test-data-set-30.txt
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ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 2|2|CD|O
Δfur|δfur|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
OmpR|ompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 2.5|2.5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 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|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|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 300|300|CD|O mM|mm|NN|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|O KCl|kcl|NN|O ,|,|,|O 0.3|0.3|CD|O mM|mm|NN|O NaCl|nacl|NN|O ,|,|,|O 6|6|CD|O mM|mm|NN|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|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|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 250|250|CD|O mM|mm|NN|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|O NaCl|nacl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 600|600|CD|O mM|mm|NN|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|O NaCl|nacl|NN|O wash|wash|NN|O buffer|buffer|NN|O -LRB-|-lrb-|-LRB-|O 100|100|CD|O mM|mm|NN|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 300|300|CD|O mM|mm|NN|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|O Tris|Tris|NNP|O pH|ph|NN|O 8|8|CD|O ,|,|,|O 10|10|CD|O mM|mm|NN|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
growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O
ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|Substrain
Cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
The|the|DT|O cultured|culture|VBN|O cells|cell|NNS|O were|be|VBD|O inoculated|inoculate|VBN|O with|with|IN|O 1:100|1:100|CD|O dilution|dilution|NN|O into|into|IN|O 50|50|CD|O mL|ml|NN|O of|of|IN|O the|the|DT|O fresh|fresh|JJ|O M9|m9|NN|Med medium|medium|NN|Med containing|contain|VBG|O 2|2|CD|Supp g/L|g/l|NN|Supp glucose|glucose|NN|Supp in|in|IN|O either|either|CC|O the|the|DT|O presence|presence|NN|Supp or|or|CC|Supp absence|absence|NN|Supp of|of|IN|Supp 1|1|CD|Supp g/L|g/l|NN|Supp arginine|arginine|NN|Supp and|and|CC|O continued|continue|VBD|O to|to|TO|O culture|culture|NN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp until|until|IN|O reaching|reach|VBG|O an|a|DT|O appropriate|appropriate|JJ|O cell|cell|NN|O density|density|NN|O -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD ≈|≈|CD|OD 0.5|0.5|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O B|b|NN|O
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O A|a|NN|O
cultured|culture|VBN|O in|in|IN|O :|:|:|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp fructose|fructose|NN|Supp
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
WT|wt|JJ|O fructose|fructose|NN|O 2|2|CD|O
EC18n178|ec18n178|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O heat|heat|NN|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
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
ΔompR|δompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 1|1|CD|O
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
ΔompR|δompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 4|4|CD|O µM|µm|NN|O IPTG|iptg|NN|O
σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
Cra|Cra|NNP|O acetate|acetate|NN|O 1|1|CD|O
Escherichia|escherichia|FW|O coli|coli|FW|O K-12|k-12|NN|O
Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O B|b|NN|O
RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
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
EC18n168|ec18n168|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
RpoB|rpob|NN|O WT|wt|NN|O 2|2|CD|O
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
Escherichia|escherichia|FW|O coli|coli|FW|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
Δcra|δcra|NN|O glucose|glucose|NN|O 1|1|CD|O
∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O A|a|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
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|Gtype
MG1655|mg1655|NN|Substrain PhtpG|phtpg|NN|Gtype :|:|:|Gtype :|:|:|Gtype lacZ|lacz|NN|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|Gtype -RRB-|-rrb-|-RRB-|Gtype
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
WT|wt|NN|O NaCl|nacl|NN|O 2|2|CD|O
Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|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 in|in|IN|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 10|10|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp .|.|.|O
Cra|Cra|NNP|O acetate|acetate|NN|O 2|2|CD|O
EC18n171|ec18n171|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
Δcra|δcra|NN|O acetate|acetate|NN|O 1|1|CD|O
SoxS|soxs|NN|O PQ|pq|NN|O 2|2|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
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 <Air>|<air>|NN|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 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|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
SeqA|seqa|NN|O old|old|JJ|O rep1|rep1|NN|O
ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 2|2|CD|O
genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
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 <Air>|<air>|NN|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
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 Δfur|δfur|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|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|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|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|O .|.|.|O
RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 1|1|CD|O
genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
EC18n180|ec18n180|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-rpoB|anti-rpob|JJ|Anti -LRB-|-lrb-|-LRB-|O Santa|Santa|NNP|O Cruz|Cruz|NNP|O Biotech|Biotech|NNP|O ,|,|,|O sc-56766|sc-56766|NN|O -RRB-|-rrb-|-RRB-|O
Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
CsiR|CsiR|NNP|O _|_|VBD|O ChIPSeq|chipseq|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype lacZ|lacz|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype tonB|tonb|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype feoA|feoa|NN|Gtype ,|,|,|Gtype -LCB-|-lcb-|-LRB-|Gtype delta|delta|NN|Gtype -RCB-|-rcb-|-RRB-|Gtype zupT|zupt|NN|Gtype K12|k12|NN|Gtype
MG1655|mg1655|NN|Substrain PhtpG|phtpg|NN|Gtype :|:|:|Gtype :|:|:|Gtype lacZ|lacz|NN|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
RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O and|and|CC|O rifampicin|rifampicin|NN|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
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.|FW|OD coli|coli|FW|OD K-12|k-12|NN|OD MG1655|mg1655|NN|OD WT|wt|NN|OD ,|,|,|OD ΔoxyR|δoxyr|NN|OD ,|,|,|OD ΔsoxR|δsoxr|NN|OD ,|,|,|OD and|and|CC|OD ΔsoxS|δsoxs|NN|OD were|be|VBD|OD grown|grow|VBN|OD to|to|TO|OD mid-log|mid-log|JJ|OD phase|phase|NN|OD <Air>|<air>|NN|OD aerobically|aerobically|RB|OD at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|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|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.|FW|OD coli|coli|FW|OD K-12|k-12|NN|OD MG1655|mg1655|NN|OD WT|wt|NN|OD ,|,|,|OD gadE|gade|NN|OD ,|,|,|OD gadW|gadw|NN|OD and|and|CC|OD gadX|gadx|NN|OD mutant|mutant|JJ|OD cells|cell|NNS|OD were|be|VBD|OD grown|grow|VBN|OD to|to|TO|OD mid-log|mid-log|JJ|OD phase|phase|NN|OD -LRB-|-lrb-|-LRB-|OD OD600|od600|NN|OD
RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
Δfur|δfur|NN|O with|with|IN|O Fe|Fe|NNP|O 1|1|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655star|mg1655star|NN|O
genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
EC18n186|ec18n186|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
SeqA|seqa|NN|O new|new|JJ|O rep2|rep2|NN|O
ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 1|1|CD|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|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
culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
LB|lb|NN|O 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
agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
Input|input|NN|O ChIP-Seq|chip-seq|NN|O
PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|NN|O 2|2|CD|O
Cra|cra|NN|O glucose|glucose|NN|O 1|1|CD|O
RNAP|rnap|NN|O old|old|JJ|O rep1|rep1|NN|O
Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
All|all|DT|O sequencing|sequencing|NN|O reads|read|VBZ|O were|be|VBD|O mapped|map|VBN|O to|to|TO|O E.|e.|FW|O coli|coli|FW|O MG1655|mg1655|NN|O reference|reference|NN|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion -RRB-|-rrb-|-RRB-|O using|use|VBG|O CLC|clc|NN|O Genomics|genomic|NNS|O Workbench5|workbench5|NN|O with|with|IN|O the|the|DT|O length|length|NN|O fraction|fraction|NN|O of|of|IN|O 0.9|0.9|CD|O and|and|CC|O the|the|DT|O similarity|similarity|NN|O of|of|IN|O 0.99|0.99|CD|O .|.|.|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 Δfur|δfur|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|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|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|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|O .|.|.|O
Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O B|b|NN|O -|-|:|O 8|8|CD|O µM|µm|NN|O IPTG|iptg|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 <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|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|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|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 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
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O C|c|NN|O
antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
EC18n167|ec18n167|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O B|b|NN|O
M63|m63|NN|O 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
Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O A|a|NN|O
∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
M9|m9|NN|Med minimal|minimal|JJ|Med complete|complete|JJ|Med media|media|NNS|Med ,|,|,|O cultures|culture|NNS|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O at|at|IN|O 30|30|CD|Temp degrees|degree|NNS|Temp C|c|NN|Temp in|in|IN|O a|a|DT|O gyratory|gyratory|JJ|Agit water|water|NN|Agit bath|bath|NN|Agit shaking|shake|VBG|Agit at|at|IN|Agit 240|240|CD|Agit rpm|rpm|NN|Agit