Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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Estefani Gaytan Nunez
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1 --------------------------------- PARAMETERS --------------------------------
2 -Path of CoreNLP output: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CoreNLP/output/
3 -File with CoreNLP-tagging sentences: raw-metadata-senteneces.txt.conll
4 -Path of training data set: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
5 -File with training data set: training-data-set-70.txt
6 -Path of test data set: /home/egaytan/GROWTH-CONDITIONS-GEO-EXTRACTION/CRF/data-sets
7 -File with test data set: test-data-set-30.txt
8 --------------------------------- PROCESSING --------------------------------
9 -Number of sentences: 405
10 - agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
11 - agent|agent|NN|O :|:|:|O DPD|dpd|NN|Supp
12 - agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp and|and|CC|Supp rifampicin|rifampicin|NN|Supp
13 - agent|agent|NN|O :|:|:|O Fe|Fe|NNP|Supp
14 - <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
15 - <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
16 - 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
17 - antibody|antibody|NN|O :|:|:|O 9E10|9e10|CD|Anti Myc|myc|NN|Anti tag|tag|NN|Anti antibody|antibody|NN|O
18 - antibody|antibody|NN|O :|:|:|O Affinity|Affinity|NNP|Anti Purified|purify|VBN|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
19 - antibody|antibody|NN|O :|:|:|O anti-FLAG|anti-flag|JJ|Anti mAb|mab|NN|Anti
20 - antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti FNR|fnr|NN|Anti antibody|antibody|NN|Anti
21 - 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
22 - antibody|antibody|NN|O :|:|:|O Pre-cleared|pre-cleared|JJ|Anti IHF|ihf|NN|Anti polyclonal|polyclonal|JJ|Anti antibody|antibody|NN|Anti
23 - antibody|antibody|NN|O :|:|:|O RNA|rna|NN|Anti Polymerase|polymerase|NN|Anti ß|ß|NN|Anti monoclonal|monoclonal|JJ|Anti antibody|antibody|NN|Anti from|from|IN|O NeoClone|NeoClone|NNP|O -LRB-|-lrb-|-LRB-|O W0002|w0002|NN|O -RRB-|-rrb-|-RRB-|O
24 - At|at|IN|O OD450|od450|NN|OD
25 - A|a|NN|OD total|total|NN|OD of|of|IN|OD six|six|CD|OD samples|sample|NNS|OD were|be|VBD|OD analyzed|analyze|VBN|OD .|.|.|OD oxyR-8myc|oxyr-8myc|NN|OD ,|,|,|OD soxR-8myc|soxr-8myc|NN|OD ,|,|,|OD and|and|CC|OD soxS-8myc|soxs-8myc|NN|OD tagged|tag|VBD|OD cells|cell|NNS|OD were|be|VBD|OD cultured|culture|VBN|OD in|in|IN|OD M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med 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
26 - A|a|NN|O total|total|NN|O of|of|IN|O two|two|CD|O samples|sample|NNS|O were|be|VBD|O analyzed|analyze|VBN|O .|.|.|O ompR-8myc|ompr-8myc|NN|O tagged|tag|VBD|O cells|cell|NNS|O were|be|VBD|O cultured|culture|VBN|O in|in|IN|O M9|m9|NN|Med minimal|minimal|JJ|Med media|media|NNS|Med 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 0.3|0.3|CD|Supp M|m|NN|Supp of|of|IN|Supp NaCl|nacl|NN|Supp at|at|IN|O mid-log|mid-log|NN|Phase pahse|pahse|NN|Phase for|for|IN|O 30|30|CD|Supp min|min|NN|Supp with|with|IN|O agitation|agitation|NN|O .|.|.|O
27 - carbon|carbon|NN|O source|source|NN|O :|:|:|O acetate|acetate|NN|Supp
28 - carbon|carbon|NN|O source|source|NN|O :|:|:|O fructose|fructose|NN|Supp
29 - carbon|carbon|NN|O source|source|NN|O :|:|:|O glucose|glucose|NN|Supp
30 - 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
31 - 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 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
32 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 70|70|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O or|or|CC|O anaerobically|anaerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O and|and|CC|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O until|until|IN|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.3-0.35|0.3-0.35|CD|OD -RRB-|-rrb-|-RRB-|O .|.|.|O
33 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O <Air>|<air>|NN|O aerobically|aerobically|RB|O -LRB-|-lrb-|-LRB-|O 25|25|CD|O %|%|NN|O O2|o2|CD|O ,|,|,|O 70|70|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 0.35|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
34 - 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 .|.|.|O
35 - 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
36 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|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 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
37 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.15|0.15|CD|OD in|in|IN|O 100|100|CD|O ml|ml|NN|O LB|lb|NN|Med -LRB-|-lrb-|-LRB-|O +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp -RRB-|-rrb-|-RRB-|O .|.|.|O
38 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp to|to|TO|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD about|about|IN|OD 0.15|0.15|CD|OD in|in|IN|O 50|50|CD|O ml|ml|NN|O LB|lb|NN|Med -LRB-|-lrb-|-LRB-|O +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp -RRB-|-rrb-|-RRB-|O before|before|IN|O crosslinking|crosslink|VBG|O .|.|.|O
39 - 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
40 - 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 and|and|CC|O the|the|DT|O remainder|remainder|NN|O kept|keep|VBD|O at|at|IN|O 30|30|CD|Temp °C|°c|NN|Temp -LRB-|-lrb-|-LRB-|Temp see|see|VB|Temp control|control|JJ|Temp sample|sample|NN|Temp -RRB-|-rrb-|-RRB-|Temp .|.|.|O
41 - 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
42 - 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
43 - 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 <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
44 - Cells|cell|NNS|O were|be|VBD|O grown|grow|VBN|O with|with|IN|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp and|and|CC|Supp 300|300|CD|Supp µL|µl|NN|Supp Cm20|cm20|NN|Supp <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
45 - 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
46 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti
47 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-myc|anti-myc|JJ|Anti -LRB-|-lrb-|-LRB-|O Santa|Santa|NNP|O Cruz|Cruz|NNP|O Biotech|Biotech|NNP|O ,|,|,|O sc-28207|sc-28207|NN|O -RRB-|-rrb-|-RRB-|O
48 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O anti-RpoB|anti-rpob|JJ|Anti -LRB-|-lrb-|-LRB-|O Neoclone|Neoclone|NNP|O ,|,|,|O WP002|wp002|NN|O -RRB-|-rrb-|-RRB-|O
49 - 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
50 - 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
51 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O none|none|NN|Anti
52 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O RNA|rna|NN|Anti polymerase|polymerase|NN|Anti subunit|subunit|NN|Anti β|β|NN|Anti
53 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O SeqA|seqa|NN|Anti
54 - chip|chip|NN|O antibody|antibody|NN|O :|:|:|O σ32|σ32|NN|Anti
55 - 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
56 - 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
57 - 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
58 - culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O cultures|culture|NNS|O
59 - culture|culture|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O cultures|culture|NNS|O
60 - 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 acetate|acetate|NN|Supp
61 - 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
62 - 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 glucose|glucose|NN|Supp
63 - 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
64 - E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O cra-8myc|cra-8myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O was|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|O phase|phase|NN|O <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|O minimal|minimal|JJ|O media|media|NNS|O supplemented|supplement|VBN|O with|with|IN|O 0.2|0.2|CD|O %|%|NN|O glucose|glucose|NN|O ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
65 - 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|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
66 - 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
67 - 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|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
68 - 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|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|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
69 - 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 <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 fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
70 - 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 <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|O ,|,|,|O fructose|fructose|NN|O and|and|CC|O acetate|acetate|NN|O .|.|.|O
71 - 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
72 - 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
73 - E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|wt|NN|O and|and|CC|O ΔompR|δompr|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase <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 Then|then|RB|O cells|cell|NNS|O were|be|VBD|O treated|treat|VBN|O with|with|IN|O 0.3|0.3|CD|Supp M|m|NN|Supp of|of|IN|Supp NaCl|nacl|NN|Supp at|at|IN|O mid-log|mid-log|JJ|O pahse|pahse|NN|O for|for|IN|O 30|30|CD|Supp min|min|NN|Supp with|with|IN|O agitation|agitation|NN|O .|.|.|O
74 - E.|E.|NNP|O coli|coli|NN|O K-12|k-12|NN|O MG1655|mg1655|NN|O WT|WT|NNP|O ,|,|,|O GadE-8-myc|gade-8-myc|NN|O ,|,|,|O GadW-8-myc|gadw-8-myc|NN|O ,|,|,|O and|and|CC|O GadX-8-myc|gadx-8-myc|NN|O tagged|tag|VBD|O strains|strain|NNS|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD
75 - 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
76 - 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
77 - 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 .|.|.|O
78 - 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
79 - 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 <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
80 - 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 <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
81 - 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 <Air>|<air>|NN|O anaerobically|anaerobically|RB|O in|in|IN|O L|L|NNP|Med broth|broth|NN|Med supplemented|supplement|VBN|O with|with|IN|O glucose|glucose|NN|Supp .|.|.|O
82 - 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 <Air>|<air>|NN|O anaerobically|anaerobically|RB|O 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
83 - 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 <Air>|<air>|NN|O anaerobically|anaerobically|RB|O 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
84 - 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
85 - Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|NN|O and|and|CC|O ∆|∆|NN|O fnr|fnr|NN|O were|be|VBD|O grown|grow|VBN|O to|to|TO|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O O.D.|o.d.|NN|OD 600nm|600nm|JJ|OD 0.3|0.3|CD|OD -RRB-|-rrb-|-RRB-|O <Air>|<air>|NN|O anerobically|anerobically|RB|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O N2|n2|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O CO2|co2|NN|O -RRB-|-rrb-|-RRB-|O at|at|IN|O 37|37|CD|Temp °C|°c|NN|Temp in|in|IN|O MOPS|MOPS|NNP|Med +|+|CC|O 0.2|0.2|CD|Supp %|%|NN|Supp glucose|glucose|NN|Supp media|media|NNS|O -LRB-|-lrb-|-LRB-|O Ref|ref|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O
86 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O Escherichia|escherichia|FW|O coli|coli|FW|O MG1655|mg1655|NN|O K-12|k-12|NN|O genome|genome|NN|O version|version|NN|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion
87 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O ASM584v2|asm584v2|NN|Gversion
88 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913.2|000913.2|CD|Gversion
89 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O NC|nc|NN|Gversion _|_|CD|Gversion 000913|000913|CD|Gversion
90 - Genome|Genome|NNP|O _|_|NNP|O build|build|VB|O :|:|:|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion -LRB-|-lrb-|-LRB-|O GenBank|genbank|NN|O -RRB-|-rrb-|-RRB-|O
91 - genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O cra|cra|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
92 - genotype|genotype|NN|O :|:|:|O delta|delta|NN|O -|-|:|O crp|crp|NN|Gtype Knock-out|knock-out|JJ|Gtype strain|strain|NN|Gtype
93 - genotype|genotype|NN|O :|:|:|O ArgR-8myc|argr-8myc|NN|Gtype
94 - genotype|genotype|NN|O :|:|:|O gadE-8myc|gade-8myc|NN|Gtype
95 - genotype|genotype|NN|O :|:|:|O gadW-8myc|gadw-8myc|NN|Gtype
96 - genotype|genotype|NN|O :|:|:|O gadX-8myc|gadx-8myc|NN|Gtype
97 - genotype|genotype|NN|O :|:|:|O Lrp-8myc|lrp-8myc|JJ|Gtype
98 - genotype|genotype|NN|O :|:|:|O ompR-8myc|ompr-8myc|NN|Gtype
99 - genotype|genotype|NN|O :|:|:|O ompR|ompr|NN|Gtype deletion|deletion|NN|Gtype mutant|mutant|JJ|Gtype
100 - genotype|genotype|NN|O :|:|:|O PurR-8myc|purr-8myc|NN|Gtype
101 - genotype|genotype|NN|O :|:|:|O TrpR-8myc|trpr-8myc|NN|Gtype
102 - genotype|genotype|NN|O :|:|:|O wildtype|wildtype|JJ|Gtype
103 - genotype|genotype|NN|O :|:|:|O Wildtype|wildtype|NN|Gtype
104 - genotype|genotype|NN|O :|:|:|O WT|WT|NNP|Gtype
105 - genotype|genotype|NN|O :|:|:|O ΔseqA|δseqa|NN|Gtype
106 - genotype/variation|genotype/variation|NN|O :|:|:|O Combined|Combined|NNP|Gtype input|input|NN|Gtype
107 - genotype/variation|genotype/variation|NN|O :|:|:|O cra-8myc-tagged|cra-8myc-tagged|JJ|Gtype
108 - genotype/variation|genotype/variation|NN|O :|:|:|O delta|delta|NN|Gtype _|_|SYM|Gtype cra|cra|FW|Gtype
109 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadE|delta-gade|NN|Gtype
110 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadW|delta-gadw|NN|Gtype
111 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-gadX|delta-gadx|NN|Gtype
112 - 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
113 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-oxyR|delta-oxyr|NN|Gtype
114 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxR|delta-soxr|NN|Gtype
115 - genotype/variation|genotype/variation|NN|O :|:|:|O delta-soxS|delta-soxs|NN|Gtype
116 - genotype/variation|genotype/variation|NN|O :|:|:|O -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
117 - genotype/variation|genotype/variation|NN|O :|:|:|O fur-8myc|fur-8myc|JJ|Gtype
118 - 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
119 - 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
120 - 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
121 - genotype/variation|genotype/variation|NN|O :|:|:|O oxyR-8myc|oxyr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
122 - genotype/variation|genotype/variation|NN|O :|:|:|O soxR-8myc|soxr-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
123 - genotype/variation|genotype/variation|NN|O :|:|:|O soxS-8myc|soxs-8myc|NN|Gtype -|-|:|O tagged|tag|VBN|O
124 - genotype/variation|genotype/variation|NN|O :|:|:|O wild|wild|JJ|Gtype type|type|NN|Gtype
125 - genotype/variation|genotype/variation|NN|O :|:|:|O Wild-type|wild-type|JJ|Gtype
126 - genotype/variation|genotype/variation|NN|O :|:|:|O WT|WT|NNP|Gtype
127 - genotype/variation|genotype/variation|NN|O :|:|:|O Δfur|δfur|NN|Gtype
128 - genoype|genoype|NN|O :|:|:|O dFNR|dfnr|NN|Gtype
129 - genoype|genoype|NN|O :|:|:|O Wild-Type|wild-type|JJ|Gtype
130 - growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<Air>|NNP|O Aerobic|Aerobic|NNP|O
131 - growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O anaerobic|anaerobic|JJ|O
132 - growth|growth|NN|O condition|condition|NN|O :|:|:|O <Air>|<air>|NN|O Anaerobic|anaerobic|JJ|O
133 - growth|growth|NN|O condition|condition|NN|O :|:|:|O 16|16|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
134 - growth|growth|NN|O condition|condition|NN|O :|:|:|O 4|4|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
135 - growth|growth|NN|O condition|condition|NN|O :|:|:|O 8|8|CD|Supp µM|µm|NN|Supp IPTG|iptg|NN|Supp
136 - growth|growth|NN|O condition|condition|NN|O :|:|:|O Adenine|Adenine|NNP|Supp
137 - growth|growth|NN|O condition|condition|NN|O :|:|:|O glucose|glucose|NN|Supp
138 - growth|growth|NN|O medium|medium|NN|O :|:|:|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
139 - growth|growth|NN|O medium|medium|NN|O :|:|:|O MOPS|MOPS|NNP|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med media|media|NNS|Med containing|contain|VBG|O 1|1|CD|Supp µM|µm|NN|Supp FeSO4|feso4|NN|Supp
140 - growth|growth|NN|O phase|phase|NN|O :|:|:|O exponential|exponential|JJ|Phase
141 - growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|NN|Phase
142 - growth|growth|NN|O phase|phase|NN|O :|:|:|O mid-log|mid-log|JJ|Phase phase|phase|NN|Phase -LRB-|-lrb-|-LRB-|O OD600|od600|NN|OD
143 - growth|growth|NN|OD phase|phase|NN|OD :|:|:|OD stationary|stationary|JJ|Phase
144 - ∆|∆|CD|Gtype fnr|fnr|NN|Gtype ChIP|chip|NN|O DNA|dna|NN|O from|from|IN|O PK4854|pk4854|NN|Gtype
145 - ChIP-Seq|chip-seq|NN|Gversion
146 - 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
147 - library|library|NN|O strategy|strategy|NN|O :|:|:|O ChIP-exo|ChIP-exo|NNP|Technique
148 - medium|medium|NN|O :|:|:|O LB|LB|NNP|Med
149 - medium|medium|NN|O :|:|:|O M63|m63|NN|Med
150 - 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
151 - ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 1|1|CD|O
152 - ArgR|argr|NN|O _|_|CD|O Arginine|arginine|NN|O _|_|NN|O 2|2|CD|O
153 - ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
154 - ArgR|argr|NN|O _|_|CD|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
155 - ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
156 - ChIP-exo|ChIP-exo|NNP|O GadE|GadE|NNP|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
157 - ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
158 - ChIP-exo|chip-exo|NN|O GadW|gadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
159 - ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
160 - ChIP-exo|chip-exo|NN|O GadX|gadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
161 - ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
162 - ChIP-exo|ChIP-exo|NNP|O RpoS|rpos|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
163 - Cra|Cra|NNP|O acetate|acetate|NN|O 1|1|CD|O
164 - Cra|Cra|NNP|O acetate|acetate|NN|O 2|2|CD|O
165 - Cra|Cra|NNP|O fructose|fructose|NN|O 1|1|CD|O
166 - Cra|Cra|NNP|O fructose|fructose|NN|O 2|2|CD|O
167 - Cra|cra|NN|O glucose|glucose|NN|O 1|1|CD|O
168 - Cra|cra|NN|O glucose|glucose|NN|O 2|2|CD|O
169 - Crosslink|Crosslink|NNP|O
170 - CsiR|CsiR|NNP|O _|_|VBD|O ChIPSeq|chipseq|NN|O
171 - CsiR|csir|NN|O _|_|CD|O RNASeq|rnaseq|NN|O
172 - EC18n122|ec18n122|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 4|4|CD|O
173 - 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
174 - 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
175 - EC18n169|ec18n169|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
176 - EC18n170|ec18n170|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 2|2|CD|O
177 - 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
178 - EC18n177|ec18n177|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
179 - 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
180 - EC18n179|ec18n179|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
181 - 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
182 - EC18n181|ec18n181|NN|O RpoH|rpoh|NN|O 20|20|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 1|1|CD|O
183 - EC18n182|ec18n182|NN|O RpoH|rpoh|NN|O 0|0|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
184 - EC18n183|ec18n183|NN|O RpoH|rpoh|NN|O 2.5|2.5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
185 - EC18n184|ec18n184|NN|O RpoH|rpoh|NN|O 5|5|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
186 - EC18n185|ec18n185|NN|O RpoH|rpoh|NN|O 10|10|CD|O min|min|NN|O Time|Time|NNP|O course|course|NN|O 3|3|CD|O
187 - 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
188 - Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
189 - Ecoli|ecolus|NNS|O _|_|VBP|O dFNR|dfnr|NN|O _|_|CD|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
190 - Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep1|rep1|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
191 - Ecoli|Ecoli|NNP|O _|_|NNP|O wild-type|wild-type|JJ|O _|_|NN|O rep2|rep2|NN|O _|_|NN|O anaerobic|anaerobic|JJ|O
192 - Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|O
193 - FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O A|a|NN|O
194 - FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O Affinity|affinity|NN|O Purified|purify|VBN|O -|-|:|O B|b|NN|O
195 - FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
196 - FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
197 - FNR|fnr|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O C|c|NN|O
198 - ∆|∆|CD|O fnr|fnr|SYM|O -|-|:|O Anaeroibc|anaeroibc|NN|O
199 - FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O A|a|NN|O
200 - FNR|fnr|SYM|O -|-|:|O ∆|∆|SYM|O hns|hn|VBZ|O ∆|∆|SYM|O stpA|stpa|NN|O B|b|NN|O
201 - ∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
202 - ∆|∆|CD|O fur|fur|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
203 - ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
204 - ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
205 - ∆|∆|CD|O fur|fur|NN|O Anaerobic|anaerobic|JJ|O -LSB-|-lsb-|-LRB-|O IP|IP|NNP|O vs|vs|CC|O nput|nput|NN|O -RSB-|-rsb-|-RRB-|O
206 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O A|A|NNP|O
207 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O B|B|NNP|O
208 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Aerobic|Aerobic|NNP|O C|C|NNP|O
209 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O A|A|NNP|O
210 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O B|b|NN|O
211 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|anaerobic|JJ|O C|c|NN|O
212 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O ,|,|,|O Iron|Iron|NNP|O Deficient|Deficient|NNP|O A|A|NNP|O
213 - Fur|Fur|NNP|O IP|IP|NNP|O ChIP-Seq|ChIP-Seq|NNP|O Anaerobic|Anaerobic|NNP|O ,|,|,|O Iron|Iron|NNP|O Deficient|deficient|JJ|O B|b|NN|O
214 - ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O A|a|NN|O
215 - ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O B|b|NN|O
216 - ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O A|a|NN|O
217 - ∆|∆|CD|O fur|fur|NN|O ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O B|b|NN|O
218 - Fur|Fur|NNP|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
219 - Fur|Fur|NNP|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
220 - Fur|Fur|NNP|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
221 - Fur|Fur|NNP|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
222 - HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O A|a|NN|O
223 - HNS|hns|SYM|O -|-|:|O Aerobic|aerobic|JJ|O B|b|NN|O
224 - HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
225 - HNS|hns|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
226 - IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O A|a|NN|O
227 - IHF|ihf|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O B|b|NN|O
228 - Input|input|NN|O ChIP-Seq|chip-seq|NN|O
229 - LB|lb|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
230 - LB|lb|NN|O 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
231 - LB|lb|NN|O 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
232 - LB|lb|NN|O 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
233 - 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
234 - 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 HS2|hs2|NN|O
235 - LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
236 - LB|lb|NN|O 2.0|2.0|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L2|l2|NN|O HS2|hs2|NN|O
237 - LB|lb|NN|O 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
238 - LB|lb|NN|O 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
239 - LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O HS1|hs1|NN|O
240 - LB|lb|NN|O 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
241 - LB|lb|NN|O 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
242 - 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 HS1|hs1|NN|O
243 - 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
244 - LB|lb|NN|O 2.0|2.0|CD|O B2|b2|NN|O TEX|TEX|NNP|O pos|po|VBZ|O L2|l2|NN|O HS2|hs2|NN|O
245 - Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 1|1|CD|O
246 - Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 2|2|CD|O
247 - Lrp|Lrp|NNP|O _|_|NNP|O Leu|Leu|NNP|O _|_|SYM|O 3|3|CD|O
248 - Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 1|1|CD|O
249 - Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 2|2|CD|O
250 - Lrp|Lrp|NNP|O _|_|SYM|O NH4Cl|nh4cl|NN|O _|_|NN|O 3|3|CD|O
251 - M63|m63|NN|O 0.4|0.4|CD|O B1|b1|NN|O TEX|TEX|NNP|O neg|neg|NNP|O L1|l1|NN|O GA|ga|NN|O
252 - M63|m63|NN|O 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
253 - M63|m63|NN|O 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
254 - M63|m63|NN|O 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
255 - 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 HS1|hs1|NN|O
256 - 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
257 - Nac|Nac|NNP|O _|_|NNP|O ChIPSeq|ChIPSeq|NNP|O
258 - Nac|Nac|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
259 - NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep1|rep1|NN|O
260 - NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep2|rep2|NN|O
261 - NsrR|nsrr|NN|O _|_|CD|O Flagtag|Flagtag|NNP|O _|_|CD|O rep3|rep3|NN|O
262 - NtrC|ntrc|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
263 - OmpR|ompr|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O
264 - OmpR|ompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
265 - OmpR|ompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
266 - OxyR|oxyr|NN|O PQ|pq|NN|O 1|1|CD|O
267 - OxyR|oxyr|NN|O PQ|pq|NN|O 2|2|CD|O
268 - pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 1|1|CD|O
269 - pT7|pt7|NN|O _|_|CD|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
270 - Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
271 - Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 4|4|CD|O µM|µm|NN|O IPTG|iptg|NN|O
272 - Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O A|a|NN|O -|-|:|O 8|8|CD|O µM|µm|NN|O IPTG|iptg|NN|O
273 - 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
274 - 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
275 - 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
276 - Ptac|ptac|NN|O :|:|:|O :|:|:|O fnr|fnr|SYM|O -|-|:|O C|c|NN|O -|-|:|O 16|16|CD|O µM|µm|NN|O IPTG|iptg|NN|O
277 - PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|SYM|O 1|1|CD|O
278 - PurR|purr|NN|O _|_|CD|O Adenine|Adenine|NNP|O _|_|NN|O 2|2|CD|O
279 - PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 1|1|CD|O
280 - PurR|purr|NN|O _|_|CD|O glucose|glucose|NN|O _|_|NN|O 2|2|CD|O
281 - RNAP|rnap|NN|O old|old|JJ|O rep1|rep1|NN|O
282 - RNAP|rnap|NN|O old|old|JJ|O rep2|rep2|NN|O
283 - RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 1|1|CD|O
284 - RpoB|rpob|NN|O ∆|∆|CD|O cra|cra|NN|O 2|2|CD|O
285 - RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 1|1|CD|O
286 - RpoB|rpob|NN|O ∆|∆|CD|O crp|crp|NN|O 2|2|CD|O
287 - 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
288 - RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
289 - RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|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
290 - RpoB|rpob|NN|O with|with|IN|O DPD|dpd|NN|O and|and|CC|O rifampicin|rifampicin|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
291 - 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
292 - RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
293 - 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
294 - RpoB|rpob|NN|O with|with|IN|O Fe|Fe|NNP|O and|and|CC|O rifampicin|rifampicin|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O ChIP-exo|chip-exo|NN|O -RRB-|-rrb-|-RRB-|O
295 - RpoB|rpob|NN|O WT|wt|NN|O 1|1|CD|O
296 - RpoB|rpob|NN|O WT|wt|NN|O 2|2|CD|O
297 - RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
298 - RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
299 - RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 20|20|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
300 - RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 2.5|2.5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
301 - RpoH|rpoh|NN|O induced|induce|VBN|O -LRB-|-lrb-|-LRB-|O 5|5|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
302 - ∆|∆|CD|O ryhB|ryhb|NN|O Aerobic|aerobic|JJ|O
303 - ∆|∆|CD|O ryhB|ryhb|NN|O Anaerobic|anaerobic|JJ|O
304 - SeqA|seqa|NN|O new|new|JJ|O deltaSeqA|deltaseqa|NN|O
305 - SeqA|seqa|NN|O new|new|JJ|O rep1|rep1|NN|O
306 - SeqA|seqa|NN|O new|new|JJ|O rep2|rep2|NN|O
307 - SeqA|seqa|NN|O old|old|JJ|O deltaSeqA|deltaseqa|NN|O
308 - SeqA|seqa|NN|O old|old|JJ|O rep1|rep1|NN|O
309 - SeqA|seqa|NN|O old|old|JJ|O rep2|rep2|NN|O
310 - SoxR|soxr|NN|O PQ|pq|NN|O 1|1|CD|O
311 - SoxR|soxr|NN|O PQ|pq|NN|O 2|2|CD|O
312 - SoxS|soxs|NN|O PQ|pq|NN|O 1|1|CD|O
313 - SoxS|soxs|NN|O PQ|pq|NN|O 2|2|CD|O
314 - ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O A|a|NN|O
315 - ß|ß|SYM|O -|-|:|O Aerobic|aerobic|JJ|O -|-|:|O B|b|NN|O
316 - ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O A|a|NN|O
317 - ß|ß|SYM|O -|-|:|O Anaerobic|anaerobic|JJ|O -|-|:|O B|b|NN|O
318 - TrpR|trpr|NN|O _|_|NN|O glucose|glucose|NN|O
319 - TrpR|trpr|NN|O _|_|CD|O Trp|trp|NN|O
320 - Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O A|a|NN|O
321 - Wild-type|wild-type|JJ|O Aerobic|aerobic|JJ|O B|b|NN|O
322 - Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O A|a|NN|O
323 - Wild-type|wild-type|JJ|O Anaerobic|anaerobic|JJ|O B|b|NN|O
324 - Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 0|0|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
325 - Wild|Wild|NNP|O type|type|NN|O control|control|NN|O -LRB-|-lrb-|-LRB-|O 10|10|CD|O min|min|NN|O -RRB-|-rrb-|-RRB-|O
326 - 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
327 - 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
328 - 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
329 - WT|wt|JJ|O acetate|acetate|NN|O 1|1|CD|O
330 - WT|wt|JJ|O acetate|acetate|NN|O 2|2|CD|O
331 - WT|WT|NNP|O _|_|SYM|O ChIPSeq|ChIPSeq|NNP|O _|_|SYM|O 1|1|CD|O
332 - WT|wt|JJ|O _|_|NN|O ChIPSeq|chipseq|NN|O _|_|NN|O 2|2|CD|O
333 - WT|wt|JJ|O fructose|fructose|NN|O 1|1|CD|O
334 - WT|wt|JJ|O fructose|fructose|NN|O 2|2|CD|O
335 - WT|wt|JJ|O glucose|glucose|NN|O 1|1|CD|O
336 - WT|wt|JJ|O glucose|glucose|NN|O 2|2|CD|O
337 - WT|wt|NN|O NaCl|nacl|NN|O 1|1|CD|O
338 - WT|wt|NN|O NaCl|nacl|NN|O 2|2|CD|O
339 - WT|wt|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
340 - WT|wt|JJ|O pH5|ph5|NN|O .5|.5|NN|O 2|2|CD|O
341 - WT|WT|NNP|O PQ|PQ|NNP|O 1|1|CD|O
342 - WT|WT|NNP|O PQ|PQ|NNP|O 2|2|CD|O
343 - WT|WT|NNP|O _|_|SYM|O RNASeq|rnaseq|NN|O
344 - WT|wt|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
345 - WT|wt|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
346 - WT|wt|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
347 - WT|wt|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
348 - Δcra|δcra|NN|O acetate|acetate|NN|O 1|1|CD|O
349 - Δcra|δcra|NN|O acetate|acetate|NN|O 2|2|CD|O
350 - Δcra|δcra|NN|O fructose|fructose|NN|O 1|1|CD|O
351 - Δcra|δcra|NN|O fructose|fructose|NN|O 2|2|CD|O
352 - Δcra|δcra|NN|O glucose|glucose|NN|O 1|1|CD|O
353 - Δcra|δcra|NN|O glucose|glucose|NN|O 2|2|CD|O
354 - 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
355 - Δfur|δfur|NN|O with|with|IN|O DPD|dpd|NN|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
356 - 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
357 - Δfur|δfur|NN|O with|with|IN|O Fe|Fe|NNP|O 2|2|CD|O -LRB-|-lrb-|-LRB-|O RNA-seq|rna-seq|NN|O -RRB-|-rrb-|-RRB-|O
358 - ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
359 - ΔgadE|δgade|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
360 - ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
361 - ΔgadW|δgadw|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
362 - ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 1|1|CD|O
363 - ΔgadX|δgadx|NN|O pH5|ph5|NN|O .5|.5|CD|O 2|2|CD|O
364 - ΔompR|δompr|NN|O NaCl|nacl|NN|O 1|1|CD|O
365 - ΔompR|δompr|NN|O NaCl|nacl|NN|O 2|2|CD|O
366 - ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 1|1|CD|O
367 - ΔoxyR|δoxyr|NN|O PQ|pq|NN|O 2|2|CD|O
368 - ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 1|1|CD|O
369 - ΔsoxR|δsoxr|NN|O PQ|pq|NN|O 2|2|CD|O
370 - ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 1|1|CD|O
371 - ΔsoxS|δsoxs|VBZ|O PQ|pq|NN|O 2|2|CD|O
372 - σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep1|rep1|NN|O
373 - σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O rep2|rep2|NN|O
374 - σ32|σ32|NN|O 30|30|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
375 - σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep1|rep1|NN|O
376 - σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O rep2|rep2|NN|O
377 - σ32|σ32|NN|O 43|43|CD|O °C|°c|NN|O short|short|JJ|O RNase|rnase|NN|O
378 - σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O control|control|NN|O
379 - σ32|σ32|NN|O ChIP|chip|NN|O DNA|dna|NN|O ,|,|,|O heat|heat|NN|O
380 - Escherichia|escherichia|FW|O coli|coli|FW|O K-12|k-12|NN|O
381 - Escherichia|escherichia|FW|O coli|coli|FW|O
382 - Escherichia|escherichia|FW|O coli|coli|FW|O str|str|NN|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655star|mg1655star|NN|Substrain
383 - 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
384 - Escherichia|escherichia|FW|O coli|coli|FW|O str|str|FW|O .|.|.|O K-12|k-12|NN|O substr|substr|NN|O .|.|.|O MG1655|mg1655|NN|O
385 - 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
386 - Resulting|result|VBG|O reads|read|VBZ|O were|be|VBD|O aligned|align|VBN|O to|to|TO|O the|the|DT|O published|publish|VBN|O E.|e.|FW|O coli|coli|FW|O K-12|k-12|NN|O MG1655|mg1655|NN|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O U00096|u00096|NN|Gversion .2|.2|NN|Gversion -RRB-|-rrb-|-RRB-|O using|use|VBG|O the|the|DT|O software|software|NN|O package|package|NN|O SOAP|soap|NN|O -LRB-|-lrb-|-LRB-|O Li|Li|NNP|O et|et|FW|O al|al|FW|O ,|,|,|O 2009|2009|CD|O -RRB-|-rrb-|-RRB-|O ,|,|,|O allowing|allow|VBG|O no|no|RB|O more|more|JJR|O than|than|IN|O two|two|CD|O mismatches|mismatch|NNS|O -LRB-|-lrb-|-LRB-|O Supplemental|Supplemental|NNP|O File|File|NNP|O -RRB-|-rrb-|-RRB-|O .|.|.|O Reads|read|VBZ|O aligning|align|VBG|O to|to|TO|O repeated|repeated|JJ|O elements|element|NNS|O in|in|IN|O the|the|DT|O genome|genome|NN|O -LRB-|-lrb-|-LRB-|O e.g.|e.g.|FW|O rRNA|rrna|NN|O -RRB-|-rrb-|-RRB-|O were|be|VBD|O removed|remove|VBN|O from|from|IN|O analysis|analysis|NN|O .|.|.|O For|for|IN|O reads|read|VBZ|O that|that|IN|O had|have|VBD|O no|no|DT|O mapping|mapping|NN|O locations|location|NNS|O for|for|IN|O the|the|DT|O first|first|JJ|O 36|36|CD|O bp|bp|NN|O ,|,|,|O the|the|DT|O 3-30|3-30|CD|O bp|bp|NN|O subsequences|subsequence|NNS|O were|be|VBD|O used|use|VBN|O in|in|IN|O the|the|DT|O subsequent|subsequent|JJ|O mapping|mapping|NN|O to|to|TO|O the|the|DT|O reference|reference|NN|O genome|genome|NN|O .|.|.|O Reads|read|NNS|O that|that|WDT|O had|have|VBD|O unique|unique|JJ|O mapping|mapping|NN|O locations|location|NNS|O and|and|CC|O did|do|VBD|O not|not|RB|O match|match|VB|O annotated|annotated|JJ|O rRNA|rrna|NN|O genes|gene|NNS|O were|be|VBD|O used|use|VBN|O for|for|IN|O further|further|JJ|O analysis|analysis|NN|O .|.|.|O For|for|IN|O each|each|DT|O gene|gene|NN|O ,|,|,|O the|the|DT|O tag|tag|NN|O density|density|NN|O was|be|VBD|O estimated|estimate|VBN|O as|as|IN|O the|the|DT|O number|number|NN|O of|of|IN|O aligned|align|VBN|O sequencing|sequencing|NN|O tags|tag|NNS|O divided|divide|VBN|O by|by|IN|O gene|gene|NN|O size|size|NN|O in|in|IN|O kb|kb|NN|O .|.|.|O Per-gene|per-gene|JJ|O tag|tag|NN|O density|density|NN|O was|be|VBD|O normalized|normalize|VBN|O using|use|VBG|O quantile|quantile|JJ|O normalization|normalization|NN|O -LRB-|-lrb-|-LRB-|O Supplemental|Supplemental|NNP|O Files|Files|NNP|O -RRB-|-rrb-|-RRB-|O .|.|.|O The|the|DT|O tag|tag|NN|O density|density|NN|O data|datum|NNS|O were|be|VBD|O analyzed|analyze|VBN|O for|for|IN|O statistically|statistically|RB|O significant|significant|JJ|O differential|differential|JJ|O expression|expression|NN|O using|use|VBG|O BaySeq|BaySeq|NNP|O -LRB-|-lrb-|-LRB-|O Hardcastle|Hardcastle|NNP|O &|&|CC|O Kelly|Kelly|NNP|O ,|,|,|O 2010|2010|CD|O -RRB-|-rrb-|-RRB-|O with|with|IN|O a|a|DT|O FDR|FDR|NNP|O of|of|IN|O 0.01|0.01|CD|O ,|,|,|O and|and|CC|O genes|gene|NNS|O were|be|VBD|O organized|organize|VBN|O into|into|IN|O operons|operon|NNS|O using|use|VBG|O data|datum|NNS|O from|from|IN|O EcoCyc|EcoCyc|NNP|O -LRB-|-lrb-|-LRB-|O Keseler|Keseler|NNP|O et|et|FW|O al|al|FW|O ,|,|,|O 2011|2011|CD|O -RRB-|-rrb-|-RRB-|O .|.|.|O
387 - Sequenced|sequence|VBD|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
388 - 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
389 - strain|strain|NN|O :|:|:|O ∆|∆|CD|Gtype hns|hn|NNS|Gtype /|/|:|Gtype ∆|∆|SYM|Gtype stpA|stpa|NN|Gtype
390 - strain|strain|NN|O :|:|:|O PK4854|pk4854|NN|Gtype
391 - strain|strain|NN|O :|:|:|O PK8263|pk8263|NN|Gtype
392 - strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O K-12|k-12|NN|O WT|wt|JJ|Gtype
393 - strain|strain|NN|O :|:|:|O K-12|k-12|NN|O MG1655|mg1655|NN|O
394 - strain|strain|NN|O :|:|:|O MG1655|mg1655|NN|O
395 - strain|strain|NN|O :|:|:|O K-12|k-12|NN|O
396 - 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
397 - 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
398 - acetate|acetate|NN|Supp
399 - Sodium|sodium|NN|Supp phosphate|phosphate|NN|Supp -LRB-|-lrb-|-LRB-|Supp 1/100|1/100|CD|Supp vol|vol|NN|Supp .|.|.|Supp of|of|IN|Supp 1M|1m|NN|Supp ,|,|,|Supp pH|ph|NN|Supp 7.6|7.6|CD|Supp ;|;|:|Supp 10|10|CD|Supp mM|mm|NN|Supp final|final|JJ|Supp -RRB-|-rrb-|-RRB-|Supp was|be|VBD|O added|add|VBN|O to|to|TO|O the|the|DT|O mid-log|mid-log|NN|Phase cultures|culture|NNS|O followed|follow|VBN|O by|by|IN|O formaldehyde|formaldehyde|NN|O to|to|TO|O 1|1|CD|O %|%|NN|O final|final|JJ|O ,|,|,|O and|and|CC|O aerobic|aerobic|JJ|O or|or|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O was|be|VBD|O continued|continue|VBN|O for|for|IN|O 10|10|CD|O min|min|NN|O .|.|.|O Cold|Cold|NNP|O 2.5|2.5|CD|O M|m|NN|O glycine|glycine|NN|O was|be|VBD|O added|add|VBN|O to|to|TO|O 100mM|100mm|NN|O and|and|CC|O the|the|DT|O mixture|mixture|NN|O was|be|VBD|O incubated|incubate|VBN|O at|at|IN|O 4|4|CD|O °C|°c|NN|O with|with|IN|O aerobic|aerobic|JJ|O or|or|CC|O anaerobic|anaerobic|JJ|O sparging|sparging|NN|O for|for|IN|O 30|30|CD|O minutes|minute|NNS|O to|to|TO|O stop|stop|VB|O the|the|DT|O crosslinking|crosslinking|NN|O .|.|.|O Cells|cell|NNS|O were|be|VBD|O spun|spin|VBN|O at|at|IN|O 3500|3500|CD|O x|x|CC|O g|g|NN|O ,|,|,|O and|and|CC|O washed|wash|VBN|O repeatedly|repeatedly|RB|O with|with|IN|O phosphate|phosphate|NN|O buffered|buffer|VBN|O saline|saline|NN|O before|before|IN|O being|be|VBG|O frozen|freeze|VBN|O at|at|IN|O -80|-80|CD|O °C|°c|NN|O .|.|.|O
400 - ChIP-Seq|chip-seq|NN|Technique
401 - RNA-Seq|rna-seq|NN|Technique
402 - 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|O medium|medium|NN|O containing|contain|VBG|O 2|2|CD|O g/L|g/l|NN|O glucose|glucose|NN|O in|in|IN|O either|either|CC|O the|the|DT|O presence|presence|NN|O or|or|CC|O 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|O °C|°c|NN|O 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|O ≈|≈|CD|O 0.5|0.5|CD|O -RRB-|-rrb-|-RRB-|O .|.|.|O
403 - 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
404 - 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|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|OD of|of|IN|OD 2.0|2.0|CD|OD a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
405 - 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
406 - To|to|TO|O harvest|harvest|VB|O total|total|JJ|O RNA|rna|NN|O samples|sample|NNS|O ,|,|,|O overnight|overnight|JJ|O cultures|culture|NNS|O of|of|IN|O wild|wild|JJ|Gtype type|type|NN|Gtype MG1655|mg1655|NN|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O at|at|IN|O 37|37|CD|O ˚C|˚c|NN|O were|be|VBD|O diluted|dilute|VBN|O back|back|RB|O 1:500|1:500|CD|O in|in|IN|O either|either|CC|O fresh|fresh|JJ|O LB|lb|NN|O or|or|CC|O M63|m63|NN|Med minimal|minimal|JJ|Med glucose|glucose|NN|Med medium|medium|NN|O and|and|CC|O allowed|allow|VBN|O to|to|TO|O grow|grow|VB|O until|until|IN|O the|the|DT|O cultures|culture|NNS|O reached|reach|VBD|O an|a|DT|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O and|and|CC|O 2.0|2.0|CD|O for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O LB|lb|NN|O and|and|CC|O an|a|DT|O OD600|od600|NN|OD of|of|IN|OD ~|~|NN|OD 0.4|0.4|CD|OD for|for|IN|O cultures|culture|NNS|O grown|grow|VBN|O in|in|IN|O M63|m63|NN|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O ~|~|NN|O 0.4|0.4|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 25|25|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O -LRB-|-lrb-|-LRB-|O 95|95|CD|O %|%|NN|O Ethanol|ethanol|NN|O ,|,|,|O 5|5|CD|O %|%|NN|O acid|acid|NN|O phenol|phenol|NN|O -RRB-|-rrb-|-RRB-|O .|.|.|O For|for|IN|O samples|sample|NNS|O grown|grow|VBN|O to|to|TO|O OD600|od600|NN|O of|of|IN|O 2.0|2.0|CD|O a|a|DT|O total|total|JJ|O volume|volume|NN|O of|of|IN|O 5|5|CD|O ml|ml|NN|O of|of|IN|O cells|cell|NNS|O were|be|VBD|O harvested|harvest|VBN|O and|and|CC|O combined|combine|VBN|O with|with|IN|O 1|1|CD|O ml|ml|NN|O of|of|IN|O stop|stop|NN|O solution|solution|NN|O .|.|.|O
407 - 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 at|at|IN|O mid-log|mid-log|NN|Phase pahse|pahse|NN|Phase for|for|IN|O 20|20|CD|Supp min|min|NN|Supp
408 - 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 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
409 - 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
410 - 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 20|20|CD|Supp mg/L|mg/l|NN|Supp tryptophan|tryptophan|NN|Supp .|.|.|O
411 - 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 10|10|CD|Supp mM|mm|NN|Supp leucine|leucine|NN|Supp .|.|.|O
412 - 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
413 - 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 W2|w2|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 1g/L|1g/l|NN|Supp arginine|arginine|NN|Supp .|.|.|O
414 - 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 W2|w2|NN|Med medium|medium|NN|Med supplemented|supplement|VBN|O with|with|IN|O 2g/L|2g/l|NN|Supp glutamine|glutamine|NN|Supp .|.|.|O