test-data-set-30.txt
33.9 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 _|_|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-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|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 _|_|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-arcA|delta-arca|NN|Gtype _|_|CD|O glucose|glucose|NN|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 delta-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|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 _|_|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-fnr|delta-fnr|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
affyexp|affyexp|JJ|O _|_|NN|O wt|wt|JJ|Gtype _|_|NN|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O anaerobic|anaerobic|JJ|Air _|_|NN|O 2|2|CD|O .|.|.|O CEL|CEL|NNP|O
Anaerobic|anaerobic|JJ|Air cultures|culture|NNS|O
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|O minimal|minimal|JJ|O medium|medium|NN|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|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|O respiration|respiration|NN|O 20|20|CD|Supp mmol|mmol|NN|Supp potassium|potassium|NN|Supp nitrate|nitrate|JJ|Supp was|be|VBD|O added|add|VBN|O .|.|.|O
antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
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
ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|Supp _|_|NN|O 2|2|CD|O
ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|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|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
carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
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|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 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
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 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
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|O medium|medium|NN|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
Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O in|in|IN|O LB|LB|NNP|Med media|media|NNS|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
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-ArcA|chip-arca|NN|O _|_|CD|O ArcA8myc|arca8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|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 _|_|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 _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 1|1|CD|O
chip-Fnr|chip-fnr|JJ|O _|_|NN|O Fnr8myc|fnr8myc|NN|Gtype _|_|CD|O glucose|glucose|NN|Supp _|_|CD|O NH4CL|nh4cl|NN|Supp _|_|CD|O NO3|no3|NN|Supp _|_|NN|O 2|2|CD|O
Cra|Cra|NNP|O glucose|glucose|NN|Supp 2|2|CD|O
culture|culture|NN|O condition|condition|NN|O :|:|:|O Aerobic|Aerobic|NNP|Air cultures|culture|NNS|O
Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|Gtype _|_|CD|O rep1|rep1|NN|O _|_|CD|O anaerobic|anaerobic|JJ|Air
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 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
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 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|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|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
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 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 fructose|fructose|NN|O and|and|CC|O acetate|acetate|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 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
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 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.|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|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 minimal|minimal|JJ|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 100ug/L|100ug/l|NN|Supp adenine|adenine|NN|Supp .|.|.|O
Escherichia|escherichia|FW|O coli|coli|FW|O ,|,|,|O expressing|express|VBG|O NsrR|nsrr|NN|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 and|and|CC|O nitrate|nitrate|VBP|Supp .|.|.|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O A|a|NN|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O C|c|NN|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|Anaerobic|NNP|Air A|A|NNP|O
Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|Technique Anaerobic|anaerobic|JJ|Air C|c|NN|O
Fur|Fur|NNP|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
genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
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
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 and|and|CC|Gtype the|the|DT|Gtype small|small|JJ|Gtype RNA|rna|NN|Gtype RyhB|ryhb|NN|Gtype
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 Wild-type|wild-type|JJ|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
genotype/variation|genotype/variation|NN|O :|:|:|O harboring|harbor|VBG|O Fnr-8myc|fnr-8myc|JJ|Gtype
genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
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
growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
∆|∆|CD|Gtype fur|fur|NN|Gtype Anaerobic|anaerobic|JJ|Air A|a|DT|O
NsrR|nsrr|NN|Gtype _|_|CD|Gtype Flagtag|flagtag|NN|Gtype _|_|CD|O rep2|rep2|NN|O
Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O B|b|NN|O -|-|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
Ptac|ptac|NN|Gtype :|:|:|Gtype :|:|:|Gtype fnr|fnr|NN|Gtype -|-|:|O B|b|NN|O -|-|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
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
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
WT|wt|JJ|Gtype acetate|acetate|NN|Supp 2|2|CD|O
WT|wt|JJ|Gtype fructose|fructose|NN|Supp 1|1|CD|O
WT|wt|JJ|Gtype fructose|fructose|NN|Supp 2|2|CD|O
WT|wt|JJ|Gtype glucose|glucose|NN|Supp 1|1|CD|O
WT|wt|JJ|Gtype PQ|pq|NN|Supp 1|1|CD|O
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
Δcra|δcra|NN|Gtype acetate|acetate|NN|Supp 1|1|CD|O
ΔgadX|δgadx|NN|Gtype pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
ΔompR|δompr|NN|Gtype NaCl|nacl|NN|Supp 2|2|CD|O
ΔoxyR|δoxyr|NN|Gtype PQ|pq|NN|Supp 1|1|CD|O
ΔsoxS|δsoxs|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
HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air B|b|NN|O
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 1|1|CD|O
Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|Supp _|_|NN|O 2|2|CD|O
Lrp|lrp|NN|O _|_|CD|O NH4Cl|nh4cl|NN|Supp _|_|CD|O 3|3|CD|O
medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
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 B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|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
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 pos|po|VBZ|O L1|l1|NN|O HS2|hs2|NN|O
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
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
NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
OmpR|ompr|NN|O NaCl|nacl|NN|Supp 2|2|CD|O
OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|Technique
OxyR|oxyr|NN|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
PurR|purr|NN|O _|_|SYM|O Adenine|Adenine|NNP|Supp _|_|SYM|O 1|1|CD|O
PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|Supp _|_|NN|O 1|1|CD|O
RpoB|rpob|NN|O ∆|∆|CD|Gtype cra|cra|NN|Gtype 1|1|CD|O
RpoB|rpob|NN|O ∆|∆|CD|Gtype crp|crp|NN|Gtype 1|1|CD|O
RpoB|rpob|NN|O ∆|∆|CD|Gtype crp|crp|NN|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 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 and|and|CC|O rifampicin|rifampicin|NN|Supp 1|1|CD|O -LRB-|-lrb-|-LRB-|Technique ChIP-exo|chip-exo|NN|Technique -RRB-|-rrb-|-RRB-|Technique
SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|Gtype
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
ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|Air -|-|:|O B|b|NN|O
ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|Air -|-|:|O A|a|NN|O
strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
strain|strain|NN|O :|:|:|O K-12|k-12|NN|Strain
ChIP-exo|chip-exo|NN|Technique GadX|gadx|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 1|1|CD|O
ChIP-exo|chip-exo|NN|Technique GadX|gadx|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 2|2|CD|O
ChIP-exo|ChIP-exo|NNP|Technique RpoS|rpos|NN|O pH5|ph5|NN|pH .5|.5|CD|pH 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
treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|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|Supp leucine|leucine|NN|Supp .|.|.|O
treatment|treatment|NN|O :|:|:|O glucose|glucose|NN|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
TrpR|trpr|NN|O _|_|CD|O Trp|Trp|NNP|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 short|short|JJ|O RNase|rnase|NN|O
σ32|σ32|NN|O 43|43|CD|Temp °C|°c|NN|Temp rep1|rep1|NN|O