCACACGUCU|gaucggaagagcacacgucu|NN|_ -LSB-|-lsb-|-LRB-|_ idT|idt|NN|_ -RSB-|-rsb-|-RRB-|_ -3|-3|CD|_ '|'|''|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ was|be|VBD|_ phosphorylated|phosphorylate|VBN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ end|end|NN|_ using|use|VBG|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ The|the|DT|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ adapter|adapter|NN|_ was|be|VBD|_ ligated|ligate|VBN|_ to|to|TO|_ the|the|DT|_ 3|3|CD|_ '|'|''|_ ends|end|NNS|_ of|of|IN|_ the|the|DT|_ rRNA|rrna|NN|_ depleted|deplete|VBN|_ RNA|rna|NN|_ using|use|VBG|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ I|i|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ 1.5|1.5|CD|_ mg|mg|NN|_ of|of|IN|_ RNA|rna|NN|_ was|be|VBD|_ incubated|incubate|VBN|_ at|at|IN|_ 20|20|CD|_ °C|°c|NN|_ for|for|IN|_ 6|6|CD|_ hours|hour|NNS|_ in|in|IN|_ 1X|1x|NN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ reaction|reaction|NN|_ buffer|buffer|NN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP ATP|atp|NN|SUPP ,|,|,|_ 30|30|CD|_ µM|µm|NN|_ 3|3|CD|_ '|'|''|_ RNA|rna|NN|_ adapter|adapter|NN|_ ,|,|,|_ 10|10|CD|_ %|%|NN|_ DMSO|dmso|NN|_ ,|,|,|_ 10|10|CD|_ U|u|NN|_ of|of|IN|_ T4|t4|NN|_ RNA|rna|NN|_ ligase|ligase|NN|_ I|I|PRP|_ ,|,|,|_ and|and|CC|_ 40|40|CD|_ U|u|NN|_ of|of|IN|_ RNasin|rnasin|NN|_ -LRB-|-lrb-|-LRB-|_ Promega|promega|NN|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ a|a|DT|_ 20|20|CD|_ ml|ml|NN|_ reaction|reaction|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ then|then|RB|_ fragmented|fragmented|JJ|_ in|in|IN|_ equivalents|equivalent|NNS|_ of|of|IN|_ 100|100|CD|_ ng|ng|NN|_ using|use|VBG|_ the|the|DT|_ RNA|rna|NN|_ fragmentation|fragmentation|NN|_ reagents|reagent|NNS|_ -LRB-|-lrb-|-LRB-|_ Ambion|Ambion|NNP|_ ®|®|NNP|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ at|at|IN|_ 70|70|CD|_ °C|°c|NN|_ for|for|IN|_ 3|3|CD|_ min|min|NN|_ and|and|CC|_ subsequently|subsequently|RB|_ phosphorylated|phosphorylate|VBN|_ at|at|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ ends|end|VBZ|_ using|use|VBG|_ T4|t4|NN|_ PNK|pnk|NN|_ -LRB-|-lrb-|-LRB-|_ New|New|NNP|_ England|England|NNP|_ Biolabs|Biolabs|NNP|_ -RRB-|-rrb-|-RRB-|_ per|per|IN|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ to|to|TO|_ allow|allow|VB|_ for|for|IN|_ ligation|ligation|NN|_ of|of|IN|_ the|the|DT|_ 5|5|CD|_ '|'|''|_ adapter|adapter|NN|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ size-selected|size-selected|JJ|_ -LRB-|-lrb-|-LRB-|_ ≈|≈|JJ|_ 150-300|150-300|CD|_ nt|nt|NNS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ purified|purify|VBN|_ over|over|IN|_ a|a|DT|_ denaturing|denature|VBG|_ 8|8|CD|_ %|%|NN|_ polyacrylamide|polyacrylamide|NN|_
Total|Total|NNP|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ using|use|VBG|_ the|the|DT|_ hot|hot|JJ|_ phenol|phenol|NN|_ method|method|NN|_ as|as|IN|_ described|describe|VBN|_ in|in|IN|_ -LRB-|-lrb-|-LRB-|_ Lybecker|Lybecker|NNP|_ et|et|FW|_ al.|al.|FW|_ ,|,|,|_ 2014|2014|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 2|2|CD|_ state|state|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 3|3|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 4|4|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 5|5|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 6|6|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 7|7|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
0x58|0x58|NN|_ replicate|replicate|VBP|_ 3|3|CD|_ state|state|NN|_ 8|8|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|NN|_ +|+|CC|_
Control|Control|NNP|_ pAN1201|pan1201|NN|_ replicate|replicate|VB|_ 1|1|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Control|Control|NNP|_ pAN1201|pan1201|NN|_ replicate|replicate|VB|_ 2|2|CD|_ -LRB-|-lrb-|-LRB-|_ IPTG|iptg|SYM|_ -|-|:|_
Culture|culture|NN|_ grown|grow|VBN|_ in|in|IN|_ 14|14|CD|_ ml|ml|NN|_ tube|tube|NN|_
Cultures|culture|NNS|_ were|be|VBD|_ spun|spin|VBN|_ down|down|RP|_ at|at|IN|_ 4|4|CD|_ °C|°c|NN|_ ,|,|,|_ 15,000|15,000|CD|_ ×|×|CD|_ g|g|NN|_ for|for|IN|_ 3|3|CD|_ minutes|minute|NNS|_ .|.|.|_ Supernatants|supernatant|NNS|_ were|be|VBD|_ discarded|discard|VBN|_ after|after|IN|_ centrifugation|centrifugation|NN|_ and|and|CC|_ cell|cell|NN|_ pellets|pellet|NNS|_ were|be|VBD|_ flash|flash|NN|_ frozen|freeze|VBN|_ in|in|IN|_ liquid|liquid|JJ|_ nitrogen|nitrogen|NN|_ for|for|IN|_ storage|storage|NN|_ at|at|IN|_ -80|-80|CD|_ °C|°c|NN|_ .|.|.|_ Cells|cell|NNS|_ were|be|VBD|_ lysed|lyse|VBN|_ with|with|IN|_ 1|1|CD|_ mg|mg|NN|_ of|of|IN|_ lysozme|lysozme|NN|_ -LRB-|-lrb-|-LRB-|_ Sigma|Sigma|NNP|_ Aldrich|Aldrich|NNP|_ L6871|L6871|NNP|_ -RRB-|-rrb-|-RRB-|_ in|in|IN|_ 10|10|CD|_ mM|mm|NN|KWSUPP Tris-HCl|tris-hcl|NN|_ -LRB-|-lrb-|-LRB-|_ pH|ph|NN|_ 8.0|8.0|CD|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 75825|75825|CD|_ -RRB-|-rrb-|-RRB-|_ supplemented|supplement|VBN|_ with|with|IN|_ 0.1|0.1|CD|_ mM|mm|NN|KWSUPP EDTA|edta|NN|_ -LRB-|-lrb-|-LRB-|_ USB|usb|JJ|_ 15694|15694|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ RNA|rna|NN|_ was|be|VBD|_ extracted|extract|VBN|_ with|with|IN|_ PureLink|purelink|NN|_ RNA|rna|NN|_ Mini|Mini|NNP|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Life|Life|NNP|_ Technologies|Technologies|NNPS|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ further|further|JJ|_ purified|purify|VBN|_ and|and|CC|_ concentrated|concentrate|VBN|_ with|with|IN|_ RNA|rna|NN|_ Clean|Clean|NNP|_ &|&|CC|_ Concentrator-5|Concentrator-5|NNP|_ -LRB-|-lrb-|-LRB-|_ Zymo|Zymo|NNP|_ Research|Research|NNP|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ assure|assure|VB|_ sample|sample|NN|_ quality|quality|NN|_ .|.|.|_ The|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ analyzed|analyze|VBN|_ using|use|VBG|_ a|a|DT|_ Bioanalyzer|Bioanalyzer|NNP|_ -LRB-|-lrb-|-LRB-|_ Agilent|Agilent|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ Ribo-Zero|Ribo-Zero|NNP|_ rRNA|rrna|NN|_ Removal|removal|NN|_ Kit|kit|NN|_ for|for|IN|_ bacteria|bacterium|NNS|_ -LRB-|-lrb-|-LRB-|_ Illumina|Illumina|NNP|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ deplete|deplete|VB|_ rRNA|rrna|NN|_ from|from|IN|_ the|the|DT|_ samples|sample|NNS|_ .|.|.|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Genome|Genome|NNP|_ _|_|NNP|_ build|build|VB|_ :|:|:|_ NC|NC|NNP|_ _|_|NNP|_ 010473.1|010473.1|CD|_
Individual|Individual|NNP|_ colonies|colony|NNS|_ were|be|VBD|_ inoculated|inoculate|VBN|_ into|into|IN|_ MOPS|MOPS|NNP|MED EZ|EZ|NNP|_ Rich|Rich|NNP|_ Defined|Defined|NNP|_ Medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ Teknova|teknova|NN|_ ,|,|,|_ CA|CA|NNP|_ ,|,|,|_ M2105|m2105|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ 0.2|0.2|CD|_ %|%|NN|_ glycerol|glycerol|NN|SUPP carbon|carbon|NN|_ source|source|NN|_ and|and|CC|_ 50|50|CD|_ μg|μg|NN|_
Normalized|normalize|VBN|_ FPKM|fpkm|NN|_ values|value|NNS|_ were|be|VBD|_ generated|generate|VBN|_ from|from|IN|_ the|the|DT|_ raw|raw|JJ|_ gene|gene|NN|_ counts|count|NNS|_ by|by|IN|_ custom|custom|NN|_ scripts|script|NNS|_ that|that|WDT|_ calculated|calculate|VBD|_ and|and|CC|_ applied|apply|VBD|_ a|a|DT|_ trimmed|trimmed|RBR|_ mean|mean|VB|_ of|of|IN|_ M-values|m-value|NNS|_ -LRB-|-lrb-|-LRB-|_ TMM|tmm|NN|_ -RRB-|-rrb-|-RRB-|_ factor|factor|NN|_ using|use|VBG|_ edgeR|edger|NN|_ version|version|NN|_ 3.8.6|3.8.6|CD|_ .|.|.|_
Read|Read|NNP|_ counts|count|VBZ|_ for|for|IN|_ each|each|DT|_ host|host|NN|_ and|and|CC|_ circuit|circuit|NN|_ gene|gene|NN|_ was|be|VBD|_ carried|carry|VBN|_ out|out|RP|_ using|use|VBG|_ the|the|DT|_ htseq-count|htseq-count|JJ|_ command|command|NN|_ of|of|IN|_ the|the|DT|_ HTSeq|htseq|NN|_ toolkit|toolkit|NN|_ with|with|IN|_ user-defined|user-defined|JJ|_ GFF|gff|NN|_ annotations|annotation|NNS|_ of|of|IN|_ the|the|DT|_ reference|reference|NN|_ sequences|sequence|NNS|_ and|and|CC|_ the|the|DT|_ options|option|NNS|_ '|'|POS|_ -|-|:|_ s|s|NNS|_ reverse|reverse|JJ|_ -|-|:|_ a|a|DT|_ 10|10|CD|_ -|-|:|_ m|m|NN|_ union|union|NN|_ '|'|''|_ .|.|.|_
Reads|read|VBZ|_ mapped|map|VBN|_ to|to|TO|_ reference|reference|NN|_ using|use|VBG|_ BWA|bwa|NN|_ versiopn|versiopn|NN|_ 0.7.4|0.7.4|CD|_ with|with|IN|_ default|default|NN|_ settings|setting|NNS|_
RNA-Seq|rna-seq|JJ|_
strain|strain|NN|_ :|:|:|_ NEB|NEB|NNP|_ 10-beta|10-beta|JJ|_
Strand|strand|NN|_ specific|specific|JJ|_ RNAtag-seq|rnatag-seq|NN|_ libraries|library|NNS|_ were|be|VBD|_ created|create|VBN|_ by|by|IN|_ the|the|DT|_ Broad|Broad|NNP|_ Technology|Technology|NNP|_ Labs|Labs|NNPS|_ specialized|specialized|JJ|_ service|service|NN|_ facility|facility|NN|_ -LRB-|-lrb-|-LRB-|_ SSF|ssf|NN|_ -RRB-|-rrb-|-RRB-|_ using|use|VBG|_ the|the|DT|_ standard|standard|JJ|_ protocol|protocol|NN|_ described|describe|VBN|_ in|in|IN|_ Shishkin|Shishkin|NNP|_ et|et|FW|_ al.|al.|FW|_ .|.|.|_ Nature|Nature|NNP|_ Methods|method|NNS|_ 2016|2016|CD|_ .|.|.|_
Supplementary|Supplementary|NNP|_ _|_|VBD|_ files|file|NNS|_ _|_|IN|_ format|format|NN|_ _|_|NN|_ and|and|CC|_ _|_|NN|_ content|content|NN|_ :|:|:|_ CSV|CSV|NNP|_ files|file|NNS|_ of|of|IN|_ raw|raw|JJ|_ read|read|NN|_ counts|count|NNS|_ and|and|CC|_ normalized|normalize|VBN|_ gene|gene|NN|_ expression|expression|NN|_ in|in|IN|_ FPKM|FPKM|NNP|_ units|unit|NNS|_ .|.|.|_
BW25113|bw25113|NN|_ luxS|luxs|NN|GEN LB|lb|NN|_ 30C|30c|CD|_ free-living|free-living|JJ|_ cells|cell|NNS|_ 100|100|CD|_ uM|um|NN|_ AI2|ai2|NN|_ 3h|3h|VBP|_
BW25113|bw25113|NN|_ luxS|luxs|NN|GEN LB|lb|NN|_ 30C|30c|CD|_ free-living|free-living|JJ|_ cells|cell|NNS|_ no|no|DT|_ AI2|ai2|NN|_ for|for|IN|_ 3h|3h|JJ|_
BW25113|bw25113|NN|_ luxS|luxs|NN|GEN LB|lb|NN|_ 37C|37c|NN|_ free-living|free-living|JJ|_ cells|cell|NNS|_ 100|100|CD|_ uM|um|NN|_ AI2|ai2|NN|_ 3h|3h|VBP|_
BW25113|bw25113|NN|_ luxS|luxs|NN|GEN LB|lb|NN|_ 37C|37c|NN|_ free-living|free-living|JJ|_ cells|cell|NNS|_ no|no|DT|_ AI2|ai2|NN|_ 3h|3h|NN|_
BW25113|bw25113|NN|_ sdiA|sdia|NN|GEN LB|lb|NN|_ 30C|30c|NN|_ OD|od|NN|_ 4.0|4.0|CD|_ free-living|free-living|JJ|_ cells|cell|NNS|_
BW25113|bw25113|NN|_ sdiA|sdia|NN|GEN mutant|mutant|JJ|_ LB|lb|NN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP indole|indole|NN|_ 7-h|7-h|JJ|_ 30C|30c|NN|_ biofilm|biofilm|NN|_ cell|cell|NN|_
BW25113|bw25113|NN|_ sdiA|sdia|NN|GEN mutant|mutant|JJ|_ LB|lb|NN|_ with|with|IN|_ DMF|dmf|NN|_ 7-h|7-h|JJ|_ 30C|30c|NN|_ biofilm|biofilm|NN|_ cell|cell|NN|_
BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN Biofilm|biofilm|NN|_ 100|100|CD|_ uM|um|NN|_ indole|indole|FW|_ 7h|7h|FW|_ LB|lb|NN|_ 30C|30c|NN|_
BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN Biofilm|biofilm|NN|_ 100|100|CD|_ uM|um|NN|_ indole|indole|FW|_ 7h|7h|FW|_ LB|lb|NN|_ 37C|37c|NN|_
BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN Biofilm|biofilm|NN|_ DMF|dmf|NN|_ 7h|7h|VBP|_ LB|lb|NN|_ 37C|37c|NN|_
BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN LB|lb|NN|_ 30C|30c|NN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ with|with|IN|_ DMF|dmf|NN|_ 7h|7h|VBP|_
BW25113|bw25113|NN|_ w|w|NN|_
Channel|Channel|NNP|_ 1|1|CD|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
MAS|mas|FW|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|Setting|NNP|_
MAS|MAS|NNP|_ 5.0|5.0|CD|_ Expression|expression|NN|_ Analysis|analysis|NN|_ Default|Default|NNP|_ Setting|Setting|NNP|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 7|7|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ and|and|CC|_ 100|100|CD|_ uM|um|NN|_ indole|indole|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 7|7|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ and|and|CC|_ DMF|dmf|NN|_ at|at|IN|_ 30ºC|30ºC|NNP|_
RNA|RNA|NNP|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 7|7|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ and|and|CC|_ DMF|dmf|NN|_ at|at|IN|_ 37ºC|37ºc|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ tnaA|tnaa|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 7|7|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ and|and|CC|_ with|with|IN|_ 100|100|CD|_ uM|um|NN|_ indole|indole|NN|_ at|at|IN|_ 30ºC|30ºC|NNP|_
RNA|RNA|NNP|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ w|w|NN|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ sdiA|sdia|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 7|7|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ at|at|IN|_ 30ºC|30ºc|NN|_ with|with|IN|_ 1|1|CD|_ mM|mm|NN|KWSUPP indole|indole|NN|_ presence|presence|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ biofilm|biofilm|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ sdiA|sdia|NN|GEN mutant|mutant|NN|_ after|after|IN|_ 7|7|CD|_ hours|hour|NNS|_ of|of|IN|_ growth|growth|NN|_ in|in|IN|_ LB|lb|NN|_ with|with|IN|_ glasswool|glasswool|NN|_ at|at|IN|_ 30ºC|30ºc|NN|_ with|with|IN|_ DMF|dmf|NN|_ presence|presence|NN|_ .|.|.|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ free|free|JJ|_ living|living|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ luxS|luxs|NN|GEN mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ when|when|WRB|_ growth|growth|NN|_ to|to|TO|_ OD600|od600|NN|_ 0.5|0.5|CD|_ at|at|IN|_ 30ºC|30ºC|NNP|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 100|100|CD|_ uM|um|NN|_ AI2|ai2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ and|and|CC|_ 3-h|3-h|JJ|_ further|further|JJ|_ incubation|incubation|NN|_ was|be|VBD|_ applied|apply|VBN|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ free|free|JJ|_ living|living|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ luxS|luxs|NN|GEN mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ when|when|WRB|_ growth|growth|NN|_ to|to|TO|_ OD600|od600|NN|_ 0.5|0.5|CD|_ at|at|IN|_ 30ºC|30ºC|NNP|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ no|no|DT|_ AI2|ai2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ and|and|CC|_ 3-h|3-h|JJ|_ further|further|JJ|_ incubation|incubation|NN|_ was|be|VBD|_ applied|apply|VBN|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ free|free|JJ|_ living|living|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ luxS|luxs|NN|GEN mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ when|when|WRB|_ growth|growth|NN|_ to|to|TO|_ OD600|od600|NN|_ 0.5|0.5|CD|_ at|at|IN|_ 37ºC|37ºc|NN|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ 100|100|CD|_ uM|um|NN|_ AI2|ai2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ and|and|CC|_ 3-h|3-h|JJ|_ further|further|JJ|_ incubation|incubation|NN|_ was|be|VBD|_ applied|apply|VBN|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ free|free|JJ|_ living|living|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ luxS|luxs|NN|GEN mutant|mutant|NN|_ -LRB-|-lrb-|-LRB-|_ when|when|WRB|_ growth|growth|NN|_ to|to|TO|_ OD600|od600|NN|_ 0.5|0.5|CD|_ at|at|IN|_ 37ºC|37ºc|NN|_ in|in|IN|_ LB|LB|NNP|_ ,|,|,|_ no|no|DT|_ AI2|ai2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ and|and|CC|_ 3-h|3-h|JJ|_ further|further|JJ|_ incubation|incubation|NN|_ was|be|VBD|_ applied|apply|VBN|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ extracted|extract|VBN|_ from|from|IN|_ free|free|JJ|_ living|living|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ sdiA|sdia|NN|GEN mutant|mutant|NN|_ when|when|WRB|_ growth|growth|NN|_ to|to|TO|_ OD600|od600|NN|_ 4.0|4.0|CD|_ at|at|IN|_ 30ºC|30ºC|NNP|_ in|in|IN|_ LB|LB|NNP|_
RNA|RNA|NNP|_ extracted|extract|VBN|_ from|from|IN|_ free|free|JJ|_ living|living|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ wild|wild|JJ|_ type|type|NN|_ when|when|WRB|_ growth|growth|NN|_ to|to|TO|_ OD600|od600|NN|_ 4.0|4.0|CD|_ at|at|IN|_ 30ºC|30ºC|NNP|_ in|in|IN|_ LB|LB|NNP|_
RNA|RNA|NNP|_ extracted|extract|VBN|_ from|from|IN|_ suspension|suspension|NN|_ cells|cell|NNS|_ of|of|IN|_ E.|e.|FW|_ coli|coli|FW|_ K-12|k-12|NN|_ BW25113|bw25113|NN|_ w|w|NN|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 0.25|0.25|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD600|od600|CD|_ 0.5|0.5|CD|_ ,|,|,|_ 100|100|CD|_ uM|um|NN|_ AI-2|ai-2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ .|.|.|_ after|after|IN|_ further|further|JJ|_ 3-h|3-h|JJ|_ incubation|incubation|NN|_ ,|,|,|_ 2.0|2.0|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ frozen|frozen|JJ|_ in|in|IN|_ -80|-80|CD|_ C|c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 0.25|0.25|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD600|od600|CD|_ 0.5|0.5|CD|_ ,|,|,|_ no|no|DT|_ AI-2|ai-2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ .|.|.|_ after|after|IN|_ further|further|JJ|_ 3-h|3-h|JJ|_ incubation|incubation|NN|_ ,|,|,|_ 2.0|2.0|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ frozen|frozen|JJ|_ in|in|IN|_ -80|-80|CD|_ C|c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 0.25|0.25|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD600|od600|CD|_ 4.0|4.0|CD|_ ,|,|,|_ 2.0|2.0|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ frozen|frozen|JJ|_ in|in|IN|_ -80|-80|CD|_ C|c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 0.25|0.25|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD600|od600|CD|_ 0.5|0.5|CD|_ ,|,|,|_ 100|100|CD|_ uM|um|NN|_ AI-2|ai-2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ .|.|.|_ after|after|IN|_ further|further|JJ|_ 3-h|3-h|JJ|_ incubation|incubation|NN|_ ,|,|,|_ 2.0|2.0|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ frozen|frozen|JJ|_ in|in|IN|_ -80|-80|CD|_ C|c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 0.25|0.25|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 25|25|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ to|to|TO|_ OD600|od600|CD|_ 0.5|0.5|CD|_ ,|,|,|_ no|no|DT|_ AI-2|ai-2|NN|_ was|be|VBD|_ added|add|VBN|_ in|in|IN|_ .|.|.|_ after|after|IN|_ further|further|JJ|_ 3-h|3-h|JJ|_ incubation|incubation|NN|_ ,|,|,|_ 2.0|2.0|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ removed|remove|VBN|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ frozen|frozen|JJ|_ in|in|IN|_ -80|-80|CD|_ C|c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ 7|7|CD|_ hours|hour|NNS|_ ,|,|,|_ 2.0|2.0|CD|_ ml|ml|NN|_ of|of|IN|_ cell|cell|NN|_ culture|culture|NN|_ was|be|VBD|_ removed|remove|VBN|_ from|from|IN|_ suspension|suspension|NN|_ part|part|NN|_ and|and|CC|_ cells|cell|NNS|_ were|be|VBD|_ pelleted|pelleted|JJ|_ and|and|CC|_ frozen|frozen|JJ|_ in|in|IN|_ -80|-80|CD|_ C|c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ 1|1|CD|_ mM|mm|NN|KWSUPP indole|indole|NN|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ DMF|dmf|NN|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ DMF|dmf|NN|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ DMF|dmf|NN|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ with|with|IN|_ 100|100|CD|_ uM|um|NN|_ indole|indole|NN|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ with|with|IN|_ 100|100|CD|_ uM|um|NN|_ indole|indole|NN|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 37|37|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ overnight|overnight|JJ|_ culture|culture|NN|_ -LRB-|-lrb-|-LRB-|_ 2.5|2.5|CD|_ ml|ml|NN|_ -RRB-|-rrb-|-RRB-|_ was|be|VBD|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ 250|250|CD|_ ml|ml|NN|_ of|of|IN|_ fresh|fresh|JJ|_ LB|lb|NN|MED medium|medium|NN|MED with|with|IN|_ 10|10|CD|_ g|g|NN|_ of|of|IN|_ submerged|submerged|JJ|_ glass|glass|NN|_ wool|wool|NN|_ -LRB-|-lrb-|-LRB-|_ Corning|Corning|NNP|_ Glass|Glass|NNP|_ Works|Works|NNP|_ ,|,|,|_ Corning|Corning|NNP|_ ,|,|,|_ NY|NY|NNP|_ -RRB-|-rrb-|-RRB-|_ for|for|IN|_ forming|form|VBG|_ biofilm|biofilm|NN|_ .|.|.|_ After|after|IN|_ incubation|incubation|NN|_ for|for|IN|_ 7|7|CD|_ h|h|NN|_ at|at|IN|_ 30|30|CD|_ °C|°c|NN|_ with|with|IN|_ shaking|shake|VBG|_ -LRB-|-lrb-|-LRB-|_ 250|250|CD|_ rpm|rpm|NN|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ was|be|VBD|_ carefully|carefully|RB|_ and|and|CC|_ quickly|quickly|RB|_ removed|remove|VBD|_ and|and|CC|_ rinsed|rinse|VBD|_ with|with|IN|_ 100|100|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ Biofilm|biofilm|NN|_ cells|cell|NNS|_ were|be|VBD|_ removed|remove|VBN|_ by|by|IN|_ sonicating|sonicate|VBG|_ the|the|DT|_ glass|glass|NN|_ wool|wool|NN|_ in|in|IN|_ 200|200|CD|_ ml|ml|NN|_ of|of|IN|_ sterile|sterile|JJ|_ 0.85|0.85|CD|_ %|%|NN|_ NaCl|nacl|NN|_ solution|solution|NN|_ at|at|IN|_ 0|0|CD|_ °C|°c|NN|_ .|.|.|_ After|after|IN|_ breaking|break|VBG|_ the|the|DT|_ cells|cell|NNS|_ with|with|IN|_ a|a|DT|_ bead|bead|NN|_ beater|beater|NN|_ ,|,|,|_ and|and|CC|_ the|the|DT|_ total|total|JJ|_ RNA|rna|NN|_ was|be|VBD|_ isolated|isolate|VBN|_ with|with|IN|_ Qiagen|Qiagen|NNP|_ RNeasy|RNeasy|NNP|_ mini|minus|NNS|_ Kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Cat|cat|NN|_ #|#|#|_ 74104|74104|CD|_ -RRB-|-rrb-|-RRB-|_
10|10|CD|_ _|_|CD|_ ESBL019|esbl019|NN|_ Filamented|Filamented|NNP|_ Repl|Repl|NNP|_ 3|3|CD|_
11|11|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Transition|transition|NN|_ Repl|repl|NN|_ 3|3|CD|_
12|12|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Reverted|revert|VBD|_ Repl|repl|JJ|_ 3|3|CD|_
13|13|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Coliform|coliform|NN|_ Repl|repl|NN|_ 4|4|CD|_
14|14|CD|_ _|_|CD|_ ESBL019|esbl019|NN|_ Filamented|Filamented|NNP|_ Repl|Repl|NNP|_ 4|4|CD|_
15|15|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Transition|transition|NN|_ Repl|repl|NN|_ 4|4|CD|_
16|16|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Reverted|revert|VBD|_ Repl|repl|JJ|_ 4|4|CD|_
1|1|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Coliform|coliform|NN|_ Repl|repl|NN|_ 1|1|CD|_
2|2|CD|_ _|_|CD|_ ESBL019|esbl019|NN|_ Filamented|Filamented|NNP|_ Repl|Repl|NNP|_ 1|1|CD|_
3|3|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Transition|transition|NN|_ Repl|repl|NN|_ 1|1|CD|_
4|4|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Reverted|revert|VBD|_ Repl|repl|NN|_ 1|1|CD|_
5|5|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Coliform|coliform|NN|_ Repl|repl|NN|_ 2|2|CD|_
6|6|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Filamented|filament|VBD|_ Repl|repl|NN|_ 2|2|CD|_
75th|75th|JJ|_ percentile|percentile|NN|_ shift|shift|NN|_ normalisation|normalisation|NN|_ and|and|CC|_ baseline|baseline|NN|_ adjusted|adjusted|JJ|_
7|7|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Transition|transition|NN|_ Repl|repl|NN|_ 2|2|CD|_
8|8|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Reverted|revert|VBD|_ Repl|repl|NN|_ 2|2|CD|_
9|9|CD|_ _|_|NN|_ ESBL019|esbl019|NN|_ Coliform|coliform|NN|_ Repl|repl|NN|_ 3|3|CD|_
ESBL019|esbl019|NN|_ Coliform|coliform|NN|_
ESBL019|esbl019|NN|_ Filamented|filamented|JJ|_
ESBL019|esbl019|NN|_ Reverted|revert|VBD|_
ESBL019|esbl019|NN|_ Transition|transition|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
Four|four|CD|_ morphologic|morphologic|JJ|_ states|state|NNS|_ of|of|IN|_ ESBL019|esbl019|NN|_ were|be|VBD|_ used|use|VBN|_ during|during|IN|_ the|the|DT|_ experiments|experiment|NNS|_ .|.|.|_ A|a|DT|_ first|first|JJ|_ ESBL019|esbl019|NN|_ morphological|morphological|JJ|_ state|state|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ resuspension|resuspension|NN|_ of|of|IN|_ ESBL019|esbl019|NN|_ in|in|IN|_ cell|cell|NN|_ culture|culture|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ CCM|ccm|NN|_ -RRB-|-rrb-|-RRB-|_ without|without|IN|_ ceftibuten|ceftibuten|NN|_ supplementation|supplementation|NN|_ prior|prior|RB|_ to|to|TO|_ its|its|PRP$|_ inoculation|inoculation|NN|_ of|of|IN|_ primary|primary|JJ|_ human|human|JJ|_ bladder|bladder|NN|_ epithelial|epithelial|JJ|_ cells|cell|NNS|_ -LRB-|-lrb-|-LRB-|_ HBEP|hbep|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ designated|designate|VBN|_ ;|;|:|_ ESBL019|esbl019|NN|_ Coliform|coliform|NN|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ A|a|DT|_ second|second|JJ|_ ESBL019|esbl019|NN|_ morphological|morphological|JJ|_ state|state|NN|_ was|be|VBD|_ prepared|prepare|VBN|_ by|by|IN|_ resuspension|resuspension|NN|_ in|in|IN|_ CCM|CCM|NNP|_ and|and|CC|_ then|then|RB|_ used|use|VBN|_ to|to|TO|_ inoculate|inoculate|VB|_ HBEP|hbep|NN|_ cells|cell|NNS|_ with|with|IN|_ ceftibuten|ceftibuten|NN|_ supplementation|supplementation|NN|_ -LRB-|-lrb-|-LRB-|_ 480ng|480ng|CD|_
morphology|morphology|NN|_ :|:|:|_ Coliform|coliform|NN|_
morphology|morphology|NN|_ :|:|:|_ Filamented|filamented|JJ|_
morphology|morphology|NN|_ :|:|:|_ Reverted|revert|VBN|_ -LRB-|-lrb-|-LRB-|_ reverted|revert|VBD|_ back|back|RB|_ from|from|IN|_ a|a|DT|_ Filamented|filamented|JJ|_ shape|shape|NN|_ into|into|IN|_ a|a|DT|_ coli|coli|NN|_ shape|shape|NN|_ -RRB-|-rrb-|-RRB-|_
morphology|morphology|NN|_ :|:|:|_ Transition|transition|NN|_ -LRB-|-lrb-|-LRB-|_ from|from|IN|_ Coli|Coli|NNP|_ into|into|IN|_ Filamented|Filamented|NNP|_ -RRB-|-rrb-|-RRB-|_
RNA|rna|NN|_ isolation|isolation|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ an|a|DT|_ RNeasy|rneasy|NN|_ mini|minus|NNS|_ kit|kit|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|Qiagen|NNP|_ Technologies|Technologies|NNPS|_ ,|,|,|_ Hilden|Hilden|NNP|_ ,|,|,|_ Germany|Germany|NNP|_ -RRB-|-rrb-|-RRB-|_ ,|,|,|_ according|accord|VBG|_ to|to|TO|_ the|the|DT|_ manufacturer|manufacturer|NN|_ 's|'s|POS|_ protocol|protocol|NN|_ .|.|.|_ DNA|dna|NN|_ decontamination|decontamination|NN|_ treatment|treatment|NN|_ was|be|VBD|_ performed|perform|VBN|_ using|use|VBG|_ Turbo|Turbo|NNP|_ DNase|dnase|NN|_ -LRB-|-lrb-|-LRB-|_ Qiagen|qiagen|NN|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ the|the|DT|_ quantity|quantity|NN|_ and|and|CC|_ purity|purity|NN|_ of|of|IN|_ the|the|DT|_ purified|purify|VBN|_ RNA|rna|NN|_ samples|sample|NNS|_ were|be|VBD|_ determined|determine|VBN|_ using|use|VBG|_ a|a|DT|_ spectrophotometer|spectrophotometer|NN|_ Nanodrop-1000|nanodrop-1000|NN|_ -LRB-|-lrb-|-LRB-|_ Nanodrop|Nanodrop|NNP|_ Technologies|Technologies|NNPS|_ Inc.|Inc.|NNP|_ ,|,|,|_ Wilmington|Wilmington|NNP|_ ,|,|,|_ DE|de|NN|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ by|by|IN|_ measuring|measure|VBG|_ the|the|DT|_ absorbance|absorbance|NN|_ -LRB-|-lrb-|-LRB-|_ A260|a260|NN|_ ,|,|,|_ 230|230|CD|_ ,|,|,|_ 280|280|CD|_ -RRB-|-rrb-|-RRB-|_ and|and|CC|_ calculating|calculate|VBG|_ absorbance|absorbance|NN|_ ratios|ratio|NNS|_ -LRB-|-lrb-|-LRB-|_ A260|a260|NN|_
strain|strain|NN|_ :|:|:|_ beta-lactamase|beta-lactamase|NN|_ -LRB-|-lrb-|-LRB-|_ ESBL|esbl|NN|_ -RRB-|-rrb-|-RRB-|_ -|-|:|_ producing|produce|VBG|_ UPEC|upec|NN|_ -LRB-|-lrb-|-LRB-|_ ESBL019|esbl019|NN|_ -RRB-|-rrb-|-RRB-|_
The|the|DT|_ E.|e.|FW|_ coli|coli|FW|_ isolate|isolate|NN|_ ESBL019|esbl019|NN|_ was|be|VBD|_ originally|originally|RB|_ isolated|isolate|VBN|_ from|from|IN|_ a|a|DT|_ patient|patient|NN|_ at|at|IN|_ Örebro|Örebro|NNP|_ University|University|NNP|_ hospital|hospital|NN|_ ,|,|,|_ Sweden|Sweden|NNP|_ and|and|CC|_ was|be|VBD|_ maintained|maintain|VBN|_ on|on|IN|_ tryptic|tryptic|JJ|_ soy|soy|NN|_ agar|agar|NN|_ -LRB-|-lrb-|-LRB-|_ TSA|tsa|NN|_ -RRB-|-rrb-|-RRB-|_ -LRB-|-lrb-|-LRB-|_ Becton|Becton|NNP|_ Dickinson|Dickinson|NNP|_ ,|,|,|_ Le|Le|NNP|_ Pont|Pont|NNP|_ Claix|Claix|NNP|_ ,|,|,|_ France|France|NNP|_ -RRB-|-rrb-|-RRB-|_ .|.|.|_ ESBL019|esbl019|NN|_ was|be|VBD|_ grown|grow|VBN|_ in|in|IN|_ Luria|Luria|NNP|MED broth|broth|NN|MED -LRB-|-lrb-|-LRB-|_ Difco|Difco|NNP|_ Laboratories|Laboratories|NNPS|_ ,|,|,|_ Detroit|Detroit|NNP|_ ,|,|,|_ MI|MI|NNP|_ ,|,|,|_ USA|USA|NNP|_ -RRB-|-rrb-|-RRB-|_ overnight|overnight|JJ|_ on|on|IN|_ shake|shake|NN|_ at|at|IN|_ 200|200|CD|_ rpm|rpm|NN|_ 37|37|CD|_ °C|°c|NN|_ prior|prior|RB|_ to|to|TO|_ experiments|experiment|NNS|_ .|.|.|_ The|the|DT|_ bacteria|bacterium|NNS|_ were|be|VBD|_ resuspended|resuspend|VBN|_ in|in|IN|_ sterile|sterile|JJ|_ phosphate|phosphate|NN|_ buffered|buffer|VBN|_ saline|saline|NN|_ prior|prior|RB|_ to|to|TO|_ inoculation|inoculation|NN|_ of|of|IN|_ CnT-21|cnt-21|NN|_ cell|cell|NN|_ culture|culture|NN|_ medium|medium|NN|_ -LRB-|-lrb-|-LRB-|_ CCM|ccm|NN|_ -RRB-|-rrb-|-RRB-|_ with|with|IN|_ or|or|CC|_ without|without|IN|_ ceftibuten|ceftibuten|NN|_ -LRB-|-lrb-|-LRB-|_ 480|480|CD|_ ng|ng|NN|_
Escherichia|escherichia|FW|Organism coli|coli|FW|Organism
lexA|lexa|NN|GEN 10|10|CD|_ '|'|''|_ after|after|IN|_ UV|uv|NN|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ MG1655|mg1655|NN|_
lexA|lexa|NN|GEN 10|10|CD|_ min|min|NN|_ after|after|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
lexA|lexa|NN|GEN 20|20|CD|_ '|'|''|_ after|after|IN|_ NOuv|NOuv|NNP|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ MG1655|mg1655|NN|_
lexA|lexa|NN|GEN 20|20|CD|_ '|'|''|_ after|after|IN|_ UV|uv|NN|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ MG1655|mg1655|NN|_
lexA|lexa|NN|GEN 20|20|CD|_ min|min|NN|_ after|after|IN|_ NOuv|NOuv|NNP|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
lexA|lexa|NN|GEN 20|20|CD|_ min|min|NN|_ after|after|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
lexA|lexa|NN|GEN 40|40|CD|_ '|'|''|_ after|after|IN|_ UV|uv|NN|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ MG1655|mg1655|NN|_
lexA|lexa|NN|GEN 40|40|CD|_ min|min|NN|_ after|after|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
lexA|lexa|NN|GEN 5|5|CD|_ '|'|''|_ after|after|IN|_ UV|uv|NN|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ MG1655|mg1655|NN|_
lexA|lexa|NN|GEN 5|5|CD|_ min|min|NN|_ after|after|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
lexA|lexa|NN|GEN 60|60|CD|_ '|'|''|_ after|after|IN|_ NOuv|NOuv|NNP|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ MG1655|mg1655|NN|_
lexA|lexa|NN|GEN 60|60|CD|_ '|'|''|_ after|after|IN|_ UV|uv|NN|_ vs.|vs.|CC|_ 0|0|CD|_ '|'|''|_ ,|,|,|_ MG1655|mg1655|NN|_
lexA|lexa|NN|GEN 60|60|CD|_ min|min|NN|_ after|after|IN|_ NOuv|NOuv|NNP|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
lexA|lexa|NN|GEN 60|60|CD|_ min|min|NN|_ after|after|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_ ,|,|,|_ 2|2|CD|_ ug|ug|NN|_ pdN6|pdn6|NN|_
lexA|lexa|NN|GEN vs.|vs.|CC|_ wt|wt|JJ|_ ,|,|,|_ before|before|IN|_ UV|uv|NN|_ treatment|treatment|NN|_ ,|,|,|_ MG1655|mg1655|NN|_
untreated|untreated|JJ|_ cells|cell|NNS|_ ,|,|,|_ 25|25|CD|_ ug|ug|NN|_ total|total|JJ|_ RNA|rna|NN|_