test-data-set-30-NER.txt
32.2 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
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 1|1|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|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 3|3|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|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 _|_|NN|_|O 1|1|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|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 2|2|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|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 _|_|CD|_|O 3|3|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|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 _|_|NN|_|O 1|1|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|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 _|_|NN|_|O 2|2|CD|_|O .|.|.|_|O CEL|CEL|NNP|_|O
agent|agent|NN|_|O :|:|:|_|O Fe|Fe|NNP|_|Supp
Aerobic|Aerobic|NNP|_|Air cultures|culture|NNS|_|O
All|All|NNP|_|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|_|Supp 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|_|O mmol|mmol|NN|_|O potassium|potassium|NN|_|O nitrate|nitrate|NN|SUPP|O was|be|VBD|_|O added|add|VBN|_|O .|.|.|_|O
antibody|antibody|NN|_|O :|:|:|_|O Pre-cleared|pre-cleared|JJ|_|Anti H-NS|h-ns|NN|_|Anti polyclonal|polyclonal|JJ|_|Anti antibody|antibody|NN|_|Anti
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 10|10|CD|_|O min|min|NN|_|O after|after|IN|_|O induction|induction|NN|_|O
A|a|NN|_|O total|total|NN|_|O of|of|IN|_|O six|six|CD|_|O samples|sample|NNS|_|O were|be|VBD|_|O analyzed|analyze|VBN|_|O .|.|.|_|O oxyR-8myc|oxyr-8myc|NN|_|O ,|,|,|_|O soxR-8myc|soxr-8myc|NN|_|O ,|,|,|_|O and|and|CC|_|O soxS-8myc|soxs-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 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
carbon|carbon|NN|_|O source|source|NN|_|O :|:|:|_|O acetate|acetate|NN|SUPP|Supp
carbon|carbon|NN|_|O source|source|NN|_|O :|:|:|_|O fructose|fructose|NN|_|Supp
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|_|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 ~|~|NN|_|OD 0.3-0.35|0.3-0.35|CD|_|OD -RRB-|-rrb-|-RRB-|_|O .|.|.|_|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|_|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 ~|~|NN|_|OD 0.3-0.35|0.3-0.35|CD|_|OD -RRB-|-rrb-|-RRB-|_|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 .|.|.|_|O
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 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 .|.|.|_|O
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O 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
Cells|cell|NNS|_|O were|be|VBD|_|O grown|grow|VBN|_|O with|with|IN|_|O 4|4|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
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O anti-myc|anti-myc|JJ|_|Anti
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
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O biotin|biotin|NN|SUPP|Anti conjugated|conjugate|VBN|_|Anti anti-c-myc|anti-c-myc|JJ|_|Anti antibody|antibody|NN|_|Anti
chip|chip|NN|_|O antibody|antibody|NN|_|O :|:|:|_|O Custom|Custom|NNP|_|O anti-Fur|anti-fur|JJ|_|Anti polyclonal|polyclonal|JJ|_|Anti antibody|antibody|NN|_|Anti
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 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 NO3|no3|NN|_|Supp _|_|CD|_|O 3|3|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 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 3|3|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 NO3|no3|NN|_|Supp _|_|NN|_|O 1|1|CD|_|O
Cra|Cra|NNP|TF|O fructose|fructose|NN|_|Supp 2|2|CD|_|O
CsiR|csir|NN|TF|O _|_|CD|_|O RNASeq|rnaseq|NN|_|Technique
culture|culture|NN|_|O condition|condition|NN|_|O :|:|:|_|O Aerobic|Aerobic|NNP|_|Air cultures|culture|NNS|_|O
culture|culture|NN|_|O condition|condition|NN|_|O :|:|:|_|O anaerobic|anaerobic|JJ|_|Air fermentive|fermentive|JJ|_|O condition|condition|NN|_|O
culture|culture|NN|_|O condition|condition|NN|_|O :|:|:|_|O nitrate|nitrate|JJ|SUPP|Supp respiratory|respiratory|JJ|_|O condition|condition|NN|_|O
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 fructose|fructose|NN|_|Supp
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 glucose|glucose|NN|SUPP|Supp
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|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
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 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|_|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 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|_|O .|.|.|_|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 supplemented|supplement|VBN|_|O with|with|IN|_|O 100ug/L|100ug/l|NN|_|Supp adenine|adenine|NN|_|Supp .|.|.|_|O
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O ,|,|,|_|O expressing|express|VBG|_|O NsrR|nsrr|NN|TF|Gtype with|with|IN|_|O a|a|DT|_|O C-terminal|c-terminal|JJ|_|O Flag-tag|flag-tag|NN|_|Gtype ,|,|,|_|O was|be|VBD|_|O grown|grow|VBN|_|O anaerobically|anaerobically|RB|_|Air in|in|IN|_|O L|L|NNP|_|Med broth|broth|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O glucose|glucose|NN|SUPP|Supp .|.|.|_|O
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O ,|,|,|_|O expressing|express|VBG|_|O NsrR|nsrr|NN|TF|Gtype with|with|IN|_|O a|a|DT|_|O C-terminal|c-terminal|JJ|_|O Flag-tag|flag-tag|NN|_|Gtype ,|,|,|_|O was|be|VBD|_|O grown|grow|VBN|_|O anaerobically|anaerobically|RB|_|Air in|in|IN|_|O L|L|NNP|_|Med broth|broth|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O glucose|glucose|NN|SUPP|Supp .|.|.|_|O
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O ,|,|,|_|O expressing|express|VBG|_|O NsrR|nsrr|NN|TF|Gtype with|with|IN|_|O a|a|DT|_|O C-terminal|c-terminal|JJ|_|O Flag-tag|flag-tag|NN|_|Gtype ,|,|,|_|O was|be|VBD|_|O grown|grow|VBN|_|O anaerobically|anaerobically|RB|_|Air in|in|IN|_|O L|L|NNP|_|Med broth|broth|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O glucose|glucose|NN|SUPP|Supp .|.|.|_|O
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O ,|,|,|_|O expressing|express|VBG|_|O NsrR|nsrr|NN|TF|Gtype with|with|IN|_|O a|a|DT|_|O C-terminal|c-terminal|JJ|_|O Flag-tag|flag-tag|NN|_|Gtype ,|,|,|_|O was|be|VBD|_|O grown|grow|VBN|_|O anaerobically|anaerobically|RB|_|Air in|in|IN|_|O L|L|NNP|_|Med broth|broth|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O glucose|glucose|NN|SUPP|Supp and|and|CC|_|O nitrate|nitrate|VBP|SUPP|Supp .|.|.|_|O
Escherichia|escherichia|FW|Organism|O coli|coli|FW|Organism|O ,|,|,|_|O expressing|express|VBG|_|O NsrR|nsrr|NN|TF|Gtype with|with|IN|_|O a|a|DT|_|O C-terminal|c-terminal|JJ|_|O Flag-tag|flag-tag|NN|_|Gtype ,|,|,|_|O was|be|VBD|_|O grown|grow|VBN|_|O anaerobically|anaerobically|RB|_|Air in|in|IN|_|O L|L|NNP|_|Med broth|broth|NN|_|Med supplemented|supplement|VBN|_|O with|with|IN|_|O glucose|glucose|NN|SUPP|Supp and|and|CC|_|O nitrate|nitrate|VBP|SUPP|Supp .|.|.|_|O
FNR|fnr|SYM|TF|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air -|-|:|_|O Affinity|affinity|NN|_|O Purified|purify|VBN|_|O -|-|:|_|O B|b|NN|_|O
FNR|fnr|SYM|TF|O -|-|:|_|O ∆|∆|CD|_|Gtype hns|hn|NNS|GEN|Gtype ∆|∆|VBP|_|Gtype stpA|stpa|NN|GEN|Gtype A|a|NN|_|O
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Aerobic|Aerobic|NNP|_|Air A|A|NNP|_|O
Fur|Fur|NNP|TF|O IP|IP|NNP|_|O ChIP-Seq|ChIP-Seq|NNP|_|Technique Anaerobic|anaerobic|JJ|_|Air C|c|NN|_|O
Fur|Fur|NNP|TF|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
Genome|Genome|NNP|_|O _|_|NNP|_|O build|build|VB|_|O :|:|:|_|O NC|nc|NN|_|Gversion _|_|CD|_|Gversion 000913.2|000913.2|CD|_|Gversion
genotype|genotype|NN|_|O :|:|:|_|O delta|delta|NN|_|O -|-|:|_|O cra|cra|NN|GEN|Gtype Knock-out|knock-out|JJ|_|Gtype strain|strain|NN|_|Gtype
genotype|genotype|NN|_|O :|:|:|_|O ArgR-8myc|argr-8myc|NN|_|Gtype
genotype|genotype|NN|_|O :|:|:|_|O gadW-8myc|gadw-8myc|NN|_|Gtype
genotype|genotype|NN|_|O :|:|:|_|O gadX-8myc|gadx-8myc|NN|_|Gtype
genotype|genotype|NN|_|O :|:|:|_|O TrpR-8myc|trpr-8myc|NN|_|Gtype
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O Combined|Combined|NNP|_|Gtype input|input|NN|_|Gtype
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O Δfnr|δfnr|NN|_|Gtype
genotype/variation|genotype/variation|NN|_|O :|:|:|_|O harboring|harbor|VBG|_|O ArcA-8myc|arca-8myc|NN|_|Gtype
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O Aerobic|Aerobic|NNP|_|Air
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O Anaerobic|anaerobic|JJ|_|Air
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O 16|16|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
growth|growth|NN|_|O condition|condition|NN|_|O :|:|:|_|O 4|4|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
∆|∆|CD|_|Gtype fur|fur|NN|GEN|Gtype ∆|∆|CD|_|Gtype ryhB|ryhb|NN|GEN|Gtype Anaerobic|anaerobic|JJ|_|Air B|b|NN|_|O
NsrR|nsrr|NN|TF|Gtype _|_|CD|_|Gtype Flagtag|flagtag|NN|_|Gtype _|_|CD|_|O rep3|rep3|NN|_|O
Ptac|ptac|NN|_|Gtype :|:|:|_|Gtype :|:|:|_|Gtype fnr|fnr|NN|GEN|Gtype -|-|:|_|O B|b|NN|_|O -|-|:|_|O 16|16|CD|_|Supp µM|µm|NN|_|Supp IPTG|iptg|NN|_|Supp
Wild-type|wild-type|JJ|_|Gtype Aerobic|aerobic|JJ|_|Air A|a|DT|_|O
Wild-type|wild-type|JJ|_|Gtype Aerobic|aerobic|JJ|_|Air B|b|NN|_|O
Wild-type|wild-type|JJ|_|Gtype Anaerobic|anaerobic|JJ|_|Air A|a|DT|_|O
Wild-type|wild-type|JJ|_|Gtype Anaerobic|anaerobic|JJ|_|Air B|b|NN|_|O
Wild|Wild|NNP|_|Gtype type|type|NN|_|Gtype control|control|NN|_|O -LRB-|-lrb-|-LRB-|_|O 0|0|CD|_|O min|min|NN|_|O -RRB-|-rrb-|-RRB-|_|O
WT|wt|JJ|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
WT|wt|JJ|_|Gtype fructose|fructose|NN|_|Supp 1|1|CD|_|O
WT|wt|JJ|_|Gtype glucose|glucose|NN|SUPP|Supp 1|1|CD|_|O
WT|wt|JJ|_|Gtype NaCl|nacl|NN|_|Supp 1|1|CD|_|O
WT|wt|JJ|_|Gtype PQ|pq|NN|_|Supp 2|2|CD|_|O
WT|wt|JJ|_|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
WT|wt|JJ|_|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
Δcra|δcra|NN|_|Gtype glucose|glucose|NN|SUPP|Supp 2|2|CD|_|O
Δfur|δfur|NN|_|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
ΔgadE|δgade|NN|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 1|1|CD|_|O
ΔgadW|δgadw|NN|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|O
ΔgadX|δgadx|NN|_|Gtype pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|O
ΔsoxR|δsoxr|NN|_|Gtype PQ|pq|NN|_|Supp 1|1|CD|_|O
ΔsoxS|δsoxs|NN|_|Gtype PQ|pq|NN|_|Supp 2|2|CD|_|O
HNS|hns|SYM|_|O -|-|:|_|O Aerobic|aerobic|JJ|_|Air A|a|DT|_|O
IHF|ihf|SYM|TF|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air B|b|NN|_|O
Lrp|Lrp|NNP|TF|O _|_|SYM|_|O NH4Cl|nh4cl|NN|_|Supp _|_|NN|_|O 1|1|CD|_|O
Lrp|Lrp|NNP|TF|O _|_|SYM|_|O NH4Cl|nh4cl|NN|_|Supp _|_|NN|_|O 2|2|CD|_|O
medium|medium|NN|_|O :|:|:|_|O M63|m63|NN|_|Med
LB|lb|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
LB|lb|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
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 HS1|hs1|NN|_|O
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B1|b1|NN|_|O TEX|TEX|NNP|_|O pos|po|VBZ|_|O L1|l1|NN|_|O GA|ga|NN|_|O
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B1|b1|NN|_|O TEX|TEX|NNP|_|O pos|po|VBZ|_|O L2|l2|NN|_|O HS2|hs2|NN|_|O
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 HS2|hs2|NN|_|O
LB|lb|NN|_|Med 2.0|2.0|CD|_|O B2|b2|NN|_|O TEX|TEX|NNP|_|O neg|neg|NNP|_|O L2|l2|NN|_|O HS2|hs2|NN|_|O
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 HS2|hs2|NN|_|O
M63|m63|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
M63|m63|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
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 aerobically|aerobically|RB|_|Air 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
OmpR|ompr|NN|TF|O _|_|CD|_|O ChIPSeq|chipseq|NN|_|Technique
OxyR|oxyr|NN|TF|O PQ|pq|NN|_|Supp 2|2|CD|_|O
pT7|pt7|NN|_|O _|_|CD|_|O ChIPSeq|chipseq|NN|_|Technique _|_|NN|_|O 2|2|CD|_|O
RpoB|rpob|NN|_|O ∆|∆|CD|_|Gtype cra|cra|NN|GEN|Gtype 2|2|CD|_|O
RpoB|rpob|NN|_|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
RpoB|rpob|NN|_|O with|with|IN|_|O DPD|dpd|NN|_|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
RpoB|rpob|NN|_|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
RpoB|rpob|NN|_|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
RpoB|rpob|NN|_|O with|with|IN|_|O Fe|Fe|NNP|_|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
Samples|sample|NNS|_|O for|for|IN|_|O transcriptome|transcriptome|NN|_|O analysis|analysis|NN|_|O were|be|VBD|_|O taken|take|VBN|_|O from|from|IN|_|O exponentially|exponentially|RB|_|Phase growing|grow|VBG|_|Phase cells|cell|NNS|_|Phase .|.|.|_|O From|from|IN|_|O the|the|DT|_|O cells|cell|NNS|_|O treated|treat|VBN|_|O by|by|IN|_|O RNAprotect|rnaprotect|NN|_|O Bacteria|bacterium|NNS|_|O Reagent|reagent|NN|_|O -LRB-|-lrb-|-LRB-|_|O Qiagen|qiagen|NN|_|O -RRB-|-rrb-|-RRB-|_|O ,|,|,|_|O total|total|JJ|_|O RNA|rna|NN|_|O samples|sample|NNS|_|O were|be|VBD|_|O isolated|isolate|VBN|_|O using|use|VBG|_|O RNeasy|rneasy|JJ|_|O columns|column|NNS|_|O -LRB-|-lrb-|-LRB-|_|O Qiagen|Qiagen|NNP|_|O -RRB-|-rrb-|-RRB-|_|O in|in|IN|_|O accordance|accordance|NN|_|O with|with|IN|_|O manufacturer|manufacturer|NN|_|O 's|'s|POS|_|O instruction|instruction|NN|_|O .|.|.|_|O
SeqA|seqa|NN|_|O new|new|JJ|_|O deltaSeqA|deltaseqa|NN|_|Gtype
Sequenced|sequence|VBN|_|O reads|read|VBZ|_|O were|be|VBD|_|O mapped|map|VBN|_|O onto|onto|IN|_|O NC|nc|NN|_|Gversion _|_|CD|_|Gversion 000913|000913|CD|_|Gversion reference|reference|NN|_|O genome|genome|NN|_|O sequence|sequence|NN|_|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 X|x|NN|_|O 1000|1000|CD|_|O -|-|:|_|O n|n|NN|_|O 2|2|CD|_|O -3|-3|CD|_|O 3|3|LS|_|O -|-|:|_|O S|s|NN|_|O
ß|ß|SYM|_|O -|-|:|_|O Aerobic|aerobic|JJ|_|Air -|-|:|_|O A|a|NN|_|O
ß|ß|SYM|_|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air -|-|:|_|O A|a|NN|_|O
ß|ß|SYM|_|O -|-|:|_|O Anaerobic|anaerobic|JJ|_|Air -|-|:|_|O B|b|NN|_|O
strain|strain|NN|_|O :|:|:|_|O ∆|∆|CD|_|Gtype hns|hn|NNS|GEN|Gtype /|/|:|_|Gtype ∆|∆|SYM|_|Gtype stpA|stpa|NN|GEN|Gtype
strain|strain|NN|_|O :|:|:|_|O PK4854|pk4854|NN|_|Gtype
strain|strain|NN|_|O :|:|:|_|O PK8263|pk8263|NN|_|Gtype
ChIP-exo|ChIP-exo|NNP|_|Technique RpoS|rpos|NN|_|O pH5|ph5|NN|_|pH .5|.5|CD|_|pH 2|2|CD|_|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|JJ|_|Phase phase|phase|NN|_|Phase for|for|IN|_|O 20|20|CD|_|Supp min|min|NN|_|Supp
σ32|σ32|NN|_|O 30|30|CD|_|Temp °C|°c|NN|_|Temp rep1|rep1|NN|_|O
σ32|σ32|NN|_|O 30|30|CD|_|Temp °C|°c|NN|_|Temp rep2|rep2|NN|_|O