training-data-set-70-NER.txt
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cultured|culture|VBN|_|O in|in|IN|_|O :|:|:|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp acetate|acetate|NN|SUPP|Supp
ChIP-exo|chip-exo|NN|_|Technique GadX|gadx|NN|TF|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
Δfur|δfur|NN|_|Gtype with|with|IN|_|O DPD|dpd|NN|_|Supp 1|1|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique RNA-seq|rna-seq|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
Δcra|δcra|NN|_|Gtype fructose|fructose|NN|_|Supp 1|1|CD|_|O
Fur|Fur|NNP|TF|O with|with|IN|_|O Fe|Fe|NNP|_|Supp 2|2|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique ChIP-exo|chip-exo|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
SoxR|soxr|NN|TF|O PQ|pq|NN|_|Supp 1|1|CD|_|O
Ptac|ptac|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O A|a|NN|_|O -|-|:|_|O 4|4|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
ChIP-exo|ChIP-exo|NNP|_|Technique GadE|gade|NN|TF|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
ß|ß|SYM|_|O -|-|:|_|O Aerobic|aerobic|JJ|_|Air -|-|:|_|O B|b|NN|_|O
treatment|treatment|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Med -LRB-|-lrb-|-LRB-|_|Med 2|2|CD|_|Med g/L|g/l|NN|_|Med -RRB-|-rrb-|-RRB-|_|Med minimal|minimal|JJ|_|Med M9|m9|NN|_|Med medium|medium|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 10|10|CD|_|Supp mM|mm|NN|KWSUPP|Supp leucine|leucine|NN|SUPP|Supp .|.|.|_|O
genotype|genotype|NN|_|O :|:|:|_|O ompR|ompr|NN|GEN|Gtype deletion|deletion|NN|_|Gtype mutant|mutant|JJ|_|Gtype
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|WT|NNP|_|O ,|,|,|_|O GadE-8-myc|gade-8-myc|NN|_|O ,|,|,|_|O GadW-8-myc|gadw-8-myc|NN|_|O ,|,|,|_|O and|and|CC|_|O GadX-8-myc|gadx-8-myc|NN|_|O tagged|tag|VBD|_|O strains|strain|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|OD =|=|JJ|_|OD 0.3|0.3|CD|_|OD -RRB-|-rrb-|-RRB-|_|O aerobically|aerobically|RB|_|Air -LRB-|-lrb-|-LRB-|_|O 250|250|CD|_|Agit rpm|rpm|NN|_|Agit -RRB-|-rrb-|-RRB-|_|O at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp at|at|IN|_|O pH|ph|NN|_|pH 5.5|5.5|CD|_|pH .|.|.|_|O
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype ∆|∆|CD|_|Gtype ryhB|ryhb|NN|GEN|Gtype Aerobic|aerobic|JJ|_|Air B|b|NN|_|O
antibody|antibody|NN|_|O :|:|:|_|O 9E10|9e10|CD|_|Anti Myc|myc|NN|_|Anti tag|tag|NN|GEN|Anti antibody|antibody|NN|_|O
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O 8|8|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
Δcra|δcra|NN|_|Gtype fructose|fructose|NN|_|Supp 2|2|CD|_|O
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O σ32|σ32|NN|_|Anti
Δfur|δfur|NN|_|Gtype with|with|IN|_|O Fe|Fe|NNP|_|Supp 1|1|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique RNA-seq|rna-seq|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O delta|delta|NN|_|Gtype _|_|SYM|_|Gtype cra|cra|FW|GEN|Gtype
affyexp|affyexp|JJ|_|O _|_|NN|_|O delta-fnr|delta-fnr|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|NN|_|O 1|1|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
RpoB|rpob|NN|_|O WT|wt|JJ|_|Gtype 2|2|CD|_|O
FNR|fnr|SYM|TF|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air -|-|:|_|O Affinity|affinity|NN|_|O Purified|purify|VBN|_|O -|-|:|_|O A|a|NN|_|O
MG1655|mg1655|NN|_|Substrain PhtpG|phtpg|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype lacZ|lacz|NN|GEN|Gtype delta|delta|NN|_|Gtype lacX74/pTG2|lacx74/ptg2|NN|_|Gtype -LRB-|-lrb-|-LRB-|_|Gtype vector|vector|NN|_|Gtype carrying|carrying|NN|_|Gtype inducible|inducible|JJ|_|Gtype Ptrc|ptrc|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype rpoH|rpoh|NN|GEN|Gtype -RRB-|-rrb-|-RRB-|_|Gtype
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype Anaerobic|anaerobic|JJ|_|Air -LSB-|-lsb-|-LRB-|_|O IP|IP|NNP|_|O vs|vs|CC|_|O nput|nput|NN|_|O -RSB-|-rsb-|-RRB-|_|O
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype Aerobic|aerobic|JJ|_|Air B|b|NN|_|O
ArgR|argr|NN|TF|O _|_|CD|_|O Arginine|arginine|NN|_|Supp _|_|NN|_|O 1|1|CD|_|O
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|wt|NN|_|O ,|,|,|_|O ΔoxyR|δoxyr|NN|_|O ,|,|,|_|O ΔsoxR|δsoxr|NN|_|O ,|,|,|_|O and|and|CC|_|O ΔsoxS|δsoxs|NN|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|O phase|phase|NN|_|O aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp .|.|.|_|O Then|then|RB|_|O cells|cell|NNS|_|O were|be|VBD|_|O treated|treat|VBN|_|O with|with|IN|_|O 250|250|CD|_|O uM|um|NN|_|O of|of|IN|_|O paraquat|paraquat|NN|SUPP|O at|at|IN|_|O mid-log|mid-log|JJ|_|O pahse|pahse|NN|_|O for|for|IN|_|O 20|20|CD|_|O min|min|NN|_|O with|with|IN|_|O agitation|agitation|NN|_|O .|.|.|_|O
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|WT|NNP|_|O ,|,|,|_|O and|and|CC|_|O Δcra|Δcra|NNP|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp ,|,|,|_|O fructose|fructose|NN|_|O and|and|CC|_|O acetate|acetate|NN|SUPP|O .|.|.|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O lacking|lack|VBG|_|Gtype the|the|DT|_|Gtype transcription|transcription|NN|_|Gtype factor|factor|NN|_|Gtype Fur|Fur|NNP|TF|Gtype
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|wt|NN|_|O and|and|CC|_|O Fur-8-myc|fur-8-myc|NN|_|O tagged|tag|VBD|_|O strains|strain|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp .|.|.|_|O For|for|IN|_|O iron|iron|NN|_|O treated|treat|VBN|_|O cells|cell|NNS|_|O ,|,|,|_|O 0.1|0.1|CD|_|O mM|mm|NN|KWSUPP|O of|of|IN|_|O FeCl2|fecl2|NN|_|O were|be|VBD|_|O treated|treat|VBN|_|O from|from|IN|_|O the|the|DT|_|O beginning|beginning|NN|_|O of|of|IN|_|O culture|culture|NN|_|O ,|,|,|_|O and|and|CC|_|O for|for|IN|_|O DPD|dpd|NN|_|O treated|treat|VBN|_|O cells|cell|NNS|_|O ,|,|,|_|O 0.2|0.2|CD|_|Supp mM|mm|NN|KWSUPP|Supp of|of|IN|_|Supp DPD|dpd|NN|_|Supp were|be|VBD|_|O added|add|VBN|_|O at|at|IN|_|O early-log|early-log|JJ|_|O phase|phase|NN|_|O and|and|CC|_|O continued|continue|VBD|_|O to|to|TO|_|O culture|culture|NN|_|O for|for|IN|_|O additional|additional|JJ|_|O 2h|2h|NN|_|Supp .|.|.|_|O For|for|IN|_|O the|the|DT|_|O rifampicin-treated|rifampicin-treated|JJ|_|O cultures|culture|NNS|_|O ,|,|,|_|O the|the|DT|_|O rifampicin|rifampicin|NN|SUPP|O dissolved|dissolve|VBN|_|O in|in|IN|_|O methanol|methanol|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O a|a|DT|_|O final|final|JJ|_|O concentration|concentration|NN|_|O of|of|IN|_|O 150|150|CD|_|O mg/mL|mg/ml|NN|_|O at|at|IN|_|O mid-log|mid-log|JJ|_|O phase|phase|NN|_|O and|and|CC|_|O stirred|stir|VBD|_|O for|for|IN|_|O 20|20|CD|_|O min|min|NN|_|O .|.|.|_|O
PurR|purr|NN|TF|O _|_|CD|_|O Adenine|Adenine|NNP|_|Supp _|_|NN|_|O 2|2|CD|_|O
M63|m63|NN|_|Med 0.4|0.4|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O neg|neg|NNP|_|O L1|l1|NN|_|O HS2|hs2|NN|_|O
σ32|σ32|NN|_|O 30|30|CD|_|Temp °C|°c|NN|_|Temp short|short|JJ|_|O RNase|rnase|NN|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O oxyR-8myc|oxyr-8myc|NN|_|Gtype -|-|:|_|O tagged|tag|VBN|_|O
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O anti-myc|anti-myc|JJ|_|Anti -LRB-|-lrb-|-LRB-|_|O Santa|Santa|NNP|_|O Cruz|Cruz|NNP|_|O Biotech|Biotech|NNP|_|O ,|,|,|_|O sc-28207|sc-28207|NN|_|O -RRB-|-rrb-|-RRB-|_|O
M63|m63|NN|_|Med 0.4|0.4|CD|_|O B1|b1|NN|_|O TEX|TEX|NNP|_|O pos|po|VBZ|_|O L1|l1|NN|_|O GA|ga|NN|_|O
To|to|TO|_|O harvest|harvest|VB|_|O total|total|JJ|_|O RNA|rna|NN|_|O samples|sample|NNS|_|O ,|,|,|_|O overnight|overnight|JJ|_|O cultures|culture|NNS|_|O of|of|IN|_|O wild|wild|JJ|_|Gtype type|type|NN|_|Gtype MG1655|mg1655|NN|_|O grown|grow|VBN|_|O in|in|IN|_|O LB|lb|NN|_|O at|at|IN|_|O 37|37|CD|_|O ˚C|˚c|NN|_|O were|be|VBD|_|O diluted|dilute|VBN|_|O back|back|RB|_|O 1:500|1:500|CD|_|O in|in|IN|_|O either|either|CC|_|O fresh|fresh|JJ|_|O LB|lb|NN|_|O or|or|CC|_|O M63|m63|NN|_|O minimal|minimal|JJ|_|O glucose|glucose|NN|SUPP|O medium|medium|NN|_|O and|and|CC|_|O allowed|allow|VBN|_|O to|to|TO|_|O grow|grow|VB|_|O until|until|IN|_|O the|the|DT|_|O cultures|culture|NNS|_|O reached|reach|VBD|_|O an|a|DT|_|O OD600|od600|NN|_|O of|of|IN|_|O ~|~|NN|_|O 0.4|0.4|CD|_|O and|and|CC|_|O 2.0|2.0|CD|_|O for|for|IN|_|O cultures|culture|NNS|_|O grown|grow|VBN|_|O in|in|IN|_|O LB|lb|NN|_|O and|and|CC|_|O an|a|DT|_|O OD600|od600|NN|_|O of|of|IN|_|O ~|~|NN|_|O 0.4|0.4|CD|_|O for|for|IN|_|O cultures|culture|NNS|_|O grown|grow|VBN|_|O in|in|IN|_|O M63|m63|NN|_|O .|.|.|_|O For|for|IN|_|O samples|sample|NNS|_|O grown|grow|VBN|_|O to|to|TO|_|O OD600|od600|NN|_|O of|of|IN|_|O ~|~|NN|_|O 0.4|0.4|CD|_|O a|a|DT|_|O total|total|JJ|_|O volume|volume|NN|_|O of|of|IN|_|O 25|25|CD|_|O ml|ml|NN|_|O of|of|IN|_|O cells|cell|NNS|_|O were|be|VBD|_|O harvested|harvest|VBN|_|O and|and|CC|_|O combined|combine|VBN|_|O with|with|IN|_|O 5|5|CD|_|O ml|ml|NN|_|O of|of|IN|_|O stop|stop|NN|_|O solution|solution|NN|_|O -LRB-|-lrb-|-LRB-|_|O 95|95|CD|_|O %|%|NN|_|O Ethanol|ethanol|NN|_|O ,|,|,|_|O 5|5|CD|_|O %|%|NN|_|O acid|acid|NN|_|O phenol|phenol|NN|_|O -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O For|for|IN|_|O samples|sample|NNS|_|O grown|grow|VBN|_|O to|to|TO|_|O OD600|od600|NN|_|OD of|of|IN|_|OD 2.0|2.0|CD|_|OD a|a|DT|_|O total|total|JJ|_|O volume|volume|NN|_|O of|of|IN|_|O 5|5|CD|_|O ml|ml|NN|_|O of|of|IN|_|O cells|cell|NNS|_|O were|be|VBD|_|O harvested|harvest|VBN|_|O and|and|CC|_|O combined|combine|VBN|_|O with|with|IN|_|O 1|1|CD|_|O ml|ml|NN|_|O of|of|IN|_|O stop|stop|NN|_|O solution|solution|NN|_|O .|.|.|_|O
growth|growth|NN|_|O phase|phase|NN|_|O :|:|:|_|O mid-log|mid-log|NN|_|Phase
treatment|treatment|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Med -LRB-|-lrb-|-LRB-|_|Med 2|2|CD|_|Med g/L|g/l|NN|_|Med -RRB-|-rrb-|-RRB-|_|Med minimal|minimal|JJ|_|Med W2|w2|NN|_|Med medium|medium|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 1g/L|1g/l|NN|_|Supp arginine|arginine|NN|SUPP|Supp .|.|.|_|O
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Aerobic|Aerobic|NNP|_|Air C|C|NNP|_|O
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype Aerobic|aerobic|JJ|_|Air A|a|DT|_|O
affyexp|affyexp|JJ|_|O _|_|NN|_|O delta-arcA|delta-arca|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|CD|_|O 3|3|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
SoxR|soxr|NN|TF|O PQ|pq|NN|_|Supp 2|2|CD|_|O
RNA-Seq|rna-seq|NN|_|Technique
NtrC|ntrc|NN|TF|O _|_|CD|_|O ChIPSeq|chipseq|NN|_|Technique
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype Anaerobic|anaerobic|JJ|_|Air A|a|DT|_|O
Anaerobic|anaerobic|JJ|_|Air cultures|culture|NNS|_|O
affyexp|affyexp|JJ|_|O _|_|NN|_|O delta-arcA|delta-arca|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 2|2|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
genotype|genotype|NN|_|O :|:|:|_|O Wildtype|wildtype|NN|_|Gtype
treatment|treatment|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Med -LRB-|-lrb-|-LRB-|_|Med 2|2|CD|_|Med g/L|g/l|NN|_|Med -RRB-|-rrb-|-RRB-|_|Med minimal|minimal|JJ|_|Med W2|w2|NN|_|Med medium|medium|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 2g/L|2g/l|NN|_|Supp glutamine|glutamine|NN|_|Supp .|.|.|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O in|in|IN|_|O 65|65|CD|_|O ml|ml|NN|_|O LB|lb|NN|MED|O medium|medium|NN|MED|O at|at|IN|_|O 30|30|CD|_|O °C|°c|NN|_|O to|to|TO|_|O an|a|DT|_|O OD600|od600|NN|_|OD of|of|IN|_|OD about|about|IN|_|OD 0.3|0.3|CD|_|OD .|.|.|_|O Subsequently|subsequently|RB|_|O 30|30|CD|_|O ml|ml|NN|_|O of|of|IN|_|O culture|culture|NN|_|O were|be|VBD|_|O transformed|transform|VBN|_|O to|to|TO|_|O a|a|DT|_|O pre|pre|JJ|_|O warmed|warm|VBN|_|O flask|flask|NN|_|Vess at|at|IN|_|O 43|43|CD|_|Temp °C|°c|NN|_|Temp -LRB-|-lrb-|-LRB-|_|Temp see|see|VB|_|Temp heat|heat|NN|_|Temp sample|sample|NN|_|Temp -RRB-|-rrb-|-RRB-|_|Temp and|and|CC|_|O the|the|DT|_|O remainder|remainder|NN|_|O kept|keep|VBD|_|O at|at|IN|_|O 30|30|CD|_|Temp °C|°c|NN|_|Temp .|.|.|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O WT|WT|NNP|_|Gtype
ChIP-Seq|chip-seq|NN|_|Gversion
agent|agent|NN|_|O :|:|:|_|O DPD|dpd|NN|_|Supp and|and|CC|_|Supp rifampicin|rifampicin|NN|SUPP|Supp
OmpR|ompr|NN|TF|O NaCl|nacl|NN|_|Supp 1|1|CD|_|O
growth|growth|NN|_|O medium|medium|NN|_|O :|:|:|_|O MOPS|MOPS|NNP|MED|Med minimal|minimal|JJ|_|Med glucose|glucose|NN|SUPP|Med media|media|NNS|_|Med containing|contain|VBG|_|O 1|1|CD|_|Supp µM|µm|NN|_|Supp FeSO4|feso4|NN|_|Supp
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Anaerobic|anaerobic|JJ|_|Air B|b|NN|_|O
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype ∆|∆|CD|_|Gtype ryhB|ryhb|NN|GEN|Gtype Anaerobic|anaerobic|JJ|_|Air A|a|DT|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O in|in|IN|_|O LB|LB|NNP|MED|Med media|media|NNS|MED|Med with|with|IN|_|O 1mM|1mm|NN|_|Supp IPTG|iptg|NN|_|Supp at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp with|with|IN|_|O shaking|shake|VBG|_|O for|for|IN|_|O 2|2|CD|_|Supp hours|hour|NNS|_|Supp
antibody|antibody|NN|_|O :|:|:|_|O Pre-cleared|pre-cleared|JJ|_|Anti IHF|ihf|NN|TF|Anti polyclonal|polyclonal|JJ|_|Anti antibody|antibody|NN|_|Anti
Ecoli|ecolus|NNS|_|O _|_|VBP|_|O dFNR|dfnr|NN|_|Gtype _|_|CD|_|O rep2|rep2|NN|_|O _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air
Wild|Wild|NNP|_|Gtype type|type|NN|_|Gtype control|control|NN|_|O -LRB-|-lrb-|-LRB-|_|O 5|5|CD|_|O min|min|NN|_|O -RRB-|-rrb-|-RRB-|_|O
Genome|Genome|NNP|_|O _|_|NNP|_|O build|build|VB|_|O :|:|:|_|O U00096|u00096|NN|_|Gversion .2|.2|NN|_|Gversion -LRB-|-lrb-|-LRB-|_|O GenBank|genbank|NN|_|O -RRB-|-rrb-|-RRB-|_|O
RpoB|rpob|NN|_|O with|with|IN|_|O DPD|dpd|NN|_|Supp 2|2|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique ChIP-exo|chip-exo|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
ip|ip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O affinity|affinity|NN|_|Anti purified|purify|VBN|_|Anti anti-Fur|anti-fur|JJ|_|Anti antibody|antibody|NN|_|Anti
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|wt|NN|_|O and|and|CC|_|O ΔompR|δompr|NN|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp .|.|.|_|O Then|then|RB|_|O cells|cell|NNS|_|O were|be|VBD|_|O treated|treat|VBN|_|O with|with|IN|_|O 0.3|0.3|CD|_|Supp M|m|NN|_|Supp of|of|IN|_|Supp NaCl|nacl|NN|_|Supp at|at|IN|_|O mid-log|mid-log|JJ|_|O pahse|pahse|NN|_|O for|for|IN|_|O 30|30|CD|_|Supp min|min|NN|_|Supp with|with|IN|_|O agitation|agitation|NN|_|O .|.|.|_|O
affyexp|affyexp|JJ|_|O _|_|NN|_|O delta-fnr|delta-fnr|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|NN|_|O 2|2|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
RpoB|rpob|NN|_|O ∆|∆|CD|_|Gtype crp|crp|NN|GEN|Gtype 1|1|CD|_|O
Sodium|sodium|NN|_|O phosphate|phosphate|NN|_|O -LRB-|-lrb-|-LRB-|_|O 1/100|1/100|CD|_|O vol|vol|NN|_|O .|.|.|_|O of|of|IN|_|O 1M|1m|NN|_|O ,|,|,|_|O pH|ph|NN|_|O 7.6|7.6|CD|_|O ;|;|:|_|O 10|10|CD|_|O mM|mm|NN|KWSUPP|O final|final|JJ|_|O -RRB-|-rrb-|-RRB-|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O the|the|DT|_|O mid-log|mid-log|NN|_|Phase cultures|culture|NNS|_|O followed|follow|VBN|_|O by|by|IN|_|O formaldehyde|formaldehyde|NN|_|O to|to|TO|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O and|and|CC|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O was|be|VBD|_|O continued|continue|VBN|_|O for|for|IN|_|O 10|10|CD|_|O min|min|NN|_|O .|.|.|_|O Cold|Cold|NNP|_|O 2.5|2.5|CD|_|O M|m|NN|_|O glycine|glycine|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O 100mM|100mm|NN|_|O and|and|CC|_|O the|the|DT|_|O mixture|mixture|NN|_|O was|be|VBD|_|O incubated|incubate|VBN|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O with|with|IN|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O for|for|IN|_|O 30|30|CD|_|O minutes|minute|NNS|_|O to|to|TO|_|O stop|stop|VB|_|O the|the|DT|_|O crosslinking|crosslinking|NN|_|O .|.|.|_|O Cells|cell|NNS|_|O were|be|VBD|_|O spun|spin|VBN|_|O at|at|IN|_|O 3500|3500|CD|_|O x|x|CC|_|O g|g|NN|_|O ,|,|,|_|O and|and|CC|_|O washed|wash|VBN|_|O repeatedly|repeatedly|RB|_|O with|with|IN|_|O phosphate|phosphate|NN|_|O buffered|buffer|VBN|_|O saline|saline|NN|_|O before|before|IN|_|O being|be|VBG|_|O frozen|freeze|VBN|_|O at|at|IN|_|O -80|-80|CD|_|O °C|°c|NN|_|O .|.|.|_|O Cell|cell|NN|_|O pellets|pellet|NNS|_|O -LRB-|-lrb-|-LRB-|_|O from|from|IN|_|O initial|initial|JJ|_|O 250|250|CD|_|O mL|ml|NN|_|O of|of|IN|_|O culture|culture|NN|_|O -RRB-|-rrb-|-RRB-|_|O were|be|VBD|_|O thawed|thaw|VBN|_|O and|and|CC|_|O resuspended|resuspend|VBN|_|O in|in|IN|_|O 250|250|CD|_|O μL|μl|NN|_|O of|of|IN|_|O IP|IP|NNP|_|O buffer|buffer|NN|_|O -LRB-|-lrb-|-LRB-|_|O 100|100|CD|_|O mM|mm|NN|KWSUPP|O Tris|Tris|NNP|_|O pH|ph|NN|_|O 8|8|CD|_|O ,|,|,|_|O 300|300|CD|_|O mM|mm|NN|KWSUPP|O NaCl|nacl|NN|_|O ,|,|,|_|O 1|1|CD|_|O %|%|NN|_|O TritonX-100|tritonx-100|NN|_|O -RRB-|-rrb-|-RRB-|_|O and|and|CC|_|O sonicated|sonicate|VBN|_|O using|use|VBG|_|O a|a|DT|_|O microtip|microtip|NN|_|O sonicator|sonicator|NN|_|O set|set|VBN|_|O at|at|IN|_|O 10|10|CD|_|O %|%|NN|_|O output|output|NN|_|O for|for|IN|_|O 20|20|CD|_|O second|second|JJ|_|O intervals|interval|NNS|_|O with|with|IN|_|O periods|period|NNS|_|O of|of|IN|_|O cooling|cool|VBG|_|O in|in|IN|_|O between|between|IN|_|O .|.|.|_|O Cells|cell|NNS|_|O were|be|VBD|_|O then|then|RB|_|O treated|treat|VBN|_|O for|for|IN|_|O one|one|CD|_|O hour|hour|NN|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O with|with|IN|_|O RNase|rnase|NN|_|O A|a|NN|_|O -LRB-|-lrb-|-LRB-|_|O 2|2|CD|_|O ng/ml|ng/ml|NN|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O micrococcal|micrococcal|JJ|_|O nuclease|nuclease|NN|_|O -LRB-|-lrb-|-LRB-|_|O 50|50|CD|_|O units|unit|NNS|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O 20|20|CD|_|O μM|μm|NN|_|O CaCl2|cacl2|NN|_|O ,1.2|,1.2|CD|_|O mM|mm|NN|KWSUPP|O KCl|kcl|NN|_|O ,|,|,|_|O 0.3|0.3|CD|_|O mM|mm|NN|KWSUPP|O NaCl|nacl|NN|_|O ,|,|,|_|O 6|6|CD|_|O mM|mm|NN|KWSUPP|O sucrose|sucrose|NN|_|O ,|,|,|_|O and|and|CC|_|O 10|10|CD|_|O μM|μm|NN|_|O DTT|dtt|NN|_|O .|.|.|_|O EDTA|edta|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O 10|10|CD|_|O mM|mm|NN|KWSUPP|O to|to|TO|_|O stop|stop|VB|_|O the|the|DT|_|O micrococcal|micrococcal|JJ|_|O nuclease|nuclease|NN|_|O and|and|CC|_|O the|the|DT|_|O samples|sample|NNS|_|O were|be|VBD|_|O spun|spin|VBN|_|O down|down|RP|_|O to|to|TO|_|O remove|remove|VB|_|O cell|cell|NN|_|O debris|debris|NN|_|O .|.|.|_|O The|the|DT|_|O lysate|lysate|NN|_|O was|be|VBD|_|O then|then|RB|_|O precleared|preclear|VBN|_|O through|through|IN|_|O incubation|incubation|NN|_|O with|with|IN|_|O a|a|DT|_|O 50/50|50/50|CD|_|O slurry|slurry|NN|_|O of|of|IN|_|O sepharose|sepharose|NN|_|O protein|protein|NN|_|O A|a|NN|_|O beads|bead|NNS|_|O in|in|IN|_|O IP|IP|NNP|_|O buffer|buffer|NN|_|O for|for|IN|_|O 2-3|2-3|CD|_|O hours|hour|NNS|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O .|.|.|_|O The|the|DT|_|O beads|bead|NNS|_|O were|be|VBD|_|O removed|remove|VBN|_|O by|by|IN|_|O centrifugation|centrifugation|NN|_|O and|and|CC|_|O antibody|antibody|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O the|the|DT|_|O pre-cleared|pre-cleared|JJ|_|O lysate|lysate|NN|_|O for|for|IN|_|O an|a|DT|_|O overnight|overnight|JJ|_|O incubation|incubation|NN|_|O .|.|.|_|O The|the|DT|_|O next|next|JJ|_|O day|day|NN|_|O ,|,|,|_|O 30|30|CD|_|O μl|μl|NN|_|O of|of|IN|_|O a|a|DT|_|O 50/50|50/50|CD|_|O slurry|slurry|NN|_|O of|of|IN|_|O sepharose|sepharose|NN|_|O protein|protein|NN|_|O A|a|NN|_|O beads|bead|NNS|_|O in|in|IN|_|O IP|IP|NNP|_|O buffer|buffer|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O the|the|DT|_|O lysate|lysate|NN|_|O to|to|TO|_|O capture|capture|VB|_|O antibody-protein-DNA|antibody-protein-dna|JJ|_|O complex|complex|NN|_|O for|for|IN|_|O one|one|CD|_|O hour|hour|NN|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O .|.|.|_|O Beads|bead|NNS|_|O were|be|VBD|_|O then|then|RB|_|O washed|wash|VBN|_|O once|once|RB|_|O with|with|IN|_|O 1|1|CD|_|O ml|ml|NN|_|O of|of|IN|_|O LiCl|licl|NN|_|O wash|wash|NN|_|O buffer|buffer|NN|_|O -LRB-|-lrb-|-LRB-|_|O 100|100|CD|_|O mM|mm|NN|KWSUPP|O Tris|Tris|NNP|_|O pH|ph|NN|_|O 8|8|CD|_|O ,|,|,|_|O 250|250|CD|_|O mM|mm|NN|KWSUPP|O LiCl|licl|NN|_|O ,|,|,|_|O 2|2|CD|_|O %|%|NN|_|O TritonX-100|tritonx-100|NN|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O twice|twice|RB|_|O with|with|IN|_|O 600|600|CD|_|O mM|mm|NN|KWSUPP|O NaCl|nacl|NN|_|O wash|wash|NN|_|O buffer|buffer|NN|_|O -LRB-|-lrb-|-LRB-|_|O 100|100|CD|_|O mM|mm|NN|KWSUPP|O Tris|Tris|NNP|_|O pH|ph|NN|_|O 8|8|CD|_|O ,|,|,|_|O 600|600|CD|_|O mM|mm|NN|KWSUPP|O NaCl|nacl|NN|_|O ,|,|,|_|O 2|2|CD|_|O %|%|NN|_|O TritonX-100|tritonx-100|NN|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O twice|twice|RB|_|O with|with|IN|_|O 300|300|CD|_|O mM|mm|NN|KWSUPP|O NaCl|nacl|NN|_|O wash|wash|NN|_|O buffer|buffer|NN|_|O -LRB-|-lrb-|-LRB-|_|O 100|100|CD|_|O mM|mm|NN|KWSUPP|O Tris|Tris|NNP|_|O pH|ph|NN|_|O 8|8|CD|_|O ,|,|,|_|O 300|300|CD|_|O mM|mm|NN|KWSUPP|O NaCl|nacl|NN|_|O ,|,|,|_|O 2|2|CD|_|O %|%|NN|_|O TritonX-100|tritonx-100|NN|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O and|and|CC|_|O twice|twice|RB|_|O with|with|IN|_|O TE|te|NN|_|O .|.|.|_|O Elution|elution|NN|_|O buffer|buffer|NN|_|O -LRB-|-lrb-|-LRB-|_|O 50|50|CD|_|O mM|mm|NN|KWSUPP|O Tris|Tris|NNP|_|O pH|ph|NN|_|O 8|8|CD|_|O ,|,|,|_|O 10|10|CD|_|O mM|mm|NN|KWSUPP|O EDTA|edta|NN|_|O ,|,|,|_|O 1|1|CD|_|O %|%|NN|_|O SDS|sds|NN|_|O -RRB-|-rrb-|-RRB-|_|O was|be|VBD|_|O added|add|VBN|_|O after|after|IN|_|O the|the|DT|_|O final|final|JJ|_|O wash|wash|NN|_|O step|step|NN|_|O ,|,|,|_|O and|and|CC|_|O beads|bead|NNS|_|O were|be|VBD|_|O incubated|incubate|VBN|_|O at|at|IN|_|O 65|65|CD|_|O °C|°c|NN|_|O for|for|IN|_|O 30|30|CD|_|O minutes|minute|NNS|_|O to|to|TO|_|O remove|remove|VB|_|O the|the|DT|_|O crosslinked|crosslink|VBN|_|O protein-DNA|protein-dna|JJ|_|O complexes|complex|NNS|_|O from|from|IN|_|O the|the|DT|_|O beads|bead|NNS|_|O .|.|.|_|O After|after|IN|_|O centrifugation|centrifugation|NN|_|O to|to|TO|_|O remove|remove|VB|_|O the|the|DT|_|O beads|bead|NNS|_|O ,|,|,|_|O the|the|DT|_|O samples|sample|NNS|_|O were|be|VBD|_|O incubated|incubate|VBN|_|O overnight|overnight|RB|_|O at|at|IN|_|O 65|65|CD|_|O °C|°c|NN|_|O to|to|TO|_|O reverse|reverse|VB|_|O the|the|DT|_|O protein-DNA|protein-dna|JJ|_|O formaldehyde|formaldehyde|NN|_|O crosslinks|crosslink|NNS|_|O .|.|.|_|O DNA|dna|NN|_|O was|be|VBD|_|O purified|purify|VBN|_|O using|use|VBG|_|O Qiagen|Qiagen|NNP|_|O 's|'s|POS|_|O PCR|pcr|NN|_|O Purification|purification|NN|_|O kit|kit|NN|_|O and|and|CC|_|O eluted|elute|VBN|_|O to|to|TO|_|O a|a|DT|_|O final|final|JJ|_|O volume|volume|NN|_|O of|of|IN|_|O 50|50|CD|_|O μl|μl|NN|_|O with|with|IN|_|O EB|EB|NNP|_|O .|.|.|_|O
WT|wt|JJ|_|Gtype acetate|acetate|NN|SUPP|Supp 2|2|CD|_|O
HNS|hns|SYM|_|O -|-|:|_|O Aerobic|aerobic|JJ|_|Air B|b|NN|_|O
genotype|genotype|NN|_|O :|:|:|_|O ompR-8myc|ompr-8myc|NN|_|Gtype
treatment|treatment|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Med -LRB-|-lrb-|-LRB-|_|Med 2|2|CD|_|Med g/L|g/l|NN|_|Med -RRB-|-rrb-|-RRB-|_|Med minimal|minimal|JJ|_|Med M9|m9|NN|_|Med medium|medium|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 20|20|CD|_|Supp mg/L|mg/l|NN|_|Supp tryptophan|tryptophan|NN|_|Supp .|.|.|_|O
RpoB|rpob|NN|_|O with|with|IN|_|O Fe|Fe|NNP|_|Supp and|and|CC|_|O rifampicin|rifampicin|NN|SUPP|Supp 1|1|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique ChIP-exo|chip-exo|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O Δfur|δfur|NN|_|Gtype
RpoB|rpob|NN|_|O with|with|IN|_|O DPD|dpd|NN|_|Supp and|and|CC|_|O rifampicin|rifampicin|NN|SUPP|Supp 2|2|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique ChIP-exo|chip-exo|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
growth|growth|NN|_|O phase|phase|NN|_|O :|:|:|_|O stationary|stationary|JJ|_|Phase
WT|wt|JJ|_|Gtype acetate|acetate|NN|SUPP|Supp 1|1|CD|_|O
ΔgadW|δgadw|NN|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
WT|wt|JJ|_|Gtype PQ|pq|NN|_|Supp 1|1|CD|_|O
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O RNA|rna|NN|_|Anti polymerase|polymerase|NN|_|Anti subunit|subunit|NN|_|Anti β|β|NN|_|Anti
To|to|TO|_|O harvest|harvest|VB|_|O total|total|JJ|_|O RNA|rna|NN|_|O samples|sample|NNS|_|O ,|,|,|_|O overnight|overnight|JJ|_|O cultures|culture|NNS|_|O of|of|IN|_|O wild|wild|JJ|_|Gtype type|type|NN|_|Gtype MG1655|mg1655|NN|_|O grown|grow|VBN|_|O in|in|IN|_|O LB|lb|NN|_|O at|at|IN|_|O 37|37|CD|_|O ˚C|˚c|NN|_|O were|be|VBD|_|O diluted|dilute|VBN|_|O back|back|RB|_|O 1:500|1:500|CD|_|O in|in|IN|_|O either|either|CC|_|O fresh|fresh|JJ|_|O LB|lb|NN|_|O or|or|CC|_|O M63|m63|NN|_|Med minimal|minimal|JJ|_|Med glucose|glucose|NN|SUPP|Med medium|medium|NN|_|O and|and|CC|_|O allowed|allow|VBN|_|O to|to|TO|_|O grow|grow|VB|_|O until|until|IN|_|O the|the|DT|_|O cultures|culture|NNS|_|O reached|reach|VBD|_|O an|a|DT|_|O OD600|od600|NN|_|O of|of|IN|_|O ~|~|NN|_|O 0.4|0.4|CD|_|O and|and|CC|_|O 2.0|2.0|CD|_|O for|for|IN|_|O cultures|culture|NNS|_|O grown|grow|VBN|_|O in|in|IN|_|O LB|lb|NN|_|O and|and|CC|_|O an|a|DT|_|O OD600|od600|NN|_|OD of|of|IN|_|OD ~|~|NN|_|OD 0.4|0.4|CD|_|OD for|for|IN|_|O cultures|culture|NNS|_|O grown|grow|VBN|_|O in|in|IN|_|O M63|m63|NN|_|O .|.|.|_|O For|for|IN|_|O samples|sample|NNS|_|O grown|grow|VBN|_|O to|to|TO|_|O OD600|od600|NN|_|O of|of|IN|_|O ~|~|NN|_|O 0.4|0.4|CD|_|O a|a|DT|_|O total|total|JJ|_|O volume|volume|NN|_|O of|of|IN|_|O 25|25|CD|_|O ml|ml|NN|_|O of|of|IN|_|O cells|cell|NNS|_|O were|be|VBD|_|O harvested|harvest|VBN|_|O and|and|CC|_|O combined|combine|VBN|_|O with|with|IN|_|O 5|5|CD|_|O ml|ml|NN|_|O of|of|IN|_|O stop|stop|NN|_|O solution|solution|NN|_|O -LRB-|-lrb-|-LRB-|_|O 95|95|CD|_|O %|%|NN|_|O Ethanol|ethanol|NN|_|O ,|,|,|_|O 5|5|CD|_|O %|%|NN|_|O acid|acid|NN|_|O phenol|phenol|NN|_|O -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O For|for|IN|_|O samples|sample|NNS|_|O grown|grow|VBN|_|O to|to|TO|_|O OD600|od600|NN|_|O of|of|IN|_|O 2.0|2.0|CD|_|O a|a|DT|_|O total|total|JJ|_|O volume|volume|NN|_|O of|of|IN|_|O 5|5|CD|_|O ml|ml|NN|_|O of|of|IN|_|O cells|cell|NNS|_|O were|be|VBD|_|O harvested|harvest|VBN|_|O and|and|CC|_|O combined|combine|VBN|_|O with|with|IN|_|O 1|1|CD|_|O ml|ml|NN|_|O of|of|IN|_|O stop|stop|NN|_|O solution|solution|NN|_|O .|.|.|_|O
ΔoxyR|δoxyr|NN|_|Gtype PQ|pq|NN|_|Supp 1|1|CD|_|O
ΔompR|δompr|NN|_|Gtype NaCl|nacl|NN|_|Supp 2|2|CD|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O delta-soxR|delta-soxr|NN|_|Gtype
WT|wt|JJ|_|Gtype with|with|IN|_|O DPD|dpd|NN|_|Supp 1|1|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique RNA-seq|rna-seq|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
Δfur|δfur|NN|_|Gtype with|with|IN|_|O DPD|dpd|NN|_|Supp 2|2|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique RNA-seq|rna-seq|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
Cultures|culture|NNS|_|O grown|grow|VBN|_|O in|in|IN|_|O MOPS|MOPS|NNP|MED|Med minimal|minimal|JJ|_|Med glucose|glucose|NN|SUPP|Med media|media|NNS|_|Med containing|contain|VBG|_|O 10|10|CD|_|Supp µM|µm|NN|_|Supp FeSO4|feso4|NN|_|Supp
WT|wt|JJ|_|Gtype _|_|NN|_|O ChIPSeq|chipseq|NN|_|Technique _|_|NN|_|O 1|1|CD|_|O
Ptac|ptac|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O A|a|NN|_|O -|-|:|_|O 16|16|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O -LCB-|-lcb-|-LRB-|_|Gtype delta|delta|NN|_|Gtype -RCB-|-rcb-|-RRB-|_|Gtype tonB|tonb|NN|GEN|Gtype ,|,|,|_|Gtype -LCB-|-lcb-|-LRB-|_|Gtype delta|delta|NN|_|Gtype -RCB-|-rcb-|-RRB-|_|Gtype feoA|feoa|NN|GEN|Gtype ,|,|,|_|Gtype -LCB-|-lcb-|-LRB-|_|Gtype delta|delta|NN|_|Gtype -RCB-|-rcb-|-RRB-|_|Gtype zupT|zupt|NN|GEN|Gtype K12|k12|NN|_|Gtype
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O with|with|IN|_|O 8|8|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp and|and|CC|_|Supp 300|300|CD|_|Supp µL|µl|NN|_|Supp Cm20|cm20|NN|_|Supp anaerobically|anaerobically|RB|_|Air -LRB-|-lrb-|-LRB-|_|Air 95|95|CD|_|Air %|%|NN|_|Air N2|n2|NN|_|Air and|and|CC|_|Air 5|5|CD|_|Air %|%|NN|_|Air CO2|co2|NN|_|Air -RRB-|-rrb-|-RRB-|_|Air until|until|IN|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|OD of|of|IN|_|OD 0.3|0.3|CD|_|OD -RRB-|-rrb-|-RRB-|_|O and|and|CC|_|O treated|treat|VBN|_|O with|with|IN|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O volumen|voluman|NNS|_|O formaldehyde|formaldehyde|NN|_|O for|for|IN|_|O ten|ten|CD|_|O minutes|minute|NNS|_|O .|.|.|_|O Sodium|sodium|NN|_|O phosphate|phosphate|NN|_|O -LRB-|-lrb-|-LRB-|_|O 1/100|1/100|CD|_|O vol|vol|NN|_|O .|.|.|_|O of|of|IN|_|O 1M|1m|NN|_|O ,|,|,|_|O pH|ph|NN|_|O 7.6|7.6|CD|_|O ;|;|:|_|O 10|10|CD|_|O mM|mm|NN|KWSUPP|O final|final|JJ|_|O -RRB-|-rrb-|-RRB-|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O the|the|DT|_|O mid-log|mid-log|JJ|_|O cultures|culture|NNS|_|O followed|follow|VBN|_|O by|by|IN|_|O formaldehyde|formaldehyde|NN|_|O to|to|TO|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O ,|,|,|_|O and|and|CC|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O was|be|VBD|_|O continued|continue|VBN|_|O for|for|IN|_|O 10|10|CD|_|O min|min|NN|_|O .|.|.|_|O Cold|Cold|NNP|_|O 2.5|2.5|CD|_|O M|m|NN|_|O glycine|glycine|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O 100mM|100mm|NN|_|O and|and|CC|_|O the|the|DT|_|O mixture|mixture|NN|_|O was|be|VBD|_|O incubated|incubate|VBN|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O with|with|IN|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O for|for|IN|_|O 30|30|CD|_|O minutes|minute|NNS|_|O to|to|TO|_|O stop|stop|VB|_|O the|the|DT|_|O crosslinking|crosslinking|NN|_|O .|.|.|_|O Cells|cell|NNS|_|O were|be|VBD|_|O spun|spin|VBN|_|O at|at|IN|_|O 5000|5000|CD|_|O x|x|CC|_|O g|g|NN|_|O ,|,|,|_|O and|and|CC|_|O washed|wash|VBN|_|O repeatedly|repeatedly|RB|_|O with|with|IN|_|O phosphate|phosphate|NN|_|O buffered|buffer|VBN|_|O saline|saline|NN|_|O before|before|IN|_|O being|be|VBG|_|O frozen|freeze|VBN|_|O at|at|IN|_|O -80|-80|CD|_|O °C|°c|NN|_|O .|.|.|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O -LCB-|-lcb-|-LRB-|_|Gtype delta|delta|NN|_|Gtype -RCB-|-rcb-|-RRB-|_|Gtype lacZ|lacz|NN|GEN|Gtype ,|,|,|_|Gtype -LCB-|-lcb-|-LRB-|_|Gtype delta|delta|NN|_|Gtype -RCB-|-rcb-|-RRB-|_|Gtype tonB|tonb|NN|GEN|Gtype ,|,|,|_|Gtype -LCB-|-lcb-|-LRB-|_|Gtype delta|delta|NN|_|Gtype -RCB-|-rcb-|-RRB-|_|Gtype feoA|feoa|NN|GEN|Gtype ,|,|,|_|Gtype -LCB-|-lcb-|-LRB-|_|Gtype delta|delta|NN|_|Gtype -RCB-|-rcb-|-RRB-|_|Gtype zupT|zupt|NN|GEN|Gtype K12|k12|NN|_|Gtype
growth|growth|NN|_|O phase|phase|NN|_|O :|:|:|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|OD =|=|JJ|_|OD 0.3|0.3|CD|_|OD -RRB-|-rrb-|-RRB-|_|O
treatment|treatment|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Med -LRB-|-lrb-|-LRB-|_|Med 2|2|CD|_|Med g/L|g/l|NN|_|Med -RRB-|-rrb-|-RRB-|_|Med minimal|minimal|JJ|_|Med M9|m9|NN|_|Med medium|medium|NN|_|Med supplemented|supplement|VBN|_|O without|without|IN|_|O 20|20|CD|_|Supp mg/L|mg/l|NN|_|Supp tryptophan|tryptophan|NN|_|Supp .|.|.|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O Wild-type|wild-type|JJ|_|Gtype
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|WT|NNP|_|O ,|,|,|_|O and|and|CC|_|O Δcra|Δcra|NNP|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|O ,|,|,|_|O fructose|fructose|NN|_|O and|and|CC|_|O acetate|acetate|NN|SUPP|O .|.|.|_|O
Wild|Wild|NNP|_|Gtype type|type|NN|_|Gtype control|control|NN|_|O -LRB-|-lrb-|-LRB-|_|O 10|10|CD|_|O min|min|NN|_|O -RRB-|-rrb-|-RRB-|_|O
antibody|antibody|NN|_|O :|:|:|_|O RNA|rna|NN|_|Anti Polymerase|polymerase|NN|_|Anti ß|ß|NN|_|Anti monoclonal|monoclonal|JJ|_|Anti antibody|antibody|NN|_|Anti from|from|IN|_|O NeoClone|NeoClone|NNP|_|O -LRB-|-lrb-|-LRB-|_|O W0002|w0002|NN|_|O -RRB-|-rrb-|-RRB-|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O delta-gadX|delta-gadx|NN|_|Gtype
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O 9E10|9e10|CD|_|Anti Myc|myc|NN|_|Anti tag|tag|NN|GEN|Anti antibody|antibody|NN|_|O
SoxS|soxs|NN|TF|O PQ|pq|NN|_|Supp 2|2|CD|_|O
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|wt|NN|_|O and|and|CC|_|O Fur-8-myc|fur-8-myc|NN|_|O tagged|tag|VBD|_|O strains|strain|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp .|.|.|_|O For|for|IN|_|O iron|iron|NN|_|O treated|treat|VBN|_|O cells|cell|NNS|_|O ,|,|,|_|O 0.1|0.1|CD|_|O mM|mm|NN|KWSUPP|O of|of|IN|_|O FeCl2|fecl2|NN|_|O were|be|VBD|_|O treated|treat|VBN|_|O from|from|IN|_|O the|the|DT|_|O beginning|beginning|NN|_|O of|of|IN|_|O culture|culture|NN|_|O ,|,|,|_|O and|and|CC|_|O for|for|IN|_|O DPD|dpd|NN|_|O treated|treat|VBN|_|O cells|cell|NNS|_|O ,|,|,|_|O 0.2|0.2|CD|_|Supp mM|mm|NN|KWSUPP|Supp of|of|IN|_|Supp DPD|dpd|NN|_|Supp were|be|VBD|_|O added|add|VBN|_|O at|at|IN|_|O early-log|early-log|JJ|_|O phase|phase|NN|_|O and|and|CC|_|O continued|continue|VBD|_|O to|to|TO|_|O culture|culture|NN|_|O for|for|IN|_|O additional|additional|JJ|_|O 2h|2h|NN|_|Supp .|.|.|_|O For|for|IN|_|O the|the|DT|_|O rifampicin-treated|rifampicin-treated|JJ|_|O cultures|culture|NNS|_|O ,|,|,|_|O the|the|DT|_|O rifampicin|rifampicin|NN|SUPP|Supp dissolved|dissolve|VBN|_|Supp in|in|IN|_|Supp methanol|methanol|NN|_|Supp was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O a|a|DT|_|O final|final|JJ|_|O concentration|concentration|NN|_|O of|of|IN|_|O 150|150|CD|_|Supp mg/mL|mg/ml|NN|_|Supp at|at|IN|_|O mid-log|mid-log|JJ|_|O phase|phase|NN|_|O and|and|CC|_|O stirred|stir|VBD|_|O for|for|IN|_|O 20|20|CD|_|Supp min|min|NN|_|Supp .|.|.|_|O
WT|wt|JJ|_|Gtype glucose|glucose|NN|SUPP|Supp 2|2|CD|_|O
Ecoli|ecolus|NNS|_|O _|_|VBP|_|O wild-type|wild-type|JJ|_|Gtype _|_|NN|_|O rep2|rep2|NN|_|O _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air
ΔoxyR|δoxyr|NN|_|Gtype PQ|pq|NN|_|Supp 2|2|CD|_|O
RpoB|rpob|NN|_|O ∆|∆|CD|_|Gtype cra|cra|NN|GEN|Gtype 1|1|CD|_|O
NsrR|nsrr|NN|TF|Gtype _|_|CD|_|Gtype Flagtag|flagtag|NN|_|Gtype _|_|CD|_|O rep2|rep2|NN|_|O
treated|treat|VBN|_|O with|with|IN|_|O :|:|:|_|O 250|250|CD|_|Supp uM|um|NN|_|Supp of|of|IN|_|Supp paraquat|paraquat|NN|SUPP|Supp at|at|IN|_|O mid-log|mid-log|NN|_|Phase pahse|pahse|NN|_|Phase for|for|IN|_|O 20|20|CD|_|Supp min|min|NN|_|Supp
Resulting|result|VBG|_|O reads|read|VBZ|_|O were|be|VBD|_|O aligned|align|VBN|_|O to|to|TO|_|O the|the|DT|_|O published|publish|VBN|_|O E.|e.|FW|_|O coli|coli|FW|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O genome|genome|NN|_|O -LRB-|-lrb-|-LRB-|_|O U00096|u00096|NN|_|Gversion .2|.2|NN|_|Gversion -RRB-|-rrb-|-RRB-|_|O using|use|VBG|_|O the|the|DT|_|O software|software|NN|_|O package|package|NN|_|O SOAP|soap|NN|_|O -LRB-|-lrb-|-LRB-|_|O Li|Li|NNP|_|O et|et|FW|_|O al|al|FW|_|O ,|,|,|_|O 2009|2009|CD|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O allowing|allow|VBG|_|O no|no|RB|_|O more|more|JJR|_|O than|than|IN|_|O two|two|CD|_|O mismatches|mismatch|NNS|_|O -LRB-|-lrb-|-LRB-|_|O Supplemental|Supplemental|NNP|_|O File|File|NNP|_|O -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O Reads|read|VBZ|_|O aligning|align|VBG|_|O to|to|TO|_|O repeated|repeated|JJ|_|O elements|element|NNS|_|O in|in|IN|_|O the|the|DT|_|O genome|genome|NN|_|O -LRB-|-lrb-|-LRB-|_|O e.g.|e.g.|FW|_|O rRNA|rrna|NN|_|O -RRB-|-rrb-|-RRB-|_|O were|be|VBD|_|O removed|remove|VBN|_|O from|from|IN|_|O analysis|analysis|NN|_|O .|.|.|_|O For|for|IN|_|O reads|read|VBZ|_|O that|that|IN|_|O had|have|VBD|_|O no|no|DT|_|O mapping|mapping|NN|_|O locations|location|NNS|_|O for|for|IN|_|O the|the|DT|_|O first|first|JJ|_|O 36|36|CD|_|O bp|bp|NN|_|O ,|,|,|_|O the|the|DT|_|O 3-30|3-30|CD|_|O bp|bp|NN|_|O subsequences|subsequence|NNS|_|O were|be|VBD|_|O used|use|VBN|_|O in|in|IN|_|O the|the|DT|_|O subsequent|subsequent|JJ|_|O mapping|mapping|NN|_|O to|to|TO|_|O the|the|DT|_|O reference|reference|NN|_|O genome|genome|NN|_|O .|.|.|_|O Reads|read|NNS|_|O that|that|WDT|_|O had|have|VBD|_|O unique|unique|JJ|_|O mapping|mapping|NN|_|O locations|location|NNS|_|O and|and|CC|_|O did|do|VBD|_|O not|not|RB|_|O match|match|VB|_|O annotated|annotated|JJ|_|O rRNA|rrna|NN|_|O genes|gene|NNS|_|O were|be|VBD|_|O used|use|VBN|_|O for|for|IN|_|O further|further|JJ|_|O analysis|analysis|NN|_|O .|.|.|_|O For|for|IN|_|O each|each|DT|_|O gene|gene|NN|_|O ,|,|,|_|O the|the|DT|_|O tag|tag|NN|GEN|O density|density|NN|_|O was|be|VBD|_|O estimated|estimate|VBN|_|O as|as|IN|_|O the|the|DT|_|O number|number|NN|_|O of|of|IN|_|O aligned|align|VBN|_|O sequencing|sequencing|NN|_|O tags|tag|NNS|_|O divided|divide|VBN|_|O by|by|IN|_|O gene|gene|NN|_|O size|size|NN|_|O in|in|IN|_|O kb|kb|NN|_|O .|.|.|_|O Per-gene|per-gene|JJ|_|O tag|tag|NN|GEN|O density|density|NN|_|O was|be|VBD|_|O normalized|normalize|VBN|_|O using|use|VBG|_|O quantile|quantile|JJ|_|O normalization|normalization|NN|_|O -LRB-|-lrb-|-LRB-|_|O Supplemental|Supplemental|NNP|_|O Files|Files|NNP|_|O -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O The|the|DT|_|O tag|tag|NN|GEN|O density|density|NN|_|O data|datum|NNS|_|O were|be|VBD|_|O analyzed|analyze|VBN|_|O for|for|IN|_|O statistically|statistically|RB|_|O significant|significant|JJ|_|O differential|differential|JJ|_|O expression|expression|NN|_|O using|use|VBG|_|O BaySeq|BaySeq|NNP|_|O -LRB-|-lrb-|-LRB-|_|O Hardcastle|Hardcastle|NNP|_|O &|&|CC|_|O Kelly|Kelly|NNP|_|O ,|,|,|_|O 2010|2010|CD|_|O -RRB-|-rrb-|-RRB-|_|O with|with|IN|_|O a|a|DT|_|O FDR|FDR|NNP|_|O of|of|IN|_|O 0.01|0.01|CD|_|O ,|,|,|_|O and|and|CC|_|O genes|gene|NNS|_|O were|be|VBD|_|O organized|organize|VBN|_|O into|into|IN|_|O operons|operon|NNS|_|O using|use|VBG|_|O data|datum|NNS|_|O from|from|IN|_|O EcoCyc|EcoCyc|NNP|_|O -LRB-|-lrb-|-LRB-|_|O Keseler|Keseler|NNP|_|O et|et|FW|_|O al|al|FW|_|O ,|,|,|_|O 2011|2011|CD|_|O -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O
At|at|IN|_|O OD450|od450|NN|_|OD =|=|JJ|_|OD 0.3|0.3|CD|_|OD ,|,|,|_|O cultures|culture|NNS|_|O induced|induce|VBN|_|O with|with|IN|_|O 1|1|CD|_|Supp mM|mm|NN|KWSUPP|Supp IPTG|iptg|NN|_|Supp .|.|.|_|O Cells|cell|NNS|_|O harvested|harvest|VBD|_|O 0|0|CD|_|O min|min|NN|_|O after|after|IN|_|O induction|induction|NN|_|O
ChIP-exo|ChIP-exo|NNP|_|Technique RpoS|rpos|NN|_|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype Anaerobic|anaerobic|JJ|_|Air B|b|NN|_|O
∆|∆|CD|_|Gtype ryhB|ryhb|NN|GEN|Gtype Aerobic|aerobic|JJ|_|Air
At|at|IN|_|O OD450|od450|NN|_|OD =|=|JJ|_|OD 0.3|0.3|CD|_|OD ,|,|,|_|O cultures|culture|NNS|_|O induced|induce|VBN|_|O with|with|IN|_|O 1|1|CD|_|Supp mM|mm|NN|KWSUPP|Supp IPTG|iptg|NN|_|Supp .|.|.|_|O Cells|cell|NNS|_|O harvested|harvest|VBN|_|O 20|20|CD|_|O min|min|NN|_|O after|after|IN|_|O induction|induction|NN|_|O
genotype|genotype|NN|_|O :|:|:|_|O gadE-8myc|gade-8myc|NN|_|Gtype
Cra|Cra|NNP|TF|O fructose|fructose|NN|_|Supp 1|1|CD|_|O
Cra|Cra|NNP|TF|O glucose|glucose|NN|SUPP|Supp 1|1|CD|_|O
PurR|purr|NN|TF|O _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|NN|_|O 1|1|CD|_|O
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O Adenine|Adenine|NNP|_|Supp
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O neg|neg|NNP|_|O L1|l1|NN|_|O HS1|hs1|NN|_|O
affyexp|affyexp|JJ|_|O _|_|NN|_|O delta-fnr|delta-fnr|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 3|3|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
Lrp|Lrp|NNP|TF|O _|_|SYM|_|O Leu|Leu|NNP|_|Supp _|_|NN|_|O 2|2|CD|_|O
ΔsoxR|δsoxr|NN|_|Gtype PQ|pq|NN|_|Supp 2|2|CD|_|O
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B1|b1|NN|_|O TEX|tex|NN|_|O neg|neg|NN|_|O L1|l1|NN|_|O GA|ga|NN|_|O
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|wt|NN|_|O and|and|CC|_|O Fur-8-myc|fur-8-myc|NN|_|O tagged|tag|VBD|_|O strains|strain|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp .|.|.|_|O For|for|IN|_|O iron|iron|NN|_|O treated|treat|VBN|_|O cells|cell|NNS|_|O ,|,|,|_|O 0.1|0.1|CD|_|Supp mM|mm|NN|KWSUPP|Supp of|of|IN|_|Supp FeCl2|fecl2|NN|_|Supp were|be|VBD|_|O treated|treat|VBN|_|O from|from|IN|_|O the|the|DT|_|O beginning|beginning|NN|_|O of|of|IN|_|O culture|culture|NN|_|O ,|,|,|_|O and|and|CC|_|O for|for|IN|_|O DPD|dpd|NN|_|O treated|treat|VBN|_|O cells|cell|NNS|_|O ,|,|,|_|O 0.2|0.2|CD|_|O mM|mm|NN|KWSUPP|O of|of|IN|_|O DPD|dpd|NN|_|O were|be|VBD|_|O added|add|VBN|_|O at|at|IN|_|O early-log|early-log|JJ|_|O phase|phase|NN|_|O and|and|CC|_|O continued|continue|VBD|_|O to|to|TO|_|O culture|culture|NN|_|O for|for|IN|_|O additional|additional|JJ|_|O 2h|2h|NN|_|Supp .|.|.|_|O For|for|IN|_|O the|the|DT|_|O rifampicin-treated|rifampicin-treated|JJ|_|O cultures|culture|NNS|_|O ,|,|,|_|O the|the|DT|_|O rifampicin|rifampicin|NN|SUPP|O dissolved|dissolve|VBN|_|O in|in|IN|_|O methanol|methanol|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O a|a|DT|_|O final|final|JJ|_|O concentration|concentration|NN|_|O of|of|IN|_|O 150|150|CD|_|O mg/mL|mg/ml|NN|_|O at|at|IN|_|O mid-log|mid-log|JJ|_|O phase|phase|NN|_|O and|and|CC|_|O stirred|stir|VBD|_|O for|for|IN|_|O 20|20|CD|_|O min|min|NN|_|O .|.|.|_|O
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O anti-RpoS|anti-rpos|JJ|_|Anti -LRB-|-lrb-|-LRB-|_|O neoclone|neoclone|NN|_|O ,|,|,|_|O WP009|wp009|NN|_|O -RRB-|-rrb-|-RRB-|_|O
ChIP-exo|chip-exo|NN|_|O reads|read|VBZ|_|O were|be|VBD|_|O aligned|align|VBN|_|O to|to|TO|_|O the|the|DT|_|O NC|nc|NN|_|Gversion _|_|CD|_|Gversion 000913|000913|CD|_|Gversion genome|genome|NN|_|O reference|reference|NN|_|O sequence|sequence|NN|_|O using|use|VBG|_|O using|use|VBG|_|O bowtie|bowtie|NN|_|O v1|v1|NN|_|O .0.0|.0.0|CD|_|O with|with|IN|_|O parameters|parameter|NNS|_|O -|-|:|_|O S|s|NN|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O ΔarcA|δarca|NN|_|Gtype
genotype|genotype|NN|_|O :|:|:|_|O PurR-8myc|purr-8myc|NN|_|Gtype
affyexp|affyexp|JJ|_|O _|_|NN|_|O wt|wt|JJ|_|Gtype _|_|NN|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 3|3|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
ChIP-Seq|chip-seq|NN|_|Technique
LB|lb|NN|_|Med 0.4|0.4|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O neg|neg|NNP|_|O L1|l1|NN|_|O HS2|hs2|NN|_|O
genoype|genoype|NN|_|O :|:|:|_|O dFNR|dfnr|NN|_|Gtype
library|library|NN|_|O strategy|strategy|NN|_|O :|:|:|_|O ChIP-exo|ChIP-exo|NNP|_|Technique
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O soxR-8myc|soxr-8myc|NN|_|Gtype -|-|:|_|O tagged|tag|VBN|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O fur-8myc|fur-8myc|JJ|_|Gtype
Fur|Fur|NNP|TF|O with|with|IN|_|O DPD|dpd|NN|_|Supp 1|1|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique ChIP-exo|chip-exo|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
Ptac|ptac|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O B|b|NN|_|O -|-|:|_|O 4|4|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
affyexp|affyexp|JJ|_|O _|_|NN|_|O delta-arcA|delta-arca|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|NN|_|O 2|2|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
WT|wt|JJ|_|Gtype _|_|NN|_|O RNASeq|rnaseq|NN|_|Technique
growth|growth|NN|_|O medium|medium|NN|_|O :|:|:|_|O MOPS|MOPS|NNP|MED|Med minimal|minimal|JJ|_|Med glucose|glucose|NN|SUPP|Med media|media|NNS|_|Med containing|contain|VBG|_|O 10|10|CD|_|Supp µM|µm|NN|_|Supp FeSO4|feso4|NN|_|Supp
growth|growth|NN|_|O phase|phase|NN|_|O :|:|:|_|O exponential|exponential|JJ|_|Phase
FNR|fnr|SYM|TF|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air -|-|:|_|O B|b|NN|_|O
σ32|σ32|NN|_|O 43|43|CD|_|Temp °C|°c|NN|_|Temp rep1|rep1|NN|_|O
σ32|σ32|NN|_|O 43|43|CD|_|Temp °C|°c|NN|_|Temp rep2|rep2|NN|_|O
RpoB|rpob|NN|_|O WT|wt|JJ|_|Gtype 1|1|CD|_|O
ArgR|argr|NN|TF|O _|_|CD|_|O Arginine|arginine|NN|_|Supp _|_|NN|_|O 2|2|CD|_|O
Sodium|sodium|NN|_|Supp phosphate|phosphate|NN|_|Supp -LRB-|-lrb-|-LRB-|_|Supp 1/100|1/100|CD|_|Supp vol|vol|NN|_|Supp .|.|.|_|Supp of|of|IN|_|Supp 1M|1m|NN|_|Supp ,|,|,|_|Supp pH|ph|NN|_|Supp 7.6|7.6|CD|_|Supp ;|;|:|_|Supp 10|10|CD|_|Supp mM|mm|NN|KWSUPP|Supp final|final|JJ|_|Supp -RRB-|-rrb-|-RRB-|_|Supp was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O the|the|DT|_|O mid-log|mid-log|NN|_|Phase cultures|culture|NNS|_|O followed|follow|VBN|_|O by|by|IN|_|O formaldehyde|formaldehyde|NN|_|O to|to|TO|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O ,|,|,|_|O and|and|CC|_|O aerobic|aerobic|JJ|_|O or|or|CC|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O was|be|VBD|_|O continued|continue|VBN|_|O for|for|IN|_|O 10|10|CD|_|O min|min|NN|_|O .|.|.|_|O Cold|Cold|NNP|_|O 2.5|2.5|CD|_|O M|m|NN|_|O glycine|glycine|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O 100mM|100mm|NN|_|O and|and|CC|_|O the|the|DT|_|O mixture|mixture|NN|_|O was|be|VBD|_|O incubated|incubate|VBN|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O with|with|IN|_|O aerobic|aerobic|JJ|_|O or|or|CC|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O for|for|IN|_|O 30|30|CD|_|O minutes|minute|NNS|_|O to|to|TO|_|O stop|stop|VB|_|O the|the|DT|_|O crosslinking|crosslinking|NN|_|O .|.|.|_|O Cells|cell|NNS|_|O were|be|VBD|_|O spun|spin|VBN|_|O at|at|IN|_|O 3500|3500|CD|_|O x|x|CC|_|O g|g|NN|_|O ,|,|,|_|O and|and|CC|_|O washed|wash|VBN|_|O repeatedly|repeatedly|RB|_|O with|with|IN|_|O phosphate|phosphate|NN|_|O buffered|buffer|VBN|_|O saline|saline|NN|_|O before|before|IN|_|O being|be|VBG|_|O frozen|freeze|VBN|_|O at|at|IN|_|O -80|-80|CD|_|O °C|°c|NN|_|O .|.|.|_|O
Genome|Genome|NNP|_|O _|_|NNP|_|O build|build|VB|_|O :|:|:|_|O Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O MG1655|mg1655|NN|_|O K-12|k-12|NN|_|O genome|genome|NN|_|O version|version|NN|_|O U00096|u00096|NN|_|Gversion .2|.2|NN|_|Gversion
OxyR|oxyr|NN|TF|O PQ|pq|NN|_|Supp 1|1|CD|_|O
Cra|Cra|NNP|TF|O glucose|glucose|NN|SUPP|Supp 2|2|CD|_|O
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O anaerobic|anaerobic|JJ|_|Air
Genome|Genome|NNP|_|O _|_|NNP|_|O build|build|VB|_|O :|:|:|_|O NC|nc|NN|_|Gversion _|_|CD|_|Gversion 000913|000913|CD|_|Gversion
Δcra|δcra|NN|_|Gtype glucose|glucose|NN|SUPP|Supp 1|1|CD|_|O
LB|lb|NN|_|Med 0.4|0.4|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O pos|po|VBZ|_|O L1|l1|NN|_|O HS2|hs2|NN|_|O
E.|E.|NNP|_|O coli|coli|NN|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O WT|wt|NN|_|O ,|,|,|_|O gadE|gade|NN|GEN|O ,|,|,|_|O gadW|gadw|NN|GEN|O and|and|CC|_|O gadX|gadx|NN|GEN|O mutant|mutant|JJ|_|O cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|O phase|phase|NN|_|O -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|O =|=|JJ|_|O 0.3|0.3|CD|_|O -RRB-|-rrb-|-RRB-|_|O aerobically|aerobically|RB|_|Air -LRB-|-lrb-|-LRB-|_|O 250|250|CD|_|Agit rpm|rpm|NN|_|Agit -RRB-|-rrb-|-RRB-|_|O at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp at|at|IN|_|O pH|ph|NN|_|pH 5.5|5.5|CD|_|pH .|.|.|_|O
∆|∆|CD|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O Anaeroibc|anaeroibc|NN|_|Air
NsrR|nsrr|NN|TF|Gtype _|_|CD|_|Gtype Flagtag|flagtag|NN|_|Gtype _|_|CD|_|O rep1|rep1|NN|_|O
chip-ArcA|chip-arca|NN|_|O _|_|CD|_|O ArcA8myc|arca8myc|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|NN|_|O 2|2|CD|_|O
OmpR|ompr|NN|TF|O NaCl|nacl|NN|_|Supp 2|2|CD|_|O
chip-ArcA|chip-arca|NN|_|O _|_|CD|_|O ArcA8myc|arca8myc|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 3|3|CD|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O lacking|lack|VBG|_|Gtype the|the|DT|_|Gtype transcription|transcription|NN|_|Gtype factor|factor|NN|_|Gtype Fur|Fur|NNP|TF|Gtype and|and|CC|_|Gtype the|the|DT|_|Gtype small|small|JJ|_|Gtype RNA|rna|NN|_|Gtype RyhB|ryhb|NN|_|Gtype
PurR|purr|NN|TF|O _|_|SYM|_|O Adenine|Adenine|NNP|_|Supp _|_|SYM|_|O 1|1|CD|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O in|in|IN|_|O 65|65|CD|_|O ml|ml|NN|_|O LB|lb|NN|MED|O medium|medium|NN|MED|O at|at|IN|_|O 30|30|CD|_|O °C|°c|NN|_|O to|to|TO|_|O an|a|DT|_|O OD600|od600|NN|_|OD of|of|IN|_|OD about|about|IN|_|OD 0.3|0.3|CD|_|OD .|.|.|_|O Subsequently|subsequently|RB|_|O 30|30|CD|_|O ml|ml|NN|_|O of|of|IN|_|O culture|culture|NN|_|O were|be|VBD|_|O transformed|transform|VBN|_|O to|to|TO|_|O a|a|DT|_|O pre|pre|JJ|_|O warmed|warm|VBN|_|O flask|flask|NN|_|Vess at|at|IN|_|O 43|43|CD|_|Temp °C|°c|NN|_|Temp and|and|CC|_|O the|the|DT|_|O remainder|remainder|NN|_|O kept|keep|VBD|_|O at|at|IN|_|O 30|30|CD|_|Temp °C|°c|NN|_|Temp -LRB-|-lrb-|-LRB-|_|Temp see|see|VB|_|Temp control|control|JJ|_|Temp sample|sample|NN|_|Temp -RRB-|-rrb-|-RRB-|_|Temp .|.|.|_|O
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Anaerobic|Anaerobic|NNP|_|Air ,|,|,|_|O Iron|Iron|NNP|_|Supp Deficient|Deficient|NNP|_|O A|A|NNP|_|O
Fur|Fur|NNP|TF|O with|with|IN|_|O Fe|Fe|NNP|_|Supp 1|1|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique ChIP-exo|chip-exo|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
WT|wt|JJ|_|Gtype with|with|IN|_|O Fe|Fe|NNP|_|Supp 2|2|CD|_|O -LRB-|-lrb-|-LRB-|_|Technique RNA-seq|rna-seq|NN|_|Technique -RRB-|-rrb-|-RRB-|_|Technique
strain|strain|NN|_|O :|:|:|_|O K-12|k-12|NN|_|Strain
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O MG1655|mg1655|NN|_|O K-12|k-12|NN|_|O dFNR|dfnr|NN|_|Gtype -LRB-|-lrb-|-LRB-|_|Gtype PK4854|pk4854|NN|_|Gtype -RRB-|-rrb-|-RRB-|_|Gtype
genotype|genotype|NN|_|O :|:|:|_|O wildtype|wildtype|JJ|_|Gtype
chip-Fnr|chip-fnr|JJ|_|O _|_|NN|_|O Fnr8myc|fnr8myc|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|NN|_|O 2|2|CD|_|O
chip-Fnr|chip-fnr|JJ|_|O _|_|NN|_|O Fnr8myc|fnr8myc|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 1|1|CD|_|O
Ptac|ptac|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O B|b|NN|_|O -|-|:|_|O 8|8|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
genotype|genotype|NN|_|O :|:|:|_|O ΔseqA|δseqa|NN|_|Gtype
∆|∆|CD|_|Gtype fnr|fnr|NN|GEN|Gtype ChIP|chip|NN|_|O DNA|dna|NN|_|O from|from|IN|_|O PK4854|pk4854|NN|_|Gtype
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Supp
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O lacking|lack|VBG|_|Gtype the|the|DT|_|Gtype small|small|JJ|_|Gtype RNA|rna|NN|_|Gtype RyhB|ryhb|NN|_|Gtype
E.|e.|FW|_|O coli|coli|FW|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O cra-8myc|cra-8myc|NN|_|O tagged|tag|VBD|_|O strains|strain|NNS|_|O was|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|O phase|phase|NN|_|O aerobically|aerobically|RB|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O M9|m9|NN|MED|O minimal|minimal|JJ|MED|O media|media|NNS|MED|O supplemented|supplement|VBN|_|O with|with|IN|_|O 0.2|0.2|CD|_|O %|%|NN|_|O glucose|glucose|NN|SUPP|O ,|,|,|_|O fructose|fructose|NN|_|O and|and|CC|_|O acetate|acetate|NN|SUPP|O .|.|.|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O delta-gadW|delta-gadw|NN|_|Gtype
All|all|DT|_|O strains|strain|NNS|_|O used|use|VBN|_|O in|in|IN|_|O this|this|DT|_|O study|study|NN|_|O were|be|VBD|_|O E.|e.|FW|_|O coli|coli|FW|_|O K-12|k-12|NN|_|O MG1655|mg1655|NN|_|O and|and|CC|_|O its|its|PRP$|_|O derivatives|derivative|NNS|_|O .|.|.|_|O The|the|DT|_|O deletion|deletion|NN|_|O mutants|mutant|NNS|_|O -LRB-|-lrb-|-LRB-|_|O Δfnr|δfnr|NN|_|O and|and|CC|_|O ΔarcA|δarca|NN|_|O -RRB-|-rrb-|-RRB-|_|O were|be|VBD|_|O constructed|construct|VBN|_|O by|by|IN|_|O a|a|DT|_|O λ|λ|NN|_|O red|red|JJ|_|O and|and|CC|_|O FLP-mediated|flp-mediated|JJ|_|O site-specific|site-specific|JJ|_|O recombination|recombination|NN|_|O method|method|NN|_|O .|.|.|_|O Glycerol|glycerol|NN|_|O stocks|stock|NNS|_|O of|of|IN|_|O E.|e.|FW|_|O coli|coli|FW|_|O strains|strain|NNS|_|O were|be|VBD|_|O inoculated|inoculate|VBN|_|O into|into|IN|_|O M9|m9|NN|MED|O minimal|minimal|JJ|MED|O medium|medium|NN|MED|O containing|contain|VBG|_|O 0.2|0.2|CD|_|O %|%|NN|_|O -LRB-|-lrb-|-LRB-|_|O w/v|w/v|NN|_|O -RRB-|-rrb-|-RRB-|_|O carbon|carbon|NN|_|O source|source|NN|_|O -LRB-|-lrb-|-LRB-|_|O glucose|glucose|NN|SUPP|O -RRB-|-rrb-|-RRB-|_|O and|and|CC|_|O 0.1|0.1|CD|_|O %|%|NN|_|O -LRB-|-lrb-|-LRB-|_|O w/v|w/v|NN|_|O -RRB-|-rrb-|-RRB-|_|O nitrogen|nitrogen|NN|_|O source|source|NN|_|O -LRB-|-lrb-|-LRB-|_|O NH4Cl|nh4cl|NN|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O and|and|CC|_|O cultured|culture|VBN|_|O overnight|overnight|JJ|_|O at|at|IN|_|O 37|37|CD|_|O °C|°c|NN|_|O with|with|IN|_|O constant|constant|JJ|_|O agitation|agitation|NN|_|O .|.|.|_|O The|the|DT|_|O cultures|culture|NNS|_|O were|be|VBD|_|O diluted|dilute|VBN|_|O 1:100|1:100|CD|_|O into|into|IN|_|O fresh|fresh|JJ|_|O minimal|minimal|JJ|_|Med medium|medium|NN|_|Med and|and|CC|_|O then|then|RB|_|O cultured|culture|VBN|_|O at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp to|to|TO|_|O an|a|DT|_|O appropriate|appropriate|JJ|_|O cell|cell|NN|_|O density|density|NN|_|O with|with|IN|_|O constant|constant|JJ|_|O agitation|agitation|NN|_|O .|.|.|_|O For|for|IN|_|O the|the|DT|_|O anaerobic|anaerobic|JJ|_|O cultures|culture|NNS|_|O ,|,|,|_|O the|the|DT|_|O minimal|minimal|JJ|_|O medium|medium|NN|_|O were|be|VBD|_|O flushed|flush|VBN|_|O with|with|IN|_|O nitrogen|nitrogen|NN|_|O and|and|CC|_|O then|then|RB|_|O continuously|continuously|RB|_|O monitored|monitor|VBN|_|O using|use|VBG|_|O a|a|DT|_|O polarographic-dissolved|polarographic-dissolved|JJ|_|O oxygen|oxygen|NN|_|O probe|probe|NN|_|O -LRB-|-lrb-|-LRB-|_|O Cole-Parmer|Cole-Parmer|NNP|_|O Instruments|Instruments|NNP|_|O -RRB-|-rrb-|-RRB-|_|O to|to|TO|_|O ensure|ensure|VB|_|O anaerobicity|anaerobicity|NN|_|O .|.|.|_|O For|for|IN|_|O nitrate|nitrate|JJ|SUPP|O respiration|respiration|NN|_|O 20|20|CD|_|Supp mmol|mmol|NN|_|Supp potassium|potassium|NN|_|Supp nitrate|nitrate|JJ|SUPP|Supp was|be|VBD|_|O added|add|VBN|_|O .|.|.|_|O
pT7|pt7|NN|_|O _|_|CD|_|O ChIPSeq|chipseq|NN|_|Technique _|_|NN|_|O 1|1|CD|_|O
Ecoli|ecolus|NNS|_|O _|_|VBP|_|O dFNR|dfnr|NN|_|Gtype _|_|CD|_|O rep1|rep1|NN|_|O _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air
antibody|antibody|NN|_|O :|:|:|_|O Affinity|Affinity|NNP|_|Anti Purified|purify|VBN|_|Anti FNR|fnr|NN|TF|Anti antibody|antibody|NN|_|Anti
affyexp|affyexp|JJ|_|O _|_|NN|_|O delta-fnr|delta-fnr|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 1|1|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
Cra|Cra|NNP|TF|O acetate|acetate|NN|SUPP|Supp 2|2|CD|_|O
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O str|str|NN|_|O .|.|.|_|O K-12|k-12|NN|_|Strain substr|substr|NN|_|O .|.|.|_|O MG1655star|mg1655star|NN|_|Substrain
ΔgadX|δgadx|NN|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
Δcra|δcra|NN|_|Gtype acetate|acetate|NN|SUPP|Supp 1|1|CD|_|O
A|a|NN|_|O total|total|NN|_|O of|of|IN|_|O two|two|CD|_|O samples|sample|NNS|_|O were|be|VBD|_|O analyzed|analyze|VBN|_|O .|.|.|_|O ompR-8myc|ompr-8myc|NN|_|O tagged|tag|VBD|_|O cells|cell|NNS|_|O were|be|VBD|_|O cultured|culture|VBN|_|O in|in|IN|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med media|media|NNS|MED|Med with|with|IN|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp .|.|.|_|O Then|then|RB|_|O cells|cell|NNS|_|O were|be|VBD|_|O treated|treat|VBN|_|O with|with|IN|_|O 0.3|0.3|CD|_|Supp M|m|NN|_|Supp of|of|IN|_|Supp NaCl|nacl|NN|_|Supp at|at|IN|_|O mid-log|mid-log|NN|_|Phase pahse|pahse|NN|_|Phase for|for|IN|_|O 30|30|CD|_|Supp min|min|NN|_|Supp with|with|IN|_|O agitation|agitation|NN|_|O .|.|.|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O aerobically|aerobically|RB|_|Air -LRB-|-lrb-|-LRB-|_|Air 25|25|CD|_|Air %|%|NN|_|Air O2|o2|CD|_|Air ,|,|,|_|Air 70|70|CD|_|Air %|%|NN|_|Air N2|n2|NN|_|Air and|and|CC|_|Air 5|5|CD|_|Air %|%|NN|_|Air CO2|co2|NN|_|Air -RRB-|-rrb-|-RRB-|_|Air until|until|IN|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|OD of|of|IN|_|OD 0.35|0.35|CD|_|OD -RRB-|-rrb-|-RRB-|_|O and|and|CC|_|O treated|treat|VBN|_|O with|with|IN|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O volumen|voluman|NNS|_|O formaldehyde|formaldehyde|NN|_|O for|for|IN|_|O ten|ten|CD|_|O minutes|minute|NNS|_|O .|.|.|_|O Sodium|sodium|NN|_|O phosphate|phosphate|NN|_|O -LRB-|-lrb-|-LRB-|_|O 1/100|1/100|CD|_|O vol|vol|NN|_|O .|.|.|_|O of|of|IN|_|O 1M|1m|NN|_|O ,|,|,|_|O pH|ph|NN|_|O 7.6|7.6|CD|_|O ;|;|:|_|O 10|10|CD|_|O mM|mm|NN|KWSUPP|O final|final|JJ|_|O -RRB-|-rrb-|-RRB-|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O the|the|DT|_|O mid-log|mid-log|JJ|_|O cultures|culture|NNS|_|O followed|follow|VBN|_|O by|by|IN|_|O formaldehyde|formaldehyde|NN|_|O to|to|TO|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O ,|,|,|_|O and|and|CC|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O was|be|VBD|_|O continued|continue|VBN|_|O for|for|IN|_|O 10|10|CD|_|O min|min|NN|_|O .|.|.|_|O Cold|Cold|NNP|_|O 2.5|2.5|CD|_|O M|m|NN|_|O glycine|glycine|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O 100mM|100mm|NN|_|O and|and|CC|_|O the|the|DT|_|O mixture|mixture|NN|_|O was|be|VBD|_|O incubated|incubate|VBN|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O with|with|IN|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O for|for|IN|_|O 30|30|CD|_|O minutes|minute|NNS|_|O to|to|TO|_|O stop|stop|VB|_|O the|the|DT|_|O crosslinking|crosslinking|NN|_|O .|.|.|_|O Cells|cell|NNS|_|O were|be|VBD|_|O spun|spin|VBN|_|O at|at|IN|_|O 5000|5000|CD|_|O x|x|CC|_|O g|g|NN|_|O ,|,|,|_|O and|and|CC|_|O washed|wash|VBN|_|O repeatedly|repeatedly|RB|_|O with|with|IN|_|O phosphate|phosphate|NN|_|O buffered|buffer|VBN|_|O saline|saline|NN|_|O before|before|IN|_|O being|be|VBG|_|O frozen|freeze|VBN|_|O at|at|IN|_|O -80|-80|CD|_|O °C|°c|NN|_|O .|.|.|_|O
TrpR|trpr|NN|TF|O _|_|CD|_|O glucose|glucose|NN|SUPP|Supp
IHF|ihf|SYM|TF|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air A|a|DT|_|O
E.|E.|NNP|_|O coli|coli|NN|_|O strains|strain|NNS|_|O harboring|harbor|VBG|_|O PurR-8myc|purr-8myc|NN|_|O were|be|VBD|_|O grown|grow|VBN|_|O in|in|IN|_|O minimal|minimal|JJ|_|O M9|m9|NN|_|O medium|medium|NN|_|O supplemented|supplement|VBN|_|O with|with|IN|_|O glucose|glucose|NN|SUPP|O -LRB-|-lrb-|-LRB-|_|O 2|2|CD|_|O g/L|g/l|NN|_|O -RRB-|-rrb-|-RRB-|_|O then|then|RB|_|O inoculated|inoculate|VBN|_|O into|into|IN|_|O 100mL|100ml|NN|_|O of|of|IN|_|O fresh|fresh|JJ|_|O M9|m9|NN|MED|Med minimal|minimal|JJ|MED|Med medium|medium|NN|MED|Med .|.|.|_|O
treatment|treatment|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Med -LRB-|-lrb-|-LRB-|_|Med 2|2|CD|_|Med g/L|g/l|NN|_|Med -RRB-|-rrb-|-RRB-|_|Med minimal|minimal|JJ|_|Med M9|m9|NN|_|Med medium|medium|NN|_|Med supplemented|supplement|VBN|_|O without|without|IN|_|O 10|10|CD|_|Supp mM|mm|NN|KWSUPP|Supp leucine|leucine|NN|SUPP|Supp .|.|.|_|O
To|to|TO|_|O harvest|harvest|VB|_|O total|total|JJ|_|O RNA|rna|NN|_|O samples|sample|NNS|_|O ,|,|,|_|O overnight|overnight|JJ|_|O cultures|culture|NNS|_|O of|of|IN|_|O wild|wild|JJ|_|Gtype type|type|NN|_|Gtype MG1655|mg1655|NN|_|O grown|grow|VBN|_|O in|in|IN|_|O LB|lb|NN|_|O at|at|IN|_|O 37|37|CD|_|O ˚C|˚c|NN|_|O were|be|VBD|_|O diluted|dilute|VBN|_|O back|back|RB|_|O 1:500|1:500|CD|_|O in|in|IN|_|O either|either|CC|_|O fresh|fresh|JJ|_|O LB|lb|NN|_|O or|or|CC|_|O M63|m63|NN|_|O minimal|minimal|JJ|_|O glucose|glucose|NN|SUPP|O medium|medium|NN|_|O and|and|CC|_|O allowed|allow|VBN|_|O to|to|TO|_|O grow|grow|VB|_|O until|until|IN|_|O the|the|DT|_|O cultures|culture|NNS|_|O reached|reach|VBD|_|O an|a|DT|_|O OD600|od600|NN|_|O of|of|IN|_|O ~|~|NN|_|O 0.4|0.4|CD|_|O and|and|CC|_|O 2.0|2.0|CD|_|O for|for|IN|_|O cultures|culture|NNS|_|O grown|grow|VBN|_|O in|in|IN|_|O LB|lb|NN|_|O and|and|CC|_|O an|a|DT|_|O OD600|od600|NN|_|O of|of|IN|_|O ~|~|NN|_|O 0.4|0.4|CD|_|O for|for|IN|_|O cultures|culture|NNS|_|O grown|grow|VBN|_|O in|in|IN|_|O M63|m63|NN|_|O .|.|.|_|O For|for|IN|_|O samples|sample|NNS|_|O grown|grow|VBN|_|O to|to|TO|_|O OD600|od600|NN|_|OD of|of|IN|_|OD ~|~|NN|_|OD 0.4|0.4|CD|_|OD a|a|DT|_|O total|total|JJ|_|O volume|volume|NN|_|O of|of|IN|_|O 25|25|CD|_|O ml|ml|NN|_|O of|of|IN|_|O cells|cell|NNS|_|O were|be|VBD|_|O harvested|harvest|VBN|_|O and|and|CC|_|O combined|combine|VBN|_|O with|with|IN|_|O 5|5|CD|_|O ml|ml|NN|_|O of|of|IN|_|O stop|stop|NN|_|O solution|solution|NN|_|O -LRB-|-lrb-|-LRB-|_|O 95|95|CD|_|O %|%|NN|_|O Ethanol|ethanol|NN|_|O ,|,|,|_|O 5|5|CD|_|O %|%|NN|_|O acid|acid|NN|_|O phenol|phenol|NN|_|O -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O For|for|IN|_|O samples|sample|NNS|_|O grown|grow|VBN|_|O to|to|TO|_|O OD600|od600|NN|_|O of|of|IN|_|O 2.0|2.0|CD|_|O a|a|DT|_|O total|total|JJ|_|O volume|volume|NN|_|O of|of|IN|_|O 5|5|CD|_|O ml|ml|NN|_|O of|of|IN|_|O cells|cell|NNS|_|O were|be|VBD|_|O harvested|harvest|VBN|_|O and|and|CC|_|O combined|combine|VBN|_|O with|with|IN|_|O 1|1|CD|_|O ml|ml|NN|_|O of|of|IN|_|O stop|stop|NN|_|O solution|solution|NN|_|O .|.|.|_|O
carbon|carbon|NN|_|O source|source|NN|_|O :|:|:|_|O glucose|glucose|NN|SUPP|Supp
acetate|acetate|NN|SUPP|Supp
TrpR|trpr|NN|TF|O _|_|CD|_|O Trp|Trp|NNP|_|Supp
Wild|Wild|NNP|_|Gtype type|type|NN|_|Gtype control|control|NN|_|O -LRB-|-lrb-|-LRB-|_|O 20|20|CD|_|O min|min|NN|_|O -RRB-|-rrb-|-RRB-|_|O
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O anti-RpoB|anti-rpob|JJ|_|Anti -LRB-|-lrb-|-LRB-|_|O Neoclone|Neoclone|NNP|_|O ,|,|,|_|O WP002|wp002|NN|_|O -RRB-|-rrb-|-RRB-|_|O
σ32|σ32|NN|_|O 43|43|CD|_|Temp °C|°c|NN|_|Temp short|short|JJ|_|O RNase|rnase|NN|_|O
ChIP-exo|ChIP-exo|NNP|_|Technique GadE|gade|NN|TF|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|O
agent|agent|NN|_|O :|:|:|_|O DPD|dpd|NN|_|Supp
Nac|Nac|NNP|TF|O _|_|SYM|_|O RNASeq|rnaseq|NN|_|Technique
ChIP-exo|chip-exo|NN|_|O reads|read|VBZ|_|O were|be|VBD|_|O aligned|align|VBN|_|O to|to|TO|_|O the|the|DT|_|O NC|nc|NN|_|Gversion _|_|CD|_|Gversion 000913|000913|CD|_|Gversion genome|genome|NN|_|O reference|reference|NN|_|O sequence|sequence|NN|_|O using|use|VBG|_|O using|use|VBG|_|O bowtie|bowtie|NN|_|O v1|v1|NN|_|O .0.0|.0.0|CD|_|O with|with|IN|_|O parameters|parameter|NNS|_|O -|-|:|_|O S|s|NN|_|O
affyexp|affyexp|JJ|_|O _|_|NN|_|O wt|wt|JJ|_|Gtype _|_|NN|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 1|1|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O SeqA|seqa|NN|_|Anti
antibody|antibody|NN|_|O :|:|:|_|O anti-FLAG|anti-flag|JJ|_|Anti mAb|mab|NN|_|Anti
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O soxS-8myc|soxs-8myc|NN|_|Gtype -|-|:|_|O tagged|tag|VBN|_|O
genotype|genotype|NN|_|O :|:|:|_|O Lrp-8myc|lrp-8myc|JJ|_|Gtype
M63|m63|NN|_|Med 0.4|0.4|CD|_|O B1|b1|NN|_|O TEX|tex|NN|_|O neg|neg|NN|_|O L1|l1|NN|_|O GA|ga|NN|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp to|to|TO|_|O an|a|DT|_|O OD600|od600|NN|_|OD of|of|IN|_|OD about|about|IN|_|OD 0.15|0.15|CD|_|OD in|in|IN|_|O 50|50|CD|_|O ml|ml|NN|_|O LB|lb|NN|_|Med -LRB-|-lrb-|-LRB-|_|O +|+|CC|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp -RRB-|-rrb-|-RRB-|_|O before|before|IN|_|O crosslinking|crosslink|VBG|_|O .|.|.|_|O
strain|strain|NN|_|O :|:|:|_|O MG1655|mg1655|NN|_|O K-12|k-12|NN|_|O WT|wt|JJ|_|Gtype
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype ∆|∆|CD|_|Gtype ryhB|ryhb|NN|GEN|Gtype Aerobic|aerobic|JJ|_|Air A|a|DT|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O wild|wild|JJ|_|Gtype type|type|NN|_|Gtype
Lrp|lrp|NN|TF|O _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|CD|_|O 3|3|CD|_|O
FNR|fnr|SYM|TF|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air -|-|:|_|O A|a|NN|_|O
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Anaerobic|Anaerobic|NNP|_|Air A|A|NNP|_|O
Wild|Wild|NNP|_|Gtype type|type|NN|_|Gtype control|control|NN|_|O -LRB-|-lrb-|-LRB-|_|O 2.5|2.5|CD|_|O min|min|NN|_|O -RRB-|-rrb-|-RRB-|_|O
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O pos|po|VBZ|_|O L2|l2|NN|_|O HS2|hs2|NN|_|O
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Aerobic|Aerobic|NNP|_|Air B|b|NN|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp to|to|TO|_|O an|a|DT|_|O OD600|od600|NN|_|OD of|of|IN|_|OD about|about|IN|_|OD 0.15|0.15|CD|_|OD in|in|IN|_|O 100|100|CD|_|O ml|ml|NN|_|O LB|lb|NN|_|Med -LRB-|-lrb-|-LRB-|_|O +|+|CC|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O
HNS|hns|SYM|_|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air B|b|NN|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O cra-8myc-tagged|cra-8myc-tagged|JJ|_|Gtype
Ptac|ptac|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O A|a|NN|_|O -|-|:|_|O 8|8|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
ChIP-exo|ChIP-exo|NNP|_|Technique GadW|gadw|NN|TF|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
Ptac|ptac|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O C|c|NN|_|O -|-|:|_|O 16|16|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Anaerobic|Anaerobic|NNP|_|Air ,|,|,|_|O Iron|Iron|NNP|_|Supp Deficient|deficient|JJ|_|O B|b|NN|_|O
ChIP-exo|ChIP-exo|NNP|_|Technique GadW|gadw|NN|TF|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O with|with|IN|_|O 16|16|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp and|and|CC|_|Supp 300|300|CD|_|Supp µL|µl|NN|_|Supp Cm20|cm20|NN|_|Supp anaerobically|anaerobically|RB|_|Air -LRB-|-lrb-|-LRB-|_|Air 95|95|CD|_|Air %|%|NN|_|Air N2|n2|NN|_|Air and|and|CC|_|Air 5|5|CD|_|Air %|%|NN|_|Air CO2|co2|NN|_|Air -RRB-|-rrb-|-RRB-|_|Air until|until|IN|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|OD of|of|IN|_|OD 0.3|0.3|CD|_|OD -RRB-|-rrb-|-RRB-|_|O and|and|CC|_|O treated|treat|VBN|_|O with|with|IN|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O volumen|voluman|NNS|_|O formaldehyde|formaldehyde|NN|_|O for|for|IN|_|O ten|ten|CD|_|O minutes|minute|NNS|_|O .|.|.|_|O Sodium|sodium|NN|_|O phosphate|phosphate|NN|_|O -LRB-|-lrb-|-LRB-|_|O 1/100|1/100|CD|_|O vol|vol|NN|_|O .|.|.|_|O of|of|IN|_|O 1M|1m|NN|_|O ,|,|,|_|O pH|ph|NN|_|O 7.6|7.6|CD|_|O ;|;|:|_|O 10|10|CD|_|O mM|mm|NN|KWSUPP|O final|final|JJ|_|O -RRB-|-rrb-|-RRB-|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O the|the|DT|_|O mid-log|mid-log|JJ|_|O cultures|culture|NNS|_|O followed|follow|VBN|_|O by|by|IN|_|O formaldehyde|formaldehyde|NN|_|O to|to|TO|_|O 1|1|CD|_|O %|%|NN|_|O final|final|JJ|_|O ,|,|,|_|O and|and|CC|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O was|be|VBD|_|O continued|continue|VBN|_|O for|for|IN|_|O 10|10|CD|_|O min|min|NN|_|O .|.|.|_|O Cold|Cold|NNP|_|O 2.5|2.5|CD|_|O M|m|NN|_|O glycine|glycine|NN|_|O was|be|VBD|_|O added|add|VBN|_|O to|to|TO|_|O 100mM|100mm|NN|_|O and|and|CC|_|O the|the|DT|_|O mixture|mixture|NN|_|O was|be|VBD|_|O incubated|incubate|VBN|_|O at|at|IN|_|O 4|4|CD|_|O °C|°c|NN|_|O with|with|IN|_|O anaerobic|anaerobic|JJ|_|O sparging|sparging|NN|_|O for|for|IN|_|O 30|30|CD|_|O minutes|minute|NNS|_|O to|to|TO|_|O stop|stop|VB|_|O the|the|DT|_|O crosslinking|crosslinking|NN|_|O .|.|.|_|O Cells|cell|NNS|_|O were|be|VBD|_|O spun|spin|VBN|_|O at|at|IN|_|O 5000|5000|CD|_|O x|x|CC|_|O g|g|NN|_|O ,|,|,|_|O and|and|CC|_|O washed|wash|VBN|_|O repeatedly|repeatedly|RB|_|O with|with|IN|_|O phosphate|phosphate|NN|_|O buffered|buffer|VBN|_|O saline|saline|NN|_|O before|before|IN|_|O being|be|VBG|_|O frozen|freeze|VBN|_|O at|at|IN|_|O -80|-80|CD|_|O °C|°c|NN|_|O .|.|.|_|O
ArgR|argr|NN|TF|O _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|NN|_|O 2|2|CD|_|O
WT|wt|JJ|_|Gtype NaCl|nacl|NN|_|Supp 2|2|CD|_|O
LB|lb|NN|_|Med 0.4|0.4|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O pos|po|VBZ|_|O L1|l1|NN|_|O HS1|hs1|NN|_|O
medium|medium|NN|_|O :|:|:|_|O LB|LB|NNP|_|Med
At|at|IN|_|O OD450|od450|NN|_|OD =|=|JJ|_|OD 0.3|0.3|CD|_|OD ,|,|,|_|O cultures|culture|NNS|_|O induced|induce|VBN|_|O with|with|IN|_|O 1|1|CD|_|Supp mM|mm|NN|KWSUPP|Supp IPTG|iptg|NN|_|Supp .|.|.|_|O Cells|cell|NNS|_|O harvested|harvest|VBN|_|O 2.5|2.5|CD|_|O min|min|NN|_|O after|after|IN|_|O induction|induction|NN|_|O
affyexp|affyexp|JJ|_|O _|_|NN|_|O wt|wt|JJ|_|Gtype _|_|NN|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 2|2|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
ChIP-exo|chip-exo|NN|_|Technique GadX|gadx|NN|TF|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|O
CsiR|csir|NN|TF|O _|_|CD|_|O ChIPSeq|chipseq|NN|_|Technique
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O MG1655|mg1655|NN|_|O K-12|k-12|NN|_|O WT|wt|NN|_|O and|and|CC|_|O ∆|∆|NN|_|O fnr|fnr|NN|GEN|O were|be|VBD|_|O grown|grow|VBN|_|O to|to|TO|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O O.D.|o.d.|NN|_|OD 600nm|600nm|JJ|_|OD 0.3|0.3|CD|_|OD -RRB-|-rrb-|-RRB-|_|O anerobically|anerobically|RB|_|Air -LRB-|-lrb-|-LRB-|_|Air 95|95|CD|_|Air %|%|NN|_|Air N2|n2|NN|_|Air ,|,|,|_|Air 5|5|CD|_|Air %|%|NN|_|Air CO2|co2|NN|_|Air -RRB-|-rrb-|-RRB-|_|Air at|at|IN|_|O 37|37|CD|_|Temp °C|°c|NN|_|Temp in|in|IN|_|O MOPS|MOPS|NNP|MED|Med +|+|CC|_|O 0.2|0.2|CD|_|Supp %|%|NN|_|Supp glucose|glucose|NN|SUPP|Supp media|media|NNS|_|O -LRB-|-lrb-|-LRB-|_|O Ref|ref|NN|_|O -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O
RpoB|rpob|NN|_|O ∆|∆|CD|_|Gtype crp|crp|NN|GEN|Gtype 2|2|CD|_|O
MG1655|mg1655|NN|_|Substrain PhtpG|phtpg|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype lacZ|lacz|NN|GEN|Gtype delta|delta|NN|_|Gtype lacX74/ptrc99A|lacx74/ptrc99a|NN|_|Gtype -LRB-|-lrb-|-LRB-|_|Gtype control|control|NN|_|Gtype vector|vector|NN|_|Gtype -RRB-|-rrb-|-RRB-|_|Gtype
Cra|cra|NN|TF|O acetate|acetate|NN|SUPP|Supp 1|1|CD|_|O
FNR|fnr|SYM|TF|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air -|-|:|_|O C|c|NN|_|O
genotype|genotype|NN|_|O :|:|:|_|O delta|delta|NN|_|O -|-|:|_|O crp|crp|NN|GEN|Gtype Knock-out|knock-out|JJ|_|Gtype strain|strain|NN|_|Gtype
SoxS|soxs|NN|TF|O PQ|pq|NN|_|Supp 1|1|CD|_|O
SeqA|seqa|NN|_|O old|old|JJ|_|O deltaSeqA|deltaseqa|NN|_|Gtype
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O delta-oxyR|delta-oxyr|NN|_|Gtype
agent|agent|NN|_|O :|:|:|_|O Fe|Fe|NNP|_|Supp and|and|CC|_|Supp rifampicin|rifampicin|NN|SUPP|Supp
ΔompR|δompr|NN|_|Gtype NaCl|nacl|NN|_|Supp 1|1|CD|_|O
Nac|Nac|NNP|TF|O _|_|NNP|_|O ChIPSeq|ChIPSeq|NNP|_|Technique
genoype|genoype|NN|_|O :|:|:|_|O Wild-Type|wild-type|JJ|_|Gtype
chip-Fnr|chip-fnr|JJ|_|O _|_|NN|_|O Fnr8myc|fnr8myc|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|CD|_|O 3|3|CD|_|O
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B1|b1|NN|_|O TEX|TEX|NNP|_|O neg|neg|NNP|_|O L2|l2|NN|_|O HS2|hs2|NN|_|O
PurR|purr|NN|TF|O _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|NN|_|O 2|2|CD|_|O
At|at|IN|_|O OD450|od450|NN|_|OD =|=|JJ|_|OD 0.3|0.3|CD|_|OD ,|,|,|_|O cultures|culture|NNS|_|O induced|induce|VBN|_|O with|with|IN|_|O 1|1|CD|_|Supp mM|mm|NN|KWSUPP|Supp IPTG|iptg|NN|_|Supp .|.|.|_|O Cells|cell|NNS|_|O harvested|harvest|VBN|_|O 5|5|CD|_|O min|min|NN|_|O after|after|IN|_|O induction|induction|NN|_|O
antibody|antibody|NN|_|O :|:|:|_|O Pre-cleared|pre-cleared|JJ|_|Anti FNR|fnr|NN|TF|Anti antibody|antibody|NN|_|Anti
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O pos|po|VBZ|_|O L1|l1|NN|_|O HS1|hs1|NN|_|O
WT|wt|JJ|_|Gtype _|_|NN|_|O ChIPSeq|chipseq|NN|_|Technique _|_|NN|_|O 2|2|CD|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O delta-gadE|delta-gade|NN|_|Gtype
chip-ArcA|chip-arca|NN|_|O _|_|CD|_|O ArcA8myc|arca8myc|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air _|_|NN|_|O 1|1|CD|_|O
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O harboring|harbor|VBG|_|O Fnr-8myc|fnr-8myc|JJ|_|Gtype
Lrp|Lrp|NNP|TF|O _|_|SYM|_|O Leu|Leu|NNP|_|Supp _|_|SYM|_|O 1|1|CD|_|O
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O none|none|NN|_|Anti
HNS|hns|SYM|_|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air A|a|DT|_|O
affyexp|affyexp|JJ|_|O _|_|NN|_|O wt|wt|JJ|_|Gtype _|_|NN|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|CD|_|O 3|3|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
∆|∆|CD|_|Gtype ryhB|ryhb|NN|GEN|Gtype Anaerobic|anaerobic|JJ|_|Air
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O aerobically|aerobically|RB|_|Air -LRB-|-lrb-|-LRB-|_|Air 70|70|CD|_|Air %|%|NN|_|Air N2|n2|NN|_|Air ,|,|,|_|Air 25|25|CD|_|Air %|%|NN|_|Air O2|o2|CD|_|Air ,|,|,|_|Air and|and|CC|_|Air 5|5|CD|_|Air %|%|NN|_|Air CO2|co2|NN|_|Air -RRB-|-rrb-|-RRB-|_|Air or|or|CC|_|O anaerobically|anaerobically|RB|_|O -LRB-|-lrb-|-LRB-|_|O 95|95|CD|_|O %|%|NN|_|O N2|n2|NN|_|O and|and|CC|_|O 5|5|CD|_|O %|%|NN|_|O CO2|co2|NN|_|O -RRB-|-rrb-|-RRB-|_|O until|until|IN|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|OD of|of|IN|_|OD ~|~|NN|_|OD 0.3-0.35|0.3-0.35|CD|_|OD -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O
ΔgadE|δgade|NN|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|O
M63|m63|NN|_|Med 0.4|0.4|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O neg|neg|NNP|_|O L1|l1|NN|_|O HS1|hs1|NN|_|O
FNR|fnr|SYM|TF|O -|-|:|_|O ∆|∆|CD|_|Gtype hns|hn|NNS|GEN|Gtype ∆|∆|VBP|_|Gtype stpA|stpa|NN|GEN|Gtype B|b|NN|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O aerobically|aerobically|RB|_|O -LRB-|-lrb-|-LRB-|_|O 70|70|CD|_|O %|%|NN|_|O N2|n2|NN|_|O ,|,|,|_|O 25|25|CD|_|O %|%|NN|_|O O2|o2|CD|_|O ,|,|,|_|O and|and|CC|_|O 5|5|CD|_|O %|%|NN|_|O CO2|co2|NN|_|O -RRB-|-rrb-|-RRB-|_|O or|or|CC|_|O anaerobically|anaerobically|RB|_|O -LRB-|-lrb-|-LRB-|_|O 95|95|CD|_|O %|%|NN|_|O N2|n2|NN|_|O and|and|CC|_|O 5|5|CD|_|O %|%|NN|_|O CO2|co2|NN|_|O -RRB-|-rrb-|-RRB-|_|O until|until|IN|_|O mid-log|mid-log|JJ|_|Phase phase|phase|NN|_|Phase -LRB-|-lrb-|-LRB-|_|O OD600|od600|NN|_|OD of|of|IN|_|OD ~|~|NN|_|OD 0.3-0.35|0.3-0.35|CD|_|OD -RRB-|-rrb-|-RRB-|_|O .|.|.|_|O
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O str|str|NN|_|O .|.|.|_|O K-12|k-12|NN|_|Strain substr|substr|NN|_|O .|.|.|_|O MG1655|mg1655|NN|_|Substrain
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O delta-soxS|delta-soxs|NN|_|Gtype
WT|wt|JJ|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|O
culture|culture|NN|_|O condition|condition|NN|_|O :|:|:|_|O Anaerobic|anaerobic|JJ|_|Air cultures|culture|NNS|_|O
Genome|Genome|NNP|_|O _|_|NNP|_|O build|build|VB|_|O :|:|:|_|O ASM584v2|asm584v2|NN|_|Gversion
ArgR|argr|NN|TF|O _|_|CD|_|O NH4Cl|nh4cl|NN|_|Supp _|_|NN|_|O 1|1|CD|_|O
chip-ArcA|chip-arca|NN|_|O _|_|CD|_|O ArcA8myc|arca8myc|NN|_|Gtype _|_|CD|_|O glucose|glucose|NN|SUPP|Supp _|_|CD|_|O NH4CL|nh4cl|NN|_|Supp _|_|CD|_|O NO3|no3|NN|_|Supp _|_|NN|_|O 1|1|CD|_|O
WT|wt|JJ|_|Gtype fructose|fructose|NN|_|Supp 2|2|CD|_|O
Lrp|Lrp|NNP|TF|O _|_|SYM|_|O Leu|Leu|NNP|_|Supp _|_|SYM|_|O 3|3|CD|_|O
Ecoli|ecolus|NNS|_|O _|_|VBP|_|O wild-type|wild-type|JJ|_|Gtype _|_|NN|_|O rep1|rep1|NN|_|O _|_|CD|_|O anaerobic|anaerobic|JJ|_|Air
ΔsoxS|δsoxs|NN|_|Gtype PQ|pq|NN|_|Supp 1|1|CD|_|O
genotype|genotype|NN|_|O :|:|:|_|O WT|WT|NNP|_|Gtype
Input|input|NN|_|O ChIP-Seq|chip-seq|NN|_|Technique
Δcra|δcra|NN|_|Gtype acetate|acetate|NN|SUPP|Supp 2|2|CD|_|O