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

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annot-input_bg_v2.txt 2.7 MB
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0.15|0.15|CD %|%|NN Bile|Bile|NNP Salt|Salt|NNP Mix|Mix|NNP Stress|stress|NN ,|,|, 90|90|CD minutes|minute|NNS ,|,|, static|static|JJ ,|,|, 5|5|CD %|%|NN CO2|co2|NN -LRB-|-lrb-|-LRB- EHEC|ehec|NN strain|strain|NN :|:|: 86-24|86-24|CD -RRB-|-rrb-|-RRB-
0.2|0.2|CD ppm|ppm|NN deoxynivalenol|deoxynivalenol|NN
0.2|0.2|CD ppm|ppm|NN nivalenol|nivalenol|NN
0.5|0.5|CD hour|hour|NN expression|expression|NN of|of|IN synthetic|synthetic|JJ protein|protein|NN DX|dx|NN in|in|IN E.|e.|FW coli|coli|FW
0.5|0.5|CD mg/ml|mg/ml|NN SHX|shx|NN for|for|IN 20|20|CD min|min|NN
0.5|0.5|CD MIC|mic|NN of|of|IN CYA|CYA|NNP ,|,|, biological|biological|JJ rep1|rep1|NN
0.5|0.5|CD MIC|mic|NN of|of|IN CYA|CYA|NNP ,|,|, biological|biological|JJ rep2|rep2|NN
0.5|0.5|CD MIC|mic|NN of|of|IN CYA|CYA|NNP ,|,|, biological|biological|JJ rep3|rep3|NN
0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|NN _|_|NN 0|0|CD min|min|NN
0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 15|15|CD min|min|NN
0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 30|30|CD min|min|NN
0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 5|5|CD min|min|NN
0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|NN _|_|NN 60|60|CD min|min|NN
0|0|CD '|'|'' ,|,|, before|before|IN UV|uv|NN treatment|treatment|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
0|0|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
0|0|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN ,|,|, 25ug|25ug|JJ total|total|JJ RNA|rna|NN
0|0|CD '|'|'' lexA|lexA|NNP ,|,|, before|before|IN UV|uv|NN 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
0|0|CD min|min|NN
0|0|CD min|min|NN ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN
0min-1|0min-1|NN
0min-2|0min-2|JJ
0min-3|0min-3|NN
0|0|CD '|'|'' minimal|minimal|JJ +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
0|0|CD '|'|'' minimal|minimal|JJ +02|+02|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
0|0|CD '|'|'' minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
0|0|CD min|min|NN minus|minus|CC ciprofloxacin|ciprofloxacin|NN
0|0|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
0|0|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
0|0|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
0|0|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
0|0|CD min|min|NN plus|plus|CC ciprofloxacin|ciprofloxacin|NN
0|0|CD min|min|NN ,|,|, unstressed|unstressed|JJ
0|0|CD %|%|NN rep1|rep1|NN
0|0|CD %|%|NN rep2|rep2|NN
0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|NN 0|0|CD min|min|NN
0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 15|15|CD min|min|NN
0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 30|30|CD min|min|NN
0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 5|5|CD min|min|NN
0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 60|60|CD min|min|NN
0|0|CD '|'|'' wt|wt|JJ ,|,|, before|before|IN UV|uv|NN treatment|treatment|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 1|1|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 2|2|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 3|3|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 4|4|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 5|5|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 6|6|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 7|7|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 2|2|CD state|state|NN 8|8|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 1|1|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 2|2|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 3|3|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 4|4|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 5|5|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 6|6|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 7|7|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
0x58|0x58|NN replicate|replicate|VBP 3|3|CD state|state|NN 8|8|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
1|1|CD .|.|.
10,000|10,000|CD U|U|NNP Pencillin|Pencillin|NNP G|G|NNP in|in|IN media|media|NNS
1005|1005|CD fork-blocking|fork-blocking|NN strain|strain|NN induced|induce|VBD for|for|IN Tus|Tus|NNP
1005|1005|CD fork-blocking|fork-blocking|JJ strain|strain|NN induced|induce|VBN for|for|IN Tus|Tus|NNP :|:|: fork5|fork5|CD _|_|NN 2|2|CD
1005|1005|CD fork-blocking|fork-blocking|JJ strain|strain|NN induced|induce|VBN for|for|IN Tus|Tus|NNP :|:|: fork5|fork5|CD _|_|SYM 3|3|CD
1005|1005|CD ,|,|, LB|lb|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- tus|tus|NN repressed|repress|VBN -RRB-|-rrb-|-RRB-
1005|1005|CD ,|,|, LB|lb|NN +|+|CC 0.4|0.4|CD %|%|NN arabinose|arabinose|NN ,|,|, 2.5|2.5|CD hr|hr|NN -LRB-|-lrb-|-LRB- tus|tus|NN induced|induce|VBN -RRB-|-rrb-|-RRB-
1005|1005|CD ,|,|, LB|lb|NN +|+|CC 0.4|0.4|CD %|%|NN arabinose|arabinose|NN ,|,|, 3.5|3.5|CD hr|hr|NN -LRB-|-lrb-|-LRB- tus|tus|NN induced|induce|VBN -RRB-|-rrb-|-RRB-
1005|1005|CD ,|,|, LB|lb|NN +|+|CC 0.4|0.4|CD %|%|NN arabinose|arabinose|NN ,|,|, 90|90|CD '|'|'' -LRB-|-lrb-|-LRB- tus|tus|FW induced|induce|VBN -RRB-|-rrb-|-RRB-
100ng|100ng|CD 16S|16s|NN rRNA|rrna|NN gene|gene|NN amplicon|amplicon|NN of|of|IN a|a|DT mock|mock|JJ community|community|NN
100|100|CD %|%|NN rep1|rep1|NN
100|100|CD %|%|NN rep2|rep2|NN
10A|10a|CD _|_|NN MG+PMA|mg+pma|NN _|_|CD t60|t60|NN
10B|10b|NN _|_|CD MG+PMA|MG+PMA|NNP _|_|CD t60|t60|NN
10C|10c|CD _|_|NN MG+PMA|mg+pma|NN _|_|CD t60|t60|NN
10|10|CD _|_|CD ESBL019|esbl019|NN Filamented|Filamented|NNP Repl|Repl|NNP 3|3|CD
10|10|CD .|.|. FHI9.IND.HUS|fhi9.ind.hus|NN
10|10|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
10-HT874-PS-60min1|10-ht874-ps-60min1|NN
10J|10j|NN .0|.0|CD
10|10|CD min|min|NN
10|10|CD min|min|NN
10|10|CD min|min|NN -LRB-|-lrb-|-LRB- additional|additional|JJ -RRB-|-rrb-|-RRB-
10|10|CD min|min|NN after|after|IN UVtreatment|uvtreatment|NN 1|1|CD '|'|'' ,|,|, 40J|40j|NN ,|,|, MG1655|mg1655|NN in|in|IN Davis|Davis|NNP +0.4|+0.4|CD %|%|NN glu|glu|NN
10|10|CD min|min|NN UV|uv|NN treated|treat|VBN cells|cell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
10|10|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD mixed|mix|VBN with|with|IN 5|5|CD ml|ml|NN ice|ice|NN cold|cold|JJ killing|killing|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 20mM|20mm|NN Tris|tris|NN and|and|CC 5mM|5mm|NN MgCl2|mgcl2|NN and|and|CC 20mM|20mm|NN NaN3|nan3|NN -RRB-|-rrb-|-RRB- and|and|CC cells|cell|NNS collected|collect|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 8000g|8000g|CD ,|,|, 4C|4c|NN ,|,|, 3|3|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD discarded|discard|VBN and|and|CC the|the|DT pellet|pellet|NN resuspended|resuspend|VBN in|in|IN 300μL|300μL|NNP TE|TE|NNP with|with|IN 40|40|CD μl|μl|NN 10|10|CD %|%|NN SDS|sds|NN and|and|CC 3|3|CD μl|μl|NN 0.5|0.5|CD M|m|NN EDTA|edta|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 5|5|CD min|min|NN at|at|IN 65|65|CD °C|°c|NN 750μl|750μl|CD isopropanole|isopropanole|NN was|be|VBD added|add|VBN before|before|IN centrifugation|centrifugation|NN at|at|IN 15600|15600|CD rcf|rcf|NN for|for|IN 5|5|CD min|min|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD resuspended|resuspend|VBN in|in|IN 500μL|500μl|NN TE|te|NN and|and|CC 2μL|2μl|NN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 25mg/ml|25mg/ml|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC incubated|incubate|VBN for|for|IN 30|30|CD min|min|NN at|at|IN 65|65|CD °C|°c|NN .|.|. Subsequently|subsequently|RB ,|,|, 2μL|2μl|NN proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- 25|25|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC samples|sample|NNS incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 15|15|CD min|min|NN followed|follow|VBN by|by|IN phenol|phenol|NN extraction|extraction|NN and|and|CC precipitation|precipitation|NN with|with|IN ethanol|ethanol|NN and|and|CC Na-acetate|na-acetate|NN .|.|. Precipitated|precipitate|VBN DNA|dna|NN was|be|VBD resuspended|resuspend|VBN in|in|IN 50μL|50μl|NN dH2O|dh2o|NN .|.|.
10|10|CD mM|mm|NN of|of|IN sodium|sodium|NN phosphate|phosphate|NN and|and|CC formaldehyde|formaldehyde|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD %|%|NN were|be|VBD then|then|RB added|add|VBN .|.|. After|after|IN 10|10|CD min|min|NN of|of|IN incubation|incubation|NN at|at|IN room|room|NN temperature|temperature|NN ,|,|, the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN 30|30|CD min|min|NN in|in|IN ice|ice|NN
10|10|CD ng|ng|NN of|of|IN DNA|dna|NN were|be|VBD submitted|submit|VBN to|to|TO the|the|DT University|University|NNP of|of|IN Wisconsin-Madison|Wisconsin-Madison|NNP DNA|DNA|NNP Sequencing|sequencing|NN Facility|facility|NN for|for|IN ChIP-seq|ChIP-seq|NNP library|library|NN preparation|preparation|NN .|.|. Samples|sample|NNS were|be|VBD sheared|shear|VBN to|to|TO 200-500|200-500|CD nt|nt|NNS during|during|IN the|the|DT IP|IP|NNP process|process|NN to|to|TO facilitate|facilitate|VB library|library|NN preparation|preparation|NN .|.|. All|all|DT libraries|library|NNS were|be|VBD generated|generate|VBN using|use|VBG reagents|reagent|NNS from|from|IN the|the|DT Illumina|Illumina|NNP Paired|Paired|NNP End|End|NNP Sample|Sample|NNP Preparation|Preparation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT Illumina|Illumina|NNP protocol|protocol|NN ``|``|`` Preparing|prepare|VBG Samples|sample|NNS for|for|IN ChIP|chip|NN Sequencing|sequencing|NN of|of|IN DNA|dna|NN ''|''|'' -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP part|part|NN #|#|# 11257047|11257047|CD RevA|reva|NN -RRB-|-rrb-|-RRB- as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS ,|,|, except|except|IN products|product|NNS of|of|IN the|the|DT ligation|ligation|NN reaction|reaction|NN were|be|VBD purified|purify|VBN by|by|IN gel|gel|NN electrophoresis|electrophoresis|NN using|use|VBG 2|2|CD %|%|NN SizeSelect|sizeselect|NN agarose|agarose|NN gels|gel|NNS -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- targeting|target|VBG 400|400|CD bp|bp|NN fragments|fragment|NNS .|.|. After|after|IN library|library|NN construction|construction|NN and|and|CC amplification|amplification|NN ,|,|, quality|quality|NN and|and|CC quantity|quantity|NN were|be|VBD assessed|assess|VBN using|use|VBG an|a|DT Agilent|agilent|JJ DNA|dna|NN 1000|1000|CD series|series|NN chip|chip|NN assay|assay|NN -LRB-|-lrb-|-LRB- Agilent|agilent|NN -RRB-|-rrb-|-RRB- and|and|CC QuantIT|quantit|NN PicoGreen|picogreen|NN dsDNA|dsdna|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB ,|,|, and|and|CC libraries|library|NNS were|be|VBD standardized|standardized|JJ to|to|TO 10μM|10μm|NN .|.|. Cluster|cluster|NN generation|generation|NN was|be|VBD performed|perform|VBN using|use|VBG a|a|DT cBot|cBot|NNP Single|single|JJ Read|Read|NNP Cluster|Cluster|NNP Generation|Generation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC placed|place|VBN on|on|IN the|the|DT Illumina|Illumina|NNP cBot|cBot|NNP .|.|. Single|single|JJ read|read|NN ,|,|, 75|75|CD bp|bp|NN -LRB-|-lrb-|-LRB- rep|rep|NN A|a|NN -RRB-|-rrb-|-RRB- or|or|CC 36|36|CD bp|bp|NN -LRB-|-lrb-|-LRB- rep|rep|NN B|b|NN -RRB-|-rrb-|-RRB- runs|run|NNS were|be|VBD performed|perform|VBN ,|,|, using|use|VBG standard|standard|JJ SBS|SBS|NNP kits|kit|NNS -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC SCS|scs|NN 2.6|2.6|CD on|on|IN an|a|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP IIx|IIx|NNP .|.|. Basecalling|basecall|VBG was|be|VBD performed|perform|VBN using|use|VBG the|the|DT standard|standard|JJ Illumina|Illumina|NNP Pipeline|Pipeline|NNP version|version|NN 1.6|1.6|CD .|.|.
10|10|CD ng|ng|NN of|of|IN DNA|dna|NN were|be|VBD submitted|submit|VBN to|to|TO the|the|DT University|University|NNP of|of|IN Wisconsin-Madison|Wisconsin-Madison|NNP DNA|DNA|NNP Sequencing|sequencing|NN Facility|facility|NN for|for|IN ChIP-seq|ChIP-seq|NNP library|library|NN preparation|preparation|NN .|.|. Samples|sample|NNS were|be|VBD sheared|shear|VBN to|to|TO 200-500|200-500|CD nt|nt|NNS during|during|IN the|the|DT IP|IP|NNP process|process|NN to|to|TO facilitate|facilitate|VB library|library|NN preparation|preparation|NN .|.|. All|all|DT libraries|library|NNS were|be|VBD generated|generate|VBN using|use|VBG reagents|reagent|NNS from|from|IN the|the|DT Illumina|Illumina|NNP Paired|Paired|NNP End|End|NNP Sample|Sample|NNP Preparation|Preparation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT Illumina|Illumina|NNP protocol|protocol|NN ``|``|`` Preparing|prepare|VBG Samples|sample|NNS for|for|IN ChIP|chip|NN Sequencing|sequencing|NN of|of|IN DNA|dna|NN ''|''|'' -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP part|part|NN #|#|# 11257047|11257047|CD RevA|reva|NN -RRB-|-rrb-|-RRB- as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS ,|,|, except|except|IN products|product|NNS of|of|IN the|the|DT ligation|ligation|NN reaction|reaction|NN were|be|VBD purified|purify|VBN by|by|IN gel|gel|NN electrophoresis|electrophoresis|NN using|use|VBG 2|2|CD %|%|NN SizeSelect|sizeselect|NN agarose|agarose|NN gels|gel|NNS -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- targeting|target|VBG either|either|CC 275|275|CD bp|bp|NN fragments|fragment|NNS -LRB-|-lrb-|-LRB- s70|s70|NN libraries|library|NNS -RRB-|-rrb-|-RRB- or|or|CC 400|400|CD bp|bp|NN fragments|fragment|NNS -LRB-|-lrb-|-LRB- FNR|fnr|NN libraries|library|NNS -RRB-|-rrb-|-RRB- .|.|. After|after|IN library|library|NN construction|construction|NN and|and|CC amplification|amplification|NN ,|,|, quality|quality|NN and|and|CC quantity|quantity|NN were|be|VBD assessed|assess|VBN using|use|VBG an|a|DT Agilent|agilent|JJ DNA|dna|NN 1000|1000|CD series|series|NN chip|chip|NN assay|assay|NN -LRB-|-lrb-|-LRB- Agilent|agilent|NN -RRB-|-rrb-|-RRB- and|and|CC QuantIT|quantit|NN PicoGreen|picogreen|NN dsDNA|dsdna|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB ,|,|, and|and|CC libraries|library|NNS were|be|VBD standardized|standardized|JJ to|to|TO 10μM|10μm|NN .|.|. Cluster|cluster|NN generation|generation|NN was|be|VBD performed|perform|VBN using|use|VBG a|a|DT cBot|cBot|NNP Single|single|JJ Read|Read|NNP Cluster|Cluster|NNP Generation|Generation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC placed|place|VBN on|on|IN the|the|DT Illumina|Illumina|NNP cBot|cBot|NNP .|.|. A|a|DT single|single|JJ read|read|NN ,|,|, 36|36|CD bp|bp|NN run|run|NN was|be|VBD performed|perform|VBN ,|,|, using|use|VBG standard|standard|JJ SBS|SBS|NNP kits|kit|NNS -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC SCS|scs|NN 2.6|2.6|CD on|on|IN an|a|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP IIx|IIx|NNP .|.|. A|a|DT paired|paired|JJ read|read|NN ,|,|, 100|100|CD bp|bp|NN runs|run|NNS were|be|VBD used|use|VBN for|for|IN one|one|CD replicate|replicate|VB of|of|IN each|each|DT s70|s70|NN aerobic|aerobic|JJ and|and|CC anaerobic|anaerobic|JJ growth|growth|NN conditions|condition|NNS ,|,|, using|use|VBG standard|standard|JJ SBS|SBS|NNP kits|kit|NNS -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC SCS|scs|NN 2.6|2.6|CD on|on|IN an|a|DT Illumina|Illumina|NNP HiSeq|HiSeq|NNP .|.|. Basecalling|basecall|VBG was|be|VBD performed|perform|VBN using|use|VBG the|the|DT standard|standard|JJ Illumina|Illumina|NNP Pipeline|Pipeline|NNP version|version|NN 1.6|1.6|CD .|.|.
10|10|CD pmol|pmol|NN of|of|IN a|a|DT pre-adenylated|pre-adenylated|JJ -LRB-|-lrb-|-LRB- rApp|rapp|NN -RRB-|-rrb-|-RRB- adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO 1|1|CD μg|μg|NN of|of|IN nascent|nascent|JJ -LRB-|-lrb-|-LRB- or|or|CC mature|mature|JJ -RRB-|-rrb-|-RRB- RNA|rna|NN in|in|IN a|a|DT reaction|reaction|NN volume|volume|NN of|of|IN 20|20|CD μl|μl|NN ,|,|, using|use|VBG 400|400|CD U|U|NNP T4|t4|NN RNA|rna|NN Ligase|ligase|NN 2|2|CD ,|,|, Deletion|deletion|NN Mutant|mutant|JJ -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, cat|cat|NN .|.|. LR2D11310K|lr2d11310k|NN -RRB-|-rrb-|-RRB- in|in|IN the|the|DT presence|presence|NN of|of|IN 20|20|CD %|%|NN PEG-8000|peg-8000|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 25|25|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC RNA|rna|NN was|be|VBD eluted|elute|VBN in|in|IN 20|20|CD μl|μl|NN of|of|IN Fragmentation|fragmentation|NN buffer|buffer|NN -LSB-|-lsb-|-LRB- 65|65|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8.3|8.3|CD ;|;|: 100|100|CD mM|mm|NN KCl|kcl|NN ;|;|: 5|5|CD mM|mm|NN MgCl2|mgcl2|NN -RSB-|-rsb-|-RRB- .|.|. RNA|rna|NN was|be|VBD fragmented|fragment|VBN by|by|IN incubation|incubation|NN at|at|IN 95|95|CD °C|°c|NN for|for|IN 8|8|CD minutes|minute|NNS .|.|. Fragmented|fragmented|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC eluted|elute|VBN in|in|IN 5.5|5.5|CD μl|μl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN .|.|. RNA|rna|NN was|be|VBD heat-denatured|heat-denatured|JJ at|at|IN 70|70|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS ,|,|, and|and|CC reverse|reverse|JJ transcription|transcription|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN a|a|DT final|final|JJ volume|volume|NN of|of|IN 10|10|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.5|0.5|CD mM|mm|NN dNTPs|dntp|NNS ,|,|, 5|5|CD pmol|pmol|NN of|of|IN RT|rt|NN primer|primer|NN ,|,|, 20|20|CD U|U|NNP RNaseOUT|RNaseOUT|NNP ™|™|NNP Recombinant|recombinant|JJ Ribonuclease|ribonuclease|NN Inhibitor|inhibitor|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, cat|cat|NN .|.|. 10777-019|10777-019|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC 100|100|CD U|U|NNP SuperScript|SuperScript|NNP ®|®|SYM III|iii|CD Reverse|reverse|JJ Transcriptase|transcriptase|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, cat|cat|NN .|.|. 18080-044|18080-044|CD -RRB-|-rrb-|-RRB- ,|,|, by|by|IN incubation|incubation|NN at|at|IN 50|50|CD °C|°c|NN for|for|IN 50|50|CD minutes|minute|NNS .|.|. Template|template|NN RNA|rna|NN was|be|VBD degraded|degrade|VBN by|by|IN adding|add|VBG 1|1|CD μl|μl|NN of|of|IN 1|1|CD M|m|NN NaOH|naoh|NN ,|,|, and|and|CC incubating|incubate|VBG at|at|IN 95|95|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 6|6|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. cDNA|cdna|NN fragments|fragment|NNS were|be|VBD resolved|resolve|VBN on|on|IN a|a|DT 10|10|CD %|%|NN TBE-Urea|tbe-urea|NN polyacrylamide|polyacrylamide|NN gel|gel|NN ,|,|, and|and|CC a|a|DT gel|gel|NN slice|slice|NN corresponding|correspond|VBG to|to|TO fragments|fragment|NNS in|in|IN the|the|DT range|range|NN 40-150|40-150|CD nt|nt|NN was|be|VBD cut|cut|VBN .|.|. DNA|dna|NN was|be|VBD recovered|recover|VBN by|by|IN passive|passive|NN diffusion|diffusion|NN in|in|IN Diffusion|Diffusion|NNP buffer|buffer|NN for|for|IN 16|16|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN with|with|IN moderate|moderate|JJ shaking|shake|VBG .|.|. cDNA|cdna|NN was|be|VBD precipitated|precipitate|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD ml|ml|NN Isopropanol|isopropanol|NN ,|,|, and|and|CC 2|2|CD μl|μl|NN Glycogen|glycogen|NN -LRB-|-lrb-|-LRB- 20|20|CD μg/μl|μg/μl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 8.25|8.25|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. 10|10|CD pmol|pmol|NN of|of|IN a|a|DT 5|5|CD '|'|'' -|-|: phosphorylated|phosphorylate|VBN adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 3|3|CD '|'|'' -|-|: OH|oh|NN of|of|IN cDNA|cdna|NN fragments|fragment|NNS in|in|IN a|a|DT final|final|JJ reaction|reaction|NN volume|volume|NN of|of|IN 25|25|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.05|0.05|CD mM|mm|NN ATP|atp|NN ,|,|, 20|20|CD %|%|NN PEG-4000|peg-4000|NN ,|,|, and|and|CC 100|100|CD U|U|NNP CircLigase|CircLigase|NNP ™|™|NNP II|II|NNP ssDNA|ssDNA|NNP Ligase|Ligase|NNP -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, cat|cat|NN .|.|. CL9025K|cl9025k|NN -RRB-|-rrb-|-RRB- ,|,|, by|by|IN incubation|incubation|NN at|at|IN 60|60|CD °C|°c|NN for|for|IN 4|4|CD hours|hour|NNS ,|,|, and|and|CC 68|68|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Adapter-ligated|adapter-ligated|JJ cDNA|cdna|NN fragments|fragment|NNS were|be|VBD purified|purify|VBN from|from|IN excess|excess|JJ adapter|adapter|NN using|use|VBG 1.8|1.8|CD volumes|volume|NNS of|of|IN Agencourt|Agencourt|NNP AMPure|AMPure|NNP XP|xp|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Beckman|Beckman|NNP Coulter|Coulter|NNP ,|,|, cat|cat|NN .|.|. A63881|a63881|NN -RRB-|-rrb-|-RRB- ,|,|, following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 20|20|CD μl|μl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN ,|,|, and|and|CC indexed|index|VBD sequencing|sequencing|NN adapters|adapter|NNS were|be|VBD introduced|introduce|VBN by|by|IN 15|15|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN in|in|IN the|the|DT presence|presence|NN of|of|IN 25|25|CD pmol|pmol|NN of|of|IN each|each|DT primer|primer|NN ,|,|, and|and|CC 25|25|CD μl|μl|NN NEBNext|nebnext|NN ®|®|CD High-Fidelity|high-fidelity|NN 2X|2x|NN PCR|pcr|NN Master|master|NN Mix|Mix|NNP -LRB-|-lrb-|-LRB- NEB|NEB|NNP ,|,|, cat|cat|NN .|.|. M0541L|m0541l|NN -RRB-|-rrb-|-RRB- .|.|.
10|10|CD pmol|pmol|NN of|of|IN a|a|DT pre-adenylated|pre-adenylated|JJ -LRB-|-lrb-|-LRB- rApp|rapp|NN -RRB-|-rrb-|-RRB- adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO 1|1|CD μg|μg|NN of|of|IN nascent|nascent|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- either|either|CC total|total|NN ,|,|, or|or|CC rRNA-depleted|rrna-depleted|JJ using|use|VBG Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, cat|cat|NN .|.|. MRZB12424|mrzb12424|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- in|in|IN a|a|DT reaction|reaction|NN volume|volume|NN of|of|IN 20|20|CD μl|μl|NN ,|,|, using|use|VBG 400|400|CD U|U|NNP T4|t4|NN RNA|rna|NN Ligase|ligase|NN 2|2|CD ,|,|, Deletion|deletion|NN Mutant|mutant|JJ in|in|IN the|the|DT presence|presence|NN of|of|IN 20|20|CD %|%|NN PEG-8000|peg-8000|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 25|25|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC RNA|rna|NN was|be|VBD eluted|elute|VBN in|in|IN 5.5|5.5|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. RNA|rna|NN was|be|VBD heat-denatured|heat-denatured|JJ at|at|IN 70|70|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS ,|,|, and|and|CC reverse|reverse|JJ transcription|transcription|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN a|a|DT final|final|JJ volume|volume|NN of|of|IN 10|10|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.5|0.5|CD mM|mm|NN dNTPs|dntp|NNS ,|,|, 5|5|CD pmol|pmol|NN of|of|IN RT|rt|NN primer|primer|NN ,|,|, 20|20|CD U|U|NNP RNaseOUT|RNaseOUT|NNP ™|™|NNP Recombinant|recombinant|JJ Ribonuclease|ribonuclease|NN Inhibitor|inhibitor|NN ,|,|, and|and|CC 100|100|CD U|U|NNP SuperScript|SuperScript|NNP ®|®|SYM III|iii|CD Reverse|reverse|JJ Transcriptase|transcriptase|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 50|50|CD °C|°c|NN for|for|IN 50|50|CD minutes|minute|NNS .|.|. Template|template|NN RNA|rna|NN was|be|VBD degraded|degrade|VBN by|by|IN adding|add|VBG 1|1|CD μl|μl|NN of|of|IN 1|1|CD M|m|NN NaOH|naoh|NN ,|,|, and|and|CC incubating|incubate|VBG at|at|IN 95|95|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 6|6|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. cDNA|cdna|NN fragments|fragment|NNS were|be|VBD resolved|resolve|VBN on|on|IN a|a|DT 10|10|CD %|%|NN TBE-Urea|tbe-urea|NN polyacrylamide|polyacrylamide|NN gel|gel|NN ,|,|, and|and|CC three|three|CD gel|gel|NN slices|slice|NNS corresponding|correspond|VBG to|to|TO fragments|fragment|NNS in|in|IN the|the|DT ranges|range|NNS of|of|IN 40-200|40-200|CD nt|nt|NNS ,|,|, 200-400|200-400|CD nt|nt|NNS ,|,|, and|and|CC 400-600|400-600|CD nt|nt|NNS were|be|VBD cut|cut|VBN .|.|. DNA|dna|NN was|be|VBD recovered|recover|VBN by|by|IN passive|passive|NN diffusion|diffusion|NN in|in|IN Diffusion|Diffusion|NNP buffer|buffer|NN for|for|IN 16|16|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN with|with|IN moderate|moderate|JJ shaking|shake|VBG .|.|. cDNA|cdna|NN was|be|VBD precipitated|precipitate|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD ml|ml|NN Isopropanol|isopropanol|NN ,|,|, and|and|CC 2|2|CD μl|μl|NN Glycogen|glycogen|NN -LRB-|-lrb-|-LRB- 20|20|CD μg/μl|μg/μl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 8.25|8.25|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. 10|10|CD pmol|pmol|NN of|of|IN a|a|DT 5|5|CD '|'|'' -|-|: phosphorilated|phosphorilate|VBN adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 3|3|CD '|'|'' -|-|: OH|oh|NN of|of|IN cDNA|cdna|NN fragments|fragment|NNS in|in|IN a|a|DT final|final|JJ reaction|reaction|NN volume|volume|NN of|of|IN 25|25|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.05|0.05|CD mM|mm|NN ATP|atp|NN ,|,|, 20|20|CD %|%|NN PEG-4000|peg-4000|NN ,|,|, and|and|CC 100|100|CD U|U|NNP CircLigase|CircLigase|NNP ™|™|NNP II|II|NNP ssDNA|ssDNA|NNP Ligase|Ligase|NNP ,|,|, by|by|IN incubation|incubation|NN at|at|IN 60|60|CD °C|°c|NN for|for|IN 4|4|CD hours|hour|NNS ,|,|, and|and|CC 68|68|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Adapter-ligated|adapter-ligated|JJ cDNA|cdna|NN fragments|fragment|NNS were|be|VBD purified|purify|VBN from|from|IN excess|excess|JJ adapter|adapter|NN using|use|VBG 1.8|1.8|CD volumes|volume|NNS of|of|IN Agencourt|Agencourt|NNP AMPure|AMPure|NNP XP|xp|NN beads|bead|NNS ,|,|, following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 20|20|CD μl|μl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN ,|,|, and|and|CC indexed|index|VBD sequencing|sequencing|NN adapters|adapter|NNS were|be|VBD introduced|introduce|VBN by|by|IN 15|15|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN in|in|IN the|the|DT presence|presence|NN of|of|IN 25|25|CD pmol|pmol|NN of|of|IN each|each|DT primer|primer|NN ,|,|, and|and|CC 25|25|CD μl|μl|NN NEBNext|nebnext|NN ®|®|CD High-Fidelity|high-fidelity|NN 2X|2x|NN PCR|pcr|NN Master|master|NN Mix|Mix|NNP .|.|.
10|10|CD pmol|pmol|NN of|of|IN a|a|DT pre-adenylated|pre-adenylated|JJ -LRB-|-lrb-|-LRB- rApp|rapp|NN -RRB-|-rrb-|-RRB- adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO rnpB|rnpb|NN nascent|nascent|JJ RNA|rna|NN in|in|IN a|a|DT reaction|reaction|NN volume|volume|NN of|of|IN 20|20|CD μl|μl|NN ,|,|, using|use|VBG 400|400|CD U|U|NNP T4|t4|NN RNA|rna|NN Ligase|ligase|NN 2|2|CD ,|,|, Deletion|deletion|NN Mutant|mutant|JJ in|in|IN the|the|DT presence|presence|NN of|of|IN 20|20|CD %|%|NN PEG-8000|peg-8000|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 25|25|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC RNA|rna|NN was|be|VBD eluted|elute|VBN in|in|IN 5.5|5.5|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. RNA|rna|NN was|be|VBD heat-denatured|heat-denatured|JJ at|at|IN 70|70|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS ,|,|, and|and|CC reverse|reverse|JJ transcription|transcription|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN a|a|DT final|final|JJ volume|volume|NN of|of|IN 10|10|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.5|0.5|CD mM|mm|NN dNTPs|dntp|NNS ,|,|, 5|5|CD pmol|pmol|NN of|of|IN RT|rt|NN primer|primer|NN ,|,|, 20|20|CD U|U|NNP RNaseOUT|RNaseOUT|NNP ™|™|NNP Recombinant|recombinant|JJ Ribonuclease|ribonuclease|NN Inhibitor|inhibitor|NN ,|,|, and|and|CC 100|100|CD U|U|NNP SuperScript|SuperScript|NNP ®|®|SYM III|iii|CD Reverse|reverse|JJ Transcriptase|transcriptase|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 50|50|CD °C|°c|NN for|for|IN 50|50|CD minutes|minute|NNS .|.|. Template|template|NN RNA|rna|NN was|be|VBD degraded|degrade|VBN by|by|IN adding|add|VBG 1|1|CD μl|μl|NN of|of|IN 1|1|CD M|m|NN NaOH|naoh|NN ,|,|, and|and|CC incubating|incubate|VBG at|at|IN 95|95|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 6|6|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. cDNA|cdna|NN fragments|fragment|NNS were|be|VBD resolved|resolve|VBN on|on|IN a|a|DT 10|10|CD %|%|NN TBE-Urea|tbe-urea|NN polyacrylamide|polyacrylamide|NN gel|gel|NN ,|,|, and|and|CC a|a|DT gel|gel|NN slice|slice|NN corresponding|correspond|VBG to|to|TO fragments|fragment|NNS in|in|IN the|the|DT range|range|NN of|of|IN 40-300|40-300|CD nt|nt|NNS was|be|VBD cut|cut|VBN .|.|. DNA|dna|NN was|be|VBD recovered|recover|VBN by|by|IN passive|passive|NN diffusion|diffusion|NN in|in|IN Diffusion|Diffusion|NNP buffer|buffer|NN for|for|IN 16|16|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN with|with|IN moderate|moderate|JJ shaking|shake|VBG .|.|. cDNA|cdna|NN was|be|VBD precipitated|precipitate|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD ml|ml|NN Isopropanol|isopropanol|NN ,|,|, and|and|CC 2|2|CD μl|μl|NN Glycogen|glycogen|NN -LRB-|-lrb-|-LRB- 20|20|CD μg/μl|μg/μl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 8.25|8.25|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. 10|10|CD pmol|pmol|NN of|of|IN a|a|DT 5|5|CD '|'|'' -|-|: phosphorilated|phosphorilate|VBN adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 3|3|CD '|'|'' -|-|: OH|oh|NN of|of|IN cDNA|cdna|NN fragments|fragment|NNS in|in|IN a|a|DT final|final|JJ reaction|reaction|NN volume|volume|NN of|of|IN 25|25|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.05|0.05|CD mM|mm|NN ATP|atp|NN ,|,|, 20|20|CD %|%|NN PEG-4000|peg-4000|NN ,|,|, and|and|CC 100|100|CD U|U|NNP CircLigase|CircLigase|NNP ™|™|NNP II|II|NNP ssDNA|ssDNA|NNP Ligase|Ligase|NNP ,|,|, by|by|IN incubation|incubation|NN at|at|IN 60|60|CD °C|°c|NN for|for|IN 4|4|CD hours|hour|NNS ,|,|, and|and|CC 68|68|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Adapter-ligated|adapter-ligated|JJ cDNA|cdna|NN fragments|fragment|NNS were|be|VBD purified|purify|VBN from|from|IN excess|excess|JJ adapter|adapter|NN using|use|VBG 1.8|1.8|CD volumes|volume|NNS of|of|IN Agencourt|Agencourt|NNP AMPure|AMPure|NNP XP|xp|NN beads|bead|NNS ,|,|, following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 20|20|CD μl|μl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN ,|,|, and|and|CC indexed|index|VBD sequencing|sequencing|NN adapters|adapter|NNS were|be|VBD introduced|introduce|VBN by|by|IN 15|15|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN in|in|IN the|the|DT presence|presence|NN of|of|IN 25|25|CD pmol|pmol|NN of|of|IN each|each|DT primer|primer|NN ,|,|, and|and|CC 25|25|CD μl|μl|NN NEBNext|nebnext|NN ®|®|CD High-Fidelity|high-fidelity|NN 2X|2x|NN PCR|pcr|NN Master|master|NN Mix|Mix|NNP .|.|.
10|10|CD μg|μg|NN of|of|IN total|total|JJ RNA|rna|NN sample|sample|NN was|be|VBD subjected|subject|VBN to|to|TO purification|purification|NN for|for|IN discarding|discard|VBG rRNA|rrna|NN via|via|IN the|the|DT MICROBExpress|microbexpress|NN kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. Following|follow|VBG purification|purification|NN ,|,|, the|the|DT RNA|rna|NN was|be|VBD interrupted|interrupt|VBN into|into|IN short|short|JJ fragments|fragment|NNS using|use|VBG divalent|divalent|JJ cations|cation|NNS under|under|IN elevated|elevated|JJ temperature|temperature|NN and|and|CC the|the|DT short|short|JJ fragments|fragment|NNS were|be|VBD used|use|VBN for|for|IN the|the|DT cDNA|cdna|NN synthesis|synthesis|NN using|use|VBG a|a|DT SuperScript|SuperScript|NNP Double-Stranded|Double-Stranded|NNP cDNA|cdna|NN Synthesis|synthesis|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. These|these|DT cDNA|cdna|NN fragments|fragment|NNS were|be|VBD purified|purify|VBN with|with|IN a|a|DT QIAquick|qiaquick|NN PCR|pcr|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC then|then|RB went|go|VBD through|through|IN end|end|NN reparation|reparation|NN ,|,|, adding|add|VBG poly|poly|NN -LRB-|-lrb-|-LRB- A|a|NN -RRB-|-rrb-|-RRB- and|and|CC ligation|ligation|NN of|of|IN sequencing|sequencing|NN adaptors|adaptor|NNS .|.|. These|these|DT products|product|NNS were|be|VBD purified|purify|VBN with|with|IN agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN and|and|CC fragments|fragment|NNS in|in|IN the|the|DT size|size|NN of|of|IN 200-250|200-250|CD bp|bp|NN were|be|VBD selected|select|VBN for|for|IN PCR|pcr|NN amplification|amplification|NN to|to|TO construct|construct|VB the|the|DT cDNA|cdna|NN library|library|NN .|.|.
1.1|1.1|CD A|a|DT
1.1|1.1|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 25|25|CD
11|11|CD _|_|NN ESBL019|esbl019|NN Transition|transition|NN Repl|repl|NN 3|3|CD
11|11|CD .|.|. FHI12.nIND.HUS|fhi12.nind.hus|NN
11-HT874-PS-60min2|11-ht874-ps-60min2|NN
11K|11k|CD .60|.60|CD
1.2|1.2|CD A|a|DT
1.2|1.2|CD A|a|DT _|_|NN Space|space|NN _|_|CD 25|25|CD
12|12|CD _|_|NN ESBL019|esbl019|NN Reverted|revert|VBD Repl|repl|JJ 3|3|CD
12|12|CD .|.|. FHI12.IND.HUS|fhi12.ind.hus|NN
12|12|CD _|_|SYM HF|hf|NNS _|_|VBP LP|lp|NN _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
12-HT874-PS-60min3|12-ht874-ps-60min3|NN
12L|12l|NN .120|.120|CD
1.3|1.3|CD A|a|DT
1.3|1.3|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 25|25|CD
13|13|CD _|_|NN ESBL019|esbl019|NN Coliform|coliform|NN Repl|repl|NN 4|4|CD
13|13|CD .|.|. FHI24.nIND.HUS|fhi24.nind.hus|NN
13|13|CD _|_|SYM HF|hf|NNS _|_|VBP LP|lp|NN _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
1.4|1.4|CD A|a|DT
1.4|1.4|CD A|a|DT _|_|NN Space|space|NN _|_|CD 25|25|CD
14|14|CD _|_|CD ESBL019|esbl019|NN Filamented|Filamented|NNP Repl|Repl|NNP 4|4|CD
14|14|CD _|_|SYM HF|hf|NNS _|_|VBP LP|lp|NN _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
150|150|CD minutes|minute|NNS growth|growth|NN in|in|IN LB|LB|NNP
15|15|CD '|'|'' 10|10|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
15|15|CD '|'|'' 15|15|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
15|15|CD '|'|'' +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN vs|vs|CC 0|0|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN
1.5|1.5|CD A|a|DT
1.5|1.5|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 50|50|CD
15degrees|15degree|NNS replicate|replicate|VBP 1|1|CD
15degrees|15degree|NNS replicate|replicate|VBP 2|2|CD
15degrees|15degree|NNS replicate|replicate|VBP 3|3|CD
15|15|CD _|_|NN ESBL019|esbl019|NN Transition|transition|NN Repl|repl|NN 4|4|CD
15|15|CD .|.|. FHI25.nIND.HUS|fhi25.nind.hus|NN
15|15|CD _|_|SYM HF|hf|NNS _|_|VBP LP|lp|NN _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
1.5|1.5|CD hour|hour|NN expression|expression|NN of|of|IN synthetic|synthetic|JJ protein|protein|NN DX|dx|NN in|in|IN E.|e.|FW coli|coli|FW
15|15|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
15|15|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN ,25|,25|CD ug|ug|NN total|total|JJ RNA|rna|NN
15|15|CD min|min|NN
15|15|CD min|min|NN -LRB-|-lrb-|-LRB- additional|additional|JJ -RRB-|-rrb-|-RRB-
15|15|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
15|15|CD ml|ml|NN of|of|IN culture|culture|NN was|be|VBD mixed|mix|VBN with|with|IN 30|30|CD ml|ml|NN of|of|IN RNAprotect|rnaprotect|NN bacterial|bacterial|JJ reagent|reagent|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- .|.|.
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A|A|NNP
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A1|a1|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B|B|NNP
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B1|b1|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc.at|suc.at|NN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP A|A|NNP
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP B|B|NNP
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A2|a2|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B2|b2|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB A|a|DT
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB A1|a1|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB B|b|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB B1|b1|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP A|A|NNP
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc.at|suc.at|NN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP B|B|NNP
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A2|a2|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B2|b2|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB A1|a1|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB B1|b1|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A1|a1|NN
1.5|1.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B1|b1|NN
15|15|CD '|'|'' vs|vs|CC 0|0|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN
16,000|16,000|CD g|g|NN for|for|IN 40|40|CD s|s|NNS at|at|IN room|room|NN temperature|temperature|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD discarded|discard|VBN ,|,|, and|and|CC cell|cell|NN pellets|pellet|NNS
1.6|1.6|CD A|a|DT
1.6|1.6|CD A|a|DT _|_|NN Space|space|NN _|_|CD 50|50|CD
16|16|CD _|_|CD ESBL019|esbl019|NN Reverted|revert|VBD Repl|repl|JJ 4|4|CD
16|16|CD .|.|. FHI25.IND.HUS|fhi25.ind.hus|NN
170|170|CD μl|μl|NN were|be|VBD taken|take|VBN from|from|IN each|each|DT of|of|IN four|four|CD wells|well|NNS per|per|IN time|time|NN point|point|NN and|and|CC collected|collect|VBN into|into|IN a|a|DT fresh|fresh|JJ tube|tube|NN were|be|VBD 1.360|1.360|CD ml|ml|NN of|of|IN RNA|rna|NN protection|protection|NN buffer|buffer|NN had|have|VBD previously|previously|RB been|be|VBN added|add|VBN .|.|. Samples|sample|NNS were|be|VBD left|leave|VBN for|for|IN 5|5|CD minutes|minute|NNS at|at|IN RT|rt|NN and|and|CC then|then|RB centrifuged|centrifuge|VBD at|at|IN 4|4|CD °C|°c|NN at|at|IN maximum|maximum|JJ speed|speed|NN .|.|. Supernatant|supernatant|NN was|be|VBD discarded|discard|VBN and|and|CC pellets|pellet|NNS frozen|freeze|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|. RNA|rna|NN extraction|extraction|NN was|be|VBD performed|perform|VBN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN from|from|IN Qiagen|Qiagen|NNP -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP 74104|74104|NN -RSB-|-rsb-|-RRB- .|.|. To|to|TO remove|remove|VB possible|possible|JJ traces|trace|NNS of|of|IN genomic|genomic|JJ DNA|dna|NN contamination|contamination|NN ,|,|, 2|2|CD μg|μg|NN of|of|IN each|each|DT sample|sample|NN were|be|VBD treated|treat|VBN for|for|IN a|a|DT second|second|JJ time|time|NN with|with|IN DNAseI|dnasei|NN from|from|IN Qiagen|Qiagen|NNP -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP 79254|79254|NN -RSB-|-rsb-|-RRB- .|.|. Total|total|JJ RNA|rna|NN quality|quality|NN and|and|CC integrity|integrity|NN was|be|VBD assessed|assess|VBN using|use|VBG Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP and|and|CC Agilent|Agilent|NNP RNA|rna|NN 6000|6000|CD Nano|Nano|NNP kit|kit|NN -LSB-|-lsb-|-LRB- Cat|cat|NN No|no|DT 5067-1511|5067-1511|NN -RSB-|-rsb-|-RRB- .|.|. Samples|sample|NNS had|have|VBD an|a|DT average|average|JJ RIN|rin|NN of|of|IN 9.5|9.5|CD .|.|. Enrichment|enrichment|NN of|of|IN mRNA|mrna|NN was|be|VBD performed|perform|VBN using|use|VBG MicrobExpress|MicrobExpress|NNP rRNA|rrna|NN removal|removal|NN kit|kit|NN from|from|IN Thermo|Thermo|NNP Scientific|Scientific|NNP -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP AM1905|am1905|NN -RSB-|-rsb-|-RRB- .|.|. Successful|successful|JJ rRNA|rrna|NN depletion|depletion|NN was|be|VBD assessed|assess|VBN with|with|IN analysis|analysis|NN on|on|IN Bioanalyzer|Bioanalyzer|NNP .|.|. Retrotranscription|retrotranscription|NN was|be|VBD then|then|RB performed|perform|VBN starting|start|VBG from|from|IN 50|50|CD ng|ng|NN total|total|JJ enriched|enriched|JJ mRNA|mrna|NN using|use|VBG Tetro|Tetro|NNP cDNA|cdna|NN synthesis|synthesis|NN kit|kit|NN from|from|IN Bioline|Bioline|NNP -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP BIO-65043|bio-65043|NN -RSB-|-rsb-|-RRB- and|and|CC 6|6|CD μl|μl|NN of|of|IN Random|Random|NNP Hexamers|Hexamers|NNPS -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP BIO-38028|bio-38028|NN -RSB-|-rsb-|-RRB- per|per|IN reaction|reaction|NN .|.|. Second|second|JJ cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD performed|perform|VBN adding|add|VBG to|to|TO the|the|DT first|first|JJ strand|strand|NN synthesis|synthesis|NN mix|mix|NN 5|5|CD μl|μl|NN of|of|IN Second|second|JJ strand|strand|NN synthesis|synthesis|NN buffer|buffer|NN -LSB-|-lsb-|-LRB- Cat|cat|NN No|no|DT B6117S|b6117s|NN -RSB-|-rsb-|-RRB- ,|,|, 3|3|CD μl|μl|NN of|of|IN dNTPs|dntps|NN -LSB-|-lsb-|-LRB- Cat|cat|NN No|no|DT N0446S|n0446s|NN -RSB-|-rsb-|-RRB- ,|,|, 2μl|2μl|NN of|of|IN RNAseH|rnaseh|NN -LSB-|-lsb-|-LRB- Cat|cat|NN No|no|DT M0297L|m0297l|NN -RSB-|-rsb-|-RRB- all|all|DT from|from|IN NEB|NEB|NNP ,|,|, 2|2|CD μl|μl|NN of|of|IN Polymerase|polymerase|NN I|I|PRP from|from|IN Thermo|Thermo|NNP Scientific|Scientific|NNP -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP 18010025|18010025|CD -RSB-|-rsb-|-RRB- and|and|CC 18|18|CD μl|μl|NN of|of|IN water|water|NN ,|,|, per|per|IN reaction|reaction|NN .|.|. Samples|sample|NNS were|be|VBD incubated|incubate|VBN at|at|IN 16|16|CD °C|°c|NN for|for|IN 2.5|2.5|CD h.|h.|NN Purification|purification|NN of|of|IN cDNA|cdna|NN was|be|VBD performed|perform|VBN using|use|VBG MiniElute|MiniElute|NNP PCR|pcr|NN purification|purification|NN kit|kit|NN -LSB-|-lsb-|-LRB- Cat|cat|NN No|no|DT 28004|28004|NN -RSB-|-rsb-|-RRB- with|with|IN final|final|JJ elution|elution|NN in|in|IN 10|10|CD μl|μl|NN of|of|IN DEPC-treated|depc-treated|JJ free|free|JJ water|water|NN .|.|. cDNA|cdna|NN was|be|VBD quantified|quantify|VBN using|use|VBG a|a|DT Qubit|qubit|NN fluorometer|fluorometer|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|.
17.1|17.1|CD A|a|DT
17.1|17.1|CD A|a|DT _|_|NN Space|space|NN _|_|CD 25|25|CD
17.2|17.2|CD A|a|DT
17.2|17.2|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 25|25|CD
172mM|172mm|NN SCFA|scfa|NN replicate|replicate|VBP 1|1|CD
172mM|172mm|NN SCFA|scfa|NN replicate|replicate|VBP 2|2|CD
17.3|17.3|CD A|a|DT
17.3|17.3|CD A|a|DT _|_|NN Space|space|NN _|_|CD 25|25|CD
17.4|17.4|CD A|a|DT
17.4|17.4|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 25|25|CD
17.5|17.5|CD A|a|DT
17.5|17.5|CD A|a|DT _|_|NN Space|space|NN _|_|CD 50|50|CD
17.6|17.6|CD A|a|DT
17.6|17.6|CD A|a|DT _|_|NN Space|space|NN _|_|CD 50|50|CD
17.8|17.8|CD A|a|DT
17.8|17.8|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 50|50|CD
1.7|1.7|CD A|a|DT
1.7|1.7|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 50|50|CD
17|17|CD .|.|. FHI27.nIND.HUS|fhi27.nind.hus|NN
17|17|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
18.2|18.2|CD A|a|DT
18.2|18.2|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 75|75|CD
18.3|18.3|CD A|a|DT
18.3|18.3|CD A|a|DT _|_|NN Space|space|NN _|_|CD 75|75|CD
18.4|18.4|CD A|a|DT
18.4|18.4|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 75|75|CD
18|18|CD .|.|. FHI27.IND.HUS|fhi27.ind.hus|NN
18|18|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
1.8|1.8|CD ml|ml|NN -LRB-|-lrb-|-LRB- ca.|ca.|FW 3E|3e|FW +9|+9|NN cells|cell|NNS -RRB-|-rrb-|-RRB- were|be|VBD pipetted|pipet|VBN into|into|IN 2.0|2.0|CD ml|ml|NN tubes|tube|NNS and|and|CC immediately|immediately|RB centrifuged|centrifuge|VBN at|at|IN
195|195|CD min|min|NN ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN
195min-1|195min-1|CD
195min-2|195min-2|JJ
195min-3|195min-3|JJ
195|195|CD min|min|NN ,|,|, unstressed|unstressed|JJ
19|19|CD .|.|. FHI36.nIND.nHUS|fhi36.nind.nhus|NN
19|19|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
1A|1a|NN 1y|1y|NN
1A|1a|NN 4y|4y|NN
1A|1a|NN _|_|CD MG|mg|NN _|_|NN t0|t0|NN
1A|1a|NN T0|t0|NN
1B|1b|NN _|_|CD MG|mg|NN _|_|NN t0|t0|NN
1-butanol|1-butanol|NN was|be|VBD added|add|VBN at|at|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.9|0.9|CD %|%|NN -LRB-|-lrb-|-LRB- vol/vol|vol/vol|NN -RRB-|-rrb-|-RRB- and|and|CC cells|cell|NNS were|be|VBD further|further|JJ incubated|incubate|VBN for|for|IN 30|30|CD min|min|NN .|.|.
1C|1c|NN _|_|CD MG|mg|NN _|_|NN t0|t0|NN
1|1|CD _|_|NN ESBL019|esbl019|NN Coliform|coliform|NN Repl|repl|NN 1|1|CD
1|1|CD .|.|. FHI4.nIND.HUS|fhi4.nind.hus|NN
1|1|CD _|_|SYM HF|hf|NNS _|_|VBP LP|lp|NN _|_|CD noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
1|1|CD .|.|. Holme|Holme|NNP T|t|NN ,|,|, Arvidson|Arvidson|NNP S|S|NNP ,|,|, Lindholm|Lindholm|NNP B|B|NNP ,|,|, and|and|CC Pavlu|Pavlu|NNP B.|B.|NNP 1970|1970|CD .|.|. Enzymes|enzyme|NNS :|:|: Laboratory-scale|laboratory-scale|JJ production|production|NN .|.|. Process|process|VB Biochemistry|Biochemistry|NNP 62-66|62-66|CD .|.|.
1|1|CD hour|hour|NN expression|expression|NN of|of|IN synthetic|synthetic|JJ protein|protein|NN DX|dx|NN in|in|IN E.|e.|FW coli|coli|FW
1-HT873-PA1|1-ht873-pa1|NN
1-HT873-PA1|1-ht873-pa1|NN -|-|:
1|1|CD .|.|. library|library|NN -LRB-|-lrb-|-LRB- maanova|maanova|NN -RRB-|-rrb-|-RRB-
1|1|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
1|1|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
1|1|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
1|1|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
1|1|CD ml|ml|NN aliquot|aliquot|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO pressure|pressure|VB vessel|vessel|NN and|and|CC pressurized|pressurize|VBD at|at|IN 1MPa|1mpa|NN for|for|IN 15|15|CD min|min|NN
1mL|1ml|NN aliquots|aliquot|NNS were|be|VBD harvested|harvest|VBN and|and|CC mixed|mix|VBN with|with|IN 0.5|0.5|CD mL|ml|NN Phenol/ethanol|phenol/ethanol|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- Phenol|phenol|NN in|in|IN EtOHabs|etohab|NNS -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN until|until|IN use|use|NN .|.|.
1|1|CD ml|ml|NN of|of|IN each|each|DT culture|culture|NN with|with|IN the|the|DT mycotoxin|mycotoxin|NN was|be|VBD centrifuged|centrifuge|VBN and|and|CC total|total|JJ RNA|rna|NN was|be|VBD prepared|prepare|VBN using|use|VBG Hybrid-RTM|hybrid-rtm|JJ kit|kit|NN -LRB-|-lrb-|-LRB- Gene|gene|NN All|all|DT ,|,|, Seoul|Seoul|NNP ,|,|, Korea|Korea|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocols|protocol|NNS .|.|. A|a|DT MICOBExpressTM|micobexpresstm|NN bacterial|bacterial|JJ mRNA|mrna|NN enrichment|enrichment|NN kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Texas|Texas|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO remove|remove|VB bacterial|bacterial|JJ rRNA|rrna|NN from|from|IN the|the|DT total|total|JJ RNA|rna|NN samples|sample|NNS .|.|.
1|1|CD ml|ml|NN of|of|IN overnight|overnight|JJ culture|culture|NN was|be|VBD prepared|prepare|VBN for|for|IN E.|e.|FW coli|coli|FW DY|dy|NN 330|330|CD GyrA-SPA|gyra-spa|NN or|or|CC E.|e.|FW coli|coli|FW DY|dy|NN 330|330|CD GyrA-SPA|gyra-spa|NN MuSGS|musgs|NN by|by|IN seeding|seed|VBG 2YT|2yt|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN antibiotics|antibiotic|NNS -LRB-|-lrb-|-LRB- kanamycin|kanamycin|NN 50|50|CD µg/ml|µg/ml|NN for|for|IN DY|dy|NN 330|330|CD GyrA-SPA|gyra-spa|NN and|and|CC kanamycin|kanamycin|NN 50|50|CD µg/ml|µg/ml|NN ,|,|, chloramphenicol|chloramphenicol|NN 15|15|CD µg/ml|µg/ml|NN for|for|IN DY|dy|NN 330|330|CD GyrA-SPA|gyra-spa|NN MuSGS|musgs|NN -RRB-|-rrb-|-RRB- with|with|IN cells|cell|NNS from|from|IN one|one|CD isolate|isolate|JJ colony|colony|NN .|.|.
1|1|CD ml|ml|NN of|of|IN VWPE|VWPE|NNP extract|extract|NN -LRB-|-lrb-|-LRB- 1|1|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD ml|ml|NN of|of|IN ethanol|ethanol|NN 20|20|CD %|%|NN and|and|CC 1|1|CD ml|ml|NN of|of|IN LB|lb|NN broth|broth|NN were|be|VBD added|add|VBN when|when|WRB the|the|DT OD600|od600|NN of|of|IN each|each|DT culture|culture|NN reached|reach|VBD 0.4|0.4|CD
1|1|CD .|.|. Neubauer|Neubauer|NNP ,|,|, A.|a.|NN ,|,|, J.|J.|NNP Soini|Soini|NNP ,|,|, M.|M.|NNP Bollok|Bollok|NNP ,|,|, M.|M.|NNP Zenker|Zenker|NNP ,|,|, J.|J.|NNP Sandqvist|Sandqvist|NNP ,|,|, J.|J.|NNP Myllyharju|Myllyharju|NNP ,|,|, and|and|CC P.|P.|NNP Neubauer|Neubauer|NNP .|.|. 2007|2007|CD .|.|. Fermentation|fermentation|NN process|process|NN for|for|IN tetrameric|tetrameric|JJ human|human|JJ collagen|collagen|NN prolyl|prolyl|JJ 4-hydroxylase|4-hydroxylase|NN in|in|IN Escherichia|escherichia|FW coli|coli|FW :|:|: improvement|improvement|NN by|by|IN gene|gene|NN optimisation|optimisation|NN of|of|IN the|the|DT PDI/beta|pdi/beta|NN subunit|subunit|NN and|and|CC repeated|repeat|VBN addition|addition|NN of|of|IN the|the|DT inducer|inducer|NN anhydrotetracycline|anhydrotetracycline|NN .|.|. J|J|NNP Biotechnol|Biotechnol|NNP 128:308-321|128:308-321|CD .|.|.
1|1|CD .|.|. Use|Use|NNP Agilent|Agilent|NNP software|software|NN Feature|Feature|NNP Extraction|Extraction|NNP to|to|TO analyze|analyze|VB spotted|spotted|JJ arrays|array|NNS .|.|.
2003|2003|CD ,|,|, PNAS|PNAS|NNP -RRB-|-rrb-|-RRB- .|.|. To|to|TO minimize|minimize|VB the|the|DT effect|effect|NN of|of|IN such|such|JJ contributions|contribution|NNS ,|,|, microarray|microarray|NN data|datum|NNS were|be|VBD
200|200|CD bp|bp|NN insert|insert|NN ,|,|, rRNA|rrna|NN depletion|depletion|NN
200µl|200µl|NN of|of|IN prepared|prepared|JJ E.coli|e.coli|NN O157|o157|NN cells|cell|NNS within|within|IN LB|lb|NN broth|broth|NN is|be|VBZ spreaded|spread|VBN to|to|TO LB|LB|NNP agar|agar|NN plate|plate|NN ,|,|, and|and|CC sterilized|sterilize|VBN 6|6|CD mm|mm|NN filtered|filter|VBD paper|paper|NN disk|disk|NN was|be|VBD placed|place|VBN on|on|IN the|the|DT plate|plate|NN tightly|tightly|RB ,|,|, where|where|WRB E.coli|e.coli|JJ O157|o157|NN is|be|VBZ spreaded|spread|VBN .|.|. Each|each|DT filtered|filter|VBN fractions|fraction|NNS are|be|VBP injected|inject|VBN to|to|TO each|each|DT paper|paper|NN disk|disk|NN and|and|CC Distilled|Distilled|NNP water|water|NN and|and|CC Ampicillin|ampicillin|NN were|be|VBD used|use|VBN as|as|IN negative|negative|JJ -|-|: and|and|CC positive|positive|JJ control|control|NN each|each|DT and|and|CC then|then|RB cultured|culture|VBN at|at|IN 37|37|CD ℃|℃|NN for|for|IN 24|24|CD hours|hour|NNS .|.|. Finally|finally|RB the|the|DT diameter|diameter|NN of|of|IN the|the|DT cleared|clear|VBN zone|zone|NN arisen|arise|VBN around|around|IN the|the|DT paper|paper|NN disk|disk|NN was|be|VBD measured|measure|VBN .|.|.
20|20|CD .|.|. FHI36.IND.nHUS|fhi36.ind.nhus|NN
20|20|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
20|20|CD min|min|NN after|after|IN UVtreatment|uvtreatment|NN 1|1|CD '|'|'' ,|,|, 40J|40j|NN ,|,|, MG1655|mg1655|NN in|in|IN Davis|Davis|NNP +0.4|+0.4|CD %|%|NN glu|glu|NN
20|20|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
20|20|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
20|20|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
20|20|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
20|20|CD min|min|NN Nov50|nov50|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
20|20|CD min|min|NN Nov50|nov50|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
20|20|CD min|min|NN untreatedcells|untreatedcell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
20|20|CD min|min|NN UV|uv|NN treated|treat|VBN cells|cell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
20|20|CD min|min|NN UVtreatment|uvtreatment|NN control|control|NN ,|,|, MG1655|mg1655|NN in|in|IN Davis|Davis|NNP +0.4|+0.4|CD %|%|NN glu|glu|NN
20|20|CD ug|ug|NN of|of|IN Total|total|JJ RNA|rna|NN from|from|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS OD|od|NN 600|600|CD =|=|JJ 0.8|0.8|CD
20|20|CD ug|ug|NN of|of|IN Total|total|JJ RNA|rna|NN from|from|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN at|at|IN 30|30|CD degrees|degree|NNS OD|od|NN 600|600|CD =|=|JJ 0.8|0.8|CD
2.1|2.1|CD A|a|DT
2.1|2.1|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 75|75|CD
21|21|CD .|.|. FHI43.nIND.nHUS|fhi43.nind.nhus|NN
22|22|CD .|.|. FHI43.IND.nHUS|fhi43.ind.nhus|NN
2.3|2.3|CD A|a|DT
23A1|23a1|NN
2.3|2.3|CD A|a|DT _|_|NN Earth|Earth|NNP _|_|SYM 75|75|CD
23B1|23b1|NN
23C3|23c3|NN
23|23|CD .|.|. FHI48.nIND.HUS|fhi48.nind.hus|NN
23S|23s|NN
240|240|CD minutes|minute|NNS growth|growth|NN in|in|IN LB|LB|NNP
2.4|2.4|CD A|a|DT
2.4|2.4|CD A|a|DT _|_|NN Space|space|NN _|_|CD 75|75|CD
252978410001|252978410001|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE001MS16|bce001ms16|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410001|252978410001|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE022DS6|bce022ds6|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410001|252978410001|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE063MS14|bce063ms14|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410001|252978410001|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM ETP98015|etp98015|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410002|252978410002|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE007|bce007|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410002|252978410002|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE041|bce041|NN _|_|CD MS11|ms11|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410002|252978410002|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE063|bce063|NN _|_|CD DS4|ds4|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410002|252978410002|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM ETP98028|etp98028|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410003|252978410003|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD C35662|c35662|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410003|252978410003|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 007|007|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410003|252978410003|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 017|017|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410003|252978410003|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98062|etp98062|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410004|252978410004|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE003|bce003|NN _|_|CD DS5|ds5|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410004|252978410004|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE058|bce058|NN _|_|CD MS13|ms13|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410004|252978410004|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE069|bce069|NN _|_|CD MS9|ms9|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410004|252978410004|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE129|bce129|NN _|_|CD DS2|ds2|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410005|252978410005|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE008|bce008|NN _|_|CD MS13|ms13|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410005|252978410005|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE013|bce013|NN _|_|CD DS1|ds1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410005|252978410005|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE035|bce035|NN _|_|CD MS8|ms8|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410005|252978410005|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE039|bce039|NN _|_|CD DS2|ds2|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410006|252978410006|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 012|012|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410006|252978410006|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 019|019|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410006|252978410006|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 026|026|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410006|252978410006|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 044|044|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410007|252978410007|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE002|bce002|NN _|_|CD MS12|ms12|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410007|252978410007|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE021|bce021|NN _|_|CD DS7|ds7|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410007|252978410007|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE049|bce049|NN _|_|CD MS9|ms9|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410007|252978410007|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98061|etp98061|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410008|252978410008|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 180050|180050|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410008|252978410008|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98103|etp98103|NN _|_|CD CY3.mev.refIsIB.ou|cy3.mev.refisib.ou|NN
252978410008|252978410008|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98111|etp98111|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410008|252978410008|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD TW03741|tw03741|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410009|252978410009|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1787|e1787|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410009|252978410009|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E747|e747|NN _|_|NN 0|0|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410009|252978410009|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD F595C|f595c|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410009|252978410009|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS3572A1.mev.refIsIB.out|ws3572a1.mev.refisib.out|NN
252978410010|252978410010|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN 229|229|CD _|_|NN 1|1|CD _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410010|252978410010|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p13|p13|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410010|252978410010|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p1|p1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410010|252978410010|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p4|p4|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410011|252978410011|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD DS26|ds26|NN _|_|NN 1|1|CD _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410011|252978410011|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1777|e1777|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410011|252978410011|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E9034A|e9034a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410011|252978410011|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD NN|NN|NNP _|_|SYM 34|34|CD _|_|NN 1|1|CD _|_|NN 3|3|CD _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410012|252978410012|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN 42|42|CD _|_|NN 1|1|CD _|_|NN C1|c1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410012|252978410012|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETEC|ETEC|NNP _|_|SYM 18|18|CD _|_|NN 2|2|CD _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410012|252978410012|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p12|p12|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410012|252978410012|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD LSN02|lsn02|NN _|_|CD 012560|012560|CD _|_|NN A|a|DT _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410013|252978410013|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 180600|180600|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410013|252978410013|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM ETEC|etec|NNS _|_|VBP 10|10|CD _|_|SYM 1|1|CD _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410013|252978410013|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD TW3574|tw3574|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410013|252978410013|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN TW3585|tw3585|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410014|252978410014|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E20738A|e20738a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410014|252978410014|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD PUTI|PUTI|NNP _|_|SYM O26|o26|CD _|_|SYM UMN|UMN|NNP _|_|SYM O26|o26|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410014|252978410014|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH450|sprh450|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410015|252978410015|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1392|e1392|NN _|_|CD 75|75|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410015|252978410015|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p5|p5|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410015|252978410015|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p8|p8|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410015|252978410015|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH613|sprh613|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410016|252978410016|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD D02|d02|NN _|_|NN 2|2|CD _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410016|252978410016|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN E1785|e1785|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410016|252978410016|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM ETP98068|etp98068|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410016|252978410016|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p11|p11|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410017|252978410017|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN C35776|c35776|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410017|252978410017|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1788|e1788|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410017|252978410017|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETEC|ETEC|NNP _|_|NNP JURUA|JURUA|NNP _|_|VBD 18|18|CD _|_|SYM 11|11|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410017|252978410017|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p9|p9|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410018|252978410018|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ARG3|arg3|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410018|252978410018|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1792|e1792|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410018|252978410018|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN MG1655|mg1655|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410018|252978410018|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH21|sprh21|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410019|252978410019|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1786|e1786|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410019|252978410019|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS0115A|ws0115a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410020|252978410020|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 179550|179550|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410020|252978410020|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE046|bce046|NN _|_|CD DS2|ds2|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410020|252978410020|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE046|bce046|NN _|_|CD DS7|ds7|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410020|252978410020|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98114|etp98114|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410021|252978410021|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 1080200|1080200|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410021|252978410021|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE008|bce008|NN _|_|CD MS1|ms1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410021|252978410021|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE054|bce054|NN _|_|CD MS24|ms24|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410021|252978410021|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 046|046|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410022|252978410022|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE062|bce062|NN _|_|CD DS2|ds2|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410022|252978410022|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE069|bce069|NN _|_|CD DS2|ds2|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410022|252978410022|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM ETP98038|etp98038|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410022|252978410022|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98042|etp98042|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410023|252978410023|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 173150|173150|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410023|252978410023|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 174750|174750|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410023|252978410023|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 178850|178850|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410023|252978410023|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM ETP98115|etp98115|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410024|252978410024|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE018|bce018|NN _|_|CD DS6|ds6|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410024|252978410024|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE019|bce019|NN _|_|CD MS16|ms16|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410024|252978410024|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE046|bce046|NN _|_|CD MS16|ms16|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410024|252978410024|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE069|bce069|NN _|_|CD MS15|ms15|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410025|252978410025|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE007|bce007|NN _|_|CD MS11|ms11|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410025|252978410025|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE039|bce039|NN _|_|CD MS13|ms13|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410025|252978410025|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN C35959|c35959|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410025|252978410025|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 050|050|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410026|252978410026|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E24377A|e24377a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410026|252978410026|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH|sprh|NN _|_|NN 418|418|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410026|252978410026|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS1896A|ws1896a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410026|252978410026|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS2068A|ws2068a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410027|252978410027|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD LSN03|lsn03|NN _|_|SYM 016011|016011|CD _|_|CD A|a|DT _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410027|252978410027|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH|sprh|NN _|_|NN 414|414|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410027|252978410027|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH|sprh|NN _|_|NN 420|420|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410027|252978410027|CD _|_|NN B7A|b7a|NN _|_|CD ETEC20|etec20|NN _|_|SYM 10|10|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410028|252978410028|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98073|etp98073|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410028|252978410028|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD TW3439|tw3439|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410028|252978410028|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD TW3576|tw3576|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410028|252978410028|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS3080A|ws3080a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410029|252978410029|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH|sprh|NN _|_|NN 403|403|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410029|252978410029|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH|sprh|NN _|_|NN 443|443|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410029|252978410029|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH|sprh|NN _|_|NN 604|604|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410029|252978410029|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH|sprh|NN _|_|NN 606|606|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410030|252978410030|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN C36255|c36255|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410030|252978410030|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 008|008|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410030|252978410030|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98105|etp98105|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410030|252978410030|CD _|_|NN B7A|b7a|NN _|_|CD ETP98066|etp98066|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410031|252978410031|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE054|bce054|NN _|_|CD DS4|ds4|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410031|252978410031|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE068|bce068|NN _|_|CD MS10|ms10|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410031|252978410031|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE068|bce068|NN _|_|CD MS23.mev.refIsIB.out|ms23.mev.refisib.out|NN
252978410031|252978410031|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 015|015|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410032|252978410032|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE011|bce011|NN _|_|CD DS3|ds3|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410032|252978410032|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE049|bce049|NN _|_|CD DS3|ds3|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410032|252978410032|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE062|bce062|NN _|_|CD MS24|ms24|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410032|252978410032|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE066|bce066|NN _|_|CD DS5|ds5|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410033|252978410033|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE035|bce035|NN _|_|CD DS6|ds6|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410033|252978410033|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN C35209|c35209|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410033|252978410033|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP|etp|NN _|_|SYM 98004|98004|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410033|252978410033|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98056|etp98056|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410034|252978410034|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE005|bce005|NN _|_|CD MS23|ms23|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410034|252978410034|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD BCE061|bce061|NN _|_|CD DS1|ds1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410034|252978410034|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 038|038|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410034|252978410034|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98053|etp98053|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410035|252978410035|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN BCE055|bce055|NN _|_|CD DS1|ds1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410035|252978410035|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 016|016|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410035|252978410035|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 020|020|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410035|252978410035|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 039|039|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410058|252978410058|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 178900|178900|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410058|252978410058|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 179100|179100|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410058|252978410058|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 009|009|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410058|252978410058|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 010|010|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410059|252978410059|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN 532|532|CD _|_|NN WS6866B1|ws6866b1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410059|252978410059|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 047|047|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410059|252978410059|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98097|etp98097|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410059|252978410059|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98112|etp98112|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410060|252978410060|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ARG2|arg2|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410060|252978410060|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD C35134|c35134|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410060|252978410060|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1791|e1791|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410060|252978410060|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN WS3596|ws3596|NN _|_|CD A4|a4|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410061|252978410061|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM COCAR07|cocar07|CD _|_|SYM 40|40|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410061|252978410061|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM COSIN07|cosin07|CD _|_|SYM 88|88|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410061|252978410061|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM COSIN07|cosin07|CD _|_|SYM 92|92|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410062|252978410062|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD DS168|ds168|NN _|_|NN 1|1|CD _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410062|252978410062|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD PE360|pe360|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410062|252978410062|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS4087|ws4087|NN _|_|CD A1|a1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410062|252978410062|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN WS7179|ws7179|NN _|_|CD A2|a2|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410063|252978410063|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD B7A|b7a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410063|252978410063|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM COSIN07|cosin07|CD _|_|SYM 14|14|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410063|252978410063|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH372|sprh372|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410063|252978410063|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD TW3452|tw3452|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410064|252978410064|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1789|e1789|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410064|252978410064|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E1790|e1790|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410064|252978410064|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD HS|hs|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410064|252978410064|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH609|sprh609|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410065|252978410065|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN 350C1A|350c1a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410065|252978410065|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E2528|e2528|NN _|_|CD C1|c1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410065|252978410065|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E8775|e8775|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410065|252978410065|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD M424|m424|NN _|_|CD C1|c1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410066|252978410066|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 2230|2230|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410066|252978410066|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|CD P|p|NN _|_|NN 2|2|CD _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410066|252978410066|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS1933D|ws1933d|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410066|252978410066|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS6582|ws6582|NN _|_|CD A1|a1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410067|252978410067|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD B2C|b2c|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410067|252978410067|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM ETEC|etec|NNS _|_|VBP 8|8|CD _|_|SYM 11|11|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410067|252978410067|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD F5656|f5656|NN _|_|CD C1|c1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410067|252978410067|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS7162|ws7162|NN _|_|CD A1|a1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410068|252978410068|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN CFT073|cft073|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410068|252978410068|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p|p|NN _|_|SYM 10|10|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410068|252978410068|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD M408C1|m408c1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410068|252978410068|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS3294A|ws3294a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410069|252978410069|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD 278485|278485|CD _|_|NN 1|1|CD _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410069|252978410069|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH25|sprh25|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410069|252978410069|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH421|sprh421|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410069|252978410069|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH610|sprh610|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410070|252978410070|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p7|p7|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410070|252978410070|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD NR|nr|NN _|_|SYM 12|12|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410070|252978410070|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH20|sprh20|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410070|252978410070|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH612|sprh612|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410071|252978410071|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN 292|292|CD _|_|NN 1|1|CD _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410071|252978410071|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD COCAR07|cocar07|NN _|_|NN 043|043|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410071|252978410071|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM COSIN07|cosin07|CD _|_|SYM 61|61|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410071|252978410071|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD O157|o157|NN _|_|CD h7|h7|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410072|252978410072|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM COSIN07|cosin07|CD _|_|SYM 36|36|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410072|252978410072|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ICDDR|icddr|NN _|_|NN B|b|NN _|_|CD p6|p6|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410072|252978410072|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD O63|o63|NN _|_|CD nm|nm|NN _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410072|252978410072|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH605|sprh605|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410073|252978410073|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN 214|214|CD _|_|NN 4|4|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410073|252978410073|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD E7476A|e7476a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410073|252978410073|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN WS1896|ws1896|NN _|_|CD A1|a1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410073|252978410073|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS2173A|ws2173a|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410075|252978410075|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 011|011|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410075|252978410075|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 035|035|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410075|252978410075|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM O78|o78|CD _|_|CD h11|h11|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410075|252978410075|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD sPRH445|sprh445|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410076|252978410076|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 178200|178200|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410076|252978410076|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN C35213|c35213|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410076|252978410076|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN C35605|c35605|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410076|252978410076|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP98109|etp98109|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410077|252978410077|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|SYM 174900|174900|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410077|252978410077|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN C34666|c34666|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410077|252978410077|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 002|002|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410077|252978410077|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD ETP05|etp05|NN _|_|NN 003|003|CD _|_|SYM CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410078|252978410078|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|NN 2|2|CD _|_|NN 1|1|CD _|_|NN CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410078|252978410078|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS2741|ws2741|NN _|_|CD A1|a1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410078|252978410078|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS4264|ws4264|NN _|_|CD A1|a1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
252978410078|252978410078|CD _|_|NN B7A|b7a|NN _|_|CD CY5|cy5|NN _|_|CD WS5874|ws5874|NN _|_|CD A1|a1|NN _|_|CD CY3.mev.refIsIB.out|cy3.mev.refisib.out|NN
25|25|CD .|.|. FHI79.nIND.HUS|fhi79.nind.hus|NN
25|25|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
26|26|CD .|.|. FHI79.IND.HUS|fhi79.ind.hus|NN
26|26|CD %|%|NN rep1|rep1|NN
26|26|CD %|%|NN rep2|rep2|NN
27|27|CD .|.|. FHI95.nIND.nHUS|fhi95.nind.nhus|NN
285c/control|285c/control|NN vector|vector|NN at|at|IN 30|30|CD C|c|NN 1|1|CD
285c/control|285c/control|NN vector|vector|NN at|at|IN 30|30|CD C|c|NN 2|2|CD
285c/control|285c/control|NN vector|vector|NN at|at|IN 30|30|CD C|c|NN 3|3|CD
28|28|CD .|.|. FHI95.IND.nHUS|fhi95.ind.nhus|NN
29|29|CD .|.|. St.|St.|NNP Olav40.nIND.nHUS|Olav40.nIND.nHUS|NNP
2A|2a|NN 1y|1y|NN
2A|2a|NN 4y|4y|NN
2A|2a|NN _|_|CD MG|mg|NN _|_|NN t10|t10|NN
2B|2b|NN _|_|CD MG|mg|NN _|_|NN t10|t10|NN
2C|2c|NN _|_|CD MG|mg|NN _|_|NN t10|t10|NN
2|2|CD _|_|CD ESBL019|esbl019|NN Filamented|Filamented|NNP Repl|Repl|NNP 1|1|CD
2|2|CD .|.|. FHI4.IND.HUS|fhi4.ind.hus|NN
2|2|CD _|_|SYM HF|hf|NNS _|_|VBP LP|lp|NN _|_|CD noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
2|2|CD hour|hour|NN expression|expression|NN of|of|IN synthetic|synthetic|JJ protein|protein|NN DX|dx|NN in|in|IN E.|e.|FW coli|coli|FW
2-HT873-PA2|2-ht873-pa2|NN
2-HT873-PA2|2-ht873-pa2|NN -|-|:
2|2|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
2|2|CD min|min|NN Nov10|nov10|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Sau3AI|sau3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
2|2|CD min|min|NN Nov10|nov10|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
2|2|CD min|min|NN Nov2|nov2|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
2|2|CD min|min|NN Nov2|nov2|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
2|2|CD min|min|NN Nov5|nov5|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
2|2|CD min|min|NN Nov5|nov5|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
2|2|CD ppm|ppm|NN deoxynivalenol|deoxynivalenol|NN
2|2|CD ppm|ppm|NN nivalenol|nivalenol|NN
2|2|CD .|.|. Read|Read|NNP data|datum|NNS :|:|:
2|2|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD C|c|NN
2|2|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN A|a|NN
2|2|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN B|b|NN
2|2|CD ug|ug|NN of|of|IN Genomic|genomic|JJ MG|mg|NN 1655|1655|CD -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- DNA|dna|NN
2|2|CD ug|ug|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- Genomic|genomic|JJ DNA|dna|NN
2|2|CD .|.|. Use|use|NN TM4|tm4|NN suite|suite|NN software|software|NN ExpressConverter|expressconverter|NN to|to|TO modify|modify|VB Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP file|file|NN into|into|IN *|*|NN .|.|. mev|mev|NN .|.|.
2xOriT|2xorit|NN
2|2|CD μg|μg|NN of|of|IN RNA|rna|NN from|from|IN the|the|DT cytoplasmic|cytoplasmic|JJ fraction|fraction|NN were|be|VBD diluted|dilute|VBN in|in|IN 20|20|CD μl|μl|NN of|of|IN Fragmentation|fragmentation|NN buffer|buffer|NN ,|,|, and|and|CC fragmented|fragmented|JJ by|by|IN incubation|incubation|NN at|at|IN 95|95|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS .|.|. Fragmented|fragmented|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS .|.|. End|end|NN repair|repair|NN of|of|IN RNA|rna|NN fragments|fragment|NNS was|be|VBD performed|perform|VBN in|in|IN a|a|DT final|final|JJ volume|volume|NN of|of|IN 20|20|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 20|20|CD U|U|NNP T4|t4|NN Polynucleotide|Polynucleotide|NNP Kinase|kinase|NN -LRB-|-lrb-|-LRB- NEB|neb|NN ,|,|, cat|cat|NN .|.|. M0201L|m0201l|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC 20|20|CD U|U|NNP SUPERase|SUPERase|NNP •|•|SYM In|in|IN ™|™|CD RNase|rnase|NN Inhibitor|inhibitor|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN for|for|IN 1|1|CD hour|hour|NN .|.|. End-repaired|end-repaired|JJ RNA|rna|NN was|be|VBD purified|purify|VBN again|again|RB using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC eluted|elute|VBN in|in|IN 6|6|CD μl|μl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN .|.|. 6|6|CD μl|μl|NN of|of|IN 2X|2x|NN RNA|rna|NN Loading|load|VBG Dye|dye|NN were|be|VBD added|add|VBN to|to|TO end-repaired|end-repaired|JJ RNA|rna|NN .|.|. RNA|rna|NN was|be|VBD heated|heat|VBN to|to|TO 95|95|CD °C|°c|NN for|for|IN 2|2|CD minutes|minute|NNS ,|,|, and|and|CC immediately|immediately|RB placed|place|VBN on|on|IN ice|ice|NN .|.|. Samples|sample|NNS were|be|VBD resolved|resolve|VBN on|on|IN a|a|DT 10|10|CD %|%|NN TBE-Urea|tbe-urea|NN polyacrylamide|polyacrylamide|NN gel|gel|NN ,|,|, and|and|CC a|a|DT gel|gel|NN slice|slice|NN corresponding|correspond|VBG to|to|TO fragments|fragment|NNS above|above|IN 200|200|CD nt|nt|NNS was|be|VBD cut|cut|VBN .|.|. The|the|DT gel|gel|NN slice|slice|NN was|be|VBD crushed|crush|VBN by|by|IN centrifugation|centrifugation|NN through|through|IN a|a|DT punctured|punctured|JJ 0.5|0.5|CD ml|ml|NN tube|tube|NN ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 500|500|CD μl|μl|NN of|of|IN Diffusion|Diffusion|NNP buffer|buffer|NN supplemented|supplement|VBN with|with|IN 60|60|CD U|U|NNP SUPERase|SUPERase|NNP •|•|SYM In|in|IN ™|™|CD RNase|rnase|NN Inhibitor|inhibitor|NN ,|,|, then|then|RB rotated|rotate|VBD at|at|IN 4|4|CD °C|°c|NN for|for|IN 16|16|CD hours|hour|NNS to|to|TO allow|allow|VB passive|passive|JJ diffusion|diffusion|NN of|of|IN RNA|rna|NN fragments|fragment|NNS into|into|IN buffer|buffer|NN .|.|. RNA|rna|NN was|be|VBD precipitated|precipitate|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD ml|ml|NN Isopropanol|isopropanol|NN ,|,|, and|and|CC 2|2|CD μl|μl|NN Glycogen|glycogen|NN -LRB-|-lrb-|-LRB- 20|20|CD μg/μl|μg/μl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 6|6|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. 10|10|CD pmol|pmol|NN of|of|IN a|a|DT pre-adenylated|pre-adenylated|JJ -LRB-|-lrb-|-LRB- rApp|rapp|NN -RRB-|-rrb-|-RRB- adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO size-selected|size-selected|JJ RNA|rna|NN fragments|fragment|NNS in|in|IN a|a|DT reaction|reaction|NN volume|volume|NN of|of|IN 20|20|CD μl|μl|NN ,|,|, using|use|VBG 400|400|CD U|U|NNP T4|t4|NN RNA|rna|NN Ligase|ligase|NN 2|2|CD ,|,|, Deletion|deletion|NN Mutant|mutant|JJ in|in|IN the|the|DT presence|presence|NN of|of|IN 20|20|CD %|%|NN PEG-8000|peg-8000|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 25|25|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC RNA|rna|NN was|be|VBD eluted|elute|VBN in|in|IN 5.5|5.5|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. RNA|rna|NN was|be|VBD heat-denatured|heat-denatured|JJ at|at|IN 70|70|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS ,|,|, and|and|CC reverse|reverse|JJ transcription|transcription|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN a|a|DT final|final|JJ volume|volume|NN of|of|IN 10|10|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.5|0.5|CD mM|mm|NN dNTPs|dntp|NNS ,|,|, 5|5|CD pmol|pmol|NN of|of|IN RT|rt|NN primer|primer|NN ,|,|, 20|20|CD U|U|NNP RNaseOUT|RNaseOUT|NNP ™|™|NNP Recombinant|recombinant|JJ Ribonuclease|ribonuclease|NN Inhibitor|inhibitor|NN ,|,|, and|and|CC 100|100|CD U|U|NNP SuperScript|SuperScript|NNP ®|®|SYM III|iii|CD Reverse|reverse|JJ Transcriptase|transcriptase|NN ,|,|, by|by|IN incubation|incubation|NN at|at|IN 50|50|CD °C|°c|NN for|for|IN 50|50|CD minutes|minute|NNS .|.|. Template|template|NN RNA|rna|NN was|be|VBD degraded|degrade|VBN by|by|IN adding|add|VBG 1|1|CD μl|μl|NN of|of|IN 1|1|CD M|m|NN NaOH|naoh|NN ,|,|, and|and|CC incubating|incubate|VBG at|at|IN 95|95|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS .|.|. Reaction|reaction|NN clean-up|clean-up|JJ was|be|VBD performed|perform|VBN using|use|VBG RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS ,|,|, and|and|CC cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 6|6|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. cDNA|cdna|NN fragments|fragment|NNS were|be|VBD resolved|resolve|VBN on|on|IN a|a|DT 10|10|CD %|%|NN TBE-Urea|tbe-urea|NN polyacrylamide|polyacrylamide|NN gel|gel|NN ,|,|, and|and|CC a|a|DT gel|gel|NN slice|slice|NN corresponding|correspond|VBG to|to|TO fragments|fragment|NNS in|in|IN the|the|DT range|range|NN of|of|IN 40-150|40-150|CD nt|nt|NNS was|be|VBD cut|cut|VBN -LRB-|-lrb-|-LRB- corresponding|correspond|VBG to|to|TO truncated|truncate|VBN cDNA|cdna|NN products|product|NNS -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN was|be|VBD recovered|recover|VBN by|by|IN passive|passive|NN diffusion|diffusion|NN in|in|IN Diffusion|Diffusion|NNP buffer|buffer|NN for|for|IN 16|16|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN with|with|IN moderate|moderate|JJ shaking|shake|VBG .|.|. cDNA|cdna|NN was|be|VBD precipitated|precipitate|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD ml|ml|NN Isopropanol|isopropanol|NN ,|,|, and|and|CC 2|2|CD μl|μl|NN Glycogen|glycogen|NN -LRB-|-lrb-|-LRB- 20|20|CD μg/μl|μg/μl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 8.25|8.25|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|. 10|10|CD pmol|pmol|NN of|of|IN a|a|DT 5|5|CD '|'|'' -|-|: phosphorilated|phosphorilate|VBN adapter|adapter|NN were|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 3|3|CD '|'|'' -|-|: OH|oh|NN of|of|IN cDNA|cdna|NN fragments|fragment|NNS in|in|IN a|a|DT final|final|JJ reaction|reaction|NN volume|volume|NN of|of|IN 25|25|CD μl|μl|NN ,|,|, in|in|IN the|the|DT presence|presence|NN of|of|IN 0.05|0.05|CD mM|mm|NN ATP|atp|NN ,|,|, 20|20|CD %|%|NN PEG-4000|peg-4000|NN ,|,|, and|and|CC 100|100|CD U|U|NNP CircLigase|CircLigase|NNP ™|™|NNP II|II|NNP ssDNA|ssDNA|NNP Ligase|Ligase|NNP ,|,|, by|by|IN incubation|incubation|NN at|at|IN 60|60|CD °C|°c|NN for|for|IN 4|4|CD hours|hour|NNS ,|,|, and|and|CC 68|68|CD °C|°c|NN for|for|IN 2|2|CD hours|hour|NNS .|.|. Adapter-ligated|adapter-ligated|JJ cDNA|cdna|NN fragments|fragment|NNS were|be|VBD purified|purify|VBN from|from|IN excess|excess|JJ adapter|adapter|NN using|use|VBG 1.8|1.8|CD volumes|volume|NNS of|of|IN Agencourt|Agencourt|NNP AMPure|AMPure|NNP XP|xp|NN beads|bead|NNS ,|,|, following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. cDNA|cdna|NN was|be|VBD eluted|elute|VBN in|in|IN 20|20|CD μl|μl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN ,|,|, and|and|CC indexed|index|VBD sequencing|sequencing|NN adapters|adapter|NNS were|be|VBD introduced|introduce|VBN by|by|IN 15|15|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN in|in|IN the|the|DT presence|presence|NN of|of|IN 25|25|CD pmol|pmol|NN of|of|IN each|each|DT primer|primer|NN ,|,|, and|and|CC 25|25|CD μl|μl|NN NEBNext|nebnext|NN ®|®|CD High-Fidelity|high-fidelity|NN 2X|2x|NN PCR|pcr|NN Master|master|NN Mix|Mix|NNP .|.|.
30|30|CD '|'|'' 10|10|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
30|30|CD '|'|'' 15|15|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
30|30|CD '|'|'' +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN vs|vs|CC 0|0|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN
30|30|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
30|30|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN ,25|,25|CD ug|ug|NN tot|tot|NN RNA|rna|NN
30|30|CD min|min|NN
30|30|CD min|min|NN ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN
30min-1|30min-1|JJ
30min-2|30min-2|JJ
30min-3|30min-3|JJ
30|30|CD min|min|NN minus|minus|CC ciprofloxacin|ciprofloxacin|NN
30|30|CD min|min|NN plus|plus|CC ciprofloxacin|ciprofloxacin|NN
30|30|CD min|min|NN ,|,|, unstressed|unstressed|JJ
30mM|30mm|NN SCFA|scfa|NN replicate|replicate|VBP 1|1|CD
30mM|30mm|NN SCFA|scfa|NN replicate|replicate|VBP 2|2|CD
30mM|30mm|NN SCFA|scfa|NN replicate|replicate|VBP 3|3|CD
30mM|30mm|NN SCFA|scfa|NN replicate|replicate|VB 4|4|CD
30|30|CD '|'|'' vs|vs|CC 0|0|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN
31|31|CD .|.|. St.|St.|NNP Olav104.nIND.nHUS|olav104.nind.nhus|JJ
32D|32d|NN
32|32|CD .|.|. St.|St.|NNP Olav104.IND.nHUS|olav104.ind.nhus|JJ
33D|33d|NN
33|33|CD .|.|. St.|St.|NNP Olav157.nIND.nHUS|Olav157.nIND.nHUS|NNP
34|34|CD .|.|. St.|St.|NNP Olav157.IND.nHUS|Olav157.IND.nHUS|NNP
35381|35381|CD _|_|SYM 1|1|CD
35382|35382|CD _|_|NN 2|2|CD
35B|35b|NN
3.5|3.5|CD hour|hour|NN expression|expression|NN of|of|IN synthetic|synthetic|JJ protein|protein|NN DX|dx|NN in|in|IN E.|e.|FW coli|coli|FW
35|35|CD .|.|. St.|St.|NNP Olav172.nIND.nHUS|olav172.nind.nhus|JJ
360|360|CD minutes|minute|NNS growth|growth|NN in|in|IN LB|LB|NNP
37|37|CD .|.|. St.|St.|NNP Olav174.nIND.nHUS|Olav174.nIND.nHUS|NNP
38|38|CD .|.|. St.|St.|NNP Olav174.IND.nHUS|Olav174.IND.nHUS|NNP
39A1|39a1|NN
39B1|39b1|NN
39C1|39c1|NN
39|39|CD .|.|. St.|St.|NNP Olav178.nIND.nHUS|Olav178.nIND.nHUS|NNP
3A|3a|NN 1m|1m|NN
3A|3a|NN 1y|1y|NN
3A|3a|NN 4y|4y|NN
3a|3a|NN -RRB-|-rrb-|-RRB- .|.|. If|if|IN both|both|DT channels|channel|NNS -LRB-|-lrb-|-LRB- QUERY|query|NN _|_|CD MEDIAN|MEDIAN|NNP _|_|CD INTENSITY|intensity|NN and|and|CC REF|ref|NN _|_|CD MEDIAN|MEDIAN|NNP _|_|CD INTENSITY|intensity|NN -RRB-|-rrb-|-RRB- are|be|VBP zero|zero|CD ,|,|, assign|assign|VBP the|the|DT value|value|NN \|\|CD
3A|3a|NN _|_|CD MG|mg|NN _|_|NN t30|t30|NN
3b|3b|NN -RRB-|-rrb-|-RRB- .|.|. If|if|IN one|one|CD channel|channel|NN is|be|VBZ zero|zero|CD and|and|CC the|the|DT other|other|JJ is|be|VBZ not|not|RB zero|zero|CD ,|,|, substitute|substitute|VB the|the|DT zero|zero|CD with|with|IN one|one|CD -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- and|and|CC then|then|RB ,|,|, assign|assign|VB the|the|DT log2|log2|NN ratio|ratio|NN of|of|IN QUERY|QUERY|NNP _|_|NNP MEDIAN|MEDIAN|NNP _|_|SYM INTENSITY/REF|intensity/ref|NN _|_|CD MEDIAN|MEDIAN|NNP _|_|CD INTENSITY|intensity|NN to|to|TO VALUE|VALUE|NNP
3B|3b|NN _|_|CD MG|mg|NN _|_|NN t30|t30|NN
3|3|CD .|.|. Calculate|calculate|VB the|the|DT value|value|NN of|of|IN log2|log2|NN ratio|ratio|NN -LRB-|-lrb-|-LRB- Reference/Query|reference/query|NN -RRB-|-rrb-|-RRB- from|from|IN the|the|DT normalized|normalize|VBN .|.|. mev|mev|NN file|file|NN :|:|:
3c|3c|NN -RRB-|-rrb-|-RRB- .|.|. If|if|IN neither|neither|DT channel|channel|NN is|be|VBZ zero|zero|CD ,|,|, assign|assign|VB the|the|DT log2|log2|NN ratio|ratio|NN of|of|IN QUERY|QUERY|NNP _|_|NNP MEDIAN|MEDIAN|NNP _|_|SYM INTENSITY/REF|intensity/ref|NN _|_|CD MEDIAN|MEDIAN|NNP _|_|CD INTENSITY|intensity|NN to|to|TO VALUE|VALUE|NNP .|.|.
3C|3c|NN _|_|CD MG|mg|NN _|_|NN t30|t30|NN
3C-seq|3c-seq|NN :|:|: 5|5|CD µg|µg|NN of|of|IN a|a|DT 3C|3c|NN library|library|NN was|be|VBD suspended|suspend|VBN in|in|IN water|water|NN -LRB-|-lrb-|-LRB- final|final|JJ volume|volume|NN 130|130|CD µL|µl|NN -RRB-|-rrb-|-RRB- and|and|CC sheared|shear|VBD using|use|VBG a|a|DT Covaris|Covaris|NNP S220|s220|NN instrument|instrument|NN -LRB-|-lrb-|-LRB- Duty|duty|NN cycle|cycle|NN 5|5|CD ,|,|, Intensity|intensity|NN 5|5|CD ,|,|, cycles/burst|cycles/burst|NN 200|200|CD ,|,|, time|time|NN 60|60|CD sec|sec|NN for|for|IN 4|4|CD cycles|cycle|NNS -RRB-|-rrb-|-RRB- .|.|. The|the|DT DNA|dna|NN was|be|VBD purified|purify|VBN and|and|CC processed|process|VBN according|accord|VBG to|to|TO manufacturer|manufacturer|NN instructions|instruction|NNS -LRB-|-lrb-|-LRB- Paired-End|paired-end|NN DNA|dna|NN sample|sample|NN Prep|Prep|NNP Kit|kit|NN --|--|: Illumina|Illumina|NNP --|--|: PE-930-1001|pe-930-1001|NN -RRB-|-rrb-|-RRB- ,|,|, except|except|IN that|that|DT DNA|dna|NN was|be|VBD ligated|ligate|VBN to|to|TO custom-made|custom-made|JJ adapters|adapter|NNS -LRB-|-lrb-|-LRB- see|see|VB Marbouty|Marbouty|NNP M.|M.|NNP et|et|NNP al|al|NNP ,|,|, 2015|2015|CD ,|,|, Mol|Mol|NNP Cell|cell|NN -RRB-|-rrb-|-RRB- for|for|IN 4|4|CD hours|hour|NNS at|at|IN room|room|NN temperature|temperature|NN .|.|. Tubes|tube|NNS were|be|VBD then|then|RB incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 20|20|CD minutes|minute|NNS .|.|. DNA|dna|NN fragments|fragment|NNS ranging|range|VBG in|in|IN size|size|NN from|from|IN 400|400|CD to|to|TO 900|900|CD pb|pb|NN were|be|VBD purified|purify|VBN using|use|VBG a|a|DT PippinPrep|PippinPrep|NNP apparatus|apparatus|NN -LRB-|-lrb-|-LRB- SAGE|sage|NN Science|science|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN each|each|DT library|library|NN ,|,|, four|four|CD test|test|NN PCR|pcr|NN reactions|reaction|NNS were|be|VBD performed|perform|VBN to|to|TO determine|determine|VB the|the|DT optimal|optimal|JJ number|number|NN of|of|IN PCR|pcr|NN cycles|cycle|NNS -LRB-|-lrb-|-LRB- 1|1|CD or|or|CC 2|2|CD µL|µl|NN of|of|IN the|the|DT collected|collect|VBN DNA|dna|NN ,|,|, Illumina|Illumina|NNP primers|primer|NNS PE1|pe1|NN .0|.0|NN and|and|CC PE2|pe2|NN .0|.0|CD using|use|VBG Taq|taq|NN Phusion|phusion|NN -LSB-|-lsb-|-LRB- Finnzymes|finnzyme|NNS -RSB-|-rsb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. A|a|DT large-scale|large-scale|JJ PCR|pcr|NN -LRB-|-lrb-|-LRB- 8|8|CD reactions|reaction|NNS -RRB-|-rrb-|-RRB- was|be|VBD then|then|RB set-up|set-up|JJ with|with|IN the|the|DT number|number|NN of|of|IN PCR|pcr|NN cycles|cycle|NNS determined|determine|VBN previously|previously|RB .|.|. The|the|DT PCR|pcr|NN product|product|NN was|be|VBD finally|finally|RB purified|purify|VBN on|on|IN Qiagen|Qiagen|NNP MinElute|MinElute|NNP columns|column|NNS and|and|CC subject|subject|JJ to|to|TO paired-end|paired-end|NN sequenced|sequence|VBN on|on|IN an|a|DT Illumina|Illumina|NNP sequencer|sequencer|NN .|.|.
3C-seq|3c-seq|NN libraries|library|NNS were|be|VBD proccessed|proccess|VBN using|use|VBG the|the|DT 3C-seq|3c-seq|JJ pipeline|pipeline|NN available|available|JJ at|at|IN -LRB-|-lrb-|-LRB- https://github.com/koszullab/|https://github.com/koszullab/|NN -RRB-|-rrb-|-RRB- .|.|.
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW fis|fis|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW fis|fis|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW hns|hns|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW hns|hns|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW hupAB|hupab|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 37|37|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW hupAB|hupab|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 37|37|CD °C|°c|SYM -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW matP|matp|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 22|22|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW matP|matp|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW matP|matp|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW matPDC20|matpdc20|NN cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2-5xmatS|pgbm2-5xmats|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW matPDC20|matpdc20|NN cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2|pgbm2|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW matPDC20|matpdc20|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW mukB|mukb|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 22|22|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW mukB|mukb|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 22|22|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW mukBmatP|mukbmatp|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 22|22|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2-5xmatS|pgbm2-5xmats|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2-5xmatS|pgbm2-5xmats|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2|pgbm2|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2|pgbm2|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 22|22|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 22|22|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 2|2|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 37|37|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 37|37|CD °C|°c|SYM -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN LB|lb|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN LB|lb|NN 30|30|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN stationary|stationary|JJ phase|phase|NN 30|30|CD °C|°c|NN -LRB-|-lrb-|-LRB- 30h|30h|NN -RRB-|-rrb-|-RRB-
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN stationary|stationary|JJ phase|phase|NN 30|30|CD °C|°c|NN -LRB-|-lrb-|-LRB- 30h|30h|NN -RRB-|-rrb-|-RRB- -|-|: Replicate|replicate|VB 1|1|CD
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW zapB|zapb|NN cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2-5xmatS|pgbm2-5xmats|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW zapB|zapb|NN cells|cell|NNS harbouring|harbour|VBG plasmid|plasmid|NN pGBM2|pgbm2|NN in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3C-seq|3c-seq|NN of|of|IN E.|e.|FW coli|coli|FW zapB|zapb|NN cells|cell|NNS in|in|IN exponential|exponential|JJ phase|phase|NN 30|30|CD °C|°c|NN
3|3|CD '|'|'' -|-|: end|end|NN RNA-seq|rna-seq|NN ,|,|, Cytosolic|cytosolic|JJ fraction|fraction|NN
3|3|CD '|'|'' -|-|: end|end|NN RNA-seq|rna-seq|NN ,|,|, Cytosolic|cytosolic|JJ fraction|fraction|NN ,|,|, Replicate|replicate|VB #|#|# 1|1|CD
3|3|CD '|'|'' -|-|: end|end|NN RNA-seq|rna-seq|NN ,|,|, Cytosolic|cytosolic|JJ fraction|fraction|NN ,|,|, Replicate|replicate|VB #|#|# 2|2|CD
3|3|CD '|'|'' -|-|: end|end|NN RNA-seq|rna-seq|NN ,|,|, Nucleoid|nucleoid|NN fraction|fraction|NN
3|3|CD '|'|'' -|-|: end|end|NN RNA-seq|rna-seq|NN ,|,|, Nucleoid|nucleoid|NN fraction|fraction|NN ,|,|, Replicate|replicate|VB #|#|# 1|1|CD
3|3|CD '|'|'' -|-|: end|end|NN RNA-seq|rna-seq|NN ,|,|, Nucleoid|nucleoid|NN fraction|fraction|NN ,|,|, Replicate|replicate|VB #|#|# 2|2|CD
3|3|CD _|_|NN ESBL019|esbl019|NN Transition|transition|NN Repl|repl|NN 1|1|CD
3|3|CD .|.|. FHI6.nIND.HUS|fhi6.nind.hus|NN
3|3|CD _|_|NN HF|hf|NNS _|_|VBP LP|lp|NN _|_|CD noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
3|3|CD hour|hour|NN expression|expression|NN of|of|IN synthetic|synthetic|JJ protein|protein|NN DX|dx|NN in|in|IN E.|e.|FW coli|coli|FW
3-HT873-PA3|3-ht873-pa3|NN
3-HT873-PA3|3-ht873-pa3|NN -|-|:
3|3|CD .|.|. Log|log|VB transformation|transformation|NN :|:|:
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1|1|CD
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP A|A|NNP
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP B|B|NNP
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 2|2|CD
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log1|log1|NN
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log1|log1|NN
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 2|2|CD
3|3|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1|1|CD
3XSCOTS|3xscots|CD cDNA|cdna|NN 24|24|CD h|h|NN post-infection|post-infection|JJ
3XSCOTS|3xscot|NNS cDNA|cdna|NN in|in|IN RPMI|rpmi|NN medium|medium|NN
3XSCOTS|3xscots|CD cDNA|cdna|NN obtained|obtain|VBN 24|24|CD h|h|NN post-infection|post-infection|JJ
3XSCOTS|3xscot|NNS cDNA|cdna|NN obtained|obtain|VBN 2h|2h|JJ post-infection|post-infection|JJ
3XSCOTS|3xscot|NNS cDNA|cdna|NN obtained|obtain|VBN 8h|8h|JJ post-infection|post-infection|JJ
3XSCOTS|3xscot|NNS cDNA|cdna|NN obtained|obtain|VBN 8h|8h|JJ post-infection|post-infection|JJ
3XSCOTS|3xscot|NNS cDNA|cdna|NN obtained|obtain|VBN after|after|IN 8h|8h|JJ post-infection|post-infection|JJ
3XSCOTS|3xscot|NNS cDNA|cdna|NN obtained|obtain|VBN in|in|IN RPMI|rpmi|NN
3XSCOTS|3xscots|CD cDNA|cdna|NN obtained|obtain|VBN in|in|IN RPMI|rpmi|NN medium|medium|NN
40|40|CD hours|hour|NNS 1|1|CD
40|40|CD hours|hour|NNS 2|2|CD
40|40|CD hours|hour|NNS 3|3|CD
40|40|CD hours|hour|NNS cultivation|cultivation|NN in|in|IN continuous|continuous|JJ culture|culture|NN -LRB-|-lrb-|-LRB- mineral|mineral|JJ medium|medium|NN with|with|IN 100|100|CD mg/l|mg/l|NN glucose|glucose|NN -RRB-|-rrb-|-RRB-
40|40|CD hours|hour|NNS of|of|IN cultivation|cultivation|NN in|in|IN continuous|continuous|JJ colture|colture|NN -LRB-|-lrb-|-LRB- mineral|mineral|JJ medium|medium|NN with|with|IN 100|100|CD mg/l|mg/l|NN glucose|glucose|NN -RRB-|-rrb-|-RRB-
40|40|CD min|min|NN after|after|IN UVtreatment|uvtreatment|NN 1|1|CD ,|,|, 40J|40j|NN ,|,|, MG1655|mg1655|NN in|in|IN Davis|Davis|NNP +0.4|+0.4|CD %|%|NN glu|glu|NN
40|40|CD min|min|NN Nov10|nov10|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Sau3AI|sau3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
40|40|CD min|min|NN Nov10|nov10|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
40|40|CD min|min|NN Nov2|nov2|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
40|40|CD min|min|NN Nov2|nov2|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
40|40|CD min|min|NN Nov5|nov5|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Sau3AI|sau3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
40|40|CD min|min|NN Nov5|nov5|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
40|40|CD min|min|NN untreatedcells|untreatedcell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
40|40|CD .|.|. St.|St.|NNP Olav178.IND.nHUS|Olav178.IND.nHUS|NNP
41|41|CD .|.|. St.|St.|NNP Olav179.nIND.nHUS|Olav179.nIND.nHUS|NNP
42|42|CD .|.|. St.|St.|NNP Olav179.IND.nHUS|Olav179.IND.nHUS|NNP
43|43|CD .|.|. FHI63.nIND.HUS|fhi63.nind.hus|NN
44|44|CD .|.|. FHI63.IND.HUS|fhi63.ind.hus|NN
45|45|CD .|.|. FHI66.nIND.nHUS|fhi66.nind.nhus|NN
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1|1|CD
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 2|2|CD
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log1|log1|NN
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log1|log1|NN
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 2|2|CD
4.5|4.5|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, .2|.2|NN %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1|1|CD
46degrees|46degree|NNS replicate|replicate|VBP 1|1|CD
46degrees|46degree|NNS replicate|replicate|VBP 2|2|CD
46degrees|46degree|NNS replicate|replicate|VBP 3|3|CD
46|46|CD .|.|. FHI66.IND.nHUS|fhi66.ind.nhus|NN
47|47|CD .|.|. FHI83.nIND.HUS|fhi83.nind.hus|NN
48|48|CD .|.|. FHI83.IND.HUS|fhi83.ind.hus|NN
49|49|CD .|.|. St.|St.|NNP Olav17.nIND.nHUS|Olav17.nIND.nHUS|NNP
4A|4a|NN 1m|1m|NN
4A|4a|NN 1y|1y|NN
4A|4a|NN 4y|4y|NN
4A|4a|NN _|_|CD MG|mg|NN _|_|NN t60|t60|NN
4B|4b|NN _|_|CD MG|mg|NN _|_|NN t60|t60|NN
4C|4c|NN _|_|CD MG|mg|NN _|_|NN t60|t60|NN
4|4|CD _|_|NN ESBL019|esbl019|NN Reverted|revert|VBD Repl|repl|NN 1|1|CD
4|4|CD .|.|. FHI6.IND.HUS|fhi6.ind.hus|NN
4|4|CD hour|hour|NN expression|expression|NN of|of|IN synthetic|synthetic|JJ protein|protein|NN DX|dx|NN in|in|IN E.|e.|FW coli|coli|FW
4-HT873-PS-60min1|4-ht873-ps-60min1|NN
4|4|CD .|.|. Normalization|normalization|NN by|by|IN Glowess|glowess|NN method|method|NN :|:|:
4|4|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD C|c|NN
4|4|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN A|a|NN
4|4|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN B|b|NN
500|500|CD hours|hour|NNS 1|1|CD
500|500|CD hours|hour|NNS 2|2|CD
500|500|CD hours|hour|NNS 3|3|CD
500|500|CD hours|hour|NNS of|of|IN cultivation|cultivation|NN in|in|IN continuous|continuous|JJ colture|colture|NN -LRB-|-lrb-|-LRB- mineral|mineral|JJ medium|medium|NN with|with|IN 100|100|CD mg/l|mg/l|NN glucose|glucose|NN -RRB-|-rrb-|-RRB-
500|500|CD ng|ng|NN chrom|chrom|NN .|.|. DNA|dna|NN was|be|VBD digested|digest|VBN with|with|IN 10U|10u|NN of|of|IN MseI|msei|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- in|in|IN 10μL|10μl|NN volume|volume|NN for|for|IN 3h|3h|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC heat|heat|NN inactivated|inactivate|VBD for|for|IN 20|20|CD min|min|NN at|at|IN 65|65|CD °C|°c|NN .|.|. To|to|TO prepare|prepare|VB adapters|adapter|NNS 100pmol|100pmol|CD of|of|IN MseIlong|MseIlong|NNP -LRB-|-lrb-|-LRB- AGTGGGATTCCGCATGCTAGT|AGTGGGATTCCGCATGCTAGT|NNP -RRB-|-rrb-|-RRB- and|and|CC MseIshortnewNo|mseishortnewno|NN -LRB-|-lrb-|-LRB- TAACTAGCATGC|taactagcatgc|NN -RRB-|-rrb-|-RRB- were|be|VBD annealed|anneal|VBN in|in|IN 8µl|8µl|JJ ddH2O|ddh2o|NN by|by|IN heating|heat|VBG to|to|TO 95|95|CD °C|°c|NN for|for|IN 3|3|CD min|min|NN and|and|CC than|than|IN cooling|cool|VBG to|to|TO 70|70|CD °C|°c|NN and|and|CC subsequently|subsequently|RB to|to|TO 15|15|CD °C|°c|NN with|with|IN 1|1|CD °C|°c|NN per|per|IN min|min|NN .|.|. At|at|IN 15|15|CD °C|°c|NN 10µl|10µl|JJ MseI|msei|NN digested|digest|VBD DNA|dna|NN ,|,|, 2µl|2µl|JJ ligase|ligase|NN buffer|buffer|NN and|and|CC 400U|400u|NN T4-ligase|t4-ligase|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN and|and|CC ligated|ligate|VBN over|over|IN night|night|NN .|.|. Ligase|ligase|NN was|be|VBD inactivated|inactivate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 10|10|CD min|min|NN .|.|. One|one|CD halve|halve|VBP of|of|IN the|the|DT ligation|ligation|NN mix|mix|NN was|be|VBD digested|digest|VBN with|with|IN 20|20|CD U|U|NNP DpnI|DpnI|NNP for|for|IN 2h|2h|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN a|a|DT volume|volume|NN of|of|IN 50µl|50µl|JJ and|and|CC the|the|DT other|other|JJ halve|halve|VBP treated|treated|JJ similar|similar|JJ with|with|IN water|water|NN instead|instead|RB of|of|IN DpnI|dpni|NN as|as|IN control|control|NN .|.|. 5µl|5µl|NN of|of|IN the|the|DT DNA|dna|NN was|be|VBD amplified|amplify|VBN in|in|IN a|a|DT 50|50|CD µl|µl|NN PCR|pcr|NN reaction|reaction|NN with|with|IN 0.2|0.2|CD mM|mm|NN dNTPs|dntp|NNS ,|,|, 0.5|0.5|CD µM|µm|NN primer|primer|NN MseIlong|MseIlong|NNP ,|,|, 10µl|10µl|JJ Phusion|Phusion|NNP HF|hf|NN buffer|buffer|NN and|and|CC 1U|1u|NN Phusion|phusion|NN DNA|dna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Finnzymes|finnzyme|NNS -RRB-|-rrb-|-RRB- with|with|IN the|the|DT program|program|NN 30sec|30sec|CD 98|98|CD °C|°c|NN ,|,|, 20x|20x|NN -LRB-|-lrb-|-LRB- 30sec|30sec|CD 98|98|CD °C|°c|NN ,|,|, 30|30|CD sec|sec|NN 62|62|CD °C|°c|NN ,|,|, 60sec|60sec|JJ 72|72|CD °C|°c|NN -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD min|min|NN 72|72|CD °C|°c|NN .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN with|with|IN a|a|DT Qiagen|Qiagen|NNP PCR|pcr|NN cleanup|cleanup|NN kit|kit|NN .|.|.
50|50|CD bp|bp|NN single-end|single-end|JJ reads|read|VBZ ,|,|, were|be|VBD mapped|map|VBN to|to|TO the|the|DT genome|genome|NN with|with|IN using|use|VBG bowtie2|bowtie2|NN -LRB-|-lrb-|-LRB- Langmead|langmead|NN and|and|CC Salzberg|Salzberg|NNP ,|,|, 2012|2012|CD -RRB-|-rrb-|-RRB- using|use|VBG default|default|NN parameters|parameter|NNS .|.|. Alignments|alignment|NNS with|with|IN bowtie2|bowtie2|NN mapping|map|VBG quality|quality|NN values|value|NNS lower|lower|JJR than|than|IN 40|40|CD were|be|VBD not|not|RB retained|retain|VBN for|for|IN further|further|JJ analysis|analysis|NN ,|,|, leaving|leave|VBG 128,413,654|128,413,654|CD and|and|CC 76,508,335|76,508,335|CD reads|read|VBZ .|.|.
50µl|50µl|CD of|of|IN total|total|JJ RNA|rna|NN of|of|IN the|the|DT cells|cell|NNS affected|affect|VBN by|by|IN the|the|DT Chrysanthemum|Chrysanthemum|NNP herba|herba|NN methyl|methyl|NN chloride|chloride|NN fraction|fraction|NN was|be|VBD isolated|isolate|VBN .|.|. The|the|DT RNA|rna|NN extraction|extraction|NN procedure|procedure|NN was|be|VBD carried|carry|VBN out|out|RP using|use|VBG the|the|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Briefly|briefly|RB ,|,|, 1|1|CD ml|ml|NN of|of|IN bacterial|bacterial|JJ culture|culture|NN was|be|VBD added|add|VBN to|to|TO 2|2|CD ml|ml|NN of|of|IN RNA|rna|NN protect|protect|VBP bacteria|bacterium|NNS reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- .|.|. Centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 5000|5000|CD g|g|NN for|for|IN 10|10|CD minutes|minute|NNS -RRB-|-rrb-|-RRB- of|of|IN the|the|DT mixture|mixture|NN was|be|VBD performed|perform|VBN to|to|TO precipitate|precipitate|VB the|the|DT cells|cell|NNS .|.|. The|the|DT harvested|harvest|VBN cells|cell|NNS were|be|VBD incubated|incubate|VBN in|in|IN TE|TE|NNP buffer|buffer|NN with|with|IN 1|1|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- .|.|. Total|total|JJ RNA|rna|NN was|be|VBD eluted|elute|VBN in|in|IN 50|50|CD ml|ml|NN of|of|IN RNase|rnase|NN free|free|JJ water|water|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT NanoDrop|NanoDrop|NNP Spectrophotometer|Spectrophotometer|NNP -LRB-|-lrb-|-LRB- NanoDrop|NanoDrop|NNP Technologies|Technologies|NNPS ,|,|, Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN quality|quality|NN was|be|VBD examined|examine|VBN using|use|VBG the|the|DT RNA|rna|NN 6000|6000|CD Nano|Nano|NNP Labchip|labchip|NN with|with|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
50|50|CD ng|ng|NN of|of|IN the|the|DT fragmented|fragmented|JJ RNA|rna|NN was|be|VBD converted|convert|VBN to|to|TO sequencing|sequencing|NN library|library|NN using|use|VBG TruSeq|TruSeq|NNP ®|®|NNP Stranded|Stranded|NNP mRNA|mrna|NN Sample|Sample|NNP Prep|Prep|NNP Kit|kit|NN in|in|IN accordance|accordance|NN with|with|IN manufacturer|manufacturer|NN 's|'s|POS instruction|instruction|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|.
50|50|CD OD600|od600|NN of|of|IN bacteria|bacterium|NNS have|have|VBP been|be|VBN grown|grow|VBN to|to|TO the|the|DT desired|desire|VBN growth|growth|NN stage|stage|NN and|and|CC harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN .|.|. They|they|PRP were|be|VBD lysed|lyse|VBN in|in|IN 500|500|CD µl|µl|NN of|of|IN the|the|DT lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 20|20|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH7|ph7|NN .5|.5|CD ,|,|, 150|150|CD mM|mm|NN KCl|kcl|NN ,|,|, 1|1|CD mM|mm|NN MgCl2|mgcl2|NN ,|,|, 1|1|CD mM|mm|NN DTT|dtt|NN ,|,|, 1|1|CD mM|mm|NN PMSF|pmsf|NN ,|,|, 0.2|0.2|CD %|%|NN Triton|Triton|NNP X100|x100|NN ,|,|, 20|20|CD U/ml|u/ml|NN DNase|dnase|NN I|i|CD ,|,|, Thermo|Thermo|NNP Scientific|Scientific|NNP ,|,|, 200|200|CD U/ml|u/ml|NN SUPERase-IN|superase-in|NN ,|,|, Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|. Lysis|lysis|NN was|be|VBD carried|carry|VBN out|out|RP on|on|IN a|a|DT Retsch|retsch|JJ MM400|mm400|NN machine|machine|NN at|at|IN 30|30|CD Hz|hz|NN for|for|IN 10|10|CD min|min|NN in|in|IN the|the|DT presence|presence|NN of|of|IN 750|750|CD µl|µl|NN 0.1|0.1|CD mm|mm|NN glass|glass|NN beads|bead|NNS .|.|. The|the|DT lysate|lysate|NN was|be|VBD cleared|clear|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 14,000|14,000|CD g|g|NN at|at|IN 4|4|CD °C|°c|NN for|for|IN 10|10|CD min|min|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD added|add|VBN 35|35|CD µl|µl|NN of|of|IN monoclonal|monoclonal|JJ anti-FLAG|anti-flag|JJ M2|m2|NN antibody|antibody|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP ,|,|, #F1804|#f1804|NN -RRB-|-rrb-|-RRB- and|and|CC rocked|rock|VBD for|for|IN 30|30|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Then|then|RB 75|75|CD µl|µl|NN of|of|IN pre-washed|pre-washed|JJ Protein|protein|NN A|a|DT sepharose|sepharose|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP ,|,|, #P6649|#p6649|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD rocked|rock|VBN for|for|IN additional|additional|JJ 30|30|CD min|min|NN .|.|. Afterwards|afterwards|RB ,|,|, beads|bead|NNS were|be|VBD washed|wash|VBN extensively|extensively|RB with|with|IN the|the|DT lysis|lysis|NN buffer|buffer|NN ,|,|, and|and|CC similar|similar|JJ flow-through|flow-through|JJ and|and|CC wash|wash|NN protein|protein|NN and|and|CC RNA|rna|NN samples|sample|NNS were|be|VBD collected|collect|VBN .|.|.
50|50|CD .|.|. St.|St.|NNP Olav17.IND.nHUS|Olav17.IND.nHUS|NNP
5|5|CD '|'|'' 10|10|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
5|5|CD '|'|'' 15|15|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
51|51|CD .|.|. St.|St.|NNP Olav39.IND.nHUS|Olav39.IND.nHUS|NNP
52|52|CD .|.|. St.|St.|NNP Olav63.nIND.nHUS|Olav63.nIND.nHUS|NNP
53|53|CD .|.|. St.|St.|NNP Olav63.IND.nHUS|Olav63.IND.nHUS|NNP
54|54|CD .|.|. St.|St.|NNP Olav164|Olav164|NNP .|.|. nIND.HUS|nind.hus|NN
5|5|CD '|'|'' +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN vs|vs|CC 0|0|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN
55|55|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
55|55|CD .|.|. St.|St.|NNP Olav164|Olav164|NNP .|.|. IND.HUS|ind.hus|NN
56|56|CD .|.|. St.|St.|NNP Olav176.IND.HUS|Olav176.IND.HUS|NNP
57|57|CD .|.|. St.|St.|NNP Olav39.nIND.nHUS|Olav39.nIND.nHUS|NNP
59|59|CD .|.|. St.|St.|NNP Olav173.IND.nHUS|Olav173.IND.nHUS|NNP
5A|5a|NN 1m|1m|NN
5A|5a|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t10|t10|NN
5-azacytidine-treated|5-azacytidine-treated|JJ
5B|5b|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t10|t10|NN
5C|5c|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t10|t10|NN
5|5|CD _|_|NN ESBL019|esbl019|NN Coliform|coliform|NN Repl|repl|NN 2|2|CD
5|5|CD .|.|. FHI7.nIND.HUS|fhi7.nind.hus|NN
5|5|CD _|_|SYM HF|hf|NNS _|_|VBP LP|lp|NN _|_|CD noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
5-HT873-PS-60min2|5-ht873-ps-60min2|NN
5|5|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
5|5|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN ,25|,25|CD ug|ug|NN total|total|JJ RNA|rna|NN
5|5|CD '|'|'' linker|linker|NN and|and|CC poly|poly|NN A-tail|a-tail|NN removal|removal|NN using|use|VBG READemption|reademption|NN
5|5|CD min|min|NN
5|5|CD min|min|NN -LRB-|-lrb-|-LRB- additional|additional|JJ -RRB-|-rrb-|-RRB-
5|5|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
5|5|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN first|first|RB replicate|replicate|VB
5|5|CD min|min|NN after|after|IN UVtreatment|uvtreatment|NN 1|1|CD ,|,|, 40J|40j|NN ,|,|, MG1655|mg1655|NN in|in|IN Davis|Davis|NNP +0.4|+0.4|CD %|%|NN glu|glu|NN
5|5|CD min|min|NN untreatedcells|untreatedcell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
5|5|CD ml|ml|NN bacterial|bacterial|JJ cultures|culture|NNS with|with|IN a|a|DT known|known|JJ inoculum|inoculum|NN of|of|IN E.|e.|FW coli|coli|FW cells|cell|NNS -LRB-|-lrb-|-LRB- 1.0|1.0|CD ×|×|NN 109|109|CD cfu/ml|cfu/ml|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN at|at|IN 1:1|1:1|CD -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- to|to|TO the|the|DT microemulsion|microemulsion|NN and|and|CC incubated|incubate|VBN on|on|IN a|a|DT tube|tube|NN rotator|rotator|NN at|at|IN 200|200|CD rpm|rpm|NN for|for|IN 4|4|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN for|for|IN the|the|DT subsequent|subsequent|JJ DNA|dna|NN microarray|microarray|NN analysis|analysis|NN .|.|. In|in|IN the|the|DT preliminary|preliminary|JJ experiment|experiment|NN ,|,|, a|a|DT complete|complete|JJ loss|loss|NN of|of|IN E.|e.|FW coli|coli|FW viability|viability|NN was|be|VBD achieved|achieve|VBN after|after|IN 8|8|CD h|h|NN by|by|IN the|the|DT aforementioned|aforementioned|JJ treatment|treatment|NN .|.|. The|the|DT prepared|prepared|JJ microemulsion|microemulsion|NN has|have|VBZ an|a|DT oil|oil|NN phase|phase|NN of|of|IN glycerol|glycerol|NN monolaurate|monolaurate|NN -LRB-|-lrb-|-LRB- 5.5|5.5|CD %|%|NN w/w|w/w|NN of|of|IN the|the|DT total|total|JJ emulsion|emulsion|NN -RRB-|-rrb-|-RRB- ,|,|, ethanol|ethanol|NN -LRB-|-lrb-|-LRB- 5.5|5.5|CD %|%|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC a|a|DT surfactant|surfactant|JJ phase|phase|NN of|of|IN Tween|Tween|NNP 20|20|CD -LRB-|-lrb-|-LRB- 43|43|CD %|%|NN -RRB-|-rrb-|-RRB- .|.|. Mixtures|mixture|NNS of|of|IN the|the|DT surfactant-oil|surfactant-oil|JJ phase|phase|NN were|be|VBD prepared|prepare|VBN in|in|IN stoppered|stoppered|JJ flasks|flask|NNS and|and|CC kept|keep|VBD in|in|IN a|a|DT 25|25|CD °C|°c|NN water|water|NN bath|bath|NN .|.|. Subsequently|subsequently|RB ,|,|, the|the|DT water|water|NN phase|phase|NN was|be|VBD added|add|VBN ,|,|, and|and|CC the|the|DT mixture|mixture|NN was|be|VBD treated|treat|VBN in|in|IN an|a|DT ultrasonic|ultrasonic|JJ bath|bath|NN until|until|IN the|the|DT system|system|NN became|become|VBD optically|optically|RB clear|clear|JJ ,|,|, and|and|CC allowed|allow|VBN to|to|TO equilibrate|equilibrate|VB at|at|IN 25|25|CD °C|°c|NN for|for|IN at|at|IN least|least|JJS 24|24|CD h|h|NN to|to|TO guarantee|guarantee|VB steady-state|steady-state|JJ conditions|condition|NNS .|.|.
5|5|CD ml|ml|NN of|of|IN cell|cell|NN suspension|suspension|NN were|be|VBD added|add|VBN to|to|TO 0.625|0.625|CD ml|ml|NN of|of|IN pre-chilled|pre-chilled|JJ stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN phenol/95|phenol/95|CD %|%|NN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- ,|,|, vortexed|vortexed|JJ and|and|CC incubated|incubate|VBN for|for|IN 5|5|CD min|min|NN on|on|IN ice|ice|NN .|.|. Cells|cell|NNS were|be|VBD pelleted|pellete|VBN for|for|IN 5|5|CD min|min|NN at|at|IN 5000|5000|CD g|g|NN ,|,|, flash|flash|NN frozen|freeze|VBN in|in|IN a|a|DT dry|dry|JJ ice-ethanol|ice-ethanol|NN bath|bath|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD oC|oc|NN .|.|.
5mL|5ml|NN of|of|IN culture|culture|NN was|be|VBD mixed|mix|VBN with|with|IN 5mL|5ml|NN of|of|IN hot|hot|JJ acid|acid|NN phenol|phenol|NN :|:|: chloroform|chloroform|NN .|.|. Samples|sample|NNS were|be|VBD held|hold|VBN at|at|IN 65ºC|65ºc|NN with|with|IN periodic|periodic|JJ shaking|shake|VBG for|for|IN at|at|IN least|least|JJS 10|10|CD minutes|minute|NNS before|before|IN centrifuging|centrifuge|VBG at|at|IN 4000|4000|CD rpm|rpm|NN for|for|IN 20|20|CD min|min|NN .|.|. Supernatant|supernatant|NN was|be|VBD extracted|extract|VBN again|again|RB with|with|IN acid-phenol|acid-phenol|NN :|:|: chloroform|chloroform|NN and|and|CC then|then|RB with|with|IN chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN -LRB-|-lrb-|-LRB- 24.1|24.1|CD -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD precipitated|precipitated|JJ overnight|overnight|JJ at|at|IN --|--|: 80ºC|80ºc|NN in|in|IN 2.5|2.5|CD V|v|NN 100|100|CD %|%|NN ethanol|ethanol|NN and|and|CC 1/10V|1/10v|NN 3M|3M|NNP sodium|sodium|NN acetate|acetate|NN pH|ph|NN 5.2|5.2|CD .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD purified|purify|VBN and|and|CC treated|treat|VBN with|with|IN DNase|dnase|NN using|use|VBG the|the|DT Rneasy|Rneasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
5|5|CD ml|ml|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD mixed|mix|VBN with|with|IN 1/10V|1/10v|NN 10|10|CD %|%|NN phenol|phenol|NN :|:|: ethanol|ethanol|NN buffer|buffer|NN to|to|TO stabilize|stabilize|VB the|the|DT RNA|rna|NN ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 4|4|CD oC|oc|NN ,|,|, 4300|4300|CD ×|×|CD g|g|NN for|for|IN 30|30|CD min|min|NN to|to|TO pellet|pellet|NN cells|cell|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN and|and|CC cell|cell|NN pellets|pellet|NNS were|be|VBD suspended|suspend|VBN in|in|IN 5|5|CD ml|ml|NN of|of|IN buffer|buffer|NN -LRB-|-lrb-|-LRB- 2|2|CD mM|mm|NN EDTA|edta|NN ,|,|, 20|20|CD mM|mm|NN NaOAc|naoac|NN ,|,|, pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- before|before|IN mixing|mix|VBG with|with|IN equal|equal|JJ volume|volume|NN of|of|IN hot|hot|JJ acid-phenol|acid-phenol|NN :|:|: chloroform|chloroform|NN -LRB-|-lrb-|-LRB- pH|ph|NN 4.5|4.5|CD with|with|IN Iso|Iso|NNP Amyl|Amyl|NNP Alcohol|Alcohol|NNP -LRB-|-lrb-|-LRB- IAA|IAA|NNP -RRB-|-rrb-|-RRB- ,|,|, 125:25:1|125:25:1|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- and|and|CC incubating|incubate|VBG at|at|IN 65|65|CD oC|oc|NN with|with|IN periodic|periodic|JJ shaking|shake|VBG for|for|IN 10|10|CD min|min|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 3220|3220|CD ×|×|CD g|g|NN for|for|IN 20|20|CD min|min|NN and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD subjected|subject|VBN to|to|TO further|further|JJ extractions|extraction|NNS with|with|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN and|and|CC chloroform|chloroform|NN :|:|: IAA|iaa|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD precipitated|precipitated|JJ overnight|overnight|JJ at|at|IN -70|-70|CD oC|oc|NN in|in|IN 2.5|2.5|CD volume|volume|NN 100|100|CD %|%|NN ethanol|ethanol|NN and|and|CC 1/10|1/10|CD volume|volume|NN 3|3|CD M|m|NN sodium|sodium|NN acetate|acetate|NN pH|ph|NN 5.2|5.2|CD .|.|. RNA|rna|NN purification|purification|NN and|and|CC DNase|dnase|NN treatment|treatment|NN of|of|IN RNA|rna|NN samples|sample|NNS were|be|VBD done|do|VBN with|with|IN the|the|DT Rneasy|Rneasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- and|and|CC RNA|rna|NN quality|quality|NN was|be|VBD assessed|assess|VBN on|on|IN a|a|DT formaldehyde-agarose|formaldehyde-agarose|NN gel|gel|NN .|.|.
5|5|CD .|.|. Save|save|VB the|the|DT plot|plot|NN files|file|VBZ
5|5|CD '|'|'' vs|vs|CC 0|0|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN
60|60|CD '|'|'' 10|10|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
60|60|CD '|'|'' 15|15|CD ug/ml|ug/ml|JJ indole|indole|NN aa|aa|NN ,|,|, minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ
60|60|CD '|'|'' +|+|CC 50|50|CD ug/ml|ug/ml|JJ Trp|trp|NN in|in|IN min|min|NN +.2|+.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN RNA|rna|NN
60|60|CD '|'|'' +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN vs|vs|CC 0|0|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN
60|60|CD '|'|'' 50|50|CD ug/ml|ug/ml|JJ tryptophan|tryptophan|NN ,|,|, minimal|minimal|JJ +02|+02|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
60|60|CD '|'|'' in|in|IN min|min|NN +.2|+.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN RNA|rna|NN
60|60|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
60|60|CD '|'|'' in|in|IN min|min|NN med|med|VBD +0.2|+0.2|CD %|%|NN glu|glu|NN +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN ,25|,25|CD ug|ug|NN tot|tot|NN RNA|rna|NN
60|60|CD min|min|NN
60|60|CD min|min|NN after|after|IN UVtreatment|uvtreatment|NN 1|1|CD ,|,|, 40J|40j|NN ,|,|, MG1655|mg1655|NN in|in|IN Davis|Davis|NNP +0.4|+0.4|CD %|%|NN glu|glu|NN
60|60|CD min|min|NN untreatedcells|untreatedcell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
60|60|CD min|min|NN UV|uv|NN treated|treat|VBN cells|cell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
60|60|CD min|min|NN UVtreatment|uvtreatment|NN control|control|NN ,|,|, MG1655|mg1655|NN in|in|IN Davis|Davis|NNP +0.4|+0.4|CD %|%|NN glu|glu|NN
60|60|CD .|.|. St.|St.|NNP Olav176.nIND.HUS|olav176.nind.hus|JJ
60|60|CD '|'|'' vs.|vs.|CC 0|0|CD '|'|'' ,|,|, 50|50|CD ug/ml|ug/ml|JJ tryptophan|tryptophan|NN ,|,|, minimal|minimal|JJ +02|+02|CD %|%|NN glu|glu|NN
60|60|CD '|'|'' vs|vs|CC 0|0|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN
60|60|CD '|'|'' vs|vs|CC 0|0|CD '|'|'' in|in|IN minimal|minimal|JJ medium|medium|NN +0.2|+0.2|CD %|%|NN glu|glu|NN ,|,|, II|ii|CD
68908|68908|CD
68909|68909|CD
68910|68910|CD
68911|68911|CD
68912|68912|CD
68913|68913|CD
68915|68915|CD
68916|68916|CD
68917|68917|CD
68919|68919|CD
68920|68920|CD
68921|68921|CD
68922|68922|CD
68923|68923|CD
68924|68924|CD
68925|68925|CD
68926|68926|CD
68927|68927|CD
68928|68928|CD
68929|68929|CD
68930|68930|CD
68931|68931|CD
68932|68932|CD
68933|68933|CD
6A|6a|NN 1m|1m|NN
6A|6a|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t30|t30|NN
6B|6b|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t30|t30|NN
6|6|CD .|.|. close|close|RB the|the|DT graph|graph|NN :|:|:
6C|6c|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t30|t30|NN
6|6|CD _|_|NN ESBL019|esbl019|NN Filamented|Filamented|NNP Repl|Repl|NNP 2|2|CD
6|6|CD .|.|. FHI7.IND.HUS|fhi7.ind.hus|NN
6|6|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
6-HT873-PS-60min3|6-ht873-ps-60min3|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A|A|NNP
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A1|a1|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B|B|NNP
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B1|b1|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP A|A|NNP
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP B|B|NNP
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD C|c|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN A|a|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN B|b|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP A2|a2|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep.|Rep.|NNP B2|b2|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB A|a|DT
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB A1|a1|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB B|b|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB B1|b1|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP A|A|NNP
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP B|B|NNP
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP A2|a2|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB A1|a1|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Replicate|replicate|VB B1|b1|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, .2|.2|NN %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP B2|b2|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP A1|a1|NN
6|6|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Rep|Rep|NNP B1|b1|NN
72|72|CD hr|hr|NN colony|colony|NN growth|growth|NN equiv|equiv|NN .|.|. to|to|TO wildtype|wildtype|JJ colony|colony|NN size|size|NN
75th|75th|JJ percentile|percentile|NN shift|shift|NN normalisation|normalisation|NN and|and|CC baseline|baseline|NN adjusted|adjusted|JJ
7A|7a|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t60|t60|NN
7B|7b|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t60|t60|NN
7C|7c|NN _|_|CD MG+H|mg+h|NN g|g|NN _|_|CD t60|t60|NN
7|7|CD _|_|NN ESBL019|esbl019|NN Transition|transition|NN Repl|repl|NN 2|2|CD
7|7|CD .|.|. FHI8.nIND.HUS|fhi8.nind.hus|NN
7G|7g|NN .0|.0|CD
7|7|CD h|h|NN 7HI|7HI|NNP biofilm|biofilm|NN cells|cell|NNS
7|7|CD h|h|NN biofilm|biofilm|NN cells|cell|NNS
7|7|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
7|7|CD h|h|NN isatin|isatin|NN biofilm|biofilm|NN cells|cell|NNS
7|7|CD h|h|NN suspension|suspension|NN cells|cell|NNS
7-HT874-PA1|7-ht874-pa1|NN
7-HT874-PA1|7-ht874-pa1|NN -|-|:
7|7|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
7|7|CD min|min|NN Nov0|nov0|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
7|7|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
7|7|CD min|min|NN Nov500|nov500|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
7|7|CD .|.|. output|output|NN :|:|:
80|80|CD min|min|NN ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN
80min-1|80min-1|CD
80min-2|80min-2|CD
80min-3|80min-3|CD
80|80|CD min|min|NN Nov10|nov10|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Sau3AI|sau3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
80|80|CD min|min|NN Nov10|nov10|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
80|80|CD min|min|NN Nov5|nov5|NN ug/ml|ug/ml|NN ,|,|, 2|2|CD ug|ug|NN Sau3AI|sau3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
80|80|CD min|min|NN Nov5|nov5|NN ug/ml|ug/ml|NN ,|,|, dnaCacrD|dnacacrd|NN 30|30|CD min|min|NN after|after|IN synchr|synchr|NN start|start|NN
80|80|CD min|min|NN ,|,|, unstressed|unstressed|JJ
81-4420|81-4420|CD
83-2315|83-2315|CD
86-1390|86-1390|CD
86-4220|86-4220|CD
873-Con1|873-con1|NN --|--|:
873-Con2|873-con2|NN --|--|:
873-Con3|873-con3|NN --|--|:
873-PA1|873-pa1|NN --|--|:
873-PA2|873-pa2|NN --|--|:
873-PA3|873-pa3|NN --|--|:
87-4725|87-4725|CD
875-Con1|875-con1|NN --|--|:
875-Con2|875-con2|NN --|--|:
875-Con3|875-con3|NN --|--|:
875-PA1|875-pa1|NN --|--|:
875-PA2|875-pa2|NN --|--|:
875-PA3|875-pa3|NN --|--|:
88-1861|88-1861|CD
88-4299|88-4299|CD
89-56-196|89-56-196|CD
8A|8a|NN _|_|CD MG+PMA|MG+PMA|NNP _|_|CD t10|t10|NN
8B|8b|NN _|_|CD MG+PMA|MG+PMA|NNP _|_|CD t10|t10|NN
8C|8c|NN _|_|CD MG+PMA|MG+PMA|NNP _|_|CD t10|t10|NN
8|8|CD _|_|NN ESBL019|esbl019|NN Reverted|revert|VBD Repl|repl|NN 2|2|CD
8|8|CD .|.|. FHI8.IND.HUS|fhi8.ind.hus|NN
8-HT874-PA2|8-ht874-pa2|NN
8-HT874-PA2|8-ht874-pa2|NN -|-|:
8|8|CD ml|ml|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD mixed|mix|VBN with|with|IN 1/10V|1/10v|NN 10|10|CD %|%|NN phenol|phenol|NN :|:|: ethanol|ethanol|NN buffer|buffer|NN to|to|TO stabilize|stabilize|VB the|the|DT RNA|rna|NN ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 4|4|CD oC|oc|NN ,|,|, 4300|4300|CD ×|×|CD g|g|NN for|for|IN 30|30|CD min|min|NN to|to|TO pellet|pellet|NN cells|cell|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN and|and|CC cell|cell|NN pellets|pellet|NNS were|be|VBD suspended|suspend|VBN in|in|IN 5|5|CD ml|ml|NN of|of|IN buffer|buffer|NN -LRB-|-lrb-|-LRB- 2|2|CD mM|mm|NN EDTA|edta|NN ,|,|, 20|20|CD mM|mm|NN NaOAc|naoac|NN ,|,|, pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- before|before|IN mixing|mix|VBG with|with|IN equal|equal|JJ volume|volume|NN of|of|IN hot|hot|JJ acid-phenol|acid-phenol|NN :|:|: chloroform|chloroform|NN -LRB-|-lrb-|-LRB- pH|ph|NN 4.5|4.5|CD with|with|IN Iso|Iso|NNP Amyl|Amyl|NNP Alcohol|Alcohol|NNP -LRB-|-lrb-|-LRB- IAA|IAA|NNP -RRB-|-rrb-|-RRB- ,|,|, 125:25:1|125:25:1|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- and|and|CC incubating|incubate|VBG at|at|IN 65|65|CD oC|oc|NN with|with|IN periodic|periodic|JJ shaking|shake|VBG for|for|IN 10|10|CD min|min|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 3220|3220|CD ×|×|CD g|g|NN for|for|IN 20|20|CD min|min|NN and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD subjected|subject|VBN to|to|TO further|further|JJ extractions|extraction|NNS with|with|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN and|and|CC chloroform|chloroform|NN :|:|: IAA|iaa|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD precipitated|precipitated|JJ overnight|overnight|JJ at|at|IN -70|-70|CD oC|oc|NN in|in|IN 2.5|2.5|CD volume|volume|NN 100|100|CD %|%|NN ethanol|ethanol|NN and|and|CC 1/10|1/10|CD volume|volume|NN 3|3|CD M|m|NN sodium|sodium|NN acetate|acetate|NN pH|ph|NN 5.2|5.2|CD .|.|. RNA|rna|NN purification|purification|NN and|and|CC DNase|dnase|NN treatment|treatment|NN of|of|IN RNA|rna|NN samples|sample|NNS were|be|VBD done|do|VBN with|with|IN the|the|DT Rneasy|Rneasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- and|and|CC RNA|rna|NN quality|quality|NN was|be|VBD assessed|assess|VBN on|on|IN a|a|DT formaldehyde-agarose|formaldehyde-agarose|NN gel|gel|NN .|.|.
8|8|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN MCM|mcm|NN 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN A|a|NN
8|8|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD C|c|NN
8|8|CD '|'|'' RNA|rna|NN Decay|decay|NN of|of|IN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN Trial|trial|NN B|b|NN
90|90|CD min|min|NN minus|minus|CC ciprofloxacin|ciprofloxacin|NN
90|90|CD min|min|NN plus|plus|CC ciprofloxacin|ciprofloxacin|NN
90|90|CD minutes|minute|NNS growth|growth|NN in|in|IN LB|LB|NNP
91-19-172|91-19-172|CD
9A|9a|NN 3y|3y|JJ
9A|9a|NN 5y|5y|JJ
9A|9a|NN _|_|CD MG+PMA|mg+pma|NN _|_|CD t30|t30|NN
9A|9a|NN T0|t0|NN
9B|9b|NN _|_|CD MG+PMA|mg+pma|NN _|_|CD t30|t30|NN
9C|9c|NN _|_|NN MG+PMA|mg+pma|NN _|_|CD t30|t30|NN
9|9|CD _|_|NN ESBL019|esbl019|NN Coliform|coliform|NN Repl|repl|NN 3|3|CD
9|9|CD .|.|. FHI9.nIND.HUS|fhi9.nind.hus|NN
9|9|CD _|_|SYM HF|hf|NNS _|_|VBP HP|HP|NNP _|_|SYM noDP|nodp|NN _|_|CD noRh|norh|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
9-HT874-PA3|9-ht874-pa3|NN
9-HT874-PA3|9-ht874-pa3|NN -|-|:
A0-A1|a0-a1|NN _|_|CD rep1|rep1|NN _|_|VBD a|a|DT
A0-A1|a0-a1|NN _|_|CD rep1|rep1|NN _|_|NN b|b|NN
A0-A1|a0-a1|NN _|_|CD rep2|rep2|NN _|_|VBD a|a|DT
A0-A1|a0-a1|NN _|_|CD rep2|rep2|NN _|_|NN b|b|NN
A0-A1|a0-a1|NN _|_|CD rep3|rep3|NN _|_|VBD a|a|DT
A0-A1|a0-a1|NN _|_|CD rep3|rep3|NN _|_|NN b|b|NN
A0-E0|a0-e0|NN _|_|CD rep1|rep1|NN _|_|VBD a|a|DT
A0-E0|a0-e0|NN _|_|CD rep1|rep1|NN _|_|NN b|b|NN
A0-E0|a0-e0|NN _|_|CD rep2|rep2|NN _|_|VBD a|a|DT
A0-E0|a0-e0|NN _|_|CD rep2|rep2|NN _|_|NN b|b|NN
A0-E0|a0-e0|NN _|_|CD rep3|rep3|NN _|_|VBD a|a|DT
A0-E0|a0-e0|NN _|_|CD rep3|rep3|NN _|_|NN b|b|NN
A10|a10|NN :|:|: LJ110|lj110|NN del|del|FW pdhr|pdhr|FW MMAcetat|mmacetat|NN
A11|a11|NN :|:|: LJ110|lj110|NN pTM30|ptm30|NN MMAcetat|mmacetat|NN
A12|a12|NN :|:|: LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN MMAcetat|mmacetat|NN
A1|a1|NN :|:|: LJ110|lj110|NN LBo|lbo|NN
A2|a2|NN :|:|: LJ110|lj110|NN del|del|FW pdhr|pdhr|FW LBo|lbo|FW
A2|a2|NN ,|,|, osmotolerant|osmotolerant|JJ mutant|mutant|JJ
A2|a2|NN Replicate|replicate|VB 1|1|CD
A2|a2|NN Replicate|replicate|VB 2|2|CD
A3|a3|NN :|:|: LJ110|lj110|NN pTM30|ptm30|NN LBo|lbo|NN
A4|a4|NN :|:|: LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN LBo|lbo|NN
A4|a4|NN ,|,|, osmotolerant|osmotolerant|JJ mutant|mutant|JJ
A4|a4|NN Replicate|replicate|VB 1|1|CD
A4|a4|NN Replicate|replicate|VB 2|2|CD
A5|a5|NN :|:|: LJ110|lj110|NN MMPyruvat|mmpyruvat|NN
A|a|DT 5|5|CD ml|ml|NN overnight|overnight|JJ culture|culture|NN of|of|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- was|be|VBD grown|grow|VBN in|in|IN Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN for|for|IN 18|18|CD h|h|NN at|at|IN 37C|37c|NN .|.|. The|the|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN fresh|fresh|JJ ,|,|, prewarmed|prewarmed|JJ Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN in|in|IN a|a|DT 125|125|CD ml|ml|NN Ehrlenmeyer|ehrlenmeyer|NN flask|flask|NN and|and|CC shaken|shake|VBN at|at|IN 37C|37c|NN ,|,|, 150|150|CD rpm|rpm|NN in|in|IN a|a|DT New|New|NNP Brunswick|Brunswick|NNP Shaking|shake|VBG water|water|NN bath|bath|NN until|until|IN the|the|DT culture|culture|NN density|density|NN reached|reach|VBD 0.4|0.4|CD .|.|. Half|half|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT second|second|JJ identical|identical|JJ flask|flask|NN containing|contain|VBG menadione|menadione|NN bisulphite|bisulphite|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN .|.|. The|the|DT flasks|flask|NNS were|be|VBD shaken|shake|VBN for|for|IN a|a|DT further|further|JJ 10|10|CD min|min|NN before|before|IN 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- TM|tm|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO stabilise|stabilise|VB the|the|DT RNA|rna|NN .|.|. This|this|DT sample|sample|NN corresponds|correspond|VBZ to|to|TO the|the|DT culture|culture|NN that|that|WDT was|be|VBD not|not|RB treated|treat|VBN with|with|IN menadione|menadione|NN .|.|. Three|three|CD independent|independent|JJ cultures|culture|NNS were|be|VBD processed|process|VBN on|on|IN different|different|JJ occasions|occasion|NNS to|to|TO make|make|VB the|the|DT 3|3|CD replicates|replicate|VBZ used|use|VBN in|in|IN this|this|DT study|study|NN .|.|.
A|a|NN 5|5|CD ml|ml|NN overnight|overnight|JJ culture|culture|NN of|of|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN was|be|VBD grown|grow|VBN in|in|IN Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN for|for|IN 18|18|CD h|h|NN at|at|IN 37C|37c|NN .|.|. The|the|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN fresh|fresh|JJ ,|,|, prewarmed|prewarmed|JJ Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN in|in|IN a|a|DT 125|125|CD ml|ml|NN Ehrlenmeyer|ehrlenmeyer|NN flask|flask|NN and|and|CC shaken|shake|VBN at|at|IN 37C|37c|NN ,|,|, 150|150|CD rpm|rpm|NN in|in|IN a|a|DT New|New|NNP Brunswick|Brunswick|NNP Shaking|shake|VBG water|water|NN bath|bath|NN until|until|IN the|the|DT culture|culture|NN density|density|NN reached|reach|VBD 0.4|0.4|CD .|.|. Half|half|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT second|second|JJ identical|identical|JJ flask|flask|NN containing|contain|VBG menadione|menadione|NN bisulphite|bisulphite|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN -LRB-|-lrb-|-LRB- this|this|DT sample|sample|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT flasks|flask|NNS were|be|VBD shaken|shake|VBN for|for|IN a|a|DT further|further|JJ 10|10|CD min|min|NN before|before|IN 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- TM|tm|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO stabilise|stabilise|VB the|the|DT RNA|rna|NN .|.|. Three|three|CD independent|independent|JJ cultures|culture|NNS were|be|VBD processed|process|VBN on|on|IN different|different|JJ occasions|occasion|NNS to|to|TO make|make|VB the|the|DT 3|3|CD replicates|replicate|VBZ used|use|VBN in|in|IN this|this|DT study|study|NN .|.|.
A|a|NN 5|5|CD ml|ml|NN overnight|overnight|JJ culture|culture|NN of|of|IN MG1655|mg1655|NN was|be|VBD grown|grow|VBN in|in|IN Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN for|for|IN 18|18|CD h|h|NN at|at|IN 37C|37c|NN .|.|. The|the|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN fresh|fresh|JJ ,|,|, prewarmed|prewarmed|JJ Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN in|in|IN a|a|DT 125|125|CD ml|ml|NN Ehrlenmeyer|ehrlenmeyer|NN flask|flask|NN and|and|CC shaken|shake|VBN at|at|IN 37C|37c|NN ,|,|, 150|150|CD rpm|rpm|NN in|in|IN a|a|DT New|New|NNP Brunswick|Brunswick|NNP Shaking|shake|VBG water|water|NN bath|bath|NN until|until|IN the|the|DT culture|culture|NN density|density|NN reached|reach|VBD 0.4|0.4|CD .|.|. Half|half|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT second|second|JJ identical|identical|JJ flask|flask|NN containing|contain|VBG menadione|menadione|NN bisulphite|bisulphite|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN .|.|. The|the|DT flasks|flask|NNS were|be|VBD shaken|shake|VBN for|for|IN a|a|DT further|further|JJ 10|10|CD min|min|NN before|before|IN 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- TM|tm|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO stabilise|stabilise|VB the|the|DT RNA|rna|NN .|.|. This|this|DT sample|sample|NN corresponds|correspond|VBZ to|to|TO the|the|DT culture|culture|NN that|that|WDT was|be|VBD not|not|RB treated|treat|VBN with|with|IN menadione|menadione|NN .|.|. Three|three|CD independent|independent|JJ cultures|culture|NNS were|be|VBD processed|process|VBN on|on|IN different|different|JJ occasions|occasion|NNS to|to|TO make|make|VB the|the|DT 3|3|CD replicates|replicate|VBZ used|use|VBN in|in|IN this|this|DT study|study|NN .|.|.
A|a|NN 5|5|CD ml|ml|NN overnight|overnight|JJ culture|culture|NN of|of|IN MG1655|mg1655|NN was|be|VBD grown|grow|VBN in|in|IN Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN for|for|IN 18|18|CD h|h|NN at|at|IN 37C|37c|NN .|.|. The|the|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN fresh|fresh|JJ ,|,|, prewarmed|prewarmed|JJ Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN in|in|IN a|a|DT 125|125|CD ml|ml|NN Ehrlenmeyer|ehrlenmeyer|NN flask|flask|NN and|and|CC shaken|shake|VBN at|at|IN 37C|37c|NN ,|,|, 150|150|CD rpm|rpm|NN in|in|IN a|a|DT New|New|NNP Brunswick|Brunswick|NNP Shaking|shake|VBG water|water|NN bath|bath|NN until|until|IN the|the|DT culture|culture|NN density|density|NN reached|reach|VBD 0.4|0.4|CD .|.|. Half|half|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT second|second|JJ identical|identical|JJ flask|flask|NN containing|contain|VBG menadione|menadione|NN bisulphite|bisulphite|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN .|.|. This|this|DT sample|sample|NN corresponds|correspond|VBZ to|to|TO the|the|DT culture|culture|NN that|that|WDT was|be|VBD not|not|RB treated|treat|VBN with|with|IN menadione|menadione|NN .|.|. The|the|DT flasks|flask|NNS were|be|VBD shaken|shake|VBN for|for|IN a|a|DT further|further|JJ 10|10|CD min|min|NN before|before|IN 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- TM|tm|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO stabilise|stabilise|VB the|the|DT RNA|rna|NN .|.|. Three|three|CD independent|independent|JJ cultures|culture|NNS were|be|VBD processed|process|VBN on|on|IN different|different|JJ occasions|occasion|NNS to|to|TO make|make|VB the|the|DT 3|3|CD replicates|replicate|VBZ used|use|VBN in|in|IN this|this|DT study|study|NN .|.|.
A|a|NN 5|5|CD ml|ml|NN overnight|overnight|JJ culture|culture|NN of|of|IN MG1655|mg1655|NN was|be|VBD grown|grow|VBN in|in|IN Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN for|for|IN 18|18|CD h|h|NN at|at|IN 37C|37c|NN .|.|. The|the|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN fresh|fresh|JJ ,|,|, prewarmed|prewarmed|JJ Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN in|in|IN a|a|DT 125|125|CD ml|ml|NN Ehrlenmeyer|ehrlenmeyer|NN flask|flask|NN and|and|CC shaken|shake|VBN at|at|IN 37C|37c|NN ,|,|, 150|150|CD rpm|rpm|NN in|in|IN a|a|DT New|New|NNP Brunswick|Brunswick|NNP Shaking|shake|VBG water|water|NN bath|bath|NN until|until|IN the|the|DT culture|culture|NN density|density|NN reached|reach|VBD 0.4|0.4|CD .|.|. Half|half|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT second|second|JJ identical|identical|JJ flask|flask|NN containing|contain|VBG menadione|menadione|NN bisulphite|bisulphite|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN -LRB-|-lrb-|-LRB- this|this|DT sample|sample|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT flasks|flask|NNS were|be|VBD shaken|shake|VBN for|for|IN a|a|DT further|further|JJ 10|10|CD min|min|NN before|before|IN 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- TM|tm|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO stabilise|stabilise|VB the|the|DT RNA|rna|NN .|.|. Three|three|CD independent|independent|JJ cultures|culture|NNS were|be|VBD processed|process|VBN on|on|IN different|different|JJ occasions|occasion|NNS to|to|TO make|make|VB the|the|DT 3|3|CD replicates|replicate|VBZ used|use|VBN in|in|IN this|this|DT study|study|NN .|.|.
A|a|NN 5|5|CD ml|ml|NN overnight|overnight|JJ culture|culture|NN of|of|IN MG1655|mg1655|NN was|be|VBD grown|grow|VBN in|in|IN Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN for|for|IN 18|18|CD h|h|NN at|at|IN 37C|37c|NN .|.|. The|the|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN fresh|fresh|JJ ,|,|, prewarmed|prewarmed|JJ Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN in|in|IN a|a|DT 125|125|CD ml|ml|NN Ehrlenmeyer|ehrlenmeyer|NN flask|flask|NN and|and|CC shaken|shake|VBN at|at|IN 37C|37c|NN ,|,|, 150|150|CD rpm|rpm|NN in|in|IN a|a|DT New|New|NNP Brunswick|Brunswick|NNP Shaking|shake|VBG water|water|NN bath|bath|NN until|until|IN the|the|DT culture|culture|NN density|density|NN reached|reach|VBD 0.4|0.4|CD .|.|. Half|half|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT second|second|JJ identical|identical|JJ flask|flask|NN containing|contain|VBG menadione|menadione|NN bisulphite|bisulphite|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN -LRB-|-lrb-|-LRB- this|this|DT sample|sample|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT flasks|flask|NNS were|be|VBD shaken|shake|VBN for|for|IN a|a|DT further|further|JJ 10|10|CD min|min|NN before|before|IN 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- TM|tm|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO stabilise|stabilise|VB the|the|DT RNA|rna|NN .|.|. Three|three|CD independent|independent|JJ cultures|culture|NNS were|be|VBD processed|process|VBN on|on|IN different|different|JJ occasions|occasion|NNS to|to|TO make|make|VB the|the|DT 3|3|CD replicates|replicate|VBZ used|use|VBN in|in|IN this|this|DT study|study|NN .|.|.
A|a|NN 5|5|CD ml|ml|NN overnight|overnight|JJ culture|culture|NN of|of|IN MG1655|mg1655|NN was|be|VBD grown|grow|VBN in|in|IN Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN for|for|IN 18|18|CD h|h|NN at|at|IN 37C|37c|NN .|.|. The|the|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN fresh|fresh|JJ ,|,|, prewarmed|prewarmed|JJ Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN in|in|IN a|a|DT 125|125|CD ml|ml|NN Ehrlenmeyer|ehrlenmeyer|NN flask|flask|NN and|and|CC shaken|shake|VBN at|at|IN 37C|37c|NN ,|,|, 150|150|CD rpm|rpm|NN in|in|IN a|a|DT New|New|NNP Bruswick|Bruswick|NNP Shaking|shake|VBG water|water|NN bath|bath|NN until|until|IN the|the|DT culture|culture|NN density|density|NN reached|reach|VBD 0.4|0.4|CD .|.|. Half|half|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT second|second|JJ identical|identical|JJ flask|flask|NN containing|contain|VBG menadione|menadione|NN bisulphite|bisulphite|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN .|.|. This|this|DT sample|sample|NN corresponds|correspond|VBZ to|to|TO the|the|DT culture|culture|NN that|that|WDT was|be|VBD not|not|RB treated|treat|VBN with|with|IN menadione|menadione|NN .|.|. The|the|DT flasks|flask|NNS were|be|VBD shaken|shake|VBN for|for|IN a|a|DT further|further|JJ 10|10|CD min|min|NN before|before|IN 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- TM|tm|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO stabilise|stabilise|VB the|the|DT RNA|rna|NN .|.|. Three|three|CD independent|independent|JJ cultures|culture|NNS were|be|VBD processed|process|VBN on|on|IN different|different|JJ occasions|occasion|NNS to|to|TO make|make|VB the|the|DT 3|3|CD replicates|replicate|VBZ used|use|VBN in|in|IN this|this|DT study|study|NN .|.|.
A6|a6|NN :|:|: LJ110|lj110|NN del|del|FW pdhr|pdhr|FW MMPyruvat|mmpyruvat|NN
A7|a7|NN :|:|: LJ110|lj110|NN pTM30|ptm30|NN MMPyruvat|mmpyruvat|NN
A8|a8|NN :|:|: LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN MMPyruvat|mmpyruvat|NN
A9|a9|NN :|:|: LJ110|lj110|NN MMAcetat|mmacetat|NN
accession|accession|NN :|:|: NC|nc|NN _|_|SYM 000913.2|000913.2|CD +|+|CC NC|NC|NNP _|_|SYM 000913.3|000913.3|CD
accession|accession|NN :|:|: U00006|u00006|NN
According|accord|VBG to|to|TO Invitrogen|Invitrogen|NNP PureLink|PureLink|NNP Micro-to-Midi|Micro-to-Midi|NNP Total|Total|NNP RNA|rna|NN Purification|purification|NN System|System|NNP
acetate|acetate|NN
acetonitrile|acetonitrile|NN
Acid|acid|NN adaptation|adaptation|NN was|be|VBD done|do|VBN in|in|IN DMEM|dmem|NN at|at|IN pH|ph|NN 5.0|5.0|CD at|at|IN room|room|NN temperature|temperature|NN ,|,|, followed|follow|VBN by|by|IN acid-stress|acid-stress|NN at|at|IN pH|ph|NN 3.0|3.0|CD for|for|IN 30|30|CD minutes|minute|NNS
Acidic|Acidic|NNP Hot|Hot|NNP Phenol|Phenol|NNP
Acid|Acid|NNP shocking|shocking|JJ was|be|VBD done|do|VBN in|in|IN DMEM|dmem|NN at|at|IN pH|ph|NN 3.0|3.0|CD at|at|IN room|room|NN temperature|temperature|NN for|for|IN 30|30|CD minutes|minute|NNS
Acid|acid|NN shocking|shocking|JJ was|be|VBD done|do|VBN in|in|IN DMEM|dmem|NN at|at|IN pH|ph|NN 3.0|3.0|CD -LRB-|-lrb-|-LRB- unbuffered|unbuffered|JJ -RRB-|-rrb-|-RRB- at|at|IN room|room|NN temperature|temperature|NN for|for|IN 15|15|CD minutes|minute|NNS
AcrA-Negative|AcrA-Negative|NNP ,|,|, Multidrug|Multidrug|NNP Efflux|Efflux|NNP Mutant|Mutant|NNP Strain|Strain|NNP
AcrB|acrb|NN -|-|: and|and|CC EmrAB-Negative|emrab-negative|JJ ,|,|, Multidrug|multidrug|JJ Efflux|Efflux|NNP Mutant|Mutant|NNP Strain|Strain|NNP
AcrB-Negative|AcrB-Negative|NNP ,|,|, Multidrug|Multidrug|NNP Efflux|Efflux|NNP Mutant|Mutant|NNP Strain|Strain|NNP
ACSH|ACSH|NNP _|_|VBD Exp|Exp|NNP _|_|NNP CIYS|CIYS|NNP
ACSH|ACSH|NNP _|_|VBD Exp|Exp|NNP _|_|NNP CNFT|CNFT|NNP
ACSH|ACSH|NNP _|_|VBD Stat1|stat1|NN _|_|CD CNFW|CNFW|NNP
ACSH|ACSH|NNP _|_|VBD Stat1|stat1|NN _|_|CD CNGG|CNGG|NNP
ACSH|ACSH|NNP _|_|VBD Trans|Trans|NNP _|_|NNP CIYT|CIYT|NNP
ACSH|ACSH|NNP _|_|VBD Trans|Trans|NNP _|_|NNP CNFU|CNFU|NNP
A|a|DT culture|culture|NN volume|volume|NN of|of|IN 7|7|CD ml|ml|NN was|be|VBD mixed|mix|VBN with|with|IN the|the|DT same|same|JJ volume|volume|NN of|of|IN boiling|boil|VBG 2|2|CD %|%|NN SDS|sds|NN ,|,|, 4mM|4mm|NN EDTA|edta|NN and|and|CC heated|heat|VBN at|at|IN 100|100|CD °C|°c|NN for|for|IN 3|3|CD to|to|TO 5|5|CD minutes|minute|NNS then|then|RB vortexed|vortex|VBD .|.|. At|at|IN this|this|DT stage|stage|NN ,|,|, the|the|DT extract|extract|NN was|be|VBD either|either|CC processed|process|VBN further|further|JJ or|or|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|.
Adapted|adapt|VBD E.|e.|FW coli|coli|FW -LRB-|-lrb-|-LRB- DST160|dst160|NN ,|,|, tolerant|tolerant|JJ to|to|TO high|high|JJ succinic|succinic|JJ acid|acid|NN concentration|concentration|NN -RRB-|-rrb-|-RRB-
Adapter|adapter|NN cutting|cut|VBG using|use|VBG cutadapt|cutadapt|NN ,|,|, version|version|NN 1.2.1|1.2.1|CD ,|,|, parameters|parameter|NNS -|-|: e|e|SYM 0.1|0.1|CD -|-|: O|o|NN 1|1|CD -|-|: m|m|NN 12|12|CD
Adapter|Adapter|NNP cutting|cut|VBG using|use|VBG cutadapt|cutadapt|NN ,|,|, version|version|NN 1.8.3|1.8.3|CD ,|,|, parameters|parameter|NNS -|-|: e|e|SYM 0.1|0.1|CD -|-|: O|o|NN 1|1|CD -|-|: m|m|NN 12|12|CD
Adapters|adapter|NNS trimmed|trim|VBD with|with|IN Cutadapt|cutadapt|NN -LRB-|-lrb-|-LRB- v1|v1|NN .12|.12|CD -RRB-|-rrb-|-RRB-
Adaptive|adaptive|JJ threshold|threshold|NN -LRB-|-lrb-|-LRB- quantitation|quantitation|NN method|method|NN -RRB-|-rrb-|-RRB- uses|use|VBZ the|the|DT parameters|parameter|NNS of|of|IN the|the|DT spot|spot|NN diameter|diameter|NN and|and|CC background|background|NN inner|inner|JJ and|and|CC outer|outer|JJ dimensions|dimension|NNS to|to|TO create|create|VB a|a|DT spot|spot|NN mask|mask|NN and|and|CC background|background|NN mask|mask|NN ,|,|, then|then|RB refines|refine|VBZ the|the|DT mask|mask|NN on|on|IN a|a|DT pixel-by-pixel|pixel-by-pixel|JJ basis|basis|NN .|.|. Total|total|JJ -LRB-|-lrb-|-LRB- normalization|normalization|NN method|method|NN -RRB-|-rrb-|-RRB- ,|,|, uses|use|VBZ the|the|DT intensity|intensity|NN of|of|IN each|each|DT spot|spot|NN in|in|IN relation|relation|NN to|to|TO all|all|DT spots|spot|NNS .|.|.
Adaptor|adaptor|NN Sequences|sequence|NNS were|be|VBD removed|remove|VBN using|use|VBG fastx|fastx|NN _|_|NN clipper|clipper|NN .|.|. -LRB-|-lrb-|-LRB- http://hannonlab.cshl.edu/fastx_toolkit/index.html|http://hannonlab.cshl.edu/fastx_toolkit/index.html|NN -RRB-|-rrb-|-RRB- -|-|: Example|example|NN :|:|: fastx|fastx|NN _|_|NN clipper|clipper|NN -|-|: a|a|DT GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGTATCTCGTATG|gatcggaagagcacacgtctgaactccagtcaccgatgtatctcgtatg|NN -|-|: i|i|FW DL4900|dl4900|FW _|_|SYM raw.fasta|raw.fasta|SYM -|-|: o|o|NN DL4900|dl4900|NN _|_|CD clipped.fasta|clipped.fasta|JJ
Add|add|VBP 100|100|CD μl|μl|NN 1|1|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- TE|te|NN buffer|buffer|NN :|:|: 10|10|CD mM|mm|NN Tris-HCL|tris-hcl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN pH|ph|NN =|=|JJ 8.0|8.0|CD containing|contain|VBG 1|1|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN -RRB-|-rrb-|-RRB- .|.|. Vortex|Vortex|NNP for|for|IN 10|10|CD s|s|NNS and|and|CC incubate|incubate|VB at|at|IN RT|rt|NN for|for|IN at|at|IN least|least|JJS 15|15|CD min|min|NN .|.|. Add|add|VB 350|350|CD μl|μl|NN Buffer|buffer|NN RLT|rlt|NN and|and|CC vortex|vortex|NN vigorously|vigorously|RB .|.|. Add|add|VB 250|250|CD μl|μl|NN 100|100|CD %|%|NN ethanol|ethanol|NN ,|,|, mix|mix|NN by|by|IN pipetting|pipetting|NN .|.|.
Adenosine|Adenosine|NNP addition|addition|NN
Adpater|adpater|NN sequences|sequence|NNS were|be|VBD clipped|clip|VBN with|with|IN CutAdapt|CutAdapt|NNP
Aeration|Aeration|NNP was|be|VBD initiated|initiate|VBN at|at|IN 1|1|CD l/min|l/min|NN when|when|WRB the|the|DT culture|culture|NN reached|reach|VBD an|a|DT OD|od|NN -LRB-|-lrb-|-LRB- 600nm|600nm|NN -RRB-|-rrb-|-RRB- of|of|IN 3|3|CD .|.|.
Aerobic|Aerobic|NNP 1|1|CD
Aerobic|Aerobic|NNP 2|2|CD
Aerobic|Aerobic|NNP 3|3|CD
Aerobic|Aerobic|NNP and|and|CC anaerobic|anaerobic|JJ cultures|culture|NNS were|be|VBD grown|grow|VBN in|in|IN 600|600|CD mL|ml|NN aliquots|aliquot|NNS of|of|IN DM25|dm25|NN and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN an|a|DT orbital|orbital|JJ shaking|shake|VBG of|of|IN 150|150|CD RPM|rpm|NN and|and|CC inoculated|inoculate|VBN with|with|IN 1/100th|1/100th|JJ volume|volume|NN of|of|IN overnight|overnight|JJ culture|culture|NN .|.|. Aerobic|aerobic|JJ cultures|culture|NNS were|be|VBD grown|grow|VBN for|for|IN 9|9|CD h|h|NN while|while|IN anaerobic|anaerobic|JJ cultures|culture|NNS were|be|VBD grown|grow|VBN for|for|IN 16|16|CD h.|h.|NN
Aerobic|aerobic|JJ culture|culture|NN
Aerobic|aerobic|JJ cultures|culture|NNS
Aerobic|Aerobic|NNP Cultures|Cultures|NNP
Aerobic|Aerobic|NNP E.|E.|NNP coli|coli|NN exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS
Aerobic|Aerobic|NNP E.|E.|NNP coli|coli|NN not|not|RB exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- control|control|NN cells|cell|NNS -RRB-|-rrb-|-RRB-
Aerobic|aerobic|JJ growth|growth|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN specified|specify|VBN media|media|NNS
aerobic|aerobic|JJ INPUT|input|NN DNA|dna|NN
Aerobic|aerobic|JJ MG1655|mg1655|NN exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS
Aerobic|aerobic|JJ MG1655|mg1655|NN not|not|RB exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- control|control|NN cells|cell|NNS -RRB-|-rrb-|-RRB-
aerobic|aerobic|JJ reference|reference|NN
affyexp|affyexp|JJ _|_|NN delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ
affyexp|affyexp|NN _|_|CD delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 1|1|CD .|.|. CEL|CEL|NNP
affyexp|affyexp|JJ _|_|NN delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 2|2|CD .|.|. CEL|CEL|NNP
affyexp|affyexp|JJ _|_|NN delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 3|3|CD .|.|. CEL|CEL|NNP
affyexp|affyexp|JJ _|_|NN delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN
affyexp|affyexp|JJ _|_|NN delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 1|1|CD .|.|. CEL|CEL|NNP
affyexp|affyexp|JJ _|_|NN delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 2|2|CD .|.|. CEL|CEL|NNP
affyexp|affyexp|JJ _|_|NN delta-arcA|delta-arca|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 3|3|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 1|1|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 2|2|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 3|3|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 1|1|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 2|2|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD delta-fnr|delta-fnr|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 3|3|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 1|1|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 2|2|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 3|3|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 1|1|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 2|2|CD .|.|. CEL|cel|NN
affyexp|affyexp|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 3|3|CD .|.|. CEL|CEL|NNP
Affymetrix|Affymetrix|NNP .|.|. CEL|CEL|NNP files|file|VBZ data|datum|NNS were|be|VBD normalized|normalize|VBN with|with|IN dChip|dchip|NN using|use|VBG the|the|DT array|array|NN of|of|IN median|median|JJ brightness|brightness|NN -LRB-|-lrb-|-LRB- BS|bs|NN -RRB-|-rrb-|-RRB- .|.|. Model|Model|NNP method|method|NN :|:|: model-base|model-base|NN expression|expression|NN ;|;|: background|background|NN substraction|substraction|NN :|:|: Mismatch|Mismatch|NNP Probe|Probe|NNP -LRB-|-lrb-|-LRB- PM/MM|PM/MM|NNP difference|difference|NN -RRB-|-rrb-|-RRB-
Affymetrix|Affymetrix|NNP GeneChip|GeneChip|NNP Operating|Operating|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- GCOS|GCOS|NNP -RRB-|-rrb-|-RRB- Version|Version|NNP 1.4|1.4|CD Details|detail|NNS :|:|: Intra-chip|intra-chip|JJ normalizations|normalization|NNS were|be|VBD performed|perform|VBN using|use|VBG Affymetrix|Affymetrix|NNP Gene|Gene|NNP Chip|Chip|NNP Operating|Operating|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- GCOS|GCOS|NNP -RRB-|-rrb-|-RRB- .|.|. Default|Default|NNP statistical|statistical|JJ parameters|parameter|NNS were|be|VBD used|use|VBN to|to|TO normalize|normalize|VB each|each|DT chip|chip|NN to|to|TO the|the|DT same|same|JJ target|target|NN intensity|intensity|NN -LRB-|-lrb-|-LRB- 1500|1500|CD -RRB-|-rrb-|-RRB- as|as|IN described|describe|VBN in|in|IN the|the|DT Affymetrix|Affymetrix|NNP GeneChip|GeneChip|NNP Expression|expression|NN Analysis|analysis|NN manual|manual|NN .|.|. All|all|DT nine|nine|CD possible|possible|JJ inter-chip|inter-chip|NN comparisons|comparison|NNS were|be|VBD performed|perform|VBN in|in|IN GCOS|gcos|NN .|.|. The|the|DT data|datum|NNS were|be|VBD subsequently|subsequently|RB exported|export|VBN to|to|TO a|a|DT Microsoft|Microsoft|NNP Excel|Excel|NNP spreadsheet|spreadsheet|NN for|for|IN manipulation|manipulation|NN .|.|. Consensus|consensus|NN ``|``|`` detection|detection|NN p-value|p-value|NN ''|''|'' ,|,|, ``|``|`` change|change|NN p-value|p-value|NN ''|''|'' ,|,|, and|and|CC ``|``|`` signal|signal|NN log|log|NN ratios|ratio|NNS ''|''|'' were|be|VBD calculated|calculate|VBN ,|,|, and|and|CC the|the|DT default|default|NN E.|e.|FW coli|coli|FW array|array|NN p-value|p-value|NN cutoff|cutoff|NN parameters|parameter|NNS were|be|VBD applied|apply|VBN to|to|TO these|these|DT consensus|consensus|NN values|value|NNS to|to|TO estimate|estimate|VB the|the|DT transcript|transcript|NN change|change|NN between|between|IN two|two|CD conditions|condition|NNS and|and|CC the|the|DT transcript|transcript|NN presence|presence|NN under|under|IN each|each|DT condition|condition|NN .|.|. Background-subtracted|background-subtracted|JJ data|datum|NNS sets|set|NNS were|be|VBD used|use|VBN to|to|TO calculate|calculate|VB up-regulated|up-regulate|VBN and|and|CC down-regulated|down-regulate|VBN genes|gene|NNS based|base|VBN on|on|IN fold|fold|JJ changes|change|NNS of|of|IN greater|greater|JJR than|than|IN 2|2|CD .|.|.
Affymetrix|Affymetrix|NNP Microarray|Microarray|NNP Suite|Suite|NNP 5.0|5.0|CD
Affymetrix|Affymetrix|NNP Microarray|Microarray|NNP Suite/GCOS|Suite/GCOS|NNP
After|after|IN 0.5|0.5|CD M|m|NN NaCl|nacl|NN treatment|treatment|NN for|for|IN 10|10|CD min|min|NN of|of|IN the|the|DT early-exponential|early-exponential|JJ phase|phase|NN cells|cell|NNS ,|,|, samples|sample|NNS were|be|VBD collected|collect|VBN .|.|.
After|after|IN 0.5|0.5|CD M|m|NN NaCl|nacl|NN treatment|treatment|NN for|for|IN 20|20|CD min|min|NN of|of|IN the|the|DT early-exponential|early-exponential|JJ phase|phase|NN cells|cell|NNS ,|,|, samples|sample|NNS were|be|VBD collected|collect|VBN .|.|.
After|after|IN 0.5|0.5|CD M|m|NN NaCl|nacl|NN treatment|treatment|NN for|for|IN 45|45|CD min|min|NN of|of|IN the|the|DT early-exponential|early-exponential|JJ phase|phase|NN cells|cell|NNS ,|,|, samples|sample|NNS were|be|VBD collected|collect|VBN .|.|.
After|after|IN 50|50|CD hours|hour|NNS ,|,|, samples|sample|NNS -LRB-|-lrb-|-LRB- 10|10|CD ml|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD harvested|harvest|VBN directly|directly|RB into|into|IN RNA|rna|NN Protect|protect|VB -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- to|to|TO stabilize|stabilize|VB RNA|rna|NN ,|,|, and|and|CC total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN as|as|IN recommended|recommend|VBN by|by|IN the|the|DT suppliers|supplier|NNS .|.|. RNA|rna|NN was|be|VBD quantified|quantify|VBN using|use|VBG a|a|DT BioPhotometer|biophotometer|NN -LRB-|-lrb-|-LRB- Eppendorf|eppendorf|NN -RRB-|-rrb-|-RRB- .|.|.
After|after|IN 5|5|CD h|h|NN of|of|IN NP-TiO2|np-tio2|NN -LRB-|-lrb-|-LRB- or|or|CC mQ|mq|NN water|water|NN for|for|IN the|the|DT control|control|NN -RRB-|-rrb-|-RRB- exposure|exposure|NN ,|,|, cells|cell|NNS were|be|VBD incubated|incubate|VBN for|for|IN 5|5|CD min|min|NN with|with|IN two|two|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP SAS|SAS|NNP ,|,|, France|France|NNP -RRB-|-rrb-|-RRB- at|at|IN room|room|NN temperature|temperature|NN .|.|. Cells|cell|NNS were|be|VBD then|then|RB pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 7,000|7,000|CD g|g|NN ,|,|, 10|10|CD min|min|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT pellet|pellet|NN stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN .|.|.
After|after|IN 60|60|CD minutes|minute|NNS into|into|IN the|the|DT incubation|incubation|NN ,|,|, the|the|DT plate|plate|NN was|be|VBD briefly|briefly|RB removed|remove|VBN so|so|RB inducer|inducer|NN could|could|MD be|be|VB added|add|VBN to|to|TO wells|well|NNS ,|,|, and|and|CC this|this|DT time|time|NN point|point|NN was|be|VBD set|set|VBN as|as|IN time|time|NN 0|0|CD .|.|. Samples|sample|NNS were|be|VBD instead|instead|RB removed|remove|VBN from|from|IN wells|well|NNS at|at|IN 15|15|CD and|and|CC 60|60|CD minutes|minute|NNS after|after|IN induction|induction|NN for|for|IN processing|processing|NN .|.|.
After|after|IN 6|6|CD hours|hour|NNS of|of|IN growth|growth|NN both|both|CC control|control|NN and|and|CC test|test|NN strains|strain|NNS were|be|VBD induced|induce|VBN with|with|IN 0.5|0.5|CD mM|mm|NN IPTG|iptg|NN and|and|CC harvested|harvest|VBN 2|2|CD hours|hour|NNS post-induction|post-induction|JJ .|.|.
After|after|IN backgroud|backgroud|NN correction|correction|NN and|and|CC total|total|JJ intensity|intensity|NN normalization|normalization|NN ,|,|, ratio|ratio|NN to|to|TO reference|reference|NN were|be|VBD calculated|calculate|VBN and|and|CC log|log|NN base|base|NN 2|2|CD transformed|transform|VBN
After|after|IN chilling|chill|VBG on|on|IN ice|ice|NN ,|,|, each|each|DT 100-ml|100-ml|JJ culture|culture|NN was|be|VBD mixed|mix|VBN with|with|IN 25|25|CD ml|ml|NN ice-cold|ice-cold|JJ ethanol/phenol|ethanol/phenol|NN solution|solution|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- ,|,|, water-saturated|water-saturated|JJ phenol|phenol|NN in|in|IN 95|95|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- ethanol|ethanol|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 7,000|7,000|CD g|g|NN for|for|IN 2|2|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN ,|,|, flash-frozen|flash-frozen|JJ with|with|IN dry|dry|JJ ice|ice|NN ,|,|, and|and|CC stored|store|VBD at|at|IN --|--|: 80|80|CD °C|°c|NN .|.|. Two|two|CD independent|independent|JJ cultures|culture|NNS for|for|IN each|each|DT sample|sample|NN were|be|VBD mixed|mix|VBN together|together|RB for|for|IN determination|determination|NN of|of|IN transcriptional|transcriptional|JJ profiles|profile|NNS .|.|. Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN the|the|DT collected|collect|VBN bacterial|bacterial|JJ cells|cell|NNS using|use|VBG TRIzol|trizol|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientifc|Scientifc|NNP -RRB-|-rrb-|-RRB- .|.|.
After|after|IN collecting|collect|VBG 50|50|CD ml|ml|NN culture|culture|NN as|as|IN `|`|`` non|non|JJ crosslinked|crosslink|VBN '|'|'' sample|sample|NN ,|,|, the|the|DT rest|rest|NN of|of|IN the|the|DT cells|cell|NNS was|be|VBD crosslinked.Crosslinked|crosslinked.crosslinked|VBN and|and|CC non|non|JJ crosslinked|crosslink|VBN cells|cell|NNS were|be|VBD washed|wash|VBN and|and|CC sonicated|sonicate|VBN .|.|. 400|400|CD µl|µl|NN of|of|IN the|the|DT sonicated|sonicated|JJ extracts|extract|NNS were|be|VBD mixed|mix|VBN with|with|IN 400|400|CD µl|µl|NN TE|te|NN buffer|buffer|NN and|and|CC incubated|incubate|VBN with|with|IN 2|2|CD µl|µl|NN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 20|20|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- at|at|IN 42|42|CD °C|°c|NN for|for|IN 1|1|CD h.|h.|NNP Next|Next|NNP ,|,|, 200|200|CD µl|µl|NN proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- 20|20|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN and|and|CC samples|sample|NNS incubated|incubate|VBN for|for|IN 2|2|CD h|h|NN at|at|IN 42|42|CD and|and|CC 6|6|CD h|h|NN at|at|IN 65|65|CD °C|°c|NN .|.|. DNA|dna|NN was|be|VBD extracted|extract|VBN with|with|IN phenol|phenol|NN and|and|CC chlorophorm|chlorophorm|NN
After|after|IN dividing|divide|VBG sequence|sequence|NN runs|run|NNS by|by|IN barcode|barcode|NN ,|,|, we|we|PRP mapped|map|VBD the|the|DT reads|read|VBZ to|to|TO the|the|DT relevant|relevant|JJ genomes|genome|NNS using|use|VBG the|the|DT ssaha2|ssaha2|NN algorithm|algorithm|NN .|.|. Minimum|Minimum|NNP score|score|NN thresholds|threshold|NNS for|for|IN ssaha|ssaha|NN were|be|VBD selected|select|VBN based|base|VBN on|on|IN the|the|DT distribution|distribution|NN of|of|IN scores|score|NNS for|for|IN all|all|DT mapped|map|VBN reads|read|VBZ of|of|IN a|a|DT 32nt|32nt|JJ barcoded|barcoded|JJ sample|sample|NN and|and|CC a|a|DT 36-nt|36-nt|JJ non-barcoded|non-barcoded|JJ sample|sample|NN -LRB-|-lrb-|-LRB- 29|29|CD was|be|VBD selected|select|VBN as|as|IN the|the|DT minimum|minimum|JJ score|score|NN for|for|IN 32nt|32nt|JJ barcoded|barcoded|JJ samples|sample|NNS ;|;|: 33|33|CD was|be|VBD the|the|DT minimum|minimum|JJ score|score|NN used|use|VBN for|for|IN 36-nt|36-nt|JJ non-barcoded|non-barcoded|JJ samples|sample|NNS -RRB-|-rrb-|-RRB- .|.|. Although|although|IN an|a|DT 18-nt|18-nt|JJ read|read|NN is|be|VBZ sufficient|sufficient|JJ to|to|TO map|map|VB more|more|JJR than|than|IN 90|90|CD %|%|NN of|of|IN the|the|DT sequencing|sequencing|NN reads|read|VBZ ,|,|, even|even|RB at|at|IN 32-36nt|32-36nt|JJ there|there|EX is|be|VBZ a|a|DT large|large|JJ fraction|fraction|NN of|of|IN the|the|DT reads|read|VBZ that|that|IN map|map|NN to|to|TO multiple|multiple|JJ locations|location|NNS within|within|IN a|a|DT genome|genome|NN or|or|CC across|across|IN genomes|genome|NNS .|.|. Reads|read|NNS that|that|WDT map|map|VBP non-uniquely|non-uniquely|JJ were|be|VBD discarded|discard|VBN .|.|.
After|after|IN each|each|DT sequenced|sequence|VBN fragments|fragment|NNS were|be|VBD aligned|align|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN using|use|VBG Bowtie|Bowtie|NNP ,|,|, the|the|DT position|position|NN of|of|IN each|each|DT alignment|alignment|NN is|be|VBZ distributed|distribute|VBN into|into|IN several|several|JJ nucleotides|nucleotide|NNS in|in|IN the|the|DT center|center|NN of|of|IN the|the|DT footprint|footprint|NN .|.|. For|for|IN each|each|DT footprint|footprint|NN read|read|NN ,|,|, the|the|DT center|center|NN residues|residue|NNS that|that|WDT are|be|VBP at|at|IN least|least|JJS 12|12|CD nucleotides|nucleotide|NNS away|away|RB from|from|IN either|either|CC ends|end|NNS were|be|VBD given|give|VBN the|the|DT same|same|JJ score|score|NN ,|,|, which|which|WDT is|be|VBZ weighted|weight|VBN by|by|IN the|the|DT length|length|NN of|of|IN the|the|DT fragment|fragment|NN -LSB-|-lsb-|-LRB- Oh|oh|UH et|et|FW al|al|FW ,|,|, .|.|. Cell|cell|NN 147|147|CD ,|,|, 1295|1295|CD -LRB-|-lrb-|-LRB- 2011|2011|CD -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- .|.|. More|more|RBR at|at|IN G.W.|G.W.|NNP Li|Li|NNP ,|,|, E.|E.|NNP Oh|oh|UH ,|,|, and|and|CC J.S.|J.S.|NNP Weissman|Weissman|NNP ,|,|, Nature|Nature|NNP -LRB-|-lrb-|-LRB- in|in|IN press|press|NN -RRB-|-rrb-|-RRB-
After|after|IN exposed|expose|VBN under|under|IN the|the|DT red|red|JJ light|light|NN with|with|IN a|a|DT specific|specific|JJ ON/OFF|on/off|NN frequency|frequency|NN for|for|IN 10|10|CD hours|hour|NNS ,|,|, 1|1|CD ml|ml|NN bacterial|bacterial|JJ culture|culture|NN was|be|VBD sampled|sample|VBN and|and|CC the|the|DT bacterial|bacterial|JJ cells|cell|NNS were|be|VBD collected|collect|VBN at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT total|total|JJ RNA|rna|NN of|of|IN E.|e.|FW coli|coli|FW was|be|VBD extracted|extract|VBN using|use|VBG RNAprep|rnaprep|NN pure|pure|JJ Cell/Bacteria|Cell/Bacteria|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- TIANGEN|TIANGEN|NNP ,|,|, DP430|dp430|NN -RRB-|-rrb-|-RRB- and|and|CC preserved|preserve|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
After|after|IN normalization|normalization|NN ,|,|, the|the|DT expression|expression|NN of|of|IN a|a|DT gene|gene|NN was|be|VBD calculated|calculate|VBN by|by|IN a|a|DT RMA-summarization|rma-summarization|NN procedure|procedure|NN within|within|IN each|each|DT growth|growth|NN condition|condition|NN .|.|.
After|after|IN normalization|normalization|NN ,|,|, the|the|DT read|read|NN counts|count|NNS were|be|VBD estimated|estimate|VBN in|in|IN the|the|DT running|run|VBG windows|window|NNS of|of|IN 35|35|CD bp|bp|NN ,|,|, and|and|CC the|the|DT ratios|ratio|NNS R|r|NN between|between|IN values|value|NNS obtained|obtain|VBN for|for|IN experimental|experimental|JJ and|and|CC control|control|JJ libraries|library|NNS were|be|VBD calculated|calculate|VBN .|.|. Peaks|peak|NNS were|be|VBD localized|localized|JJ requiring|require|VBG R|r|NN ≥|≥|CD 1.5|1.5|CD for|for|IN at|at|IN least|least|JJS 50|50|CD %|%|NN positions|position|NNS of|of|IN at|at|IN least|least|JJS 60|60|CD bp|bp|NN genomic|genomic|JJ region|region|NN in|in|IN length|length|NN .|.|.
After|after|IN quality|quality|NN controls|control|NNS of|of|IN data|datum|NNS distribution|distribution|NN the|the|DT raw|raw|JJ data|data|NN -LRB-|-lrb-|-LRB- CEL|cel|NN files|file|NNS -RRB-|-rrb-|-RRB- were|be|VBD used|use|VBN to|to|TO perform|perform|VB ,|,|, normalization|normalization|NN and|and|CC probe|probe|NN set|set|VBD summarization|summarization|NN through|through|IN RMA|RMA|NNP algorithm|algorithm|NN -LRB-|-lrb-|-LRB- Robust|robust|JJ Multiarray|Multiarray|NNP Analysis|analysis|NN -RRB-|-rrb-|-RRB- by|by|IN using|use|VBG the|the|DT Affymetrix|Affymetrix|NNP Gene|Gene|NNP Expression|expression|NN Console|Console|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- www.affymetrix.com|www.affymetrix.com|NNP -RRB-|-rrb-|-RRB- .|.|. Normalized|normalize|VBN data|datum|NNS were|be|VBD then|then|RB uploaded|upload|VBN into|into|IN OneChannelGUI|OneChannelGUI|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- http://www.bioinformatica.unito.it/oneChannelGUI/|http://www.bioinformatica.unito.it/onechannelgui/|NN -RRB-|-rrb-|-RRB- to|to|TO perform|perform|VB a|a|DT differential|differential|JJ expression|expression|NN analysis|analysis|NN .|.|. As|as|IN the|the|DT dataset|dataset|NN is|be|VBZ limited|limit|VBN in|in|IN number|number|NN of|of|IN samples|sample|NNS and|and|CC replicates|replicate|VBZ -LRB-|-lrb-|-LRB- 4|4|CD GeneChips|genechip|NNS hybridized|hybridize|VBD ,|,|, 2|2|CD replicates|replicate|VBZ for|for|IN each|each|DT condition|condition|NN -RRB-|-rrb-|-RRB- we|we|PRP decided|decide|VBD to|to|TO apply|apply|VB a|a|DT simple|simple|JJ non-parametric|non-parametric|JJ statistical|statistical|JJ method|method|NN based|base|VBN on|on|IN ranks|rank|NNS of|of|IN fold|fold|JJ changes|change|NNS to|to|TO perform|perform|VB a|a|DT two-class|two-class|JJ paired|paired|JJ differential|differential|JJ analysis|analysis|NN .|.|. To|to|TO select|select|VB only|only|RB significatively|significatively|RB differentially|differentially|RB expressed|express|VBN genes|gene|NNS we|we|PRP set|set|VBD the|the|DT following|follow|VBG parameters|parameter|NNS for|for|IN the|the|DT Rank|Rank|NNP Product|product|NN analysis|analysis|NN :|:|: 100|100|CD permutations|permutation|NNS and|and|CC 0.1|0.1|CD cut-off|cut-off|JJ percentage|percentage|NN of|of|IN false|false|JJ positives|positive|NNS -LRB-|-lrb-|-LRB- pfp|pfp|NN -RRB-|-rrb-|-RRB- which|which|WDT corresponds|correspond|VBZ to|to|TO a|a|DT p-value|p-value|NN <|<|JJR 0.01|0.01|CD .|.|.
After|after|IN reaching|reach|VBG an|a|DT OD600nm|od600nm|NN of|of|IN 0.9|0.9|CD ,|,|, cell|cell|NN cultures|culture|NNS were|be|VBD placed|place|VBN immediately|immediately|RB in|in|IN a|a|DT shaking|shake|VBG water|water|NN bath|bath|NN along|along|IN with|with|IN another|another|DT BHI|BHI|NNP flask|flask|NN carrying|carry|VBG a|a|DT type|type|NN T|t|NN thermocouple|thermocouple|NN connected|connect|VBN to|to|TO a|a|DT MultiPaq|MultiPaq|NNP 21|21|CD datalogger|datalogger|NN -LRB-|-lrb-|-LRB- Datapaq|Datapaq|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- for|for|IN temperature|temperature|NN profile|profile|NN and|and|CC the|the|DT process|process|NN lethality|lethality|NN values|value|NNS monitoring|monitor|VBG in|in|IN real|real|JJ time|time|NN .|.|. Bacteria|bacterium|NNS suspension|suspension|NN were|be|VBD heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO process|process|NN lethality|lethality|NN values|value|NNS of|of|IN 2|2|CD and|and|CC 3|3|CD ,|,|, at|at|IN 60|60|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD ,|,|, or|or|CC until|until|IN a|a|DT temperature|temperature|NN of|of|IN 71|71|CD °C|°c|NN was|be|VBD reached|reach|VBN .|.|. Just|just|RB after|after|IN heating|heating|NN ,|,|, cell|cell|NN suspension|suspension|NN was|be|VBD cooled|cool|VBN in|in|IN an|a|DT iced|iced|JJ water|water|NN bath|bath|NN under|under|IN constant|constant|JJ agitation|agitation|NN -LRB-|-lrb-|-LRB- 150|150|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- until|until|IN the|the|DT temperature|temperature|NN dropped|drop|VBD back|back|RB to|to|TO no|no|DT less|less|JJR than|than|IN 37|37|CD °C|°c|NN in|in|IN order|order|NN to|to|TO avoid|avoid|VB cold|cold|JJ stress|stress|NN .|.|. Cell|cell|NN suspensions|suspension|NNS were|be|VBD then|then|RB centrifuged|centrifuge|VBN and|and|CC the|the|DT remaining|remain|VBG cell|cell|NN pellets|pellet|NNS were|be|VBD treated|treat|VBN with|with|IN RNA|rna|NN protect|protect|VBP bacteria|bacterium|NNS reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- prior|prior|RB to|to|TO freezing|freezing|NN at|at|IN -80|-80|CD °C|°c|NN .|.|.
After|after|IN the|the|DT final|final|JJ wash|wash|NN &|&|CC staining|staining|NN step|step|NN ,|,|, Affymetrix|Affymetrix|NNP GeneChip|GeneChip|NNP ®|®|NNP E.coli|E.coli|NNP Genome|Genome|NNP array|array|NN was|be|VBD scanned|scan|VBN using|use|VBG Affymetrix|Affymetrix|NNP Model|Model|NNP 3000|3000|CD G7|G7|NNP scanner|scanner|NN and|and|CC the|the|DT image|image|NN data|datum|NNS was|be|VBD extracted|extract|VBN through|through|IN Affymetrix|Affymetrix|NNP Commnad|Commnad|NNP Console|Console|NNP software|software|NN .|.|. The|the|DT raw|raw|JJ .|.|. cel|cel|NN file|file|NN generated|generate|VBN through|through|IN above|above|IN procedure|procedure|NN meant|mean|VBD expression|expression|NN intensity|intensity|NN data|datum|NNS and|and|CC was|be|VBD used|use|VBN for|for|IN the|the|DT next|next|JJ step|step|NN .|.|.
AG102MB|ag102mb|NN is|be|VBZ an|a|DT isogenic|isogenic|JJ mutant|mutant|JJ derived|derive|VBN from|from|IN hyper-resistant|hyper-resistant|JJ AG102|ag102|NN -LRB-|-lrb-|-LRB- marR1|marr1|NN -RRB-|-rrb-|-RRB- .|.|. It|it|PRP contains|contain|VBZ a|a|DT mutation|mutation|NN at|at|IN the|the|DT acrB|acrb|NN locus|locus|NN -LRB-|-lrb-|-LRB- marR1|marr1|NN ,|,|, acrB|acrb|NN :|:|: :|:|: kan|kan|NN -RRB-|-rrb-|-RRB- resulting|result|VBG in|in|IN a|a|DT multidrug|multidrug|JJ efflux|efflux|NN negative|negative|JJ phenotype|phenotype|NN .|.|.
AG102|ag102|NN was|be|VBD previously|previously|RB derived|derive|VBN from|from|IN AG100|ag100|NN -LRB-|-lrb-|-LRB- K-12|k-12|NN -RRB-|-rrb-|-RRB- .|.|. AG102|ag102|NN is|be|VBZ drug|drug|NN hyper-resistant|hyper-resistant|JJ due|due|JJ to|to|TO a|a|DT mutation|mutation|NN in|in|IN marR|marr|NN -LRB-|-lrb-|-LRB- marR1|marr1|NN -RRB-|-rrb-|-RRB- which|which|WDT increases|increase|VBZ expression|expression|NN of|of|IN MarA|mara|NN ,|,|, a|a|DT global|global|JJ regulator|regulator|NN ,|,|, which|which|WDT in|in|IN turn|turn|NN results|result|VBZ in|in|IN overexpression|overexpression|NN of|of|IN the|the|DT AcrAB-TolC|acrab-tolc|NN multidrug|multidrug|JJ efflux|efflux|NN system|system|NN .|.|.
A|a|NN generalized|generalize|VBN linear|linear|JJ model|model|NN likelihood|likelihood|NN ratio|ratio|NN test|test|NN was|be|VBD performed|perform|VBN to|to|TO test|test|VB for|for|IN differential|differential|JJ expression|expression|NN between|between|IN groups|group|NNS -LRB-|-lrb-|-LRB- HUS|hus|NNS vs.|vs.|CC non-HUS|non-hus|JJ -RRB-|-rrb-|-RRB- and|and|CC condition|condition|NN -LRB-|-lrb-|-LRB- induced|induce|VBN vs.|vs.|CC non-induced|non-induced|JJ -RRB-|-rrb-|-RRB- ,|,|, with|with|IN FDR-adjusted|fdr-adjusted|JJ p-values|p-values|NN <|<|JJR 0.05|0.05|CD regarded|regard|VBN as|as|IN statistically|statistically|RB significant|significant|JJ
agent|agent|NN :|:|: 0.05|0.05|CD mg/ml|mg/ml|NN Phloretin|phloretin|NN
agent|agent|NN :|:|: 0.5|0.5|CD %|%|NN honey|honey|NN
agent|agent|NN :|:|: 1x|1x|NN CORM2|corm2|NN
agent|agent|NN :|:|: 1x|1x|NN vehicle|vehicle|NN
agent|agent|NN :|:|: 20x|20x|CD CORM2|corm2|NN
agent|agent|NN :|:|: 20x|20x|CD vehicle|vehicle|NN
agent|agent|NN :|:|: control|control|NN
agent|agent|NN :|:|: control|control|NN -LRB-|-lrb-|-LRB- 1|1|CD ml|ml|NN of|of|IN LB|lb|NN broth|broth|NN added|add|VBD -RRB-|-rrb-|-RRB-
agent|agent|NN :|:|: CORM-401|corm-401|NN
agent|agent|NN :|:|: DPD|dpd|NN
agent|agent|NN :|:|: DPD|dpd|NN and|and|CC rifampicin|rifampicin|NN
agent|agent|NN :|:|: ethanol|ethanol|NN -LRB-|-lrb-|-LRB- 1|1|CD ml|ml|NN of|of|IN ethanol|ethanol|NN 20|20|CD %|%|NN added|add|VBD -RRB-|-rrb-|-RRB-
agent|agent|NN :|:|: Fe|Fe|NNP
agent|agent|NN :|:|: Fe|Fe|NNP and|and|CC rifampicin|rifampicin|NN
agent|agent|NN :|:|: glycolaldehyde|glycolaldehyde|NN
agent|agent|NN :|:|: H2O|h2o|NN
agent|agent|NN :|:|: no|no|DT triclosan|triclosan|NN
agent|agent|NN :|:|: polyphenols|polyphenol|NNS -LRB-|-lrb-|-LRB- 1|1|CD ml|ml|NN of|of|IN OVWPE|ovwpe|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN added|add|VBD -RRB-|-rrb-|-RRB-
agent|agent|NN :|:|: triclosan|triclosan|NN
agent|agent|NN :|:|: ZnSO4|znso4|NN
Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- v|v|LS 10.10.1.1|10.10.1.1|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN background|background|NN subtraction|subtraction|NN and|and|CC LOWESS|lowess|NN normalization|normalization|NN .|.|.
Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- v|v|LS 8.5.1.1|8.5.1.1|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN background|background|NN subtraction|subtraction|NN and|and|CC LOWESS|lowess|NN normalization|normalization|NN .|.|.
Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP v.|v.|CC 9.5.3.1|9.5.3.1|CD was|be|VBD used|use|VBN for|for|IN background|background|NN subtraction|subtraction|NN and|and|CC LOWESS|lowess|NN normalization|normalization|NN .|.|.
Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP v.|v.|CC 9.5.3.1|9.5.3.1|CD was|be|VBD used|use|VBN for|for|IN background|background|NN subtraction|subtraction|NN and|and|CC LOWESS|lowess|NN normalization|normalization|NN .|.|.
Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP version|version|NN 10.5.1.1|10.5.1.1|CD .|.|.
Agilent|Agilent|NNP Feature|Feature|NNP Extract|extract|NN software|software|NN performed|perform|VBN background|background|NN normalization|normalization|NN and|and|CC LOWESS|lowess|NN correction|correction|NN for|for|IN dye|dye|VB bias|bias|NN .|.|. Non-E|non-e|NN .|.|. coli|coli|NN K-12|k-12|NN probes|probe|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT dataset|dataset|NN ,|,|, as|as|IN the|the|DT BW25113|bw25113|NN strain|strain|NN is|be|VBZ a|a|DT K-12|k-12|NN strain|strain|NN .|.|.
Agilent|Agilent|NNP Scan|scan|VB Control|Control|NNP Software|Software|NNP V.|V.|NNP 8.5|8.5|CD at|at|IN a|a|DT resolution|resolution|NN of|of|IN 3μm|3μm|NN .|.|. The|the|DT data|datum|NNS was|be|VBD extracted|extract|VBN using|use|VBG Agilent|Agilent|NNP Feature|Feature|NNP extraction|extraction|NN software|software|NN V|v|NN 10.10|10.10|CD
agitation|agitation|NN speed|speed|NN :|:|: 1200|1200|CD rpm|rpm|NN
agitation|agitation|NN speed|speed|NN :|:|: 600|600|CD rpm|rpm|NN
agno3|agno3|NN concentration|concentration|NN in|in|IN µm|µm|NN :|:|: 0|0|CD
agno3|agno3|NN concentration|concentration|NN in|in|IN µm|µm|NN :|:|: 5|5|CD
agno3|agno3|NN concentration|concentration|NN in|in|IN µm|µm|NN :|:|: 6.5|6.5|CD
agno3|agno3|NN concentration|concentration|NN in|in|IN µm|µm|NN :|:|: 8.5|8.5|CD
Alanine|alanine|NN addition|addition|NN
Alert|Alert|NNP
Algorithm|Algorithm|NNP :|:|: ExpressionStat|ExpressionStat|NNP 5.0|5.0|CD -LRB-|-lrb-|-LRB- Affymetrix|Affymetrix|NNP Microarray|Microarray|NNP Suite|Suite|NNP Version|Version|NNP 5.0|5.0|CD -RRB-|-rrb-|-RRB-
Aligned|Aligned|NNP reads|read|VBZ were|be|VBD designated|designate|VBN to|to|TO top|top|JJ and|and|CC bottom|bottom|JJ strands|strand|NNS using|use|VBG Samtools|Samtools|NNP
Aligned|Aligned|NNP to|to|TO NC|NC|NNP _|_|SYM 000913.3|000913.3|CD with|with|IN bwa|bwa|NN version|version|NN 0.7.7|0.7.7|CD
Alignment|alignment|NN ,|,|, Quantiatino|quantiatino|NN and|and|CC Normalization|normalization|NN ,|,|, Differential|differential|JJ Expression|expression|NN :|:|: We|we|PRP used|use|VBD the|the|DT SPARTA|SPARTA|NNP -LRB-|-lrb-|-LRB- version|version|NN 1|1|CD -RRB-|-rrb-|-RRB- software|software|NN package|package|NN for|for|IN alignment|alignment|NN ,|,|, differential|differential|JJ expression|expression|NN analysis|analysis|NN ,|,|, and|and|CC post-analysis|post-analysis|JJ diagnostics|diagnostic|NNS .|.|. SPARTA|SPARTA|NNP is|be|VBZ an|a|DT RNA-Seq|rna-seq|NN package|package|NN specifically|specifically|RB designed|design|VBN for|for|IN bacterial|bacterial|JJ studies|study|NNS .|.|. It|it|PRP uses|use|VBZ the|the|DT Bowtie|Bowtie|NNP -LRB-|-lrb-|-LRB- version|version|NN 1.1.1|1.1.1|CD -RRB-|-rrb-|-RRB- short|short|JJ read|read|NN aligner|aligner|NN ,|,|, HTSeq|htseq|NN -LRB-|-lrb-|-LRB- version|version|NN 0.6.1|0.6.1|CD -RRB-|-rrb-|-RRB- to|to|TO count|count|VB gene|gene|NN features|feature|NNS ,|,|, and|and|CC edgeR|edger|NN for|for|IN differential|differential|JJ expression|expression|NN .|.|.
Alignment|alignment|NN :|:|: reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO bespoke|bespeak|VB reference|reference|NN sequence|sequence|NN -LRB-|-lrb-|-LRB- DL4201|dl4201|NN _|_|NN in|in|IN _|_|NN lab|lab|NN _|_|CD reference|reference|NN _|_|NN genome|genome|NN -LRB-|-lrb-|-LRB- available|available|JJ on|on|IN series|series|NN record|record|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT default|default|NN parameters|parameter|NNS of|of|IN software|software|NN Bowtie|bowtie|NN 2|2|CD -LRB-|-lrb-|-LRB- Langmead|Langmead|NNP ,|,|, B.|B.|NNP and|and|CC Salzberg|Salzberg|NNP ,|,|, S.L.|S.L.|NNP -LRB-|-lrb-|-LRB- 2012|2012|CD -RRB-|-rrb-|-RRB- Fast|fast|JJ gapped-read|gapped-read|JJ alignment|alignment|NN with|with|IN Bowtie|bowtie|NN 2|2|CD .|.|. Nat|Nat|NNP Methods|method|NNS ,|,|, 9|9|CD ,|,|, 357-359|357-359|CD -RRB-|-rrb-|-RRB- .|.|.
alignment|alignment|NN :|:|: STAR|star|NN 2.4.0|2.4.0|CD i|i|FW
Alignment|alignment|NN to|to|TO the|the|DT E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN genome|genome|NN sequence|sequence|NN was|be|VBD performed|perform|VBN using|use|VBG TMAP|tmap|NN map4|map4|NN algorithm|algorithm|NN with|with|IN 5|5|CD '|'|'' and|and|CC 3|3|CD '|'|'' soft-clipping|soft-clipping|JJ and|and|CC a|a|DT minimum|minimum|JJ seed|seed|NN length|length|NN of|of|IN 20|20|CD nt|nt|NNS
A|a|DT Linker-1|linker-1|NN adapter|adapter|NN -LRB-|-lrb-|-LRB- IDT|idt|NN -RRB-|-rrb-|-RRB- was|be|VBD ligated|ligate|VBN onto|onto|IN the|the|DT 3|3|CD '|'|'' end|end|NN of|of|IN size|size|NN selected|select|VBN RNA|rna|NN fragments|fragment|NNS ,|,|, either|either|CC ribosome|ribosome|NN footprints|footprint|NNS or|or|CC fragmented|fragmented|JJ total|total|JJ RNA|rna|NN .|.|. A|a|DT cDNA|cdna|NN library|library|NN was|be|VBD created|create|VBN using|use|VBG Superscript|Superscript|NNP III|III|NNP -LRB-|-lrb-|-LRB- ThermoFisher|ThermoFisher|NNP -RRB-|-rrb-|-RRB- .|.|. After|after|IN gel|gel|NN purification|purification|NN of|of|IN the|the|DT cDNA|cdna|NN library|library|NN all|all|DT ssDNA|ssdna|NN fragments|fragment|NNS were|be|VBD circularized|circularize|VBN using|use|VBG CircLigase|CircLigase|NNP -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|. For|for|IN ribosome|ribosome|NN profiling|profiling|NN samples|sample|NNS rRNA|rrna|NN containing|contain|VBG circles|circle|NNS were|be|VBD depleted|deplete|VBN using|use|VBG oligo-biotin|oligo-biotin|JJ and|and|CC streptavidin|streptavidin|JJ coupled|couple|VBN Dynabeads|dynabead|NNS -LRB-|-lrb-|-LRB- ThermoFisher|thermofisher|NN -RRB-|-rrb-|-RRB- subtraction|subtraction|NN .|.|. A|a|DT PCR|pcr|NN amplification|amplification|NN off|off|IN the|the|DT circles|circle|NNS using|use|VBG HF|hf|NN Phusion|phusion|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- completed|complete|VBD the|the|DT libraries|library|NNS by|by|IN adding|add|VBG Illumina|Illumina|NNP Tru-Seq|Tru-Seq|NNP adapters|adapter|NNS and|and|CC a|a|DT unique|unique|JJ index|index|NN for|for|IN each|each|DT sample|sample|NN .|.|.
All|All|NNP culture|culture|NN experiments|experiment|NNS were|be|VBD performed|perform|VBN in|in|IN MOPS|MOPS|NNP medium|medium|NN supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, 19|19|CD amino|amino|NN acids|acid|NNS -LRB-|-lrb-|-LRB- without|without|IN methionine|methionine|NN -RRB-|-rrb-|-RRB- ,|,|, vitamins|vitamin|NNS ,|,|, bases|basis|NNS and|and|CC micronutrients|micronutrient|NNS -LRB-|-lrb-|-LRB- MOPS|mop|NNS rich|rich|JJ defined|define|VBN medium|medium|NN minus|minus|CC methionine|methionine|NN ,|,|, Teknova|teknova|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN an|a|DT overnight|overnight|JJ liquid|liquid|JJ culture|culture|NN at|at|IN 37|37|CD °C|°c|NN ,|,|, diluted|dilute|VBN to|to|TO an|a|DT OD420|od420|NN =|=|JJ .001|.001|CD in|in|IN fresh|fresh|JJ medium|medium|NN and|and|CC grown|grow|VBN until|until|IN OD420|od420|NN reached|reach|VBD 0.4|0.4|CD where|where|WRB samples|sample|NNS were|be|VBD collected|collect|VBN .|.|. For|for|IN 10|10|CD °C|°c|NN samples|sample|NNS ,|,|, cultures|culture|NNS were|be|VBD grown|grow|VBN to|to|TO OD420|od420|NN =|=|JJ 1.1|1.1|CD at|at|IN 37|37|CD °C|°c|NN and|and|CC cold|cold|JJ shock|shock|NN was|be|VBD performed|perform|VBN by|by|IN mixing|mix|VBG 70mL|70ml|NN of|of|IN 37|37|CD °C|°c|NN culture|culture|NN with|with|IN 130mL|130ml|NN of|of|IN 0|0|CD °C|°c|NN media|media|NNS pre-chilled|pre-chill|VBN in|in|IN ice-water|ice-water|JJ slurry|slurry|NN ,|,|, with|with|IN continued|continued|JJ growth|growth|NN of|of|IN the|the|DT culture|culture|NN in|in|IN a|a|DT 10|10|CD °C|°c|NN shaker|shaker|NN .|.|.
All|All|NNP cultures|culture|NNS grown|grow|VBN up|up|RB to|to|TO 0.6|0.6|CD OD600|od600|NN with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN .|.|. Samples|sample|NNS 1,2,5|1,2,5|CD and|and|CC 6|6|CD were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN whereas|whereas|IN samples|sample|NNS 3|3|CD and|and|CC 4|4|CD were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN .|.|.
All|All|NNP cultures|culture|NNS were|be|VBD based|base|VBN on|on|IN MOPS|mop|NNS media|media|NNS with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- Teknova|teknova|NN -RRB-|-rrb-|-RRB- ,|,|, with|with|IN either|either|CC full|full|JJ supplement|supplement|NN -LRB-|-lrb-|-LRB- Neidhardt|Neidhardt|NNP et|et|FW al.|al.|FW ,|,|, 1974|1974|CD -RRB-|-rrb-|-RRB- .|.|. An|a|DT overnight|overnight|JJ liquid|liquid|JJ culture|culture|NN was|be|VBD diluted|dilute|VBN 400-fold|400-fold|JJ into|into|IN 200|200|CD ml|ml|NN fresh|fresh|JJ media|media|NNS .|.|. The|the|DT culture|culture|NN was|be|VBD kept|keep|VBN in|in|IN a|a|DT 2.8-liter|2.8-liter|JJ flask|flask|NN at|at|IN 37C|37c|NN with|with|IN aeration|aeration|NN -LRB-|-lrb-|-LRB- 180|180|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- until|until|IN OD600|od600|NN reached|reach|VBD 0.3|0.3|CD .|.|.
All|All|NNP cultures|culture|NNS were|be|VBD based|base|VBN on|on|IN MOPS|mop|NNS media|media|NNS with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- Teknova|teknova|NN -RRB-|-rrb-|-RRB- ,|,|, with|with|IN full|full|JJ supplement|supplement|NN -LRB-|-lrb-|-LRB- Neidhardt|Neidhardt|NNP et|et|FW al.|al.|FW ,|,|, 1974|1974|CD -RRB-|-rrb-|-RRB- minus|minus|CC methionine|methionine|NN .|.|. An|a|DT overnight|overnight|JJ liquid|liquid|JJ culture|culture|NN was|be|VBD diluted|dilute|VBN 400-fold|400-fold|JJ into|into|IN 200|200|CD ml|ml|NN fresh|fresh|JJ media|media|NNS .|.|. The|the|DT culture|culture|NN was|be|VBD kept|keep|VBN in|in|IN a|a|DT 1|1|CD liter|liter|NN flask|flask|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN aeration|aeration|NN until|until|IN OD420|od420|NN reached|reach|VBD 0.4|0.4|CD .|.|.
All|All|NNP cultures|culture|NNS were|be|VBD carried|carry|VBN out|out|RP in|in|IN a|a|DT 5|5|CD l|l|NN fermentor|fermentor|JJ BIOSTAT|biostat|NN B-DCU|b-dcu|NN -LRB-|-lrb-|-LRB- Sartorius|Sartorius|NNP BBI|BBI|NNP Systems|Systems|NNPS Inc.|Inc.|NNP .|.|. Melsungen|melsungen|NN -RRB-|-rrb-|-RRB- at|at|IN controlled|control|VBN temperature|temperature|NN 37|37|CD °C|°c|NN ,|,|, pH|ph|NN 7.0|7.0|CD ,|,|, and|and|CC dissolved|dissolve|VBD oxygen|oxygen|NN tension|tension|NN 30|30|CD %|%|NN .|.|. The|the|DT culture|culture|NN volume|volume|NN was|be|VBD 2|2|CD l.|l.|NN All|all|DT reagents|reagent|NNS were|be|VBD purchased|purchase|VBN from|from|IN Sigma-Aldrich|Sigma-Aldrich|NNP ,|,|, Inc.|Inc.|NNP .|.|. The|the|DT synthetic|synthetic|JJ culture|culture|NN medium|medium|NN had|have|VBD the|the|DT following|follow|VBG composition|composition|NN -LRB-|-lrb-|-LRB- g|g|NN l-1|l-1|NN -RRB-|-rrb-|-RRB- :|:|: 8|8|CD ,|,|, glucose|glucose|NN ;|;|: 14.6|14.6|CD ,|,|, K2HPO4|k2hpo4|NN ;|;|: 3.6|3.6|CD ,|,|, NaH2PO4|nah2po4|NN ·|·|NN H2O|h2o|NN ;|;|: 2.68|2.68|CD ,|,|, -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2SO4|2so4|NN ;|;|: 2|2|CD ,|,|, Na2SO4|na2so4|NN ;|;|: 1|1|CD ,|,|, MgSO4|mgso4|NN ;|;|: 1|1|CD ,|,|, Na-citrate|na-citrate|NN ;|;|: 0.5|0.5|CD ,|,|, NH4Cl|nh4cl|NN ;|;|: 2|2|CD ml|ml|NN of|of|IN 10|10|CD mg|mg|NN l-1|l-1|NN of|of|IN thiamine|thiamine|NN ;|;|: 3|3|CD ml|ml|NN of|of|IN trace|trace|NN element|element|NN solution|solution|NN -LRB-|-lrb-|-LRB- g|g|NN l-1|l-1|NN 20.0|20.0|CD ,|,|, Na-EDTA|na-edta|NN ;|;|: 15.0|15.0|CD ,|,|, FeCl3|fecl3|NN ·|·|NN 6H2O|6h2o|NN ;|;|: 0.5|0.5|CD ,|,|, CaCl2|cacl2|NN ·|·|NN 2H2O|2h2o|NN ;|;|: 0.2|0.2|CD ,|,|, ZnSO4|znso4|NN ·|·|NN 7H2O|7h2o|NN ;|;|: 0.2|0.2|CD ,|,|, CoCl2|cocl2|NN ·|·|NN 6H2O|6h2o|NN ;|;|: 0.2|0.2|CD ,|,|, CuSO4|cuso4|NN ·|·|NN 5H2O|5h2o|NN ;|;|: 0.2|0.2|CD ,|,|, MnSO4|mnso4|NN ·|·|NN 4H2O|4h2o|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT chemostat|chemostat|NN culture|culture|NN was|be|VBD performed|perform|VBN with|with|IN adding|add|VBG feed|feed|NN medium|medium|NN
All|All|NNP cultures|culture|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB in|in|IN a|a|DT thermostatically|thermostatically|RB controlled|control|VBN 37oC|37oc|NN culture|culture|NN room|room|NN .|.|. Cultures|culture|NNS -LRB-|-lrb-|-LRB- 150|150|CD ml|ml|NN culture|culture|NN volume|volume|NN -RRB-|-rrb-|-RRB- were|be|VBD stirred|stir|VBN by|by|IN magnetic|magnetic|JJ stirrers|stirrer|NNS at|at|IN 330|330|CD rpm|rpm|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP Variomag|Variomag|NNP Multipoint|Multipoint|NNP 6in|6in|JJ -RRB-|-rrb-|-RRB- 1000|1000|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flask|flask|NN .|.|. Starting|start|VBG cultures|culture|NNS were|be|VBD inoculated|inoculate|VBN from|from|IN a|a|DT single|single|JJ colony|colony|NN and|and|CC grown|grown|JJ overnight|overnight|JJ .|.|. Each|each|DT experimental|experimental|JJ culture|culture|NN was|be|VBD then|then|RB inoculated|inoculate|VBN from|from|IN such|such|JJ an|a|DT overnight|overnight|JJ culture|culture|NN at|at|IN a|a|DT dilution|dilution|NN of|of|IN 1:20|1:20|CD into|into|IN 150|150|CD ml|ml|NN fresh|fresh|JJ MOPS|mop|NNS minimal|minimal|JJ medium|medium|NN in|in|IN a|a|DT 1000|1000|CD ml|ml|NN flask|flask|NN .|.|. The|the|DT minimal|minimal|JJ medium|medium|NN used|use|VBN for|for|IN all|all|DT experiments|experiment|NNS was|be|VBD a|a|DT modification|modification|NN of|of|IN MOPS|mop|NNS -LRB-|-lrb-|-LRB- morpholinopropane|morpholinopropane|NN sulfonate|sulfonate|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ medium|medium|NN obtained|obtain|VBN from|from|IN Teknova|Teknova|NNP ,|,|, CA|CA|NNP -LRB-|-lrb-|-LRB- product|product|NN number|number|NN M2006|m2006|NN -RRB-|-rrb-|-RRB- which|which|WDT contains|contain|VBZ 86|86|CD mM|mm|NN NaCl|nacl|NN ,|,|, 9.5|9.5|CD mM|mm|NN NH4Cl|nh4cl|NN ,|,|, 5|5|CD mM|mm|NN K2HPO4|k2hpo4|NN and|and|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN .|.|.
All|All|NNP cultures|culture|NNS were|be|VBD grown|grow|VBN at|at|IN 37C|37c|NN in|in|IN well-mixed|well-mixed|JJ minimal|minimal|JJ media|media|NNS modified|modify|VBN with|with|IN M63|m63|NN -LRB-|-lrb-|-LRB- mM63|mm63|NN :|:|: pH|ph|NN 7.0|7.0|CD ,|,|, 62|62|CD mM|mm|NN K2HPO4|k2hpo4|NN ,|,|, 39|39|CD mM|mm|NN KH2PO4|kh2po4|NN ,|,|, 15|15|CD mM|mm|NN ammonium|ammonium|NN sulfate|sulfate|NN ,|,|, 1.8|1.8|CD µM|µm|NN FeSO4-7H2O|feso4-7h2o|NN ,|,|, 15|15|CD µM|µm|NN thiamine|thiamine|NN hydrochloride|hydrochloride|NN ,|,|, 0.2|0.2|CD mM|mm|NN MgSO4-7H2O|mgso4-7h2o|NN and|and|CC 22|22|CD mM|mm|NN glucose|glucose|NN -RRB-|-rrb-|-RRB- .|.|. One|one|CD amino|amino|NN acid|acid|NN ,|,|, Ile|ile|NN or|or|CC Leu|leu|NN ,|,|, was|be|VBD added|add|VBN to|to|TO the|the|DT monoculture|monoculture|NN medium|medium|NN when|when|WRB appropriate|appropriate|JJ .|.|. Prior|prior|RB to|to|TO coculturing|coculturing|NN ,|,|, at|at|IN both|both|CC the|the|DT initial|initial|JJ inoculation|inoculation|NN and|and|CC transfer|transfer|NN ,|,|, we|we|PRP washed|wash|VBD the|the|DT E.|e.|FW coli|coli|FW cells|cell|NNS with|with|IN fresh|fresh|JJ mM63|mm63|NN without|without|IN amino|amino|NN acids|acid|NNS to|to|TO exclude|exclude|VB the|the|DT carry-over|carry-over|NN of|of|IN supplements|supplement|NNS from|from|IN the|the|DT pre-culture|pre-culture|JJ .|.|. For|for|IN coculture|coculture|NN samples|sample|NNS ,|,|, we|we|PRP used|use|VBD cell|cell|NN culture|culture|NN inserts|insert|NNS with|with|IN a|a|DT pore|pore|NN size|size|NN of|of|IN 0.45|0.45|CD µm|µm|NN at|at|IN a|a|DT density|density|NN of|of|IN 10|10|CD ^|^|CD 8/cm|8/cm|NN ^|^|NN 2|2|CD ,|,|, and|and|CC used|use|VBN six-well|six-well|JJ cell|cell|NN culture|culture|NN companion|companion|NN plates|plate|NNS for|for|IN the|the|DT inserts|insert|NNS -LRB-|-lrb-|-LRB- BD|BD|NNP Falcon|Falcon|NNP ,|,|, Franklin|Franklin|NNP Lakes|Lakes|NNP ,|,|, NJ|NJ|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- ,|,|, to|to|TO separately|separately|RB harvest|harvest|VB I|I|PRP --|--|: and|and|CC L|l|NN --|--|: populations|population|NNS from|from|IN cocultures|coculture|NNS -LRB-|-lrb-|-LRB- Hosoda|Hosoda|NNP et|et|FW al.|al.|FW ,|,|, \|\|SYM
all|all|DT cultures|culture|NNS were|be|VBD grown|grow|VBN in|in|IN 10|10|CD ml|ml|NN LB|lb|NN broth|broth|NN at|at|IN 37C/180rpm|37c/180rpm|NN for|for|IN 24|24|CD hours|hour|NNS and|and|CC flash-frozen|flash-frozen|JJ with|with|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|.
All|All|NNP data|data|NN analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG Rockhopper|Rockhopper|NNP -LRB-|-lrb-|-LRB- McClure|McClure|NNP et|et|FW al.|al.|FW ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- and|and|CC Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN as|as|IN the|the|DT reference|reference|NN genome|genome|NN .|.|.
All|all|DT data|datum|NNS was|be|VBD processed|process|VBN using|use|VBG Rockhopper|Rockhopper|NNP Ver|Ver|NNP .2.03|.2.03|CD .|.|. Rockhopper|Rockhopper|NNP is|be|VBZ an|a|DT \|\|JJ
All|all|DT raw|raw|JJ FastQ|fastq|NN files|file|NNS generated|generate|VBN were|be|VBD filtered|filter|VBN using|use|VBG FASTX-Toolkit|fastx-toolkit|NN -LRB-|-lrb-|-LRB- http://hannonlab.cshl.edu/fastx_toolkit/|http://hannonlab.cshl.edu/fastx_toolkit/|NN -RRB-|-rrb-|-RRB- .|.|.
All|all|DT RNA|rna|NN data|datum|NNS were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN Xuzhou21|xuzhou21|NN using|use|VBG SOAP2|soap2|NN .|.|.
All|All|NNP samples|sample|NNS were|be|VBD extracted|extract|VBN using|use|VBG the|the|DT hot|hot|JJ phenol|phenol|NN extraction|extraction|NN with|with|IN DNA|dna|NN digestion|digestion|NN ,|,|, following|follow|VBG standard|standard|JJ protocol|protocol|NN
All|all|DT samples|sample|NNS were|be|VBD extracted|extract|VBN using|use|VBG the|the|DT Qiagen|Qiagen|NNP Rnasey|Rnasey|NNP Mini|Mini|NNP Kit|kit|NN ,|,|, following|follow|VBG standard|standard|JJ protocol|protocol|NN
All|all|DT samples|sample|NNS were|be|VBD processed|process|VBN following|follow|VBG NEB|NEB|NNP 's|'s|POS protocol|protocol|NN from|from|IN the|the|DT NEBNext|nebnext|NN ®|®|NN ChIP-Seq|chip-seq|JJ library|library|NN preparation|preparation|NN kit|kit|NN .|.|.
All|All|NNP sequencing|sequencing|NN reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO E.|e.|FW coli|coli|FW MG1655|mg1655|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913|000913|CD -RRB-|-rrb-|-RRB- using|use|VBG CLC|clc|NN Genomics|genomic|NNS Workbench5|workbench5|NN with|with|IN the|the|DT length|length|NN fraction|fraction|NN of|of|IN 0.9|0.9|CD and|and|CC the|the|DT similarity|similarity|NN of|of|IN 0.99|0.99|CD .|.|.
All|All|NNP strains|strain|NNS used|use|VBN are|be|VBP E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN and|and|CC its|its|PRP$ derivatives|derivative|NNS .|.|. Glycerol|glycerol|NN stock|stock|NN of|of|IN the|the|DT E.|e.|FW coli|coli|FW strain|strain|NN was|be|VBD inoculated|inoculate|VBN into|into|IN 3|3|CD mL|ml|NN Luria|Luria|NNP broth|broth|NN supplemented|supplement|VBN with|with|IN 150|150|CD μg|μg|NN kanamycin|kanamycin|NN and|and|CC cultured|culture|VBN overnight|overnight|JJ at|at|IN 37|37|CD °C|°c|NN with|with|IN constant|constant|JJ agitation|agitation|NN .|.|.
All|All|NNP strains|strain|NNS used|use|VBN in|in|IN this|this|DT study|study|NN were|be|VBD E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN and|and|CC its|its|PRP$ derivatives|derivative|NNS .|.|. The|the|DT deletion|deletion|NN mutants|mutant|NNS -LRB-|-lrb-|-LRB- Δfnr|δfnr|NN and|and|CC ΔarcA|δarca|NN -RRB-|-rrb-|-RRB- were|be|VBD constructed|construct|VBN by|by|IN a|a|DT λ|λ|NN red|red|JJ and|and|CC FLP-mediated|flp-mediated|JJ site-specific|site-specific|JJ recombination|recombination|NN method|method|NN .|.|. Glycerol|glycerol|NN stocks|stock|NNS of|of|IN E.|e.|FW coli|coli|FW strains|strain|NNS were|be|VBD inoculated|inoculate|VBN into|into|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN containing|contain|VBG 0.2|0.2|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- carbon|carbon|NN source|source|NN -LRB-|-lrb-|-LRB- glucose|glucose|NN -RRB-|-rrb-|-RRB- and|and|CC 0.1|0.1|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- nitrogen|nitrogen|NN source|source|NN -LRB-|-lrb-|-LRB- NH4Cl|nh4cl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC cultured|culture|VBN overnight|overnight|JJ at|at|IN 37|37|CD °C|°c|NN with|with|IN constant|constant|JJ agitation|agitation|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN fresh|fresh|JJ minimal|minimal|JJ medium|medium|NN and|and|CC then|then|RB cultured|culture|VBN at|at|IN 37|37|CD °C|°c|NN to|to|TO an|a|DT appropriate|appropriate|JJ cell|cell|NN density|density|NN with|with|IN constant|constant|JJ agitation|agitation|NN .|.|. For|for|IN the|the|DT anaerobic|anaerobic|JJ cultures|culture|NNS ,|,|, the|the|DT minimal|minimal|JJ medium|medium|NN were|be|VBD flushed|flush|VBN with|with|IN nitrogen|nitrogen|NN and|and|CC then|then|RB continuously|continuously|RB monitored|monitor|VBN using|use|VBG a|a|DT polarographic-dissolved|polarographic-dissolved|JJ oxygen|oxygen|NN probe|probe|NN -LRB-|-lrb-|-LRB- Cole-Parmer|Cole-Parmer|NNP Instruments|Instruments|NNP -RRB-|-rrb-|-RRB- to|to|TO ensure|ensure|VB anaerobicity|anaerobicity|NN .|.|. For|for|IN nitrate|nitrate|JJ respiration|respiration|NN 20|20|CD mmol|mmol|NN potassium|potassium|NN nitrate|nitrate|NN was|be|VBD added|add|VBN .|.|.
All|All|NNP strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 25|25|CD ug/ml|ug/ml|NN streptomycin|streptomycin|NN and|and|CC 0.52|0.52|CD mM|mm|NN arginine|arginine|NN .|.|. Samples|sample|NNS were|be|VBD grown|grow|VBN to|to|TO OD|od|NN =|=|JJ 0.5|0.5|CD @|@|SYM 30|30|CD C|c|NN ;|;|: experimental|experimental|JJ samples|sample|NNS were|be|VBD then|then|RB transferred|transfer|VBN to|to|TO a|a|DT shaking|shake|VBG water|water|NN bath|bath|NN @|@|SYM 42|42|CD C.|C.|NNP
All|All|NNP strains|strain|NNS were|be|VBD grown|grow|VBN shaking|shake|VBG at|at|IN 37|37|CD °C|°c|NN in|in|IN 200mL|200ml|NN cultures|culture|NNS of|of|IN MOPS|mop|NNS complete-glucose|complete-glucose|JJ liquid|liquid|JJ media|media|NNS -LRB-|-lrb-|-LRB- unless|unless|IN otherwise|otherwise|RB annotated|annotated|JJ -RRB-|-rrb-|-RRB- in|in|IN 1L|1l|NN flasks|flask|NNS and|and|CC cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN OD|od|NN -LRB-|-lrb-|-LRB- 420nm|420nm|NN -RRB-|-rrb-|-RRB- between|between|IN 0.4|0.4|CD -|-|: 0.6|0.6|CD
All|all|PDT those|those|DT uniquely|uniquely|RB mapped|map|VBN reads|read|VBZ were|be|VBD used|use|VBN to|to|TO calculate|calculate|VB the|the|DT gene|gene|NN expression|expression|NN level|level|NN by|by|IN the|the|DT RPKM|rpkm|NN method|method|NN ,|,|, which|which|WDT is|be|VBZ able|able|JJ to|to|TO eliminate|eliminate|VB the|the|DT influence|influence|NN of|of|IN different|different|JJ gene|gene|NN length|length|NN and|and|CC sequencing|sequencing|NN discrepancy|discrepancy|NN on|on|IN the|the|DT calculation|calculation|NN of|of|IN gene|gene|NN expression|expression|NN and|and|CC thus|thus|RB the|the|DT calculated|calculate|VBN gene|gene|NN expression|expression|NN level|level|NN can|can|MD be|be|VB directly|directly|RB used|use|VBN for|for|IN comparing|compare|VBG the|the|DT difference|difference|NN of|of|IN gene|gene|NN expression|expression|NN among|among|IN samples|sample|NNS .|.|.
Ambion|Ambion|NNP RiboPure|RiboPure|NNP RNA|rna|NN Isolation|isolation|NN
Ambion|Ambion|NNP RiboPure|RiboPure|NNP RNA|rna|NN Isolation|isolation|NN
A|a|NN minimal|minimal|JJ growth|growth|NN medium|medium|NN as|as|IN described|describe|VBN in|in|IN the|the|DT study|study|NN by|by|IN Ihssen|Ihssen|NNP and|and|CC Egli|Egli|NNP -LRB-|-lrb-|-LRB- 2004|2004|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN all|all|DT experiments|experiment|NNS .|.|. Bacterial|bacterial|JJ stock|stock|NN cultures|culture|NNS were|be|VBD streaked|streak|VBN onto|onto|IN agar|agar|NN plates|plate|NNS and|and|CC incubated|incubate|VBN overnight|overnight|JJ .|.|. One|one|CD colony|colony|NN was|be|VBD then|then|RB transferred|transfer|VBN into|into|IN 20|20|CD ml|ml|NN minimal|minimal|JJ medium|medium|NN ,|,|, grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN -LRB-|-lrb-|-LRB- 250|250|CD r.p.m.|r.p.m.|NNS -RRB-|-rrb-|-RRB- over|over|IN night|night|NN culture|culture|NN -LRB-|-lrb-|-LRB- ONC|onc|NN -RRB-|-rrb-|-RRB- and|and|CC served|serve|VBD as|as|IN the|the|DT inoculum|inoculum|NN for|for|IN experiments|experiment|NNS .|.|. For|for|IN continuous|continuous|JJ culture|culture|NN experiments|experiment|NNS we|we|PRP designed|design|VBD and|and|CC constructed|construct|VBD 500|500|CD ml|ml|NN bioreactors|bioreactor|NNS according|accord|VBG to|to|TO the|the|DT study|study|NN by|by|IN Huwiler|Huwiler|NNP et|et|FW al.|al.|FW ,|,|, -LRB-|-lrb-|-LRB- 2012|2012|CD -RRB-|-rrb-|-RRB- that|that|WDT were|be|VBD half-filled|half-filled|JJ with|with|IN medium|medium|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD g|g|NN glucose|glucose|NN per|per|IN l|l|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN in|in|IN a|a|DT temperature|temperature|NN controlled|controlled|JJ water|water|NN bath|bath|NN .|.|. Before|before|IN continuous|continuous|JJ cultivation|cultivation|NN -LRB-|-lrb-|-LRB- dilution|dilution|NN rate|rate|NN =|=|JJ 0.25|0.25|CD -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD --|--|: 2|2|CD ml|ml|NN of|of|IN the|the|DT ONC|onc|NN was|be|VBD transferred|transfer|VBN and|and|CC grown|grow|VBN in|in|IN batch-mode|batch-mode|NN until|until|IN reactors|reactor|NNS became|become|VBD visibly|visibly|RB turbid|turbid|JJ .|.|. Subsequently|subsequently|RB ,|,|, cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO steady-state|steady-state|JJ -LRB-|-lrb-|-LRB- defined|define|VBN as|as|IN constant|constant|JJ optical|optical|JJ density|density|NN over|over|IN time|time|NN -RRB-|-rrb-|-RRB- and|and|CC harvested|harvest|VBN for|for|IN experimentation|experimentation|NN .|.|. For|for|IN starvation|starvation|NN experiments|experiment|NNS the|the|DT medium|medium|NN flow|flow|NN was|be|VBD stopped|stop|VBN during|during|IN steady-state|steady-state|JJ and|and|CC bacteria|bacterium|NNS were|be|VBD collected|collect|VBN after|after|IN 4|4|CD h.|h.|NN To|to|TO avoid|avoid|VB gene-expression|gene-expression|NN signatures|signature|NNS of|of|IN stationary|stationary|JJ cells|cell|NNS from|from|IN the|the|DT ONC|ONC|NNP ,|,|, batch|batch|NN cultures|culture|NNS -LRB-|-lrb-|-LRB- 1000|1000|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flasks|flask|NNS containing|contain|VBG 100|100|CD ml|ml|NN of|of|IN pre-warmed|pre-warmed|JJ medium|medium|NN -LRB-|-lrb-|-LRB- 1|1|CD g|g|NN glucose|glucose|NN per|per|IN l|l|NN -RRB-|-rrb-|-RRB- ;|;|: 37|37|CD °C|°c|NN ;|;|: 250|250|CD r.p.m.|r.p.m.|NNS -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- were|be|VBD inoculated|inoculate|VBN with|with|IN 5|5|CD ml|ml|NN of|of|IN an|a|DT exponentially|exponentially|RB growing|grow|VBG pre-culture|pre-culture|JJ that|that|IN derived|derive|VBN from|from|IN the|the|DT ONC|ONC|NNP .|.|.
Amino|amino|NN acid|acid|NN or|or|CC nucleotide|nucleotide|NN added|add|VBD to|to|TO final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD mM|mm|NN not|not|RB exceeding|exceed|VBG 1/100th|1/100th|JJ volume|volume|NN of|of|IN culture|culture|NN .|.|. After|after|IN 10|10|CD mins|min|NNS ,|,|, samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RB and|and|CC snap|snap|VB frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD C|c|NN
Among|among|IN potential|potential|JJ TSSs|tsss|NNS ,|,|, only|only|RB TSSs|tsss|NNS with|with|IN the|the|DT strongest|strongest|JJS signal|signal|NN within|within|IN 10|10|CD bp|bp|NN window|window|NN were|be|VBD kept|keep|VBN to|to|TO remove|remove|VB possible|possible|JJ noise|noise|NN signals|signal|NNS ,|,|, and|and|CC TSSs|tsss|NNS with|with|IN greater|greater|JJR than|than|IN or|or|CC equal|equal|JJ to|to|TO 40|40|CD %|%|NN of|of|IN the|the|DT strongest|strongest|JJS signal|signal|NN upstream|upstream|RB of|of|IN an|a|DT annotated|annotated|JJ gene|gene|NN were|be|VBD considered|consider|VBN as|as|IN multiple|multiple|JJ TSSs|tsss|NNS .|.|.
ampicilin|ampicilin|NN treatment|treatment|NN
Ampicilin|ampicilin|NN _|_|NN treatment|treatment|NN _|_|NN plasmidmappedreads|plasmidmappedread|NNS _|_|VBP statistical|statistical|JJ _|_|NN output.txt|output.txt|NN :|:|: NC|NC|NNP _|_|NNP 012692.1|012692.1|CD
Amp|Amp|NNP _|_|NNP Treatment|treatment|NN _|_|NN genomemappedreads|genomemappedread|NNS _|_|VBP statistical|statistical|JJ _|_|NN output.txt|output.txt|NN :|:|: NC|nc|NN _|_|SYM 000913.2|000913.2|CD
Anaerobic|anaerobic|JJ 1|1|CD
Anaerobic|anaerobic|JJ 3|3|CD
Anaerobic|anaerobic|JJ cultures|culture|NNS
Anaerobic|anaerobic|JJ Cultures|culture|NNS
Anaerobic|anaerobic|JJ E.|e.|FW coli|coli|FW exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS
Anaerobic|anaerobic|JJ E.|e.|FW coli|coli|FW not|not|RB exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- control|control|NN cells|cell|NNS -RRB-|-rrb-|-RRB-
Anaerobic|anaerobic|JJ E.|e.|FW coli|coli|FW were|be|VBD exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS
anaerobic|anaerobic|JJ INPUT|input|NN DNA|dna|NN
Anaerobic|anaerobic|JJ ,|,|, Iron|iron|JJ Deficient|deficient|JJ cultures|culture|NNS
Anaerobic|anaerobic|JJ MG1655|mg1655|NN exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS
Anaerobic|anaerobic|JJ MG1655|mg1655|NN not|not|RB exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- control|control|NN cells|cell|NNS -RRB-|-rrb-|-RRB-
Anaerobic|anaerobic|JJ MG1655|mg1655|NN were|be|VBD exposed|expose|VBN to|to|TO CO-RMs|co-rm|NNS for|for|IN 15|15|CD minutes|minute|NNS
Anaerobic|Anaerobic|NNP ,|,|, minus|minus|CC nitrate|nitrate|NN ,|,|, IP|IP|NNP
Anaerobic|Anaerobic|NNP ,|,|, plus|plus|CC nitrate|nitrate|NN ,|,|, IP|IP|NNP
anaerobic|anaerobic|JJ reference|reference|NN
analysis|analysis|NN :|:|: in|in|FW vitro|vitro|FW
analysis|analysis|NN :|:|: in|in|FW vivo|vivo|FW
Ancestral|ancestral|JJ E.|e.|FW coli|coli|FW B|b|NN REL606|rel606|NN strain|strain|NN
Ancestral|ancestral|JJ I|I|PRP -|-|: cells|cell|NNS at|at|IN amino|amino|NN acid|acid|NN starvation|starvation|NN in|in|IN monoculture|monoculture|NN
Ancestral|ancestral|JJ I|I|PRP -|-|: cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN
Ancestral|ancestral|JJ I|I|PRP -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN
Ancestral|ancestral|JJ I|I|PRP -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN ,|,|, a|a|DT biological|biological|JJ replicate|replicate|VB
Ancestral|ancestral|JJ L|l|NN -|-|: cells|cell|NNS at|at|IN amino|amino|NN acid|acid|NN starvation|starvation|NN in|in|IN monoculture|monoculture|NN
Ancestral|ancestral|JJ L|l|NN -|-|: cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN
Ancestral|ancestral|JJ L|l|NN -|-|: cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN ,|,|, a|a|DT technical|technical|JJ replicate|replicate|VB
Ancestral|ancestral|JJ L|l|NN -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN
Ancestral|ancestral|JJ L|l|NN -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN ,|,|, a|a|DT biological|biological|JJ replicate|replicate|VB
Annotation|Annotation|NNP :|:|: The|the|DT reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- Escherichia|escherichia|FW _|_|FW coli|coli|FW _|_|SYM cft073.ASM744v1.dna.chromosome.Chromosome.fa|cft073.asm744v1.dna.chromosome.chromosome.fa|NN -RRB-|-rrb-|-RRB- and|and|CC annotations|annotation|NNS -LRB-|-lrb-|-LRB- Escherichia|escherichia|FW _|_|FW coli|coli|FW _|_|SYM cft073.ASM744v1|cft073.asm744v1|NN .32|.32|CD .|.|. gtf|gtf|NN -RRB-|-rrb-|-RRB- were|be|VBD downloaded|download|VBN from|from|IN EnsemblBacteria|EnsemblBacteria|NNP
An|a|DT o/n|o/n|JJ culture|culture|NN of|of|IN E.|e.|FW coli|coli|FW TolC|tolc|NN was|be|VBD diluted|dilute|VBN to|to|TO an|a|DT OD600|od600|NN of|of|IN 0.1|0.1|CD and|and|CC supplied|supply|VBN with|with|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD µg/ml|µg/ml|NN Carolacton|carolacton|NN in|in|IN MeOH|meoh|NN .|.|. Controls|Controls|NNP received|receive|VBD the|the|DT same|same|JJ volume|volume|NN MeOH|meoh|NN .|.|. Three|three|CD early|early|JJ time-points|time-point|NNS -LRB-|-lrb-|-LRB- t|t|NN -RRB-|-rrb-|-RRB- were|be|VBD chosen|choose|VBN to|to|TO be|be|VB analyzed|analyze|VBN by|by|IN RNA-seq|rna-seq|NN .|.|. Prior|prior|RB to|to|TO addition|addition|NN of|of|IN Carolacton|carolacton|NN -LRB-|-lrb-|-LRB- t0|t0|NN -RRB-|-rrb-|-RRB- ,|,|, t5|t5|NN ,|,|, t15|t15|NN and|and|CC t30|t30|NN min|min|NN after|after|IN addition|addition|NN of|of|IN Carolacton|Carolacton|NNP .|.|. At|at|IN each|each|DT point|point|NN ,|,|, 5|5|CD ml|ml|NN of|of|IN culture|culture|NN were|be|VBD mixed|mix|VBN with|with|IN an|a|DT equal|equal|JJ volume|volume|NN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- ,|,|, incubated|incubate|VBN at|at|IN room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- RT|rt|NN -RRB-|-rrb-|-RRB- for|for|IN 5|5|CD min|min|NN ,|,|, the|the|DT cells|cell|NNS harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN ,|,|, and|and|CC the|the|DT pellet|pellet|NN frozen|frozen|JJ and|and|CC stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
An|a|DT overnight|overnight|JJ culture|culture|NN of|of|IN E.|e.|FW coli|coli|FW O104|o104|NN :|:|: H4|h4|NN strain|strain|NN LB226692|lb226692|NN was|be|VBD diluted|dilute|VBN 1:10,000|1:10,000|CD in|in|IN pre-warmed|pre-warmed|JJ LB|lb|NN medium|medium|NN -LRB-|-lrb-|-LRB- 10|10|CD g/L|g/l|NN tryptone|tryptone|NN ,|,|, 5|5|CD g/L|g/l|NN yeast|yeast|NN extract|extract|NN ,|,|, 5|5|CD g/L|g/l|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- and|and|CC cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37oC|37oc|NN ,|,|, 180|180|CD rpm|rpm|NN for|for|IN 3.5|3.5|CD h|h|NN to|to|TO an|a|DT OD600|od600|NN of|of|IN 0.52|0.52|CD .|.|.
An|a|DT overnight|overnight|JJ culture|culture|NN was|be|VBD diluted|dilute|VBN to|to|TO an|a|DT OD600|od600|NN of|of|IN 0.02|0.02|CD in|in|IN LB|LB|NNP media|media|NNS supplemented|supplement|VBN with|with|IN 100|100|CD µg/ml|µg/ml|NN of|of|IN carbenicillin|carbenicillin|NN ,|,|, 40|40|CD µg/ml|µg/ml|NN biotin|biotin|NN ,|,|, and|and|CC 70|70|CD µM|µm|NN IPTG|iptg|NN .|.|. The|the|DT back|back|JJ diluted|diluted|JJ culture|culture|NN was|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN until|until|IN reaching|reach|VBG an|a|DT OD600|od600|NN of|of|IN 0.45|0.45|CD .|.|.
An|a|DT RNeasy|rneasy|JJ kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO extract|extract|VB the|the|DT total|total|JJ RNA|rna|NN according|accord|VBG to|to|TO manufacturers|manufacturer|NNS '|'|POS instructions|instruction|NNS .|.|. Contaminating|contaminate|VBG DNA|dna|NN was|be|VBD removed|remove|VBN by|by|IN using|use|VBG on-column|on-column|JJ DNase|dnase|NN I|i|CD digestion|digestion|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT quality|quality|NN and|and|CC quantity|quantity|NN of|of|IN the|the|DT RNA|rna|NN preparations|preparation|NNS were|be|VBD determined|determine|VBN with|with|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP by|by|IN using|use|VBG the|the|DT RNA|rna|NN 6000|6000|CD nano|nano|NN assay|assay|NN Labchip|labchip|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP ,|,|, Stockport|Stockport|NNP ,|,|, United|United|NNP Kingdom|Kingdom|NNP -RRB-|-rrb-|-RRB- .|.|.
An|a|DT RNeasy|rneasy|NN midikit|midikit|NN was|be|VBD used|use|VBN to|to|TO prepare|prepare|VB total|total|JJ RNA|rna|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP Ltd.|Ltd.|NNP -RRB-|-rrb-|-RRB- .|.|. Any|any|DT contaminating|contaminate|VBG DNA|dna|NN was|be|VBD removed|remove|VBN using|use|VBG a|a|DT DNAase|dnaase|NN column|column|NN kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- .|.|.
An|a|DT RNeasy|rneasy|NN minikit|minikit|NN was|be|VBD used|use|VBN to|to|TO prepare|prepare|VB total|total|JJ RNA|rna|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP Ltd.|Ltd.|NNP -RRB-|-rrb-|-RRB- .|.|. Any|any|DT contaminating|contaminate|VBG DNA|dna|NN was|be|VBD removed|remove|VBN using|use|VBG a|a|DT DNAase|dnaase|NN column|column|NN kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP Ltd|Ltd|NNP -RRB-|-rrb-|-RRB- .|.|.
Antibodies|antibody|NNS for|for|IN beta|beta|NN of|of|IN RNAP|rnap|NN -|-|: NeoClone|NeoClone|NNP ,|,|, Cat|Cat|NNP Number|number|NN :|:|: W0002|w0002|NN ,|,|, Lot|lot|NN Number|number|NN :|:|: 2008L10-001|2008l10-001|NN Antibodies|antibody|NNS for|for|IN sigma70|sigma70|NN of|of|IN RNAP|rnap|NN -|-|: NeoClone|NeoClone|NNP ,|,|, Cat|Cat|NNP Number|number|NN :|:|: W0004|w0004|NN ,|,|, Lot|lot|NN Number|number|NN :|:|: 2008K12-001|2008k12-001|NN All|all|DT other|other|JJ antibodies|antibody|NNS -LRB-|-lrb-|-LRB- FNR|fnr|NN ,|,|, H-NS|h-ns|NN ,|,|, IHF|ihf|NN -RRB-|-rrb-|-RRB- were|be|VBD produced|produce|VBN in|in|IN this|this|DT study|study|NN and|and|CC are|be|VBP not|not|RB commercially|commercially|RB available|available|JJ .|.|.
antibody|antibody|NN :|:|: 9E10|9e10|NN Myc|myc|NN tag|tag|NN antibody|antibody|NN
antibody|antibody|NN :|:|: Affinity|affinity|NN Purified|purify|VBN FNR|fnr|NN antibody|antibody|NN
antibody|antibody|NN :|:|: Affinity|affinity|NN purified|purify|VBN FNR|fnr|NN polyclonal|polyclonal|JJ antibody|antibody|NN
antibody|antibody|NN :|:|: anti-DksA|anti-dksa|JJ rabbit|rabbit|NN polyclonal|polyclonal|JJ antisera|antisera|NNS
antibody|antibody|NN :|:|: Anti-Dps|anti-dps|JJ antibodies|antibody|NNS
antibody|antibody|NN :|:|: anti-FLAG|anti-flag|JJ mAb|mab|NN
antibody|antibody|NN :|:|: anti-RNAP|anti-rnap|JJ b|b|NN subunit|subunit|NN NT63|nt63|NN monoclonal|monoclonal|JJ antibodies|antibody|NNS
antibody|antibody|NN :|:|: anti-s70|anti-s70|JJ monoclonal|monoclonal|JJ antibodies|antibody|NNS
antibody|antibody|NN :|:|: Flag|flag|NN
antibody|antibody|NN :|:|: IgG|igg|NN
antibody|antibody|NN :|:|: INPUT|INPUT|NNP
antibody|antibody|NN manufacturer|manufacturer|NN :|:|: Upstate|upstate|JJ
antibody|antibody|NN :|:|: Monoclonal|monoclonal|JJ antibody|antibody|NN for|for|IN RNA|rna|NN polymerase|polymerase|NN Beta|beta|NN '|'|'' subunit|subunit|NN -LRB-|-lrb-|-LRB- NT73|nt73|NN -RRB-|-rrb-|-RRB-
antibody|antibody|NN :|:|: Monoclonal|monoclonal|JJ antibody|antibody|NN for|for|IN RNA|rna|NN polymerase|polymerase|NN Beta|beta|NN subunit|subunit|NN -LRB-|-lrb-|-LRB- W0002|w0002|NN -RRB-|-rrb-|-RRB-
antibody|antibody|NN :|:|: Monoclonal|monoclonal|JJ ANTI-FLAG|anti-flag|NN M2|m2|NN antibody|antibody|NN -LRB-|-lrb-|-LRB- F3165|f3165|NN -RRB-|-rrb-|-RRB- -|-|: Sigma|Sigma|NNP
antibody|antibody|NN :|:|: None|none|NN ,|,|, input|input|NN DNA|dna|NN
antibody|antibody|NN :|:|: normal|normal|JJ mouse|mouse|NN IgG|igg|NN
antibody|antibody|NN :|:|: normal|normal|JJ mouse|mouse|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Upstate|upstate|JJ -RRB-|-rrb-|-RRB-
antibody|antibody|NN :|:|: polyclonal|polyclonal|JJ antiserum|antiserum|NN was|be|VBD raised|raise|VBN against|against|IN His6-ArcA|his6-arca|NN then|then|RB Affinity|Affinity|NNP Purified|purify|VBN using|use|VBG purified|purify|VBN ArcA|arca|NN to|to|TO yield|yield|VB the|the|DT polyclonal|polyclonal|JJ antibodies|antibody|NNS used|use|VBN for|for|IN ChIP|chip|NN
antibody|antibody|NN :|:|: polycolonal|polycolonal|JJ antiserum|antiserum|NN was|be|VBD raised|raise|VBN against|against|IN His6-ArcA|his6-arca|NN then|then|RB Affinity|Affinity|NNP Purified|purify|VBN against|against|IN ArcA|arca|NN to|to|TO yield|yield|VB the|the|DT polyclonal|polyclonal|JJ antibodies|antibody|NNS used|use|VBN for|for|IN ChIP|chip|NN
antibody|antibody|NN :|:|: Pre-cleared|pre-cleared|JJ FNR|fnr|NN antibody|antibody|NN
antibody|antibody|NN :|:|: Pre-cleared|pre-cleared|JJ H-NS|h-ns|NN polyclonal|polyclonal|JJ antibody|antibody|NN
antibody|antibody|NN :|:|: Pre-cleared|pre-cleared|JJ IHF|ihf|NN polyclonal|polyclonal|JJ antibody|antibody|NN
antibody|antibody|NN :|:|: rabbit|rabbit|NN pre-immune|pre-immune|JJ IgG|igg|NN
antibody|antibody|NN :|:|: RNAP|rnap|NN beta|beta|NN subunit|subunit|NN -LRB-|-lrb-|-LRB- NT63|nt63|NN -RRB-|-rrb-|-RRB-
antibody|antibody|NN :|:|: RNA|rna|NN Polymerase|polymerase|NN ß|ß|NN monoclonal|monoclonal|JJ antibody|antibody|NN from|from|IN NeoClone|NeoClone|NNP -LRB-|-lrb-|-LRB- W0002|w0002|NN -RRB-|-rrb-|-RRB-
antibody|antibody|NN :|:|: RNA|rna|NN Polymerase|polymerase|NN σ70|σ70|NN monoclonal|monoclonal|JJ antibody|antibody|NN from|from|IN NeoClone|NeoClone|NNP -LRB-|-lrb-|-LRB- W0004|w0004|NN -RRB-|-rrb-|-RRB-
antibody|antibody|NN vendor/catalog|vendor/catalog|NN #|#|# :|:|: Sigma/Cat|sigma/cat|NN .|.|. No|no|DT .|.|. F1804|f1804|NN
APEC|apec|NN strain|strain|NN O08|o08|CD
APEC|apec|NN strain|strain|NN SCI-07|sci-07|NN
A|a|NN pool|pool|NN of|of|IN 3|3|CD E.|e.|FW coli|coli|FW clones|clone|NNS forming|form|VBG large|large|JJ colonies|colony|NNS when|when|WRB plated|plate|VBN on|on|IN TTagar|ttagar|NN and|and|CC derived|derive|VBN from|from|IN E.|e.|FW coli|coli|FW B|b|NN REL606|rel606|NN after|after|IN 150|150|CD days|day|NNS of|of|IN seasonal|seasonal|JJ evolution|evolution|NN experiment|experiment|NN in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS in|in|IN DMga|dmga|JJ medium|medium|NN .|.|.
A|a|NN pool|pool|NN of|of|IN 3|3|CD E.|e.|FW coli|coli|FW clones|clone|NNS forming|form|VBG small|small|JJ colonies|colony|NNS when|when|WRB plated|plate|VBN on|on|IN TTagar|ttagar|NN and|and|CC derived|derive|VBN from|from|IN E.|e.|FW coli|coli|FW B|b|NN REL606|rel606|NN after|after|IN 150|150|CD days|day|NNS of|of|IN seasonal|seasonal|JJ evolution|evolution|NN experiment|experiment|NN in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS in|in|IN DMga|dmga|JJ medium|medium|NN .|.|.
A|a|NN pool|pool|NN of|of|IN 3|3|CD E.|e.|FW coli|coli|FW clones|clone|NNS forming|form|VBG small|small|JJ colonies|colony|NNS when|when|WRB plated|plate|VBN on|on|IN TTagar|ttagar|NN and|and|CC derived|derive|VBN from|from|IN E.|e.|FW coli|coli|FW B|b|NN REL606|rel606|NN after|after|IN 150|150|CD days|day|NNS of|of|IN seasonal|seasonal|JJ evolution|evolution|NN experiment|experiment|NN in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS in|in|IN DMga|dmga|JJ medium|medium|NN .|.|.
AR1|ar1|SYM -|-|: /|/|: AR2|ar2|SYM -|-|:
AR1|ar1|NN -|-|: /|/|: AR2|ar2|SYM -|-|: rep|rep|NN 1|1|CD
AR1|ar1|NN -|-|: /|/|: AR2|ar2|SYM -|-|: rep|rep|NN 2|2|CD
AR1|ar1|NN -|-|: /|/|: AR2|ar2|SYM -|-|: rep|rep|NN 3|3|CD
ArcA|arca|NN -|-|: Aerobic|aerobic|JJ -|-|: Affinity|affinity|NN Purified|purify|VBN -|-|: A|a|NN
ArcA|arca|NN -|-|: Anaerobic|anaerobic|JJ -|-|: Affinity|affinity|NN Purified|purify|VBN -|-|: biological|biological|JJ rep|rep|NN A|a|DT
ArcA|arca|NN -|-|: Anaerobic|anaerobic|JJ -|-|: Affinity|affinity|NN Purified|purify|VBN -|-|: biological|biological|JJ rep|rep|NN B|b|NN
∆|∆|CD ArcA|arca|NN -|-|: Anaerobic|anaerobic|JJ -|-|: Affinity|affinity|NN Purified|purify|VBN -|-|: technical|technical|JJ rep|rep|NN A|a|DT
∆|∆|CD ArcA|arca|NN -|-|: Anaerobic|anaerobic|JJ -|-|: Affinity|affinity|NN Purified|purify|VBN -|-|: technical|technical|JJ rep|rep|NN B|b|NN
ArcA|arca|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN ChIP-seq|ChIP-seq|NNP _|_|NNP IP|IP|NNP _|_|SYM A.wig|A.wig|NNP :|:|: U00096|u00096|NN .2|.2|NN
ArcA|arca|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN ChIP-seq|ChIP-seq|NNP _|_|NNP IP|IP|NNP _|_|NNP B.wig|B.wig|NNP :|:|: U00096|u00096|NN .2|.2|NN
ArcA|arca|NN INPUT|input|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherchia|Escherchia|NNP coli|coli|NN MG1655|mg1655|NN K-12|k-12|NN ,|,|, no|no|DT antibody|antibody|NN control|control|NN
ArcA|arca|NN INPUT|input|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
ArcA|arca|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Anaerobic|Anaerobic|NNP Biological|Biological|NNP replicate|replicate|VB 1|1|CD
ArcA|arca|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Anaerobic|Anaerobic|NNP Biological|Biological|NNP replicate|replicate|VB 2|2|CD
∆|∆|SYM arcA|arcA|NNP IP|IP|NNP DNA|dna|NN from|from|IN PK9416|pk9416|NN
ArcA|arca|NN IP|IP|NNP DNA|dna|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
ArcA|arca|NN IP|IP|NNP from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
Archaea|archaea|NN
Arginine|arginine|NN addition|addition|NN
ArgR|argr|NN _|_|CD Arginine|arginine|NN _|_|NN 1|1|CD
ArgR|argr|NN _|_|CD Arginine|arginine|NN _|_|NN 2|2|CD
ArgR|argr|NN -LRB-|-lrb-|-LRB- -|-|: arg|arg|NN -RRB-|-rrb-|-RRB- rep1|rep1|NN and|and|CC rep2|rep2|NN
ArgR|argr|NN -LRB-|-lrb-|-LRB- +|+|CC arg|arg|NN -RRB-|-rrb-|-RRB- rep1|rep1|NN and|and|CC rep2|rep2|NN
ArgR|argr|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN 1|1|CD
ArgR|argr|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN 2|2|CD
Arrays|array|NNS were|be|VBD processed|process|VBN using|use|VBG Nimblegen|Nimblegen|NNP 's|'s|POS standard|standard|JJ protocol|protocol|NN for|for|IN Nimblescan|nimblescan|JJ 2.4|2.4|CD ChIP|chip|NN data|datum|NNS extraction|extraction|NN .|.|.
Arrays|array|NNS were|be|VBD processed|process|VBN using|use|VBG Nimblegen|Nimblegen|NNP 's|'s|POS standard|standard|JJ protocol|protocol|NN for|for|IN Nimblescan|Nimblescan|NNP ChIP|ChIP|NNP data|datum|NNS extraction|extraction|NN .|.|. .|.|.
As|as|IN described|describe|VBN in|in|IN description|description|NN
As|as|IN described|describe|VBN in|in|IN the|the|DT description|description|NN
A|a|NN single|single|JJ colony|colony|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW was|be|VBD inoculated|inoculate|VBN into|into|IN 250|250|CD ml|ml|NN of|of|IN LB|lb|NN medium|medium|NN without|without|IN antibiotics|antibiotic|NNS ,|,|, and|and|CC grown|grow|VBN at|at|IN 37C|37c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 150|150|CD RPM|rpm|NN -RRB-|-rrb-|-RRB- for|for|IN approximately|approximately|RB 4|4|CD hours|hour|NNS ,|,|, until|until|IN OD600|od600|NN was|be|VBD ~|~|CD 0.3|0.3|CD -LRB-|-lrb-|-LRB- log|log|NN phase|phase|NN -RRB-|-rrb-|-RRB- .|.|. EDTA|edta|NN was|be|VBD then|then|RB added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD mM|mm|NN ,|,|, and|and|CC incubated|incubate|VBN for|for|IN additional|additional|JJ 5|5|CD minutes|minute|NNS to|to|TO make|make|VB bacteria|bacterium|NNS permeable|permeable|JJ to|to|TO Actinomycin|Actinomycin|NNP D.|D.|NNP Actinomycin|Actinomycin|NNP D|D|NNP was|be|VBD then|then|RB added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 5|5|CD g/ml|g/ml|NN ,|,|, and|and|CC bacteria|bacterium|NNS were|be|VBD incubated|incubate|VBN for|for|IN additional|additional|JJ 2|2|CD minutes|minute|NNS to|to|TO block|block|VB transcription|transcription|NN .|.|. 25|25|CD ml|ml|NN aliquots|aliquot|NNS of|of|IN bacteria|bacterium|NNS were|be|VBD then|then|RB rapidly|rapidly|RB pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 4C|4c|NN .|.|. After|after|IN centrifugation|centrifugation|NN ,|,|, medium|medium|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC cells|cell|NNS from|from|IN each|each|DT 25|25|CD ml|ml|NN of|of|IN culture|culture|NN were|be|VBD resuspended|resuspend|VBN in|in|IN 1|1|CD ml|ml|NN of|of|IN structure|structure|NN probing|probe|VBG buffer|buffer|NN -LSB-|-lsb-|-LRB- 10|10|CD mM|mm|NN HEPES-KOH|hepes-koh|NN pH|ph|NN 7.9|7.9|CD ;|;|: 140|140|CD mM|mm|NN NaCl|nacl|NN ;|;|: 3|3|CD mM|mm|NN KCl|kcl|NN -RSB-|-rsb-|-RRB- .|.|. DMS|dms|NN was|be|VBD diluted|dilute|VBN 1:6|1:6|CD in|in|IN 100|100|CD %|%|NN Ethanol|ethanol|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1.76|1.76|CD M.|m.|NN Diluted|Diluted|NNP DMS|DMS|NNP was|be|VBD added|add|VBN to|to|TO bacteria|bacterium|NNS to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN ~|~|NN 105|105|CD mM|mm|NN .|.|. Samples|sample|NNS were|be|VBD incubated|incubate|VBN with|with|IN moderate|moderate|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 800|800|CD RPM|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 25C|25c|NN for|for|IN 2|2|CD minutes|minute|NNS ,|,|, after|after|IN which|which|WDT reactions|reaction|NNS were|be|VBD immediately|immediately|RB transferred|transfer|VBN to|to|TO ice|ice|NN .|.|. DTT|dtt|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.7|0.7|CD M|m|NN to|to|TO quench|quench|VB DMS|DMS|NNP ,|,|, and|and|CC samples|sample|NNS were|be|VBD vigorously|vigorously|RB vortexed|vortex|VBN for|for|IN 10|10|CD seconds|seconds|NNS .|.|. Bacteria|bacterium|NNS were|be|VBD then|then|RB pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 10,000|10,000|CD g|g|NN for|for|IN 30|30|CD seconds|seconds|NNS -LRB-|-lrb-|-LRB- 4C|4c|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN .|.|. Pellets|pellet|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN 1|1|CD ml|ml|NN Isoamyl|Isoamyl|NNP alcohol|alcohol|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP ,|,|, cat|cat|NN .|.|. W205702|w205702|NN -RRB-|-rrb-|-RRB- to|to|TO remove|remove|VB traces|trace|NNS of|of|IN water-insoluble|water-insoluble|JJ DMS|dms|NN .|.|. Bacteria|bacterium|NNS were|be|VBD then|then|RB pelleted|pellete|VBN by|by|IN additional|additional|JJ centrifugation|centrifugation|NN at|at|IN 10,000|10,000|CD g|g|NN for|for|IN 30|30|CD seconds|seconds|NNS -LRB-|-lrb-|-LRB- 4C|4c|NN -RRB-|-rrb-|-RRB- ,|,|, supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC samples|sample|NNS were|be|VBD snap-frozen|snap-frozen|JJ in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|. Pellets|pellet|NNS were|be|VBD stored|store|VBN at|at|IN -80|-80|CD C.|C.|NNP
A|A|NNP single|single|JJ large|large|JJ fastq|fastq|NN format|format|NN file|file|NN of|of|IN high|high|JJ quality|quality|NN reads|read|VBZ -LRB-|-lrb-|-LRB- Q|Q|NNP ≥|≥|SYM 30|30|CD -RRB-|-rrb-|-RRB- was|be|VBD split|split|VBN into|into|IN about|about|IN 10|10|CD smaller|smaller|JJR files|file|NNS by|by|IN using|use|VBG a|a|DT shell|shell|NN script|script|NN splitReads.sh|splitreads.sh|JJ
Aspartate|aspartate|NN addition|addition|NN
aspC|aspc|NN KO|ko|NN rep1|rep1|NN
aspC|aspc|NN KO|ko|NN rep2|rep2|NN
aspC|aspc|NN KO|ko|NN rep3|rep3|NN
Assignment|assignment|NN to|to|TO restriction|restriction|NN fragment|fragment|NN
Astat|astat|NN _|_|NN chemostat|chemostat|NN
A-stat|a-stat|NN gene|gene|NN expression|expression|NN changes|change|NNS 0.3|0.3|CD /|/|: 0.47|0.47|CD h-1|h-1|NN dye-flip|dye-flip|JJ repl|repl|NN .3|.3|NN
A-stat|a-stat|NN gene|gene|NN expression|expression|NN changes|change|NNS 0.47|0.47|CD /|/|: 0.3|0.3|CD h-1|h-1|NN repl|repl|NN .1|.1|CD
A-stat|a-stat|NN gene|gene|NN expression|expression|NN changes|change|NNS 0.47|0.47|CD /|/|: 0.3|0.3|CD h-1|h-1|NN repl|repl|NN .2.1|.2.1|CD
A-stat|a-stat|NN gene|gene|NN expression|expression|NN changes|change|NNS 0.47|0.47|CD /|/|: 0.3|0.3|CD h-1|h-1|NN repl|repl|NN .2.2|.2.2|CD
A-stat|a-stat|NN ,|,|, specific|specific|JJ growth|growth|NN rate|rate|NN 0.48|0.48|CD 1/h|1/h|JJ
AT1|at1|NN
AT1|at1|NN biological|biological|JJ replicate|replicate|VBP
At|at|IN 3|3|CD h|h|NN of|of|IN culture|culture|NN ,|,|, 60|60|CD mL|ml|NN of|of|IN culture|culture|NN -LRB-|-lrb-|-LRB- at|at|IN OD595|od595|CD nm|nm|NN =|=|JJ 0.73|0.73|CD ±|±|SYM 0.07|0.07|CD ,|,|, 0.63|0.63|CD ±|±|SYM 0.02|0.02|CD ,|,|, 0.12|0.12|CD ±|±|SYM 0.01|0.01|CD and|and|CC 0.11|0.11|CD ±|±|NN 0.02|0.02|CD for|for|IN cultures|culture|NNS subjected|subject|VBN to|to|TO 0|0|CD ,|,|, 5.0|5.0|CD ,|,|, 6.5|6.5|CD and|and|CC 8.5|8.5|CD µM|µm|NN AgNO3|agno3|NN ,|,|, respectively|respectively|RB -RRB-|-rrb-|-RRB- were|be|VBD sampled|sample|VBN and|and|CC centrifuged|centrifuge|VBN -LRB-|-lrb-|-LRB- 4000|4000|CD rpm|rpm|NN ,|,|, 5|5|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- ,|,|, then|then|RB the|the|DT pellet|pellet|NN was|be|VBD frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD resuspended|resuspend|VBN with|with|IN 1|1|CD mL|ml|NN of|of|IN TE|TE|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- Tris-HCl|tris-hcl|NN 10|10|CD mM|mm|NN ,|,|, pH|ph|NN 8|8|CD ,|,|, EDTA|edta|NN 1|1|CD mM|mm|NN ,|,|, 1|1|CD mg|mg|NN lysozyme|lysozyme|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN 5|5|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN with|with|IN a|a|DT RNeasy|rneasy|NN midi|midi|JJ kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- ,|,|, including|include|VBG the|the|DT DNase|dnase|NN I|i|CD treatment|treatment|NN described|describe|VBN in|in|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Total|total|JJ RNA|rna|NN quantity|quantity|NN and|and|CC integrity|integrity|NN were|be|VBD checked|check|VBN by|by|IN Nanodrop|Nanodrop|NNP ®|®|NNP and|and|CC Agilent|Agilent|NNP BioAnalyzer|BioAnalyzer|NNP ,|,|, respectively|respectively|RB .|.|.
ATCACG-D1|atcacg-d1|NN
ATCC2|atcc2|NN
ATCC3|atcc3|NN
At|at|IN each|each|DT time|time|NN point|point|NN ,|,|, 15|15|CD ml|ml|NN of|of|IN each|each|DT culture|culture|NN was|be|VBD mixed|mix|VBN with|with|IN 30|30|CD ml|ml|NN of|of|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- ,|,|, vortexed|vortex|VBN for|for|IN 5s|5|NNS ,|,|, incubated|incubate|VBN for|for|IN 5|5|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN ,|,|, and|and|CC centrifuged|centrifuge|VBN for|for|IN 10|10|CD min|min|NN at|at|IN 5000g|5000g|CD .|.|. The|the|DT pellet|pellet|NN was|be|VBD processed|process|VBN using|use|VBG a|a|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Midi|Midi|NNP kit|kit|NN with|with|IN on-column|on-column|JJ DNase|dnase|NN digestion|digestion|NN using|use|VBG Qiagen|Qiagen|NNP DNase|dnase|NN .|.|. The|the|DT final|final|JJ elution|elution|NN of|of|IN RNA|rna|NN from|from|IN the|the|DT column|column|NN was|be|VBD with|with|IN 160|160|CD μl|μl|NN RNase-free|rnase-free|NN water|water|NN .|.|.
At|at|IN OD|od|NN ~|~|NN 0.3|0.3|CD ,|,|, cultures|culture|NNS were|be|VBD induced|induce|VBN with|with|IN 1mM|1mm|NN IPTG|iptg|NN for|for|IN the|the|DT appropriate|appropriate|JJ length|length|NN of|of|IN time|time|NN .|.|.
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBD 0|0|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBD 10|10|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBN 15|15|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBN 20|20|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBN 2.5|2.5|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBN 30|30|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBN 5|5|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD ,|,|, cultures|culture|NNS induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN .|.|. Cells|cell|NNS harvested|harvest|VBN 60|60|CD min|min|NN after|after|IN induction|induction|NN
At|at|IN OD600|od600|NN ~|~|NN 0.3|0.3|CD ,|,|, serine|serine|NN hydroxamate|hydroxamate|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD mg/ml|mg/ml|NN ,|,|, cells|cell|NNS were|be|VBD collected|collect|VBN 40|40|CD minutes|minute|NNS later|later|RB .|.|.
At|at|IN OD600|od600|NN of|of|IN 0.5|0.5|CD ,|,|, cell|cell|NN cultures|culture|NNS were|be|VBD separated|separate|VBN into|into|IN two|two|CD flasks|flask|NNS .|.|. D-galactose|d-galactose|NN -LRB-|-lrb-|-LRB- final|final|JJ 0.3|0.3|CD %|%|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO one|one|CD and|and|CC cells|cell|NNS were|be|VBD grown|grow|VBN for|for|IN 1.5|1.5|CD h|h|NN further|further|RB .|.|.
At|at|IN OD630nm|od630nm|NN =|=|JJ 0.1|0.1|CD ,|,|, the|the|DT cultures|culture|NNS were|be|VBD filtered|filter|VBN through|through|IN 47-mm|47-mm|JJ diameter|diameter|NN polycarbonate|polycarbonate|JJ membrane|membrane|NN filter|filter|NN -LRB-|-lrb-|-LRB- 0.4|0.4|CD µm|µm|NN pore|pore|NN size|size|NN ;|;|: Millipore|Millipore|NNP -RRB-|-rrb-|-RRB- ,|,|, washed|wash|VBN with|with|IN the|the|DT same|same|JJ medium|medium|NN without|without|IN hypoxanthine|hypoxanthine|NN -LRB-|-lrb-|-LRB- Hx|hx|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC then|then|RB resuspended|resuspend|VBD at|at|IN the|the|DT same|same|JJ cell|cell|NN density|density|NN -LRB-|-lrb-|-LRB- OD630|od630|NN =|=|JJ 0.1|0.1|CD -RRB-|-rrb-|-RRB- in|in|IN the|the|DT medium|medium|NN without|without|IN Hx|hx|NN ,|,|, and|and|CC growth|growth|NN was|be|VBD continued|continue|VBN as|as|IN before|before|RB .|.|. The|the|DT OD630|od630|NN was|be|VBD followed|follow|VBN closely|closely|RB during|during|IN the|the|DT next|next|JJ two|two|CD hours|hour|NNS ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD periodically|periodically|RB diluted|dilute|VBN with|with|IN fresh|fresh|JJ ,|,|, pre-warmed|pre-warmed|JJ medium|medium|NN without|without|IN Hx|hx|NN to|to|TO keep|keep|VB OD|od|NN between|between|IN values|value|NNS 0.1|0.1|CD and|and|CC 0.3|0.3|CD -LRB-|-lrb-|-LRB- low-dilution|low-dilution|JJ protocol|protocol|NN -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS were|be|VBD taken|take|VBN for|for|IN microarray|microarray|NN analysis|analysis|NN -LRB-|-lrb-|-LRB- see|see|VB below|below|IN -RRB-|-rrb-|-RRB- at|at|IN 0|0|CD ,|,|, 15|15|CD ,|,|, 30|30|CD ,|,|, 45|45|CD ,|,|, 60|60|CD and|and|CC 120|120|CD minutes|minute|NNS .|.|. In|in|IN a|a|DT parallel|parallel|JJ procedure|procedure|NN ,|,|, the|the|DT optA1|opta1|NN gpt|gpt|NN double|double|JJ mutant|mutant|NN was|be|VBD also|also|RB followed|follow|VBN in|in|IN a|a|DT near-identical|near-identical|JJ manner|manner|NN using|use|VBG a|a|DT more|more|RBR highly|highly|RB diluted|dilute|VBN culture|culture|NN over|over|IN a|a|DT six-hour|six-hour|JJ incubation|incubation|NN period|period|NN in|in|IN the|the|DT absence|absence|NN of|of|IN hypoxanthine|hypoxanthine|NN -LRB-|-lrb-|-LRB- high-dilution|high-dilution|JJ protocol|protocol|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT effectiveness|effectiveness|NN of|of|IN the|the|DT latter|latter|JJ treatment|treatment|NN was|be|VBD followed|follow|VBN microscopically|microscopically|RB by|by|IN observing|observe|VBG the|the|DT extensive|extensive|JJ cellular|cellular|JJ filamentation|filamentation|NN associated|associate|VBN with|with|IN dGTP|dgtp|NN starvation|starvation|NN .|.|.
A|a|NN total|total|NN of|of|IN six|six|CD samples|sample|NNS were|be|VBD analyzed|analyze|VBN .|.|. oxyR-8myc|oxyr-8myc|NN ,|,|, soxR-8myc|soxr-8myc|NN ,|,|, and|and|CC soxS-8myc|soxs-8myc|NN tagged|tag|VBD cells|cell|NNS were|be|VBD cultured|culture|VBN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN .|.|. Then|then|RB cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN 250|250|CD uM|um|NN of|of|IN paraquat|paraquat|NN at|at|IN mid-log|mid-log|JJ pahse|pahse|NN for|for|IN 20|20|CD min|min|NN with|with|IN agitation|agitation|NN .|.|.
A|a|NN total|total|NN of|of|IN two|two|CD samples|sample|NNS were|be|VBD analyzed|analyze|VBN .|.|. ompR-8myc|ompr-8myc|NN tagged|tag|VBD cells|cell|NNS were|be|VBD cultured|culture|VBN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN .|.|. Then|then|RB cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN 0.3|0.3|CD M|m|NN of|of|IN NaCl|nacl|NN at|at|IN mid-log|mid-log|JJ pahse|pahse|NN for|for|IN 30|30|CD min|min|NN with|with|IN agitation|agitation|NN .|.|.
A|a|NN ,|,|, TP1|tp1|NN
A|a|NN ,|,|, TP2|tp2|NN
A|a|NN ,|,|, TP3|tp3|NN
A|a|NN ,|,|, TP4|tp4|NN
At|at|IN the|the|DT appropriate|appropriate|JJ optical|optical|JJ density|density|NN ,|,|, culture|culture|NN growth|growth|NN was|be|VBD instantaneously|instantaneously|RB arrested|arrest|VBN by|by|IN addition|addition|NN of|of|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN chilled|chill|VBN 100|100|CD %|%|NN ethanol|ethanol|NN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD stored|store|VBN at|at|IN --|--|: 80|80|CD °C|°c|NN until|until|IN they|they|PRP were|be|VBD processed|process|VBN for|for|IN RNA|rna|NN extraction|extraction|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD lysed|lyse|VBN and|and|CC total|total|JJ RNA|rna|NN was|be|VBD prepared|prepare|VBN by|by|IN the|the|DT hot|hot|JJ phenol|phenol|NN method|method|NN essentially|essentially|RB as|as|IN described|describe|VBN ,|,|, after|after|IN chromosomal|chromosomal|JJ DNA|dna|NN has|have|VBZ been|be|VBN digested|digest|VBN with|with|IN RNase-free|rnase-free|JJ DNase|dnase|NN .|.|.
At|at|IN the|the|DT appropriate|appropriate|JJ phase|phase|NN of|of|IN growth|growth|NN ,|,|, a|a|DT one-eighth|one-eighth|NN volume|volume|NN of|of|IN stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN -LSB-|-lsb-|-LRB- v/v|v/v|NN -RSB-|-rsb-|-RRB- ethanol|ethanol|NN ;|;|: 5|5|CD %|%|NN -LSB-|-lsb-|-LRB- v/v|v/v|NN -RSB-|-rsb-|-RRB- phenol|phenol|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO a|a|DT culture|culture|NN to|to|TO inhibit|inhibit|VB cell|cell|NN metabolism|metabolism|NN -LRB-|-lrb-|-LRB- Kime|Kime|NNP et|et|FW al.|al.|FW 2008|2008|CD .|.|. In|in|IN RNA|rna|NN Turnover|turnover|NN in|in|IN Bacteria|bacterium|NNS ,|,|, Archaea|Archaea|NNP and|and|CC Organelles|Organelles|NNP ,|,|, Vol|Vol|NNP 447|447|CD -LRB-|-lrb-|-LRB- ed|ed|VBN .|.|. LE|LE|NNP Maquat|Maquat|NNP ,|,|, CM|cm|NN Arraiano|arraiano|NN -RRB-|-rrb-|-RRB- ,|,|, pp.|pp.|NN 215|215|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN .|.|. When|when|WRB necessary|necessary|JJ ,|,|, cell|cell|NN pellets|pellet|NNS were|be|VBD stored|store|VBN frozen|freeze|VBN at|at|IN -80|-80|CD C.|C.|NNP
At|at|IN time|time|NN point|point|NN 0|0|CD ,|,|, rifampicin|rifampicin|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 500ug/ml|500ug/ml|NN .|.|. Samples|sample|NNS were|be|VBD collected|collect|VBN at|at|IN 0|0|CD ,|,|, 2|2|CD ,|,|, 4|4|CD ,|,|, 6|6|CD ,|,|, and|and|CC 8|8|CD minutes|minute|NNS .|.|.
Automatic|Automatic|NNP extractor|extractor|NN in|in|IN Verigene|verigene|JJ system|system|NN of|of|IN genomic|genomic|JJ DNA|dna|NN
average|average|JJ fitness|fitness|NN :|:|: 0.196851676684606|0.196851676684606|CD
average|average|JJ fitness|fitness|NN :|:|: 0.296737932583603|0.296737932583603|CD
average|average|JJ fitness|fitness|NN :|:|: 0.344592279464807|0.344592279464807|CD
average|average|JJ fitness|fitness|NN :|:|: 0.353076289611459|0.353076289611459|CD
average|average|JJ fitness|fitness|NN :|:|: 0.434286415079969|0.434286415079969|CD
average|average|JJ fitness|fitness|NN :|:|: 0.502711019240335|0.502711019240335|CD
Average|average|JJ Normalization|normalization|NN using|use|VBG GeneChip|GeneChip|NNP Operating|Operating|NNP Software|Software|NNP Version|Version|NNP 1.4|1.4|CD
AW1|aw1|NN .7|.7|CD ,|,|, steady-state|steady-state|JJ continuous|continuous|JJ cultured|culture|VBN experimental|experimental|JJ samples|sample|NNS at|at|IN 37|37|CD °C|°c|NN
AW1|aw1|NN .7|.7|CD ,|,|, steady-state|steady-state|JJ continuous|continuous|JJ cultured|culture|VBN experimental|experimental|JJ samples|sample|NNS at|at|IN 37|37|CD °C|°c|NN and|and|CC then|then|RB 15|15|CD minutes|minute|NNS heatshock|heatshock|NN at|at|IN 50|50|CD °C|°c|NN
azide|azide|NN treated|treat|VBN
B10|b10|NN DH10BGFP|dh10bgfp|NN _|_|CD pSB1C3|psb1c3|NN _|_|NN 2|2|CD
B10|b10|NN :|:|: LJ110|lj110|NN del|del|FW pdhr|pdhr|FW MMAcetat|mmacetat|NN
B11|b11|NN :|:|: LJ110|lj110|NN pTM30|ptm30|NN MMAcetat|mmacetat|NN
B12|b12|NN :|:|: LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN MMAcetat|mmacetat|NN
B17|b17|NN MG1655GFP|mg1655gfp|NN _|_|CD pSB1C3|psb1c3|NN _|_|NN 2|2|CD
B1|b1|NN :|:|: LJ110|lj110|NN LBo|lbo|NN
B22|b22|NN MG1655GFP|mg1655gfp|NN _|_|CD pSB1C3|psb1c3|NN _|_|CD H3|h3|NN _|_|NN 2|2|CD
b2618|b2618|NN _|_|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
b2618|b2618|NN _|_|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
b2618|b2618|NN _|_|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
b2618|b2618|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
B26|b26|NN MG1655GFP|mg1655gfp|NN _|_|CD Lux|lux|FW _|_|FW 2|2|CD
B2|b2|NN :|:|: LJ110|lj110|NN del|del|FW pdhr|pdhr|FW LBo|lbo|FW
B3|b3|NN DH10BGFP|dh10bgfp|NN _|_|CD pSB1C3|psb1c3|NN _|_|NN 2|2|CD
B3|b3|NN :|:|: LJ110|lj110|NN pTM30|ptm30|NN LBo|lbo|NN
B4|b4|NN DH10BGFP|dh10bgfp|NN _|_|CD pLys|ply|VBZ _|_|SYM 2|2|CD
B4|b4|NN :|:|: LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN LBo|lbo|NN
B500|b500|CD _|_|NN 1|1|CD
B5|b5|NN :|:|: LJ110|lj110|NN MMPyruvat|mmpyruvat|NN
B6|b6|NN :|:|: LJ110|lj110|NN del|del|FW pdhr|pdhr|FW MMPyruvat|mmpyruvat|NN
B7|b7|NN DH10BGFP|dh10bgfp|NN _|_|CD pD864|pd864|NN _|_|NN 2|2|CD
B7|b7|NN :|:|: LJ110|lj110|NN pTM30|ptm30|NN MMPyruvat|mmpyruvat|NN
B8|b8|NN :|:|: LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN MMPyruvat|mmpyruvat|NN
B9|b9|NN DH10BGFP|dh10bgfp|NN _|_|CD pLys|ply|VBZ _|_|SYM M1|m1|NN _|_|NN 2|2|CD
B9|b9|NN :|:|: LJ110|lj110|NN MMAcetat|mmacetat|NN
Background|background|NN correction|correction|NN and|and|CC normalization|normalization|NN -LRB-|-lrb-|-LRB- print-tip|print-tip|JJ loess|loess|NN and|and|CC quantile|quantile|NN -RRB-|-rrb-|-RRB- were|be|VBD performed|perform|VBN using|use|VBG the|the|DT limma|limma|NN R|r|NN package|package|NN .|.|.
Background|background|NN correction|correction|NN ,|,|, normalization|normalization|NN and|and|CC calculation|calculation|NN of|of|IN the|the|DT expression|expression|NN measures|measure|NNS were|be|VBD performed|perform|VBN using|use|VBG RMA|RMA|NNP procedure|procedure|NN with|with|IN the|the|DT WebArray|WebArray|NNP platform|platform|NN -LRB-|-lrb-|-LRB- http://bioinformatics.skcc.org/webarray/|http://bioinformatics.skcc.org/webarray/|NN -RRB-|-rrb-|-RRB- .|.|. Subsequently|subsequently|RB the|the|DT program|program|NN EDGE|edge|NN -LRB-|-lrb-|-LRB- http://www.biostat.washington.edu/software/jstorey/edge/|http://www.biostat.washington.edu/software/jstorey/edge/|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO estimate|estimate|VB the|the|DT conditional|conditional|JJ false|false|JJ discovery|discovery|NN rate|rate|NN -LRB-|-lrb-|-LRB- FDR|FDR|NNP -RRB-|-rrb-|-RRB- ,|,|, the|the|DT expected|expect|VBN proportion|proportion|NN of|of|IN false|false|JJ positives|positive|NNS conditioned|condition|VBN on|on|IN having|have|VBG k|k|NN `|`|`` significant|significant|JJ '|'|'' findings|finding|NNS .|.|.
background|background|NN :|:|: crp|crp|NN mutant|mutant|JJ background|background|NN ,|,|, fis|fi|VBZ flag|flag|NN tag|tag|NN
background|background|NN :|:|: fis|fis|NN mutant|mutant|JJ background|background|NN ,|,|, crp|crp|NN flag|flag|NN tag|tag|NN
background|background|NN strain|strain|NN :|:|: BW25113|bw25113|NN
background|background|NN strain|strain|NN :|:|: BW27784|bw27784|NN
background|background|NN strain|strain|NN :|:|: LJ110|lj110|NN
Background|background|NN subtractions|subtraction|NNS and|and|CC normalization|normalization|NN of|of|IN extracted|extract|VBN data|datum|NNS were|be|VBD performed|perform|VBN through|through|IN R|r|NN using|use|VBG the|the|DT Bioconductor|Bioconductor|NNP package|package|NN as|as|IN described|describe|VBN -LRB-|-lrb-|-LRB- Yang|Yang|NNP ,|,|, Y.H.|Y.H.|NNP et|et|FW al.|al.|FW .|.|. Normalization|normalization|NN for|for|IN cDNA|cdna|NN microarray|microarray|NN data|datum|NNS :|:|: a|a|DT robust|robust|JJ composite|composite|JJ method|method|NN addressing|address|VBG single|single|JJ and|and|CC multiple|multiple|JJ slide|slide|NN systematic|systematic|JJ variation|variation|NN ,|,|, Nucleic|nucleic|JJ Acid|acid|NN Res|Res|NNP 30|30|CD ,|,|, e15|e15|NN ,|,|, 2002|2002|CD ;|;|: Smyth|Smyth|NNP ,|,|, G.K.|G.K.|NNP in|in|IN Bioinformatics|Bioinformatics|NNP and|and|CC Computational|Computational|NNP Biology|Biology|NNP Solutions|Solutions|NNPS using|use|VBG R|r|NN and|and|CC Bioconductor|bioconductor|NN .|.|. 397-420|397-420|CD ,|,|, Springer|Springer|NNP ,|,|, New|New|NNP York|York|NNP ,|,|, 2005|2005|CD -RRB-|-rrb-|-RRB- .|.|.
background|background|NN :|:|: wild|wild|JJ type|type|NN ,|,|, crp|crp|NN flag|flag|NN tag|tag|NN
background|background|NN :|:|: wild|wild|JJ type|type|NN ,|,|, fis|fi|VBZ flag|flag|NN tag|tag|NN
bacteria|bacterium|NNS
Bacteria|bacterium|NNS
Bacteria|bacterium|NNS at|at|IN 58|58|CD °C|°c|NN F|f|NN =|=|JJ 2|2|CD
Bacteria|bacterium|NNS at|at|IN 58|58|CD °C|°c|NN F|f|NN =|=|JJ 3|3|CD
Bacteria|bacterium|NNS at|at|IN 60|60|CD °C|°c|NN F|f|NN =|=|JJ 3|3|CD
Bacteria|bacterium|NNS at|at|IN 71|71|CD °C|°c|NN
Bacteria|bacterium|NNS cells|cell|NNS
bacteria|bacterium|NNS grown|grow|VBN at|at|IN 37|37|CD °|°|CD C|c|NN with|with|IN shaking|shake|VBG until|until|IN log|log|NN phase|phase|NN
bacteria|bacterium|NNS grown|grow|VBN at|at|IN 37|37|CD °|°|CD C|c|NN with|with|IN shaking|shake|VBG until|until|IN log|log|NN phase|phase|NN with|with|IN ampicilin|ampicilin|NN treatment|treatment|NN
bacteria|bacterium|NNS grown|grow|VBN at|at|IN 37|37|CD °|°|CD C|c|NN with|with|IN shaking|shake|VBG until|until|IN log|log|NN phase|phase|NN with|with|IN florfenicol|florfenicol|NN treatment|treatment|NN
bacteria|bacterium|NNS grown|grow|VBN at|at|IN 37|37|CD °|°|CD C|c|NN with|with|IN shaking|shake|VBG until|until|IN log|log|NN phase|phase|NN with|with|IN streptomycin|streptomycin|NN treatment|treatment|NN
bacteria|bacterium|NNS grown|grow|VBN in|in|IN LB|lb|NN in|in|FW vitro|vitro|FW
bacteria|bacterium|NNS harvested|harvest|VBN from|from|IN blood|blood|NN of|of|IN chickens|chicken|NNS
Bacterial|bacterial|JJ cell|cell|NN
bacterial|bacterial|JJ cell|cell|NN culture|culture|NN
Bacterial|bacterial|JJ Cell|cell|NN Lysates|lysate|NNS
bacterial|bacterial|JJ cell|cell|NN lysates|lysate|NNS _|_|VBP input|input|NN
bacterial|bacterial|JJ cell|cell|NN lysates|lysate|NNS _|_|VBP RecA-ChIP-seq|reca-chip-seq|JJ
Bacterial|bacterial|JJ cell|cell|NN pellet|pellet|NN
bacterial|bacterial|JJ cells|cell|NNS
Bacterial|bacterial|JJ cells|cell|NNS
Bacterial|bacterial|JJ cells|cell|NNS from|from|IN an|a|DT overnight|overnight|JJ culture|culture|NN were|be|VBD washed|wash|VBN and|and|CC diluted|dilute|VBN in|in|IN fresh|fresh|JJ SILAC|silac|NN -LRB-|-lrb-|-LRB- stable|stable|JJ isotope|isotope|NN labeling|labeling|NN with|with|IN amino|amino|NN acids|acid|NNS in|in|IN cell|cell|NN culture|culture|NN -RRB-|-rrb-|-RRB- medium|medium|NN optimized|optimize|VBN for|for|IN non-auxotrophic|non-auxotrophic|JJ E.|e.|FW coli|coli|FW -LRB-|-lrb-|-LRB- Ping|ping|VB LY|LY|NNP et|et|FW al.|al.|FW .|.|. J|J|NNP Proteome|Proteome|NNP Res.|Res.|NNP ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- ,|,|, before|before|IN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN agitation|agitation|NN until|until|IN reaching|reach|VBG an|a|DT OD600|od600|NN of|of|IN approximately|approximately|RB 0.3|0.3|CD .|.|.
bacterial|bacterial|JJ cells|cell|NNS grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 0.5|0.5|CD
Bacterial|bacterial|JJ cells|cell|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN and|and|CC 5|5|CD %|%|NN LB|lb|NN at|at|IN 37|37|CD °C|°c|NN under|under|IN constant|constant|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- ~|~|NN 120|120|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- in|in|IN a|a|DT water|water|NN bath|bath|NN and|and|CC harvested|harvest|VBN at|at|IN OD|od|NN ~|~|NN 0.6|0.6|CD .|.|.
Bacterial|bacterial|JJ cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN dYT|dyt|JJ medium|medium|NN -LRB-|-lrb-|-LRB- Miller|Miller|NNP ,|,|, JH|JH|NNP -LRB-|-lrb-|-LRB- 1972|1972|CD -RRB-|-rrb-|-RRB- Experiments|experiment|NNS in|in|IN Molecular|molecular|JJ Genetics|Genetics|NNP -LRB-|-lrb-|-LRB- Cold|Cold|NNP Spring|Spring|NNP Harbor|Harbor|NNP Laboratory|Laboratory|NNP ,|,|, Cold|Cold|NNP Spring|Spring|NNP Harbor|Harbor|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN kanamycin|kanamycin|NN -LRB-|-lrb-|-LRB- 10|10|CD mg/L|mg/l|NN -RRB-|-rrb-|-RRB- ,|,|, ampicillin|ampicillin|NN -LRB-|-lrb-|-LRB- 100|100|CD mg/L|mg/l|NN -RRB-|-rrb-|-RRB- and|and|CC IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- at|at|IN 30|30|CD °C|°c|NN in|in|IN a|a|DT shaking|shake|VBG water|water|NN bath|bath|NN .|.|. At|at|IN a|a|DT turbidity|turbidity|NN -LRB-|-lrb-|-LRB- measured|measure|VBN at|at|IN OD536|od536|NN -RRB-|-rrb-|-RRB- of|of|IN approximately|approximately|RB 0.1|0.1|CD bacteria|bacterium|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN ambient|ambient|JJ temperature|temperature|NN and|and|CC resuspended|resuspend|VBN in|in|IN fresh|fresh|JJ dYT|dyt|NN medium|medium|NN containing|contain|VBG antibiotics|antibiotic|NNS and|and|CC 0.2|0.2|CD %|%|NN arabinose|arabinose|NN .|.|. Growth|growth|NN was|be|VBD continued|continue|VBN at|at|IN 30|30|CD °C|°c|NN and|and|CC 10|10|CD hours|hour|NNS after|after|IN inducer|inducer|NN shift|shift|NN 3|3|CD ml|ml|NN sample|sample|NN were|be|VBD withdrawn|withdraw|VBN ,|,|, treated|treat|VBN with|with|IN RNAPROTECT|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Ballerup|Ballerup|NNP -RRB-|-rrb-|-RRB- ,|,|, harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC frozen|freeze|VBN .|.|.
Bacterial|bacterial|JJ culture|culture|NN grown|grow|VBN overnight|overnight|RB at|at|IN 37C|37c|NN ,|,|, given|give|VBN 1|1|CD %|%|NN sub-culturing|sub-culturing|JJ till|till|IN OD|od|NN at|at|IN 600nm|600nm|NN was|be|VBD 0.4|0.4|CD
Bacterial|bacterial|JJ cultures|culture|NNS
Bacterial|bacterial|JJ culture|culture|NN with|with|IN 0.2|0.2|CD ppm|ppm|NN deoxynivalenol|deoxynivalenol|NN
Bacterial|bacterial|JJ culture|culture|NN with|with|IN 0.2|0.2|CD ppm|ppm|NN nivalenol|nivalenol|NN
Bacterial|bacterial|JJ culture|culture|NN with|with|IN 2|2|CD ppm|ppm|NN deoxynivalenol|deoxynivalenol|NN
Bacterial|bacterial|JJ culture|culture|NN with|with|IN 2|2|CD ppm|ppm|NN nivalenol|nivalenol|NN
Bacterial|bacterial|JJ culture|culture|NN with|with|IN acetonitrile|acetonitrile|NN
Bacterial|bacterial|JJ liquid|liquid|JJ culture|culture|NN
Bacterial|bacterial|JJ lysis|lysis|NN
bacterial|bacterial|JJ pellet|pellet|NN
Bacterial|bacterial|JJ pellets|pellet|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 350µl|350µl|CD RNAwiz|rnawiz|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- and|and|CC kept|keep|VBD at|at|IN -80|-80|CD °C|°c|NN .|.|.
Bacterial|bacterial|JJ RNA|rna|NN was|be|VBD purified|purify|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN ,|,|, and|and|CC the|the|DT samples|sample|NNS with|with|IN RNA|rna|NN Integrity|integrity|NN Number|number|NN -LRB-|-lrb-|-LRB- RIN|rin|NN -RRB-|-rrb-|-RRB- >|>|JJR 9|9|CD were|be|VBD used|use|VBN for|for|IN labeling|label|VBG
Bacterial|bacterial|JJ RNA|rna|NN was|be|VBD stabilized|stabilize|VBN in|in|FW vivo|vivo|FW ,|,|, by|by|IN using|use|VBG RNA|rna|NN protect|protect|VBP Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. Total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN by|by|IN using|use|VBG RNeasy|RNeasy|NNP Kits|kit|NNS for|for|IN RNA|rna|NN purification|purification|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
Bacterial|bacterial|JJ strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN 1:100|1:100|CD in|in|IN fresh|fresh|JJ LB|lb|NN and|and|CC grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG to|to|TO an|a|DT OD600|od600|NN =|=|JJ 0.5|0.5|CD .|.|.
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 2|2|CD -|-|: Replicate|replicate|VB 1|1|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 2|2|CD -|-|: Replicate|replicate|VB 2|2|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 2|2|CD -|-|: Replicate|replicate|VB 3|3|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 2|2|CD -|-|: Replicate|replicate|VB 4|4|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 2|2|CD -|-|: Replicate|replicate|VB 5|5|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 1|1|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 2|2|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 3|3|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 58|58|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 4|4|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 60|60|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 1|1|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 60|60|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 2|2|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 60|60|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 3|3|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN at|at|IN 60|60|CD °C|°c|NN to|to|TO a|a|DT process|process|NN lethality|lethality|NN value|value|NN of|of|IN 3|3|CD -|-|: Replicate|replicate|VB 4|4|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN to|to|TO a|a|DT core|core|NN temperature|temperature|NN of|of|IN 71|71|CD °C|°c|NN -|-|: Replicate|replicate|VB 1|1|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN to|to|TO a|a|DT core|core|NN temperature|temperature|NN of|of|IN 71|71|CD °C|°c|NN -|-|: Replicate|replicate|VB 2|2|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN to|to|TO a|a|DT core|core|NN temperature|temperature|NN of|of|IN 71|71|CD °C|°c|NN -|-|: Replicate|replicate|VB 3|3|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN to|to|TO a|a|DT core|core|NN temperature|temperature|NN of|of|IN 71|71|CD °C|°c|NN -|-|: Replicate|replicate|VB 4|4|CD
Bacteria|bacterium|NNS suspension|suspension|NN heated|heat|VBN to|to|TO a|a|DT core|core|NN temperature|temperature|NN of|of|IN 71|71|CD °C|°c|NN -|-|: Replicate|replicate|VB 5|5|CD
Bacteria|bacterium|NNS were|be|VBD cultured|culture|VBN in|in|IN an|a|DT M9|m9|NN minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN 2|2|CD g/L|g/l|NN lactose|lactose|NN and|and|CC 5|5|CD mM|mm|NN phenylethylamine|phenylethylamine|NN -LRB-|-lrb-|-LRB- PEA|pea|NN ,|,|, M9|m9|NN +|+|CC L+PEA|l+pea|NN -RRB-|-rrb-|-RRB- .|.|. To|to|TO induce|induce|VB ECAO|ecao|NN expression|expression|NN from|from|IN tynA|tyna|NN gene|gene|NN ,|,|, o/n|o/n|JJ culture|culture|NN of|of|IN wt|wt|JJ E.|e.|FW coli|coli|FW in|in|IN M9-lactose|m9-lactose|JJ medium|medium|NN was|be|VBD diluted|dilute|VBN 1:20|1:20|CD in|in|IN M9|m9|NN +|+|CC L+PEA|l+pea|NN with|with|IN 5|5|CD μM|μm|NN CuSO4|cuso4|NN .|.|. The|the|DT bacteria|bacterium|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB at|at|IN +30|+30|CD °C|°c|NN with|with|IN 250|250|CD rpm|rpm|NN shaking|shake|VBG .|.|.
Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN at|at|IN 30C|30c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- ~|~|NN 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- in|in|IN fully|fully|RB supplemented|supplement|VBN MOPS|mop|NNS glucose|glucose|NN media|media|NNS -LRB-|-lrb-|-LRB- Teknova|teknova|NN -RRB-|-rrb-|-RRB- to|to|TO OD420|od420|NN ~|~|NN 0.4|0.4|CD .|.|. Cultures|culture|NNS were|be|VBD split|split|VBN into|into|IN 4|4|CD subcultures|subculture|NNS ,|,|, and|and|CC grown|grow|VBN to|to|TO OD|od|NN ~|~|NN 0.3|0.3|CD .|.|.
Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN in|in|IN batch|batch|NN or|or|CC bioreactor|bioreactor|NN vessels|vessel|NNS in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|.
Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN broth|broth|NN overnight|overnight|JJ and|and|CC subcultured|subculture|VBN in|in|IN DMEM|DMEM|NNP
Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN broth|broth|NN overnight|overnight|JJ and|and|CC subcultured|subculture|VBN in|in|IN DMEM|DMEM|NNP prior|prior|RB to|to|TO acid|acid|NN stress|stress|NN
Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN broth|broth|NN overnight|overnight|JJ and|and|CC subcultured|subculture|VBN in|in|IN DMEM|dmem|NN to|to|TO OD600|od600|NN of|of|IN 0.4|0.4|CD .|.|. Bacteria|bacterium|NNS were|be|VBD then|then|RB spun|spin|VBN down|down|RP ,|,|, media|media|NNS removed|remove|VBD and|and|CC repalced|repalce|VBD with|with|IN DMEM|dmem|NN .|.|.
Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN broth|broth|NN overnight|overnight|JJ and|and|CC subcultured|subculture|VBN in|in|IN DMEM|dmem|NN to|to|TO OD600|od600|NN of|of|IN 0.4|0.4|CD .|.|. Bacteria|bacterium|NNS were|be|VBD then|then|RB spun|spin|VBN down|down|RP ,|,|, media|media|NNS removed|remove|VBD and|and|CC repalced|repalce|VBD with|with|IN DMEM|dmem|NN plus|plus|CC 0.15|0.15|CD %|%|NN bile|bile|NN salt|salt|NN mix|mix|NN .|.|.
Bacteria|bacterium|NNS were|be|VBD harvested|harvest|VBN with|with|IN 0.5|0.5|CD Vol|vol|NN of|of|IN 5|5|CD %|%|NN phenol|phenol|NN in|in|IN ethanol|ethanol|NN and|and|CC frozen|freeze|VBN at|at|IN -80|-80|CD C.|C.|NNP Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN frozen|frozen|JJ cultures|culture|NNS using|use|VBG RNeasy|RNeasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
Bacteria|bacterium|NNS were|be|VBD inoculated|inoculate|VBN by|by|IN direct|direct|JJ injection|injection|NN of|of|IN the|the|DT mouse|mouse|NN bladder|bladder|NN ,|,|, and|and|CC kidney|kidney|NN samples|sample|NNS were|be|VBD taken|take|VBN at|at|IN day|day|NN 2|2|CD post-infection|post-infection|JJ
Bacteria|bacterium|NNS were|be|VBD lyzed|lyze|VBN with|with|IN lyzozyme|lyzozyme|NN and|and|CC sonicated|sonicate|VBN to|to|TO shear|shear|NN DNA|dna|NN .|.|. TopoIV-DNA|topoiv-dna|JJ complexes|complex|NNS were|be|VBD isolated|isolate|VBN with|with|IN antibody|antibody|NN .|.|.
Bacterium|Bacterium|NNP
Bacteroides|Bacteroides|NNPS caccae|caccae|FW ATCC|atcc|NN 43185|43185|CD
Bacteroides|Bacteroides|NNPS fragilis|fragili|VBZ
Bacteroides|Bacteroides|NNPS ovatus|ovatus|NN ATCC|atcc|NN 8483|8483|CD
Bacteroides|Bacteroides|NNPS thetaiotaomicron|thetaiotaomicron|RB VPI-5482|vpi-5482|JJ
BAM|bam|NN files|file|NNS of|of|IN each|each|DT ChIP|chip|NN biological|biological|JJ replicate|replicate|VB and|and|CC the|the|DT input|input|NN replicate|replicate|VB samples|sample|NNS were|be|VBD used|use|VBN in|in|IN the|the|DT MACS|macs|NN peak|peak|NN calling|call|VBG program|program|NN with|with|IN the|the|DT -|-|: f|f|LS BAMPE|bampe|NN parameter|parameter|NN
BAM|bam|NN files|file|NNS of|of|IN the|the|DT resulting|result|VBG assembly|assembly|NN data|datum|NNS were|be|VBD exported|export|VBN to|to|TO JMP|JMP|NNP Genomics|Genomics|NNP -LRB-|-lrb-|-LRB- SAS|SAS|NNP -RRB-|-rrb-|-RRB- .|.|. TMM|TMM|NNP normalization|normalization|NN and|and|CC ANOVA|anova|NN analysis|analysis|NN of|of|IN the|the|DT read|read|NN samples|sample|NNS were|be|VBD conducted|conduct|VBN in|in|IN JMP|JMP|NNP Genomics|Genomics|NNPS
basal|basal|JJ media|media|NNS :|:|: M9|m9|NN +|+|CC 4|4|CD g/L|g/l|NN glc|glc|NN -LRB-|-lrb-|-LRB- glucose|glucose|NN minimal|minimal|JJ media|media|NNS -RRB-|-rrb-|-RRB-
Basecalling|basecalling|NN performed|perform|VBN by|by|IN MiSeq|miseq|NN -LRB-|-lrb-|-LRB- RTA|rta|NN -RRB-|-rrb-|-RRB-
Base|base|NN calling|call|VBG performed|perform|VBN using|use|VBG Illumina|Illumina|NNP GA|GA|NNP pipeline|pipeline|NN 1.6|1.6|CD .|.|.
Basecalling|basecalling|NN was|be|VBD done|do|VBN on|on|IN the|the|DT sequencers|sequencer|NNS using|use|VBG the|the|DT sequencer|sequencer|NN 's|'s|POS Real-Time|Real-Time|NNP Analysis|analysis|NN -LRB-|-lrb-|-LRB- RTA|rta|NN -RRB-|-rrb-|-RRB- software|software|NN .|.|. CASAVA|CASAVA|NNP was|be|VBD used|use|VBN to|to|TO process|process|VB the|the|DT basecalled|basecalled|JJ data|datum|NNS into|into|IN FASTQ|fastq|NN format|format|NN .|.|.
Base|Base|NNP calling|call|VBG was|be|VBD performed|perform|VBN by|by|IN the|the|DT DOE|DOE|NNP Joint|Joint|NNP Genome|Genome|NNP Institute|Institute|NNP using|use|VBG Illumina|Illumina|NNP software|software|NN .|.|.
Basecalling|basecalling|NN was|be|VBD performed|perform|VBN by|by|IN Torrent|Torrent|NNP Suite|Suite|NNP version|version|NN 5|5|CD software|software|NN using|use|VBG the|the|DT default|default|NN settings|setting|NNS .|.|.
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG CASAVA|CASAVA|NNP version|version|NN 1.4|1.4|CD
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG CASAVA|CASAVA|NNP version|version|NN 1.7|1.7|CD
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG CASAVA|CASAVA|NNP version|version|NN 1.8|1.8|CD
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG CASAVA|CASAVA|NNP version|version|NN 1.8.2|1.8.2|CD
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG CASAVA|CASAVA|NNP version|version|NN 1.8.2|1.8.2|CD .|.|.
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG Casava|Casava|NNP versions|version|NNS 1.6|1.6|CD or|or|CC 1.7|1.7|CD .|.|.
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG HCS|hcs|NN 2.0.5|2.0.5|CD and|and|CC RTA|RTA|NNP 1.17.20|1.17.20|CD
Basecalls|basecall|NNS performed|perform|VBN using|use|VBG Illumina|Illumina|NNP CASAVA|CASAVA|NNP .|.|.
Base|Base|NNP calls|call|VBZ performed|perform|VBN with|with|IN RTA|rta|NN v1|v1|NN .18.5|.18.5|CD
Base|base|NN calls|call|NNS were|be|VBD made|make|VBN using|use|VBG MiSeq|MiSeq|NNP Reporter|reporter|NN v.|v.|CC 2.6.2.1|2.6.2.1|CD
Basecalls|basecall|NNS were|be|VBD performed|perform|VBN using|use|VBG CASAVA|CASAVA|NNP .1.8|.1.8|CD
base|base|NN calls|call|VBZ with|with|IN quality|quality|NN metrics|metric|NNS were|be|VBD generated|generate|VBN using|use|VBG the|the|DT HiSeq|HiSeq|NNP 2500|2500|CD Control|Control|NNP software|software|NN
batch|batch|NN :|:|: 10|10|CD
batch|batch|NN :|:|: 11|11|CD
batch|batch|NN :|:|: 12|12|CD
batch|batch|NN :|:|: 13|13|CD
batch|batch|NN :|:|: 14|14|CD
batch|batch|NN :|:|: 15|15|CD
batch|batch|NN :|:|: 16|16|CD
batch|batch|NN :|:|: 17|17|CD
batch|batch|NN :|:|: 18|18|CD
batch|batch|NN :|:|: 19|19|CD
batch|batch|NN :|:|: 20|20|CD
batch|batch|NN :|:|: 21|21|CD
batch|batch|NN :|:|: 22|22|CD
batch|batch|NN :|:|: 23|23|CD
batch|batch|NN :|:|: 24|24|CD
batch|batch|NN :|:|: 25|25|CD
batch|batch|NN :|:|: 26|26|CD
batch|batch|NN :|:|: 27|27|CD
batch|batch|NN :|:|: 7|7|CD
batch|batch|NN :|:|: 8|8|CD
batch|batch|NN :|:|: 9|9|CD
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 10|10|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 120|120|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 20|20|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 40|40|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 60|60|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 10|10|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 120|120|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 20|20|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 40|40|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 60|60|CD min|min|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, prior|prior|RB to|to|TO CORM-3|corm-3|NN addition|addition|NN
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, prior|prior|RB to|to|TO CORM-3|corm-3|NN addition|addition|NN -LRB-|-lrb-|-LRB- t|t|NN =|=|JJ 0|0|CD -RRB-|-rrb-|-RRB-
Batch|batch|NN anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN hemA|hema|NN defined|define|VBN medium|medium|NN ,|,|, prior|prior|RB to|to|TO iCORM-3|icorm-3|NN addition|addition|NN
batch|batch|NN culture|culture|NN
batch|batch|NN culture|culture|NN rep1|rep1|NN ,|,|, 0.5|0.5|CD min|min|NN
batch|batch|NN culture|culture|NN rep1|rep1|NN ,|,|, 0|0|CD min|min|NN
batch|batch|NN culture|culture|NN rep1|rep1|NN ,|,|, 10|10|CD min|min|NN
batch|batch|NN culture|culture|NN rep1|rep1|NN ,|,|, 1|1|CD min|min|NN
batch|batch|NN culture|culture|NN rep1|rep1|NN ,|,|, 2|2|CD min|min|NN
batch|batch|NN culture|culture|NN rep1|rep1|NN ,|,|, 5|5|CD min|min|NN
batch|batch|NN culture|culture|NN rep2|rep2|NN ,|,|, 0.5|0.5|CD min|min|NN
batch|batch|NN culture|culture|NN rep2|rep2|NN ,|,|, 0|0|CD min|min|NN
batch|batch|NN culture|culture|NN rep2|rep2|NN ,|,|, 10|10|CD min|min|NN
batch|batch|NN culture|culture|NN rep2|rep2|NN ,|,|, 1|1|CD min|min|NN
batch|batch|NN culture|culture|NN rep2|rep2|NN ,|,|, 2|2|CD min|min|NN
batch|batch|NN culture|culture|NN rep2|rep2|NN ,|,|, 5|5|CD min|min|NN
batch|batch|NN culture|culture|NN rep3|rep3|NN ,|,|, 0.5|0.5|CD min|min|NN
batch|batch|NN culture|culture|NN rep3|rep3|NN ,|,|, 0|0|CD min|min|NN
batch|batch|NN culture|culture|NN rep3|rep3|NN ,|,|, 10|10|CD min|min|NN
batch|batch|NN culture|culture|NN rep3|rep3|NN ,|,|, 1|1|CD min|min|NN
batch|batch|NN culture|culture|NN rep3|rep3|NN ,|,|, 2|2|CD min|min|NN
batch|batch|NN culture|culture|NN rep3|rep3|NN ,|,|, 5|5|CD min|min|NN
Batch|batch|NN cultures|culture|NNS of|of|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG in|in|IN Luria-Bertani|luria-bertani|JJ medium|medium|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD %|%|NN Bacto|bacto|NN Tryptone|tryptone|NN ,|,|, 0.05|0.05|CD %|%|NN yeast|yeast|NN extract|extract|NN ,|,|, 0.05|0.05|CD %|%|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- .|.|.
Batch|batch|NN growth|growth|NN in|in|IN mineral|mineral|JJ medium|medium|NN supplied|supply|VBN with|with|IN 4|4|CD g/l|g/l|NN glucose|glucose|NN as|as|IN sole|sole|JJ carbon|carbon|NN source|source|NN -LRB-|-lrb-|-LRB- optical|optical|JJ density|density|NN 0.4|0.4|CD at|at|IN 546nm|546nm|NN -RRB-|-rrb-|-RRB-
Batch|batch|NN growth|growth|NN in|in|IN mineral|mineral|JJ medium|medium|NN supplied|supply|VBN with|with|IN 4|4|CD g/l|g/l|NN glucose|glucose|NN as|as|IN sole|sole|JJ carbon|carbon|NN source|source|NN -LRB-|-lrb-|-LRB- optical|optical|JJ density|density|NN of|of|IN 0.4|0.4|CD at|at|IN 546|546|CD nm|nm|NN -RRB-|-rrb-|-RRB-
BC-7ppm|bc-7ppm|JJ replicate|replicate|VB 1|1|CD
BC-7ppm|bc-7ppm|JJ replicate|replicate|VB 2|2|CD
BC-7ppm|bc-7ppm|JJ replicate|replicate|VB 3|3|CD
BC-9ppm|bc-9ppm|JJ replicate|replicate|VB 1|1|CD
BC-9ppm|bc-9ppm|JJ replicate|replicate|VB 2|2|CD
BC-9ppm|bc-9ppm|JJ replicate|replicate|VB 3|3|CD
bcl2fastq2|bcl2fastq2|NN v2|v2|NN .15.0|.15.0|CD -LRB-|-lrb-|-LRB- Demultiplexing|demultiplexing|NN -RRB-|-rrb-|-RRB- ,|,|, Fastqc|fastqc|NN 0.11.5|0.11.5|CD -LRB-|-lrb-|-LRB- read|read|VB quality|quality|NN -RRB-|-rrb-|-RRB- ,|,|, Cutadapt-1.9.1|cutadapt-1.9.1|NN -LRB-|-lrb-|-LRB- adaptor|adaptor|NN trimming|trim|VBG -RRB-|-rrb-|-RRB-
-LRB-|-lrb-|-LRB- B|b|NN -RRB-|-rrb-|-RRB- ,|,|, column|column|NN -LRB-|-lrb-|-LRB- X|x|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC row|row|NN -LRB-|-lrb-|-LRB- Y|y|NN -RRB-|-rrb-|-RRB- number|number|NN ,|,|, red|red|JJ foreground|foreground|NN -LRB-|-lrb-|-LRB- f|f|FW _|_|FW r|r|NN -RRB-|-rrb-|-RRB- and|and|CC background|background|NN -LRB-|-lrb-|-LRB- b|b|NN _|_|CD r|r|NN -RRB-|-rrb-|-RRB- ,|,|, green|green|JJ
bcp|bcp|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
bcp|bcp|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r2|r2|NN
bcp|bcp|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r3|r3|NN
bcp|bcp|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
Bear|Bear|NNP feces|fece|NNS isolate|isolate|VBP B1|b1|NN
Bear|Bear|NNP feces|fece|VBZ isolate|isolate|JJ B3|b3|NN
Bear|Bear|NNP feces|fece|VBZ isolate|isolate|JJ B5|b5|NN
Bear|Bear|NNP III|III|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 1|1|CD
Bear|Bear|NNP III|III|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VBP 2|2|CD
Bear|Bear|NNP II|II|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 1|1|CD
Bear|Bear|NNP II|II|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 2|2|CD
Bear|Bear|NNP I|I|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 1|1|CD
Bear|Bear|NNP I|I|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VBP 2|2|CD
Beta|beta|JJ _|_|NN ChIP|chip|NN _|_|CD A|a|DT _|_|NN cy5|cy5|NN
Beta|beta|NN _|_|CD ChIP|chip|NN _|_|NN B|b|NN _|_|CD cy5|cy5|NN
Beta|beta|NN _|_|CD ChIP|chip|NN _|_|NN control|control|NN _|_|CD A|a|DT _|_|NN cy3|cy3|NN
Beta|beta|NN _|_|CD ChIP|chip|NN _|_|NN control|control|NN _|_|NN B|b|NN _|_|CD cy3|cy3|NN
Bexp|bexp|NN _|_|CD Bstat|Bstat|NNP _|_|SYM dyeswap1|dyeswap1|CD
Bexp|bexp|NN _|_|CD Bstat|Bstat|NNP _|_|SYM dyeswap2|dyeswap2|CD
Bexp|bexp|NN _|_|CD Bstat|Bstat|NNP _|_|CD rep1|rep1|NN
Bexp|bexp|NN _|_|CD Bstat|Bstat|NNP _|_|CD rep2|rep2|NN
Bexp|bexp|NN _|_|CD Kexp|Kexp|NNP _|_|SYM dyeswap1|dyeswap1|CD
Bexp|bexp|NN _|_|CD Kexp|Kexp|NNP _|_|SYM dyeswap2|dyeswap2|CD
Bexp|bexp|NN _|_|CD Kexp|Kexp|NNP _|_|CD rep1|rep1|NN
Bexp|bexp|NN _|_|CD Kexp|Kexp|NNP _|_|CD rep2|rep2|NN
Bexp|bexp|NN _|_|CD Kstat|Kstat|NNP _|_|SYM dyeswap1|dyeswap1|CD
Bexp|bexp|NN _|_|CD Kstat|Kstat|NNP _|_|SYM dyeswap2|dyeswap2|CD
Bexp|bexp|NN _|_|CD Kstat|Kstat|NNP _|_|CD rep1|rep1|NN
Bexp|bexp|NN _|_|CD Kstat|Kstat|NNP _|_|CD rep2|rep2|NN
BGI|bgi|NN inhouse|inhouse|NN software|software|NN ``|``|`` filter|filter|NN _|_|NN fq|fq|NN ''|''|'' for|for|IN basecalling|basecalling|NN and|and|CC trimming|trim|VBG
Bicyclomycin|bicyclomycin|NN -LRB-|-lrb-|-LRB- BCM|bcm|NN ,|,|, gift|gift|NN of|of|IN Schering-Plough|Schering-Plough|NNP Animal|Animal|NNP Health|Health|NNP -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT culture|culture|NN at|at|IN the|the|DT indicated|indicate|VBN dose|dose|NN for|for|IN 20|20|CD minutes|minute|NNS .|.|. Culture|culture|NN was|be|VBD added|add|VBN to|to|TO 2|2|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN Bacterial|bacterial|JJ Reagent|reagent|NN -LRB-|-lrb-|-LRB- QIAGEN|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
BigWIG|bigwig|NN files|file|NNS were|be|VBD viewed|view|VBN and|and|CC annotated|annotated|JJ using|use|VBG Jbrowse|Jbrowse|NNP and|and|CC Integrated|Integrated|NNP Genome|Genome|NNP Viewer|Viewer|NNP .|.|.
bile|bile|NN +1|+1|CD
bile|bile|NN +2|+2|CD
bile|bile|NN +3|+3|CD
Bile|Bile|NNP salt|salt|NN stress|stress|NN was|be|VBD done|do|VBN in|in|IN DMEM|dmem|NN at|at|IN pH|ph|NN 7.4|7.4|CD -LRB-|-lrb-|-LRB- unbuffered|unbuffered|JJ -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN ,|,|, 5|5|CD %|%|NN CO2|co2|NN ,|,|, static|static|JJ incubation|incubation|NN for|for|IN 90|90|CD minutes|minute|NNS
Binning|binning|NN at|at|IN 5kb|5kb|JJ .|.|.
Bio1|bio1|NN 1m|1m|NN
Bio1|bio1|NN 1y|1y|NN
Bio2|bio2|NN 1m|1m|NN
Bio2|bio2|NN 1y|1y|NN
Bio3|bio3|NN 1m|1m|NN
Bio3|bio3|NN 1y|1y|NN
Bio4|bio4|NN 1m|1m|NN
Bio4|bio4|NN 1y|1y|NN
Bio-6|bio-6|NN
Bio|bio|NN Contro|contro|NN
Biofilms|biofilm|NNS were|be|VBD grown|grow|VBN on|on|IN nylon|nylon|NN membranes|membrane|NNS using|use|VBG agar|agar|NN as|as|IN the|the|DT source|source|NN of|of|IN nutrients|nutrient|NNS and|and|CC water|water|NN .|.|. Aliquots|aliquot|NNS of|of|IN 10|10|CD ml|ml|NN Luria|Luria|NNP agar|agar|NN were|be|VBD transferred|transfer|VBN to|to|TO petri|petri|VB dishes|dish|NNS to|to|TO produce|produce|VB layers|layer|NNS of|of|IN agar|agar|NN approximately|approximately|RB 3|3|CD mm|mm|NN in|in|IN depth|depth|NN .|.|. Nylon|nylon|NN membrane|membrane|NN filters|filter|NNS -LRB-|-lrb-|-LRB- 47|47|CD mm|mm|NN diameter|diameter|NN -RRB-|-rrb-|-RRB- with|with|IN a|a|DT 0.2|0.2|CD μm|μm|NN pore|pore|NN size|size|NN -LRB-|-lrb-|-LRB- Whatman|whatman|NN -RRB-|-rrb-|-RRB- were|be|VBD autoclaved|autoclave|VBN in|in|IN Milli-Q|milli-q|JJ water|water|NN ,|,|, dried|dry|VBD and|and|CC placed|place|VBD on|on|IN the|the|DT agar|agar|NN surface|surface|NN .|.|. A|a|DT 100|100|CD μl|μl|NN aliquot|aliquot|NN of|of|IN an|a|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- approximately|approximately|RB 108|108|CD cells|cell|NNS -RRB-|-rrb-|-RRB- was|be|VBD applied|apply|VBN to|to|TO the|the|DT membrane|membrane|NN as|as|IN a|a|DT single|single|JJ spot|spot|NN and|and|CC allowed|allow|VBN to|to|TO dry|dry|JJ .|.|. All|all|DT of|of|IN these|these|DT steps|step|NNS were|be|VBD performed|perform|VBN on|on|IN a|a|DT level|level|NN table|table|NN so|so|RB as|as|IN not|not|RB to|to|TO introduce|introduce|VB unwanted|unwanted|JJ gradients|gradient|NNS .|.|. Dishes|dish|NNS were|be|VBD then|then|RB inverted|inverted|JJ and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD oC|oc|NN for|for|IN 24|24|CD h.|h.|NN
Biofilms|biofilm|NNS were|be|VBD individually|individually|RB removed|remove|VBN from|from|IN the|the|DT incubator|incubator|NN and|and|CC ,|,|, using|use|VBG a|a|DT small|small|JJ scalpel|scalpel|NN blade|blade|NN and|and|CC sterile|sterile|JJ forceps|forceps|NNS ,|,|, the|the|DT distinctive|distinctive|JJ outer|outer|JJ perimeter|perimeter|NN of|of|IN biofilm|biofilm|NN growth|growth|NN was|be|VBD cut|cut|VBN away|away|RB from|from|IN the|the|DT rest|rest|NN of|of|IN the|the|DT biofilm|biofilm|NN .|.|. The|the|DT two|two|CD resulting|result|VBG sections|section|NNS of|of|IN membrane|membrane|NN were|be|VBD submerged|submerge|VBN in|in|IN separate|separate|JJ volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN and|and|CC vortexed|vortex|VBN to|to|TO release|release|VB the|the|DT cells|cell|NNS .|.|. The|the|DT sections|section|NNS of|of|IN membrane|membrane|NN were|be|VBD then|then|RB removed|remove|VBN from|from|IN the|the|DT resulting|result|VBG suspension|suspension|NN before|before|IN RNA|rna|NN extraction|extraction|NN .|.|.
biological|biological|JJ replicate|replicate|VB :|:|: 1|1|CD
biological|biological|JJ replicate|replicate|VB :|:|: 2|2|CD
biological|biological|JJ replicate|replicate|VB :|:|: 318|318|CD
biological|biological|JJ replicate|replicate|VB :|:|: 320|320|CD
biological|biological|JJ replicate|replicate|VB :|:|: 327|327|CD
biological|biological|JJ replicate|replicate|VB :|:|: Replicate|replicate|VB 1|1|CD
Biological|Biological|NNP replicates|replicate|VBZ per|per|IN genotype|genotype|NN were|be|VBD incubated|incubate|VBN at|at|IN 1|1|CD mg/L|mg/l|NN of|of|IN ciprofloxacin|ciprofloxacin|NN during|during|IN 60|60|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- that|that|WDT means|mean|VBZ 250xMIC|250xmic|NN for|for|IN E.|e.|FW coli|coli|FW ATCC|atcc|NN 25922|25922|CD ,|,|, 8xMIC|8xmic|NN for|for|IN EC14|ec14|NN ,|,|, 2xMIC|2xmic|NN for|for|IN EC19|ec19|NN and|and|CC 1xMIC|1xmic|NN for|for|IN EC24|ec24|NN -RRB-|-rrb-|-RRB- .|.|.
biological|biological|JJ replicate|replicate|VB :|:|: t|t|NN =|=|JJ 0|0|CD Replicate|replicate|NN 1|1|CD
biological|biological|JJ replicate|replicate|VB :|:|: t|t|NN =|=|JJ 0|0|CD replicate|replicate|VBP 2|2|CD
biomass|biomass|VBP collected|collect|VBN in|in|IN the|the|DT transition|transition|NN between|between|IN exponential|exponential|JJ to|to|TO stationary|stationary|JJ phase|phase|NN
Biomass|Biomass|NNP was|be|VBD snap|snap|JJ frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD C|c|NN prior|prior|JJ to|to|TO extraction|extraction|NN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Midi|Midi|NNP kits|kit|NNS .|.|. RNA|rna|NN integrity|integrity|NN was|be|VBD verified|verify|VBN with|with|IN a|a|DT 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- .|.|.
bioremediation|bioremediation|NN treatment|treatment|NN :|:|: Alert|Alert|NNP -LRB-|-lrb-|-LRB- ex|ex|FW situ|situ|FW -RRB-|-rrb-|-RRB-
bioremediation|bioremediation|NN treatment|treatment|NN :|:|: Eureka|Eureka|NNP -LRB-|-lrb-|-LRB- in|in|FW situ|situ|FW -RRB-|-rrb-|-RRB-
Biotinylated|biotinylate|VBN GST|gst|NN protein|protein|NN
BL21|bl21|NN _|_|NN 1|1|CD
BL21|bl21|NN _|_|NN 2|2|CD
BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- _|_|CD adhE|adhe|NN mutant|mutant|JJ
BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- ,|,|, adhE|adhe|NN mutant|mutant|JJ
BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- HPA|hpa|NN 0mM|0mm|NN
BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- HPA|hpa|NN 3mM|3mm|NN
BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- with|with|IN 3|3|CD mM|mm|NN of|of|IN heptanoic|heptanoic|JJ acid|acid|NN
BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- without|without|IN heptanoic|heptanoic|JJ acid|acid|NN
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 1|1|LS -RRB-|-rrb-|-RRB-
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 2|2|LS -RRB-|-rrb-|-RRB-
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 3|3|LS -RRB-|-rrb-|-RRB-
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB-
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.46|0.46|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 1|1|LS -RRB-|-rrb-|-RRB-
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.46|0.46|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 2|2|LS -RRB-|-rrb-|-RRB-
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.46|0.46|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 3|3|LS -RRB-|-rrb-|-RRB-
BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.46|0.46|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 1|1|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 2|2|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 3|3|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.39|0.39|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 1|1|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.39|0.39|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 2|2|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.39|0.39|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 3|3|LS -RRB-|-rrb-|-RRB-
BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.39|0.39|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 1|1|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 2|2|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 3|3|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.29|0.29|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 1|1|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.29|0.29|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 2|2|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.29|0.29|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 3|3|LS -RRB-|-rrb-|-RRB-
BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.29|0.29|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB-
bla|bla|NN _|_|NN 0|0|CD min|min|NN
bla|bla|NN _|_|CD 10|10|CD min|min|NN
bla|bla|NN _|_|CD 15|15|CD min|min|NN
bla|bla|NN _|_|NN 1|1|CD min|min|NN
bla|bla|NN _|_|NN 2|2|CD min|min|NN
bla|bla|NN _|_|CD 4|4|CD min|min|NN
bla|bla|NN _|_|CD 6|6|CD min|min|NN
bla|bla|NN _|_|CD 8|8|CD min|min|NN
Blautia|blautia|NN coccoides|coccoide|NNS
Blautia|blautia|NN hydrogenotrophica|hydrogenotrophica|NN DSM|DSM|NNP 10507|10507|CD
Blood|Blood|NNP culture|culture|NN
Blood|Blood|NNP culture|culture|NN bottle|bottle|NN
Blue|blue|JJ _|_|NN 1|1|CD
Blue|blue|JJ _|_|NN 2|2|CD
BnTR1|bntr1|NN ,|,|, 37|37|CD °C|°c|NN ,|,|, replicate|replicate|VB 1|1|CD
BnTR1|bntr1|NN ,|,|, 37|37|CD °C|°c|NN ,|,|, replicate|replicate|VB 2|2|CD
BnTR1|bntr1|NN ,|,|, 37|37|CD °C|°c|NN ,|,|, replicate|replicate|VB 3|3|CD
BnTR1|bntr1|NN _|_|NN 37|37|CD _|_|CD rep1|rep1|NN
BnTR1|bntr1|NN _|_|NN 37|37|CD _|_|CD rep2|rep2|NN
BnTR1|bntr1|NN _|_|NN 37|37|CD _|_|CD rep3|rep3|NN
BnTR1|bntr1|NN ,|,|, 42|42|CD °C|°c|NN ,|,|, replicate|replicate|VB 1|1|CD
BnTR1|bntr1|NN ,|,|, 42|42|CD °C|°c|NN ,|,|, replicate|replicate|VB 2|2|CD
BnTR1|bntr1|NN ,|,|, 42|42|CD °C|°c|NN ,|,|, replicate|replicate|VB 3|3|CD
BnTR1|bntr1|NN _|_|CD 42|42|CD _|_|NN rep1|rep1|NN
BnTR1|bntr1|NN _|_|CD 42|42|CD _|_|NN rep2|rep2|NN
BnTR1|bntr1|NN _|_|CD 42|42|CD _|_|NN rep3|rep3|NN
Bordetella|bordetella|NN sp.|sp.|NN .|.|. IITR-02|iitr-02|NN
bovine-biased-1|bovine-biased-1|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
bovine-biased-2|bovine-biased-2|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
bovine-biased-3|bovine-biased-3|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
bovine-biased-4|bovine-biased-4|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
bowtie2-build|bowtie2-build|JJ final|final|JJ _|_|NN reference|reference|NN _|_|CD seqs/REL606|seqs/rel606|NN .|.|. fa|fa|NN indexes/REL606|indexes/rel606|NN
Bowtie|bowtie|NN 2|2|CD -LRB-|-lrb-|-LRB- Langmead|langmead|NN B|b|NN &|&|CC Salzberg|Salzberg|NNP SL|SL|NNP ,|,|, 2012|2012|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN with|with|IN default|default|NN parameters|parameter|NNS ,|,|, to|to|TO remove|remove|VB any|any|DT sequence|sequence|NN reads|read|VBZ aligning|align|VBG to|to|TO ribosomal|ribosomal|JJ RNA|rna|NN ,|,|, transfer|transfer|NN RNA|rna|NN and|and|CC non-coding|non-coding|JJ RNA|rna|NN sequences|sequence|NNS .|.|.
bowtie2|bowtie2|NN v2|v2|NN .2.3|.2.3|CD was|be|VBD used|use|VBN for|for|IN alignment|alignment|NN
Bowtie|bowtie|NN alignments|alignment|NNS against|against|IN the|the|DT E.|e.|FW coli|coli|FW genome|genome|NN were|be|VBD converted|convert|VBN to|to|TO wiggle|wiggle|VB files|file|NNS .|.|. For|for|IN ribosome|ribosome|NN footprints|footprint|NNS and|and|CC mRNA-seq|mrna-seq|NN ,|,|, the|the|DT position|position|NN of|of|IN each|each|DT alignment|alignment|NN is|be|VBZ distributed|distribute|VBN into|into|IN several|several|JJ nucleotides|nucleotide|NNS in|in|IN the|the|DT center|center|NN of|of|IN each|each|DT read|read|NN .|.|. For|for|IN each|each|DT read|read|NN ,|,|, the|the|DT center|center|NN residues|residue|NNS that|that|WDT are|be|VBP at|at|IN least|least|JJS 10|10|CD nucleotides|nucleotide|NNS away|away|RB from|from|IN either|either|CC ends|end|NNS were|be|VBD given|give|VBN the|the|DT same|same|JJ score|score|NN ,|,|, which|which|WDT is|be|VBZ weighted|weight|VBN by|by|IN the|the|DT length|length|NN of|of|IN the|the|DT fragment|fragment|NN -LSB-|-lsb-|-LRB- Oh|oh|UH et|et|FW al|al|FW ,|,|, .|.|. Cell|cell|NN 147|147|CD ,|,|, 1295|1295|CD -LRB-|-lrb-|-LRB- 2011|2011|CD -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- .|.|. Scores|score|NNS therefore|therefore|RB represent|represent|VBP the|the|DT number|number|NN of|of|IN read|read|VBN alignments|alignment|NNS attributed|attribute|VBD to|to|TO each|each|DT genomic|genomic|JJ position|position|NN under|under|IN each|each|DT scoring|score|VBG scheme|scheme|NN .|.|. For|for|IN DMS-seq|dms-seq|NN ,|,|, the|the|DT position|position|NN of|of|IN each|each|DT alignment|alignment|NN was|be|VBD the|the|DT position|position|NN immediately|immediately|RB 5|5|CD '|'|'' of|of|IN the|the|DT 5|5|CD '|'|'' end|end|NN of|of|IN the|the|DT read|read|NN .|.|.
Bowtie|Bowtie|NNP alignments|alignment|NNS against|against|IN the|the|DT E|e|NN coli|coli|NN genome|genome|NN were|be|VBD converted|convert|VBN to|to|TO wiggle|wiggle|VB files|file|NNS .|.|. The|the|DT position|position|NN of|of|IN each|each|DT alignment|alignment|NN is|be|VBZ distributed|distribute|VBN into|into|IN several|several|JJ nucleotides|nucleotide|NNS in|in|IN the|the|DT center|center|NN of|of|IN the|the|DT footprint|footprint|NN .|.|. For|for|IN each|each|DT footprint|footprint|NN read|read|NN ,|,|, the|the|DT center|center|NN residues|residue|NNS that|that|WDT are|be|VBP at|at|IN least|least|JJS 10|10|CD nucleotides|nucleotide|NNS away|away|RB from|from|IN either|either|CC ends|end|NNS were|be|VBD given|give|VBN the|the|DT same|same|JJ score|score|NN ,|,|, which|which|WDT is|be|VBZ weighted|weight|VBN by|by|IN the|the|DT length|length|NN of|of|IN the|the|DT fragment|fragment|NN -LSB-|-lsb-|-LRB- Oh|oh|UH et|et|FW al|al|FW ,|,|, .|.|. Cell|cell|NN 147|147|CD ,|,|, 1295|1295|CD -LRB-|-lrb-|-LRB- 2011|2011|CD -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- .|.|. Scores|score|NNS therefore|therefore|RB represent|represent|VBP the|the|DT number|number|NN of|of|IN read|read|VBN alignments|alignment|NNS attributed|attribute|VBD to|to|TO each|each|DT genomic|genomic|JJ position|position|NN under|under|IN each|each|DT scoring|score|VBG scheme|scheme|NN .|.|.
Bowtie|Bowtie|NNP alignments|alignment|NNS against|against|IN the|the|DT reference|reference|NN genome|genome|NN were|be|VBD converted|convert|VBN to|to|TO wiggle|wiggle|VB files|file|NNS .|.|. The|the|DT position|position|NN of|of|IN each|each|DT alignment|alignment|NN was|be|VBD mapped|map|VBN to|to|TO the|the|DT 3|3|CD '|'|'' end|end|NN of|of|IN the|the|DT nascent|nascent|JJ transcript|transcript|NN .|.|.
Briefly|briefly|RB ,|,|, hot|hot|JJ phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN was|be|VBD done|do|VBN by|by|IN mixing|mix|VBG the|the|DT cell|cell|NN culture|culture|NN in|in|IN 1/2|1/2|CD volume|volume|NN of|of|IN 99|99|CD °C|°c|NN lysis|lysis|NN solution|solution|NN -LRB-|-lrb-|-LRB- 2|2|CD %|%|NN SDS|sds|NN ,|,|, 16|16|CD mM|mm|NN EDTA|edta|NN ,|,|, 200|200|CD mM|mm|NN NaCl|nacl|NN made|make|VBN in|in|IN RNAse-free|rnase-free|JJ H2O|h2o|NN -RRB-|-rrb-|-RRB- for|for|IN 10|10|CD min|min|NN .|.|. The|the|DT suspension|suspension|NN was|be|VBD extracted|extract|VBN twice|twice|RB with|with|IN 1|1|CD volume|volume|NN of|of|IN 65|65|CD °C|°c|NN acid|acid|NN phenol/chloroform|phenol/chloroform|NN -LRB-|-lrb-|-LRB- pH|ph|NN 4.5|4.5|CD -RRB-|-rrb-|-RRB- ,|,|, once|once|RB in|in|IN chloroform/isoamyl|chloroform/isoamyl|JJ alcohol|alcohol|NN ,|,|, and|and|CC precipitated|precipitate|VBD with|with|IN isopropanol|isopropanol|NN .|.|. Pellets|pellet|NNS were|be|VBD washed|wash|VBN with|with|IN 1|1|CD mL|ml|NN of|of|IN 70|70|CD %|%|NN ethanol|ethanol|NN ,|,|, dried|dry|VBD and|and|CC purified|purify|VBN using|use|VBG QIAGEN|QIAGEN|NNP RNeasy|RNeasy|NNP kit|kit|NN .|.|. Final|final|JJ RNA|rna|NN was|be|VBD eluted|elute|VBN with|with|IN 100|100|CD µL|µl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN .|.|. Following|follow|VBG purification|purification|NN ,|,|, DNAse|dnase|NN treatment|treatment|NN with|with|IN TURBO|TURBO|NNP DNase|dnase|NN kit|kit|NN was|be|VBD performed|perform|VBN according|accord|VBG to|to|TO manufacturer|manufacturer|NN 's|'s|POS manual|manual|NN ,|,|, except|except|IN that|that|DT twice|twice|JJ amount|amount|NN of|of|IN recommended|recommend|VBN DNase|dnase|NN inactivation|inactivation|NN reagent|reagent|NN was|be|VBD used|use|VBN .|.|. The|the|DT integrity|integrity|NN of|of|IN DNA-free|dna-free|JJ RNA|rna|NN was|be|VBD analyzed|analyze|VBN on|on|IN either|either|CC native|native|JJ agarose|agarose|NN gel|gel|NN or|or|CC on|on|IN Agilent|Agilent|NNP Bioanalyzer|Bioanalyzer|NNP RNA|rna|NN 6000|6000|CD Nano|Nano|NNP chip|chip|NN .|.|.
Briefly|briefly|RB ,|,|, total|total|JJ RNA|rna|NN were|be|VBD isolated|isolate|VBN from|from|IN cell|cell|NN culture|culture|NN with|with|IN Total|total|JJ RNA|rna|NN Extraction|extraction|NN Kit|kit|NN -LRB-|-lrb-|-LRB- RBC|rbc|NN Bioscience|bioscience|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO manufacturer|manufacturer|NN 's|'s|POS specifications|specification|NNS .|.|. DNA|dna|NN was|be|VBD degraded|degrade|VBN by|by|IN DNAse|dnase|NN -LRB-|-lrb-|-LRB- Promega|promega|NN -RRB-|-rrb-|-RRB- .|.|.
Broiler|broiler|NN Fecal|fecal|JJ
BRP|brp|NN Induction|induction|NN 10|10|CD Minutes|Minutes|NNPS against|against|IN 5|5|CD Minutes|Minutes|NNPS
BRP|BRP|NNP Induction|induction|NN -10|-10|CD minutes|minute|NNS against|against|IN 60|60|CD minutes|minute|NNS
BRP|BRP|NNP Induction|induction|NN 20|20|CD minutes|minute|NNS against|against|IN 10|10|CD minutes|minute|NNS
BRP|BRP|NNP Induction|induction|NN 30|30|CD minutes|minute|NNS against|against|IN 20|20|CD minutes|minute|NNS
BRP|BRP|NNP Induction|induction|NN 45|45|CD minutes|minute|NNS against|against|IN 30|30|CD minutes|minute|NNS
BRP|BRP|NNP Induction|induction|NN 5|5|CD minutes|minute|NNS against|against|IN 2|2|CD minutes|minute|NNS
BRP|BRP|NNP Induction|induction|NN 60|60|CD minutes|minute|NNS against|against|IN 45|45|CD minutes|minute|NNS
B|b|NN strain|strain|NN _|_|RB wild|wild|JJ type|type|NN
B|b|NN strain|strain|NN ,|,|, wild|wild|JJ type|type|NN
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|SYM 1-1|1-1|CD
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|NN 1-2|1-2|CD
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|SYM 2-1|2-1|CD
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|SYM 2-2|2-2|CD
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|SYM 3-1|3-1|CD
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|SYM 3-2|3-2|CD
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|SYM 4-1|4-1|CD
Butanol|Butanol|NNP _|_|NNP Challenge|Challenge|NNP _|_|VBD Step|step|NN _|_|SYM 4-2|4-2|CD
BW25113|bw25113|NN
BW25113|bw25113|NN _|_|CD adhE|adhe|NN mutant|mutant|JJ
BW25113|bw25113|NN ,|,|, adhE|adhe|NN mutant|mutant|JJ
BW25113|bw25113|NN ,|,|, H2O2|h2o2|NN
BW25113|bw25113|NN HEPES-glu|hepes-glu|NN 30|30|CD min|min|NN 4.5|4.5|CD %|%|NN deoxycholate|deoxycholate|NN
BW25113|bw25113|NN hha|hha|NN deletion|deletion|NN mutant|mutant|JJ LB|lb|NN 4|4|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN hha|hha|NN mutant|mutant|JJ LB|lb|NN glu|glu|NN 15|15|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN hha|hha|NN mutant|mutant|JJ LB|lb|NN glu|glu|NN 24|24|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN hha|hha|NN mutant|mutant|JJ LB|lb|NN glu|glu|NN 4|4|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN luxS|luxs|NN LB|lb|NN 30C|30c|CD free-living|free-living|JJ cells|cell|NNS 100|100|CD uM|um|NN AI2|ai2|NN 3h|3h|VBP
BW25113|bw25113|NN luxS|luxs|NN LB|lb|NN 30C|30c|CD free-living|free-living|JJ cells|cell|NNS no|no|DT AI2|ai2|NN for|for|IN 3h|3h|JJ
BW25113|bw25113|NN luxS|luxs|NN LB|lb|NN 37C|37c|NN free-living|free-living|JJ cells|cell|NNS 100|100|CD uM|um|NN AI2|ai2|NN 3h|3h|VBP
BW25113|bw25113|NN luxS|luxs|NN LB|lb|NN 37C|37c|NN free-living|free-living|JJ cells|cell|NNS no|no|DT AI2|ai2|NN 3h|3h|NN
BW25113|bw25113|NN mqsR|mqsr|NN mutant|mutant|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN suspension|suspension|NN cell|cell|NN
BW25113|bw25113|NN mqsR/pBS|mqsr/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: mqsR|mqsr|NN 2-1|2-1|CD in|in|IN LB|lb|NN with|with|IN ampicillin|ampicillin|NN
BW25113|bw25113|NN mqsR/pBS|mqsr/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: mqsR|mqsr|NN in|in|IN LB|lb|NN with|with|IN ampicillin|ampicillin|NN
BW25113-pCA24N|bw25113-pca24n|NN
BW25113-pCA24N|bw25113-pca24n|NN _|_|CD arT|art|NN LB|lb|NN 90|90|CD min|min|NN 1|1|CD mM|mm|NN IPTG|iptg|NN
BW25113/pCA24N|bw25113/pca24n|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN 2|2|CD mM|mm|NN IPTG|iptg|NN suspension|suspension|NN cell|cell|NN
BW25113/pCA24N|bw25113/pca24n|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN then|then|RB 2|2|CD mM|mm|NN IPTG|iptg|NN for|for|IN 15|15|CD min|min|NN short|short|JJ time|time|NN suspension|suspension|NN cell|cell|NN
BW25113-pCA24N|bw25113-pca24n|NN _|_|CD dosP|dosp|NN
BW25113-pCA24N|bw25113-pca24n|NN LB|lb|NN 90|90|CD min|min|NN 1|1|CD mM|mm|NN IPTG|iptg|NN
BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN 2|2|CD mM|mm|NN IPTG|iptg|NN suspension|suspension|NN cell|cell|NN
BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN then|then|RB 2|2|CD mM|mm|NN IPTG|iptg|NN for|for|IN 15|15|CD min|min|NN short|short|JJ time|time|NN suspension|suspension|NN cell|cell|NN
BW25113|bw25113|NN sdiA-empty|sdia-empty|JJ vector|vector|NN 12h|12h|NN biofilm|biofilm|NN cells|cell|NNS at|at|IN 30oC|30oC|NNP
BW25113|bw25113|NN sdiA|sdia|NN LB|lb|NN 30C|30c|NN OD|od|NN 4.0|4.0|CD free-living|free-living|JJ cells|cell|NNS
BW25113|bw25113|NN sdiA|sdia|NN mutant|mutant|JJ LB|lb|NN with|with|IN 1|1|CD mM|mm|NN indole|indole|NN 7-h|7-h|JJ 30C|30c|NN biofilm|biofilm|NN cell|cell|NN
BW25113|bw25113|NN sdiA|sdia|NN mutant|mutant|JJ LB|lb|NN with|with|IN DMF|dmf|NN 7-h|7-h|JJ 30C|30c|NN biofilm|biofilm|NN cell|cell|NN
BW25113|bw25113|NN sdiA-SdiA1E11|sdia-sdia1e11|NN 12h|12h|NN biofilm|biofilm|NN cells|cell|NNS at|at|IN 30oC|30oC|NNP
BW25113|bw25113|NN sdiA-WTSdiA|sdia-wtsdia|NN 12h|12h|NN biofilm|biofilm|NN cells|cell|NNS at|at|IN 30oC|30oC|NNP
BW25113|bw25113|NN tnaA|tnaa|NN Biofilm|biofilm|NN 100|100|CD uM|um|NN indole|indole|FW 7h|7h|FW LB|lb|NN 30C|30c|NN
BW25113|bw25113|NN tnaA|tnaa|NN Biofilm|biofilm|NN 100|100|CD uM|um|NN indole|indole|FW 7h|7h|FW LB|lb|NN 37C|37c|NN
BW25113|bw25113|NN tnaA|tnaa|NN Biofilm|biofilm|NN DMF|dmf|NN 7h|7h|VBP LB|lb|NN 37C|37c|NN
BW25113|bw25113|NN tnaA|tnaa|NN LB|lb|NN 30C|30c|NN biofilm|biofilm|NN cells|cell|NNS with|with|IN DMF|dmf|NN 7h|7h|VBP
BW25113|bw25113|NN ,|,|, water|water|NN -LRB-|-lrb-|-LRB- negative|negative|JJ control|control|NN -RRB-|-rrb-|-RRB-
BW25113|bw25113|NN with|with|IN deoxycholate|deoxycholate|NN stress|stress|NN
BW25113|bw25113|NN w/t|w/t|NN 7h|7h|VBP LB|lb|NN 30C|30c|NN biofilm|biofilm|NN
BW25113|bw25113|NN w/t|w/t|NN 7h|7h|VBP LB|lb|NN 30C|30c|NN free-living|free-living|JJ
BW25113|bw25113|NN wt|wt|JJ at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN suspension|suspension|NN cell|cell|NN
BW25113|bw25113|NN w/t|w/t|NN LB|lb|NN 30C|30c|NN OD|od|NN 4.0|4.0|CD free-living|free-living|JJ cells|cell|NNS
BW25113|bw25113|NN w/t|w/t|NN LB|lb|NN 4|4|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN w/t|w/t|NN LB|lb|NN glu|glu|NN 15|15|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN W/T|w/t|NN LBglu|lbglu|NN 24h|24h|JJ biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN w/t|w/t|NN LB|lb|NN glu|glu|NN 24|24|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN w/t|w/t|NN LB|lb|NN glu|glu|NN 4|4|CD hr|hr|NN biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN ychH|ychh|NN ,|,|, H2O2|h2o2|NN
BW25113|bw25113|NN ychH|ychh|NN ,|,|, water|water|NN -LRB-|-lrb-|-LRB- negative|negative|JJ control|control|NN -RRB-|-rrb-|-RRB-
BW25113|bw25113|NN ygiW|ygiw|NN ,|,|, H2O2|h2o2|NN
BW25113|bw25113|NN ygiW|ygiw|NN ,|,|, water|water|NN -LRB-|-lrb-|-LRB- negative|negative|JJ control|control|NN -RRB-|-rrb-|-RRB-
BW25113|bw25113|NN ymgB|ymgb|NN LBglu|lbglu|NN 24h|24h|JJ biofilm|biofilm|NN cells|cell|NNS
BW25113|bw25113|NN ΔmqsRA|δmqsra|NN HEPES-glu|hepes-glu|NN 30|30|CD min|min|NN 4.5|4.5|CD %|%|NN deoxycholate|deoxycholate|NN
BW25113|bw25113|NN ΔmqsRA|δmqsra|NN with|with|IN deoxycholate|deoxycholate|NN stress|stress|NN
BWG|bwg|NN _|_|CD butanol|butanol|NN _|_|CD 3passages|3passage|NNS
BWG|bwg|NN _|_|NN replicated|replicate|VBN
BWY|bwy|NN _|_|NN butanol|butanol|NN _|_|CD 3passages|3passage|NNS
BWY|bwy|NN _|_|NN replicated|replicate|VBN
BZNT|bznt|JJ
Call|call|VB peaks|peak|NNS to|to|TO and|and|CC FDR|FDR|NNP 0.1|0.1|CD ,|,|, MOSAiCs|MOSAiCs|NNP
CAR005|car005|NN
CAR005|car005|NN strain|strain|NN
carbon|carbon|NN source|source|NN :|:|: acetate|acetate|NN
carbon|carbon|NN source|source|NN :|:|: fructose|fructose|NN
carbon|carbon|NN source|source|NN :|:|: gluconate|gluconate|NN
carbon|carbon|NN source|source|NN :|:|: glucose|glucose|NN
carbon|carbon|NN source|source|NN :|:|: Glucose|glucose|NN
carbon|carbon|NN source|source|NN :|:|: glycerol|glycerol|NN
carbon|carbon|NN source|source|NN :|:|: Glycerol|glycerol|NN
carbon|carbon|NN source|source|NN :|:|: glycerol|glycerol|NN +|+|CC propionate|propionate|NN
carbon|carbon|NN source|source|NN :|:|: lactate|lactate|NN
CASAVA|CASAVA|NNP version|version|NN 1.4|1.4|CD
cas|ca|VBZ _|_|SYM RNAA|RNAA|NNP
Cattle|Cattle|NNP feces|fece|NNS isolate|isolate|VBP C1A|c1a|NN
Cattle|cattle|JJ feces|fece|NNS isolate|isolate|VBP C4A|c4a|NN
Cattle|cattle|JJ feces|fece|NNS isolate|isolate|VBP C6D|c6d|NN
Cattle|Cattle|NNP III|III|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 1|1|CD
Cattle|Cattle|NNP III|III|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 2|2|CD
Cattle|Cattle|NNP II|II|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 1|1|CD
Cattle|Cattle|NNP II|II|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 2|2|CD
Cattle|Cattle|NNP I|I|PRP versus|versus|CC MG1655|mg1655|NN technical|technical|JJ replicate|replicate|VB 1|1|CD
Cattle|Cattle|NNP I|I|PRP versus|versus|CC MG1655|mg1655|NN technical|technical|JJ replicate|replicate|VBP 2|2|CD
Caulobacter|caulobacter|NN crescentus|crescentus|NN and|and|CC derivatives|derivative|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN in|in|IN PYE|pye|NN -LRB-|-lrb-|-LRB- Peptone|peptone|NN yeast|yeast|NN extract|extract|NN -RRB-|-rrb-|-RRB- or|or|CC LB|lb|NN
CCCP-1|cccp-1|NN ,|,|, biological|biological|JJ rep1|rep1|NN
CCCP-2|cccp-2|NN ,|,|, biological|biological|JJ rep2|rep2|NN
CCCP-3|cccp-3|NN ,|,|, biological|biological|JJ rep3|rep3|NN
ccdB|ccdb|NN _|_|CD K12|k12|NN _|_|NN 0|0|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD K12|k12|NN _|_|NN 120|120|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD K12|k12|NN _|_|CD 30|30|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD K12|k12|NN _|_|NN 60|60|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD K12|k12|NN _|_|NN 90|90|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|NN 0|0|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|NN 0|0|CD _|_|NN r2|r2|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|NN 120|120|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|CD 30|30|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|CD 30|30|CD _|_|NN r2|r2|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|NN 60|60|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|NN 60|60|CD _|_|NN r2|r2|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|NN 90|90|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD MG1063|mg1063|NN _|_|NN 90|90|CD _|_|NN r2|r2|NN
ccdB|ccdb|NN _|_|CD W1863|w1863|NN _|_|NN 0|0|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD W1863|w1863|NN _|_|CD 30|30|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD W1863|w1863|NN _|_|NN 60|60|CD _|_|NN r1|r1|NN
ccdB|ccdb|NN _|_|CD W1863|w1863|NN _|_|NN 90|90|CD _|_|CD r1|r1|NN
cDNA|cdna|NN _|_|NN A|a|NN _|_|CD cy3|cy3|NN
cDNA|cdna|NN _|_|NN B|b|NN _|_|CD cy5|cy5|NN
cDNA|cdna|NN libraries|library|NNS for|for|IN the|the|DT Illumina|Illumina|NNP sequencing|sequencing|NN platform|platform|NN were|be|VBD constructed|construct|VBN by|by|IN vertis|vertis|NN Biotechnology|Biotechnology|NNP AG|AG|NNP ,|,|, Germany|Germany|NNP ,|,|, as|as|IN described|describe|VBN previously|previously|RB -LRB-|-lrb-|-LRB- Berezikov|Berezikov|NNP et|et|FW al.|al.|FW ,2006|,2006|CD -RRB-|-rrb-|-RRB- ,|,|, without|without|IN the|the|DT RNA|rna|NN size-fractionation|size-fractionation|NN step|step|NN prior|prior|RB to|to|TO cDNA|cdna|NN synthesis|synthesis|NN .|.|. Briefly|briefly|RB ,|,|, RNA|rna|NN samples|sample|NNS were|be|VBD polyA-tailed|polya-tailed|JJ using|use|VBG polyA|polya|NN polymerase|polymerase|NN .|.|. Then|then|RB ,|,|, the|the|DT 5|5|CD '|'|'' -|-|: PPP|ppp|NN termini|terminus|NNS were|be|VBD converted|convert|VBN to|to|TO 5|5|CD '|'|'' -|-|: P|p|NN using|use|VBG tobacco|tobacco|NN acid|acid|NN pyrophosphatase|pyrophosphatase|NN -LRB-|-lrb-|-LRB- TAP|tap|NN -RRB-|-rrb-|-RRB- to|to|TO allow|allow|VB for|for|IN the|the|DT ligation|ligation|NN of|of|IN the|the|DT 5|5|CD '|'|'' end|end|NN RNA|rna|NN adapter|adapter|NN .|.|. First-strand|first-strand|JJ cDNA|cdna|NN was|be|VBD synthesized|synthesize|VBN by|by|IN an|a|DT oligo|oligo|JJ -LRB-|-lrb-|-LRB- dT|dt|NN -RRB-|-rrb-|-RRB- -|-|: adapter|adapter|NN primer|primer|NN and|and|CC the|the|DT M-MLV|m-mlv|NN reverse|reverse|JJ transcriptase|transcriptase|NN .|.|. In|in|IN a|a|DT PCR-based|pcr-based|JJ amplification|amplification|NN step|step|NN using|use|VBG a|a|DT high|high|JJ fidelity|fidelity|NN DNA|dna|NN polymerase|polymerase|NN the|the|DT cDNA|cdna|NN concentration|concentration|NN was|be|VBD increased|increase|VBN to|to|TO 20-30|20-30|CD ng/µl|ng/µl|NN .|.|. A|a|DT library-specific|library-specific|JJ barcode|barcode|NN for|for|IN multiplex|multiplex|JJ sequencing|sequencing|NN was|be|VBD part|part|NN of|of|IN a|a|DT 3|3|CD '|'|'' -|-|: sequencing|sequencing|NN adapter|adapter|NN .|.|.
cDNA|cdna|NN libraries|library|NNS were|be|VBD barcoded|barcode|VBN with|with|IN the|the|DT TruSeq|TruSeq|NNP RNA|rna|NN Sample|sample|NN Prep|Prep|NNP Kit|kit|NN v2|v2|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP Inc.|Inc.|NNP ,|,|, San|San|NNP Diego|Diego|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. Libraries|library|NNS were|be|VBD sequenced|sequence|VBN on|on|IN the|the|DT Illumina|Illumina|NNP MiSeq|MiSeq|NNP to|to|TO produce|produce|VB 50|50|CD bp|bp|NN single|single|JJ reads|read|VBZ .|.|. All|all|DT steps|step|NNS in|in|IN library|library|NN construction|construction|NN and|and|CC sequencing|sequencing|NN were|be|VBD performed|perform|VBN according|accord|VBG to|to|TO manufacturer|manufacturer|NN 's|'s|POS standards|standard|NNS .|.|.
cDNA|cdna|NN libraries|library|NNS were|be|VBD constructed|construct|VBN at|at|IN Purdue|Purdue|NNP using|use|VBG an|a|DT adapted|adapt|VBN SOLiD|SOLiD|NNP Total|Total|NNP RNA-Seq|RNA-Seq|NNP Kit|kit|NN .|.|. Total|total|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- DNase|dnase|NN I|i|CD digested|digest|VBN -RRB-|-rrb-|-RRB- was|be|VBD fragmented|fragment|VBN by|by|IN RNase|rnase|NN III|iii|CD .|.|. RNA|rna|NN samples|sample|NNS labeled|label|VBN as|as|IN TEX|TEX|NNP were|be|VBD also|also|RB subsequently|subsequently|RB digested|digest|VBN with|with|IN Terminator|Terminator|NNP Exonuclease|Exonuclease|NNP -LRB-|-lrb-|-LRB- TEX|TEX|NNP -RRB-|-rrb-|-RRB- .|.|. Pyrophosphate|pyrophosphate|NN groups|group|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT 5|5|CD ′|′|NN terminus|terminus|NN using|use|VBG tobacco|tobacco|NN acid|acid|NN pyrophosphatase|pyrophosphatase|NN -LRB-|-lrb-|-LRB- TAP|tap|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC an|a|DT RNA|rna|NN adapter|adapter|NN was|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 5|5|CD ′|′|NN end|end|NN of|of|IN the|the|DT RNA|rna|NN .|.|. First-strand|first-strand|JJ synthesis|synthesis|NN was|be|VBD performed|perform|VBN using|use|VBG standard|standard|JJ SOLiD|solid|NN 4|4|CD Total|total|JJ RNA-Seq|rna-seq|NN protocol|protocol|NN .|.|. RNA-seq|rna-seq|NN via|via|IN SOLiD|solid|JJ 4|4|CD sequencing|sequencing|NN of|of|IN libraries|library|NNS prepared|prepare|VBN by|by|IN ligation|ligation|NN based|base|VBN chemistry|chemistry|NN to|to|TO provide|provide|VB strand-specific|strand-specific|JJ datasets|dataset|NNS .|.|.
cDNA|cdna|NN libraries|library|NNS were|be|VBD constructed|construct|VBN at|at|IN Vertis|Vertis|NNP in|in|IN Germany|Germany|NNP using|use|VBG a|a|DT ligation|ligation|NN based|base|VBN stratagey|stratagey|NN for|for|IN Illumina|Illumina|NNP whole|whole|JJ transcriptome|transcriptome|NN sequencing|sequencing|NN .|.|. Total|total|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- DNase|dnase|NN I|i|CD digested|digest|VBN -RRB-|-rrb-|-RRB- was|be|VBD fragmented|fragment|VBN by|by|IN RNase|rnase|NN III|iii|CD .|.|. RNA|rna|NN samples|sample|NNS labeled|label|VBN as|as|IN TEX|TEX|NNP were|be|VBD also|also|RB subsequently|subsequently|RB digested|digest|VBN with|with|IN Terminator|Terminator|NNP Exonuclease|Exonuclease|NNP -LRB-|-lrb-|-LRB- TEX|TEX|NNP -RRB-|-rrb-|-RRB- .|.|. Pyrophosphate|pyrophosphate|NN groups|group|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT 5|5|CD ′|′|NN terminus|terminus|NN using|use|VBG tobacco|tobacco|NN acid|acid|NN pyrophosphatase|pyrophosphatase|NN -LRB-|-lrb-|-LRB- TAP|tap|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC an|a|DT RNA|rna|NN adapter|adapter|NN was|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 5|5|CD ′|′|NN end|end|NN of|of|IN the|the|DT RNA|rna|NN .|.|. First-strand|first-strand|JJ synthesis|synthesis|NN was|be|VBD performed|perform|VBN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS .|.|.
cDNA|cdna|NN library|library|NN of|of|IN the|the|DT nascent|nascent|JJ RNA|rna|NN was|be|VBD constructed|construct|VBN according|accord|VBG to|to|TO Churchman|Churchman|NNP and|and|CC Weissman|Weissman|NNP ,|,|, Nature|Nature|NNP 2011|2011|CD -LRB-|-lrb-|-LRB- PMID|pmid|NN :|:|: 21248844|21248844|CD -RRB-|-rrb-|-RRB- .|.|.
cDNA|cdna|NN made|make|VBN from|from|IN strain|strain|NN KMD|kmd|NN extracted|extract|VBN from|from|IN mouse|mouse|NN kidney|kidney|NN on|on|IN day|day|NN 2|2|CD post|post|NN infection|infection|NN
cDNA|cdna|NN made|make|VBN from|from|IN strain|strain|NN PC1012|pc1012|NN -LRB-|-lrb-|-LRB- marArobsoxS|mararobsoxs|NN -RRB-|-rrb-|-RRB- extracted|extract|VBN from|from|IN mouse|mouse|NN kidney|kidney|NN on|on|IN day|day|NN 2|2|CD post|post|NN infection|infection|NN
cDNA|cdna|NN of|of|IN EPEC|epec|NN strain|strain|NN
cDNA|cdna|NN reads|read|VBZ were|be|VBD trimmed|trim|VBN so|so|RB that|that|IN the|the|DT quality|quality|NN at|at|IN each|each|DT base|base|NN position|position|NN was|be|VBD above|above|IN 30|30|CD -LRB-|-lrb-|-LRB- ~|~|CD 15-20|15-20|CD bp|bp|NN -RRB-|-rrb-|-RRB- and|and|CC then|then|RB mapped|map|VBD either|either|CC to|to|TO the|the|DT E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN published|publish|VBN genome|genome|NN sequence|sequence|NN -LRB-|-lrb-|-LRB- Genbank|Genbank|NNP accession|accession|NN no|no|DT .|.|. NC|nc|NN _|_|SYM 000913|000913|CD -RRB-|-rrb-|-RRB- or|or|CC to|to|TO the|the|DT pAR060302|par060302|NN published|publish|VBN sequence|sequence|NN -LRB-|-lrb-|-LRB- Genbank|Genbank|NNP accession|accession|NN no|no|DT .|.|. NC|nc|NN _|_|SYM 092692|092692|CD -RRB-|-rrb-|-RRB- using|use|VBG BOWTIE|BOWTIE|NNP .|.|. The|the|DT E.|e.|FW coli|coli|FW strain|strain|NN DH5α|dh5α|NN has|have|VBZ an|a|DT incomplete|incomplete|JJ annotation|annotation|NN and|and|CC for|for|IN this|this|DT reason|reason|NN the|the|DT E.|e.|FW coli|coli|FW K-12|k-12|NN annotation|annotation|NN was|be|VBD used|use|VBN ,|,|, representing|represent|VBG an|a|DT estimation|estimation|NN of|of|IN differentially|differentially|RB expressed|express|VBN genes|gene|NNS due|due|JJ to|to|TO exposure|exposure|NN of|of|IN antimicrobials|antimicrobial|NNS .|.|. Mapped|map|VBN reads|read|VBZ for|for|IN 3|3|CD seperate|seperate|JJ sequencing|sequencing|NN runs|run|NNS were|be|VBD combined|combine|VBN because|because|IN some|some|DT sequencing|sequencing|NN runs|run|NNS were|be|VBD not|not|RB fully|fully|RB completed|complete|VBN due|due|JJ to|to|TO technical|technical|JJ difficulties|difficulty|NNS .|.|. For|for|IN each|each|DT condition|condition|NN ,|,|, graphs|graph|NNS representing|represent|VBG the|the|DT number|number|NN of|of|IN mapped|map|VBN reads|read|VBZ per|per|IN nucleotide|nucleotide|NN were|be|VBD generated|generate|VBN and|and|CC visualized|visualize|VBN using|use|VBG the|the|DT Integrated|Integrated|NNP Genome|Genome|NNP Viewer|Viewer|NNP -LRB-|-lrb-|-LRB- IGV|igv|NN -RRB-|-rrb-|-RRB- .|.|. Images|image|NNS were|be|VBD created|create|VBN using|use|VBG XplasMap|xplasmap|NN -LRB-|-lrb-|-LRB- http://www.iayork.com/XPlasMap/|http://www.iayork.com/xplasmap/|NN -RRB-|-rrb-|-RRB- and|and|CC IGV|igv|NN .|.|. The|the|DT reads|read|VBZ mapped|map|VBN per|per|IN kilobase|kilobase|NN of|of|IN gene|gene|NN per|per|IN million|million|CD -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- reads|read|VBZ was|be|VBD calculated|calculate|VBN using|use|VBG either|either|CC the|the|DT E.|e.|FW coli|coli|FW chromosome|chromosome|NN or|or|CC the|the|DT pAR060302|par060302|NN annotation|annotation|NN and|and|CC was|be|VBD used|use|VBN for|for|IN global|global|JJ normalization|normalization|NN .|.|. The|the|DT per|per|IN kilobase|kilobase|NN cDNA|cdna|NN length|length|NN normalized|normalize|VBD the|the|DT effect|effect|NN of|of|IN different|different|JJ length|length|NN of|of|IN cDNAs|cdna|NNS such|such|JJ that|that|IN the|the|DT sequence|sequence|NN reads|read|VBZ have|have|VB a|a|DT equal|equal|JJ chance|chance|NN to|to|TO map|map|VB on|on|IN the|the|DT long|long|JJ cDNA|cdna|NN regions|region|NNS and|and|CC the|the|DT short|short|JJ cDNA|cdna|NN regions|region|NNS .|.|. After|after|IN RPKM|rpkm|NN normalization|normalization|NN ,|,|, each|each|DT sample|sample|NN is|be|VBZ comparable|comparable|JJ to|to|TO each|each|DT other|other|JJ .|.|. An|a|DT R|r|NN package|package|NN ,|,|, DEGseq|degseq|NN ,|,|, was|be|VBD used|use|VBN to|to|TO identify|identify|VB differentially|differentially|RB expressed|express|VBN genes|gene|NNS between|between|IN the|the|DT control|control|NN and|and|CC each|each|DT antibiotic|antibiotic|JJ treatment|treatment|NN condition|condition|NN .|.|.
cDNA|cdna|NN were|be|VBD synthesized|synthesize|VBN from|from|IN the|the|DT reverse|reverse|JJ transcription|transcription|NN of|of|IN Total|total|JJ RNA|rna|NN using|use|VBG the|the|DT Life|Life|NNP Technologies|Technologies|NNPS SuperScript|SuperScript|NNP II|II|NNP Double-Strand|Double-Strand|NNP Synthesis|synthesis|NN Kit|kit|NN
CEL|cel|NN files|file|NNS were|be|VBD quantified|quantify|VBN with|with|IN Distribution|distribution|NN Free|Free|NNP Weighted|Weighted|NNP method|method|NN -LRB-|-lrb-|-LRB- DFW|dfw|NN -RRB-|-rrb-|-RRB- ,|,|, using|use|VBG the|the|DT statistical|statistical|JJ language|language|NN R|r|NN -LRB-|-lrb-|-LRB- R-2.7.2|r-2.7.2|NN -RRB-|-rrb-|-RRB- and|and|CC Bioconductor|Bioconductor|NNP 2.2|2.2|CD .|.|.
cell|cell|NN culture|culture|NN
Cell|cell|NN culture|culture|NN
Cell|cell|NN cultures|culture|NNS were|be|VBD cross|cross|JJ linked|link|VBN by|by|IN addition|addition|NN of|of|IN 27|27|CD µl|µl|NN of|of|IN formaldehyde|formaldehyde|NN -LRB-|-lrb-|-LRB- 37|37|CD %|%|NN -RRB-|-rrb-|-RRB- per|per|IN ml|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN 1|1|CD %|%|NN -RRB-|-rrb-|-RRB- .|.|. Crosslinking|crosslinking|NN was|be|VBD performed|perform|VBN at|at|IN slow|slow|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 100|100|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- for|for|IN 20|20|CD min|min|NN followed|follow|VBN by|by|IN quenching|quench|VBG with|with|IN 0.2|0.2|CD ml|ml|NN of|of|IN 2.5|2.5|CD M|m|NN glycine|glycine|NN per|per|IN ml|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN 0.5|0.5|CD M|m|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN from|from|IN 15|15|CD ml|ml|NN by|by|IN centrifugation|centrifugation|NN and|and|CC washed|wash|VBN twice|twice|RB with|with|IN cold|cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- pH7|ph7|NN .5|.5|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT pellet|pellet|NN wa|wa|NN resuspended|resuspend|VBN in|in|IN 300μL|300μL|NNP TE|TE|NNP with|with|IN 40|40|CD μl|μl|NN 10|10|CD %|%|NN SDS|sds|NN and|and|CC 3|3|CD μl|μl|NN 0.5|0.5|CD M|m|NN EDTA|edta|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 5|5|CD min|min|NN at|at|IN 65|65|CD °C|°c|NN 750μl|750μl|CD isopropanole|isopropanole|NN was|be|VBD added|add|VBN before|before|IN centrifugation|centrifugation|NN at|at|IN 15600|15600|CD rcf|rcf|NN for|for|IN 5|5|CD min|min|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD resuspended|resuspend|VBN in|in|IN 500μL|500μl|NN TE|te|NN and|and|CC 3μL|3μl|NN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 25mg/ml|25mg/ml|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC incubated|incubate|VBN for|for|IN 30|30|CD min|min|NN at|at|IN 65|65|CD °C|°c|NN .|.|. Subsequently|subsequently|RB ,|,|, 100μL|100μl|NN proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- 25|25|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC samples|sample|NNS incubated|incubate|VBN at|at|IN 42|42|CD °C|°c|NN for|for|IN 2|2|CD h|h|NN and|and|CC 65|65|CD °C|°c|NN for|for|IN 6|6|CD h|h|NN to|to|TO reverse|reverse|VB the|the|DT crosslink|crosslink|NN followed|follow|VBN by|by|IN phenol|phenol|NN extraction|extraction|NN and|and|CC precipitation|precipitation|NN with|with|IN ethanol|ethanol|NN and|and|CC Na-acetate|na-acetate|NN .|.|. Precipitated|precipitate|VBN DNA|dna|NN was|be|VBD resuspended|resuspend|VBN in|in|IN 50μL|50μl|NN dH2O|dh2o|NN .|.|.
Cell|cell|NN culture|culture|NN was|be|VBD rapidly|rapidly|RB filtered|filter|VBN in|in|IN 250|250|CD mL|ml|NN increments|increment|NNS at|at|IN 37|37|CD °C|°c|NN over|over|IN 0.22|0.22|CD μm|μm|NN nitrocellulose|nitrocellulose|NN filters|filters|NNS -LRB-|-lrb-|-LRB- GE|GE|NNP -RRB-|-rrb-|-RRB- and|and|CC frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN to|to|TO simultaneously|simultaneously|RB halt|halt|VB all|all|DT transcriptional|transcriptional|JJ progress|progress|NN .|.|. Frozen|frozen|JJ cells|cell|NNS -LRB-|-lrb-|-LRB- 100|100|CD μg|μg|NN -RRB-|-rrb-|-RRB- were|be|VBD pulverized|pulverize|VBN on|on|IN a|a|DT Qiagen|Qiagen|NNP TissueLyser|TissueLyser|NNP II|II|NNP mixer|mixer|NN mill|mill|NN 6|6|CD times|time|NNS at|at|IN 15|15|CD Hz|hz|NN for|for|IN 3|3|CD min|min|NN in|in|IN the|the|DT presence|presence|NN of|of|IN 500|500|CD μL|μl|NN frozen|frozen|JJ lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 20|20|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 0.4|0.4|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 0.1|0.1|CD %|%|NN NP-40|np-40|NN ,|,|, 100|100|CD mM|mm|NN NH4Cl|nh4cl|NN ,|,|, 50|50|CD U/mL|u/ml|NN SUPERase|superase|NN •|•|SYM In|in|IN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- and|and|CC 1X|1x|NN protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- Complete|complete|JJ ,|,|, EDTA-free|edta-free|NN ,|,|, Roche|Roche|NNP -RRB-|-rrb-|-RRB- ,|,|, supplemented|supplement|VBN with|with|IN 10|10|CD mM|mm|NN MnCl2|mncl2|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD resuspended|resuspend|VBN on|on|IN ice|ice|NN by|by|IN pipetting|pipetting|NN .|.|. RQ1|rq1|NN DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- 110|110|CD U|U|NNP total|total|NN ,|,|, Promega|Promega|NNP -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC incubated|incubate|VBN for|for|IN 20|20|CD min|min|NN on|on|IN ice|ice|NN .|.|. The|the|DT reaction|reaction|NN was|be|VBD quenched|quench|VBN with|with|IN EDTA|edta|NN -LRB-|-lrb-|-LRB- 25|25|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- ,|,|, which|which|WDT releases|release|VBZ polysomes|polysome|NNS from|from|IN the|the|DT transcript|transcript|NN and|and|CC reduces|reduce|VBZ contamination|contamination|NN from|from|IN ribosomal|ribosomal|JJ RNA|rna|NN and|and|CC ribosome-associated|ribosome-associated|JJ tRNAs|trna|NNS .|.|. The|the|DT lysate|lysate|NN was|be|VBD clarified|clarify|VBN at|at|IN 4|4|CD °C|°c|NN by|by|IN centrifugation|centrifugation|NN at|at|IN 20,000|20,000|CD g|g|NN for|for|IN 10|10|CD min|min|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD loaded|load|VBN onto|onto|IN a|a|DT PD|pd|NN MiniTrap|MiniTrap|NNP G-25|G-25|NNP column|column|NN -LRB-|-lrb-|-LRB- GE|GE|NNP Healthcare|Healthcare|NNP -RRB-|-rrb-|-RRB- and|and|CC eluted|elute|VBN with|with|IN lysis|lysis|NN buffer|buffer|NN supplemented|supplement|VBN with|with|IN 1|1|CD mM|mm|NN EDTA|edta|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN from|from|IN the|the|DT clarified|clarify|VBN lysate|lysate|NN using|use|VBG the|the|DT miRNeasy|miRNeasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
Cell|cell|NN exposure|exposure|NN to|to|TO NP-TiO2|np-tio2|NN was|be|VBD conducted|conduct|VBN in|in|IN 50|50|CD ml|ml|NN of|of|IN sterile|sterile|JJ Milli-Q|milli-q|JJ water|water|NN supplemented|supplement|VBN with|with|IN 10|10|CD mM|mm|NN NaCl|nacl|NN .|.|. Briefly|briefly|RB ,|,|, 500|500|CD µl|µl|NN of|of|IN the|the|DT E.|e.|FW coli|coli|FW bacterial|bacterial|JJ suspension|suspension|NN and|and|CC 500|500|CD µl|µl|NN of|of|IN the|the|DT NP-TiO2|np-tio2|NN stock|stock|NN suspension|suspension|NN -LRB-|-lrb-|-LRB- or|or|CC mQ|mq|NN water|water|NN for|for|IN the|the|DT control|control|NN -RRB-|-rrb-|-RRB- were|be|VBD prepared|prepare|VBN as|as|IN previously|previously|RB described|describe|VBN and|and|CC then|then|RB added|add|VBD to|to|TO the|the|DT NaCl|nacl|NN solution|solution|NN to|to|TO obtain|obtain|VB final|final|JJ concentrations|concentration|NNS of|of|IN 10E7|10e7|CD cells/ml|cells/ml|NNS and|and|CC 100|100|CD mg/l|mg/l|NN of|of|IN TiO2|tio2|NN nanoparticles|nanoparticle|NNS .|.|. The|the|DT flasks|flask|NNS were|be|VBD then|then|RB incubated|incubate|VBN at|at|IN 20|20|CD °C|°c|NN on|on|IN a|a|DT dark|dark|JJ rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 150|150|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- for|for|IN 5|5|CD h.|h.|NN
cell|cell|NN pellets|pellet|NNS
Cell|Cell|NNP pellets|pellet|NNS -LRB-|-lrb-|-LRB- from|from|IN initial|initial|JJ 250|250|CD mL|ml|NN of|of|IN culture|culture|NN -RRB-|-rrb-|-RRB- were|be|VBD thawed|thaw|VBN and|and|CC resuspended|resuspend|VBN in|in|IN 250|250|CD μL|μl|NN of|of|IN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- and|and|CC sonicated|sonicate|VBN using|use|VBG a|a|DT microtip|microtip|NN sonicator|sonicator|NN set|set|VBN at|at|IN 10|10|CD %|%|NN output|output|NN for|for|IN 20|20|CD second|second|JJ intervals|interval|NNS with|with|IN periods|period|NNS of|of|IN cooling|cool|VBG in|in|IN between|between|IN .|.|. Cells|cell|NNS were|be|VBD then|then|RB treated|treat|VBN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN with|with|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 2|2|CD ng/ml|ng/ml|NN -RRB-|-rrb-|-RRB- ,|,|, micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- 50|50|CD units|unit|NNS -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD μM|μm|NN CaCl2|cacl2|NN ,1.2|,1.2|CD mM|mm|NN KCl|kcl|NN ,|,|, 0.3|0.3|CD mM|mm|NN NaCl|nacl|NN ,|,|, 6|6|CD mM|mm|NN sucrose|sucrose|NN ,|,|, and|and|CC 10|10|CD μM|μm|NN DTT|dtt|NN .|.|. EDTA|edta|NN was|be|VBD added|add|VBN to|to|TO 10|10|CD mM|mm|NN to|to|TO stop|stop|VB the|the|DT micrococcal|micrococcal|JJ nuclease|nuclease|NN and|and|CC the|the|DT samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RP to|to|TO remove|remove|VB cell|cell|NN debris|debris|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB precleared|preclear|VBN through|through|IN incubation|incubation|NN with|with|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN for|for|IN 2-3|2-3|CD hours|hour|NNS at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC antibody|antibody|NN was|be|VBD added|add|VBN to|to|TO the|the|DT pre-cleared|pre-cleared|JJ lysate|lysate|NN for|for|IN an|a|DT overnight|overnight|JJ incubation|incubation|NN .|.|. The|the|DT next|next|JJ day|day|NN ,|,|, 30|30|CD μl|μl|NN of|of|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT lysate|lysate|NN to|to|TO capture|capture|VB antibody-protein-DNA|antibody-protein-dna|JJ complex|complex|NN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Beads|bead|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN 1|1|CD ml|ml|NN of|of|IN LiCl|licl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 600|600|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 600|600|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 300|300|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC twice|twice|RB with|with|IN TE|te|NN .|.|. Elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN after|after|IN the|the|DT final|final|JJ wash|wash|NN step|step|NN ,|,|, and|and|CC beads|bead|NNS were|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO remove|remove|VB the|the|DT crosslinked|crosslink|VBN protein-DNA|protein-dna|JJ complexes|complex|NNS from|from|IN the|the|DT beads|bead|NNS .|.|. After|after|IN centrifugation|centrifugation|NN to|to|TO remove|remove|VB the|the|DT beads|bead|NNS ,|,|, the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 65|65|CD °C|°c|NN to|to|TO reverse|reverse|VB the|the|DT protein-DNA|protein-dna|JJ formaldehyde|formaldehyde|NN crosslinks|crosslink|NNS .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS PCR|pcr|NN Purification|purification|NN kit|kit|NN and|and|CC eluted|elute|VBN to|to|TO a|a|DT final|final|JJ volume|volume|NN of|of|IN 50|50|CD μl|μl|NN with|with|IN EB|EB|NNP .|.|.
Cell|cell|NN pellets|pellet|NNS -LRB-|-lrb-|-LRB- from|from|IN initial|initial|JJ 50|50|CD ml|ml|NN of|of|IN culture|culture|NN -RRB-|-rrb-|-RRB- were|be|VBD thawed|thaw|VBN and|and|CC resuspended|resuspend|VBN in|in|IN 250ul|250ul|NN of|of|IN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- and|and|CC sonicated|sonicate|VBN using|use|VBG a|a|DT microtip|microtip|NN sonicator|sonicator|NN set|set|VBN at|at|IN 10|10|CD %|%|NN output|output|NN for|for|IN 20|20|CD second|second|JJ intervals|interval|NNS with|with|IN periods|period|NNS of|of|IN cooling|cool|VBG in|in|IN between|between|IN .|.|. Cells|cell|NNS were|be|VBD then|then|RB treated|treat|VBN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN with|with|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 2|2|CD ng/ml|ng/ml|NN -RRB-|-rrb-|-RRB- micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- 50|50|CD units|unit|NNS -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD µM|µm|NN CaCl2|cacl2|NN ,1.2|,1.2|CD mM|mm|NN KCl|kcl|NN ,|,|, 0.3|0.3|CD mM|mm|NN NaCl|nacl|NN ,|,|, 6|6|CD mM|mm|NN sucrose|sucrose|NN ,|,|, and|and|CC 10|10|CD µM|µm|NN DTT|dtt|NN .|.|. After|after|IN treatment|treatment|NN ,|,|, a|a|DT distribution|distribution|NN of|of|IN DNA|dna|NN fragments|fragment|NNS ranging|range|VBG from|from|IN 200-600|200-600|CD bp|bp|NN was|be|VBD detected|detect|VBN by|by|IN agarose-gel|agarose-gel|JJ electrophoretic|electrophoretic|JJ separation|separation|NN of|of|IN a|a|DT small|small|JJ sample|sample|NN that|that|WDT was|be|VBD de-crosslinked|de-crosslinked|JJ by|by|IN incubation|incubation|NN at|at|IN 65|65|CD °C|°c|NN for|for|IN >|>|JJR 4|4|CD hr|hr|NN .|.|. EDTA|edta|NN was|be|VBD added|add|VBN to|to|TO 10|10|CD mM|mm|NN to|to|TO stop|stop|VB the|the|DT micrococcal|micrococcal|JJ nuclease|nuclease|NN and|and|CC the|the|DT samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RP to|to|TO remove|remove|VB cell|cell|NN debris|debris|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB incubated|incubate|VBN with|with|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS and|and|CC protein|protein|NN G|g|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN for|for|IN 2-3|2-3|CD hours|hour|NNS at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC antibody|antibody|NN was|be|VBD added|add|VBN to|to|TO the|the|DT pre-cleared|pre-cleared|JJ lysate|lysate|NN for|for|IN an|a|DT overnight|overnight|JJ incubation|incubation|NN .|.|. The|the|DT next|next|JJ day|day|NN ,|,|, 30|30|CD µl|µl|NN of|of|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN and|and|CC G|g|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT lysate|lysate|NN to|to|TO capture|capture|VB antibody-protein-DNA|antibody-protein-dna|JJ complex|complex|NN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Beads|bead|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN 1|1|CD ml|ml|NN of|of|IN 250|250|CD mM|mm|NN LiCl|licl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 600|600|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 600|600|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 300|300|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC twice|twice|RB with|with|IN TE|te|NN .|.|. Elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN after|after|IN the|the|DT final|final|JJ wash|wash|NN step|step|NN ,|,|, and|and|CC beads|bead|NNS were|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS toremove|toremove|VBP the|the|DT crosslinked|crosslink|VBN protein-DNA|protein-dna|JJ complexes|complex|NNS from|from|IN the|the|DT beads|bead|NNS .|.|. After|after|IN centrifugation|centrifugation|NN to|to|TO remove|remove|VB the|the|DT beads|bead|NNS ,|,|, the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 65|65|CD °C|°c|NN to|to|TO reverse|reverse|VB the|the|DT protein-DNA|protein-dna|JJ formaldehyde|formaldehyde|NN crosslinks|crosslink|NNS .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS PCR|pcr|NN Purification|purification|NN kit|kit|NN and|and|CC eluted|elute|VBN to|to|TO a|a|DT final|final|JJ volume|volume|NN of|of|IN 50ul|50ul|JJ with|with|IN EB|EB|NNP .|.|.
Cell|cell|NN pellets|pellet|NNS -LRB-|-lrb-|-LRB- from|from|IN initial|initial|JJ 50|50|CD ml|ml|NN of|of|IN culture|culture|NN -RRB-|-rrb-|-RRB- were|be|VBD thawed|thaw|VBN and|and|CC resuspended|resuspend|VBN in|in|IN 250ul|250ul|NN of|of|IN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- and|and|CC sonicated|sonicate|VBN using|use|VBG a|a|DT microtip|microtip|NN sonicator|sonicator|NN set|set|VBN at|at|IN 10|10|CD %|%|NN output|output|NN for|for|IN 20|20|CD second|second|JJ intervals|interval|NNS with|with|IN periods|period|NNS of|of|IN cooling|cool|VBG in|in|IN between|between|IN .|.|. Cells|cell|NNS were|be|VBD then|then|RB treated|treat|VBN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN with|with|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 2|2|CD ng/ml|ng/ml|NN -RRB-|-rrb-|-RRB- micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- 50|50|CD units|unit|NNS -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD μM|μm|NN CaCl2|cacl2|NN ,1.2|,1.2|CD mM|mm|NN KCl|kcl|NN ,|,|, 0.3|0.3|CD mM|mm|NN NaCl|nacl|NN ,|,|, 6|6|CD mM|mm|NN sucrose|sucrose|NN ,|,|, and|and|CC 10|10|CD μM|μm|NN DTT|dtt|NN .|.|. After|after|IN treatment|treatment|NN ,|,|, a|a|DT distribution|distribution|NN of|of|IN DNA|dna|NN fragments|fragment|NNS ranging|range|VBG from|from|IN 200-600|200-600|CD bp|bp|NN was|be|VBD detected|detect|VBN by|by|IN agarose-gel|agarose-gel|JJ electrophoretic|electrophoretic|JJ separation|separation|NN of|of|IN a|a|DT small|small|JJ sample|sample|NN that|that|WDT was|be|VBD de-crosslinked|de-crosslinked|JJ by|by|IN incubation|incubation|NN at|at|IN 65|65|CD °C|°c|NN for|for|IN >|>|JJR 4|4|CD hr|hr|NN .|.|. EDTA|edta|NN was|be|VBD added|add|VBN to|to|TO 10|10|CD mM|mm|NN to|to|TO stop|stop|VB the|the|DT micrococcal|micrococcal|JJ nuclease|nuclease|NN and|and|CC the|the|DT samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RP to|to|TO remove|remove|VB cell|cell|NN debris|debris|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB incubated|incubate|VBN with|with|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS and|and|CC protein|protein|NN G|g|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN for|for|IN 2-3|2-3|CD hours|hour|NNS at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC antibody|antibody|NN was|be|VBD added|add|VBN to|to|TO the|the|DT pre-cleared|pre-cleared|JJ lysate|lysate|NN for|for|IN an|a|DT overnight|overnight|JJ incubation|incubation|NN .|.|. The|the|DT next|next|JJ day|day|NN ,|,|, 30|30|CD μl|μl|NN of|of|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN and|and|CC G|g|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT lysate|lysate|NN to|to|TO capture|capture|VB antibody-protein-DNA|antibody-protein-dna|JJ complex|complex|NN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Beads|bead|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN 1|1|CD ml|ml|NN of|of|IN 250|250|CD mM|mm|NN LiCl|licl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 600|600|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 600|600|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 300|300|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC twice|twice|RB with|with|IN TE|te|NN .|.|. Elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN after|after|IN the|the|DT final|final|JJ wash|wash|NN step|step|NN ,|,|, and|and|CC beads|bead|NNS were|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS toremove|toremove|VBP the|the|DT crosslinked|crosslink|VBN protein-DNA|protein-dna|JJ complexes|complex|NNS from|from|IN the|the|DT beads|bead|NNS .|.|. After|after|IN centrifugation|centrifugation|NN to|to|TO remove|remove|VB the|the|DT beads|bead|NNS ,|,|, the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 65|65|CD °C|°c|NN to|to|TO reverse|reverse|VB the|the|DT protein-DNA|protein-dna|JJ formaldehyde|formaldehyde|NN crosslinks|crosslink|NNS .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS PCR|pcr|NN Purification|purification|NN kit|kit|NN and|and|CC eluted|elute|VBN to|to|TO a|a|DT final|final|JJ volume|volume|NN of|of|IN 50ul|50ul|JJ with|with|IN EB|EB|NNP .|.|.
Cell|cell|NN pellets|pellet|NNS -LRB-|-lrb-|-LRB- from|from|IN initial|initial|JJ 50|50|CD ml|ml|NN of|of|IN culture|culture|NN -RRB-|-rrb-|-RRB- were|be|VBD thawed|thaw|VBN and|and|CC resuspended|resuspend|VBN in|in|IN 250ul|250ul|NN of|of|IN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- and|and|CC sonicated|sonicate|VBN using|use|VBG a|a|DT microtip|microtip|NN sonicator|sonicator|NN set|set|VBN at|at|IN 10|10|CD %|%|NN output|output|NN for|for|IN 20|20|CD second|second|JJ intervals|interval|NNS with|with|IN periods|period|NNS of|of|IN cooling|cool|VBG in|in|IN between|between|IN .|.|. Cells|cell|NNS were|be|VBD then|then|RB treated|treat|VBN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN with|with|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 2|2|CD ng/ml|ng/ml|NN -RRB-|-rrb-|-RRB- micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- 50|50|CD units|unit|NNS -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD μM|μm|NN CaCl2|cacl2|NN ,1.2|,1.2|CD mM|mm|NN KCl|kcl|NN ,|,|, 0.3|0.3|CD mM|mm|NN NaCl|nacl|NN ,|,|, 6|6|CD mM|mm|NN sucrose|sucrose|NN ,|,|, and|and|CC 10|10|CD μM|μm|NN DTT|dtt|NN .|.|. After|after|IN treatment|treatment|NN ,|,|, a|a|DT distribution|distribution|NN of|of|IN DNA|dna|NN fragments|fragment|NNS ranging|range|VBG from|from|IN 200-600|200-600|CD bp|bp|NN was|be|VBD detected|detect|VBN by|by|IN agarose-gel|agarose-gel|JJ electrophoretic|electrophoretic|JJ separation|separation|NN of|of|IN a|a|DT small|small|JJ sample|sample|NN that|that|WDT was|be|VBD de-crosslinked|de-crosslinked|JJ by|by|IN incubation|incubation|NN at|at|IN 65|65|CD °C|°c|NN for|for|IN >|>|JJR 4|4|CD hr|hr|NN .|.|. EDTA|edta|NN was|be|VBD added|add|VBN to|to|TO 10|10|CD mM|mm|NN to|to|TO stop|stop|VB the|the|DT micrococcal|micrococcal|JJ nuclease|nuclease|NN and|and|CC the|the|DT samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RP to|to|TO remove|remove|VB cell|cell|NN debris|debris|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB incubated|incubate|VBN with|with|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS and|and|CC protein|protein|NN G|g|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN for|for|IN 2-3|2-3|CD hours|hour|NNS at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC no|no|DT antibody|antibody|NN was|be|VBD added|add|VBN to|to|TO the|the|DT pre-cleared|pre-cleared|JJ lysate|lysate|NN for|for|IN an|a|DT overnight|overnight|JJ incubation|incubation|NN .|.|. The|the|DT next|next|JJ day|day|NN ,|,|, 30|30|CD μl|μl|NN of|of|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN and|and|CC G|g|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT lysate|lysate|NN to|to|TO capture|capture|VB antibody-protein-DNA|antibody-protein-dna|JJ complex|complex|NN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Beads|bead|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN 1|1|CD ml|ml|NN of|of|IN 250|250|CD mM|mm|NN LiCl|licl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 600|600|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 600|600|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 300|300|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC twice|twice|RB with|with|IN TE|te|NN .|.|. Elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN after|after|IN the|the|DT final|final|JJ wash|wash|NN step|step|NN ,|,|, and|and|CC beads|bead|NNS were|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS toremove|toremove|VBP the|the|DT crosslinked|crosslink|VBN protein-DNA|protein-dna|JJ complexes|complex|NNS from|from|IN the|the|DT beads|bead|NNS .|.|. After|after|IN centrifugation|centrifugation|NN to|to|TO remove|remove|VB the|the|DT beads|bead|NNS ,|,|, the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 65|65|CD °C|°c|NN to|to|TO reverse|reverse|VB the|the|DT protein-DNA|protein-dna|JJ formaldehyde|formaldehyde|NN crosslinks|crosslink|NNS .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS PCR|pcr|NN Purification|purification|NN kit|kit|NN and|and|CC eluted|elute|VBN to|to|TO a|a|DT final|final|JJ volume|volume|NN of|of|IN 50ul|50ul|JJ with|with|IN EB|EB|NNP .|.|.
Cell|cell|NN pellets|pellet|NNS were|be|VBD lysed|lyse|VBN and|and|CC RNA|rna|NN collected|collect|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNeasy|RNeasy|NNP Plus|Plus|NNP Mini|Mini|NNP Kit|kit|NN with|with|IN Qiagen|Qiagen|NNP Bacteria|bacterium|NNS Protect|protect|VB RNA|rna|NN kit|kit|NN .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD then|then|RB treated|treat|VBN with|with|IN DNase|dnase|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN .|.|.
Cell|cell|NN pellets|pellet|NNS were|be|VBD lysed|lyse|VBN in|in|IN Tissue|tissue|NN and|and|CC Cell|cell|NN lysis|lysis|NN solution|solution|NN -LRB-|-lrb-|-LRB- EpiCentre|EpiCentre|NNP -RRB-|-rrb-|-RRB- and|and|CC proteinase|proteinase|NN K.|K.|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN and|and|CC DNase|dnase|NN treated|treat|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. The|the|DT amount|amount|NN of|of|IN total|total|JJ RNA|rna|NN in|in|IN each|each|DT sample|sample|NN was|be|VBD quantified|quantify|VBN using|use|VBG the|the|DT Qubit|Qubit|NNP 2.0|2.0|CD Flurometer|Flurometer|NNP -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC quality|quality|NN was|be|VBD assessed|assess|VBN using|use|VBG the|the|DT RNA6000|rna6000|NN Nano|Nano|NNP Chip|Chip|NNP on|on|IN the|the|DT Bioanalyzer|Bioanalyzer|NNP 2100|2100|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- .|.|.
cells|cell|NNS
Cells|cell|NNS -LRB-|-lrb-|-LRB- 10|10|CD ml|ml|NN -RRB-|-rrb-|-RRB- for|for|IN transcriptomic|transcriptomic|JJ analysis|analysis|NN were|be|VBD collected|collect|VBN into|into|IN tubes|tube|NNS containing|contain|VBG 1.25|1.25|CD ml|ml|NN ice-cold|ice-cold|JJ 5|5|CD %|%|NN -LRB-|-lrb-|-LRB- vol/vol|vol/vol|NN -RRB-|-rrb-|-RRB- unbuffered|unbuffered|JJ phenol|phenol|NN in|in|IN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- EP|ep|NN -RRB-|-rrb-|-RRB- and|and|CC pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 10,000|10,000|CD g|g|NN ,|,|, 4|4|CD °C|°c|NN ,|,|, 3|3|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. To|to|TO remove|remove|VB residual|residual|JJ traces|trace|NNS of|of|IN hydrolysate|hydrolysate|NN ,|,|, cell|cell|NN pellets|pellet|NNS were|be|VBD twice|twice|RB resuspended|resuspend|VBN in|in|IN ice-cold|ice-cold|JJ GMM|gmm|NN plus|plus|CC 0.125|0.125|CD volume|volume|NN of|of|IN EP|ep|NN ,|,|, repelleted|repellete|VBN ,|,|, then|then|RB flash|flash|VBP frozen|freeze|VBN in|in|IN dry|dry|JJ ice-ethanol|ice-ethanol|NN ,|,|, and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN .|.|.
cells|cell|NNS 12|12|CD min|min|NN after|after|IN treatment|treatment|NN by|by|IN norfloxacin|norfloxacin|NN
cells|cell|NNS 24|24|CD min|min|NN after|after|IN treatment|treatment|NN by|by|IN norfloxacin|norfloxacin|NN
cells|cell|NNS 36|36|CD min|min|NN after|after|IN treatment|treatment|NN by|by|IN norfloxacin|norfloxacin|NN
cells|cell|NNS 48|48|CD min|min|NN after|after|IN treatment|treatment|NN by|by|IN norfloxacin|norfloxacin|NN
cells|cell|NNS 60|60|CD min|min|NN after|after|IN treatment|treatment|NN by|by|IN norfloxacin|norfloxacin|NN
Cells|cell|NNS aerobically|aerobically|RB grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN MOPS/0|mops/0|NN .5|.5|CD %|%|NN glucose|glucose|NN at|at|IN 37C|37c|NN and|and|CC ~|~|NN 250|250|CD RPM|rpm|NNS .|.|.
Cells|cell|NNS at|at|IN appropriate|appropriate|JJ cell|cell|NN density|density|NN were|be|VBD cross-linked|cross-link|VBN by|by|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 25|25|CD min|min|NN .|.|. Following|follow|VBG quenching|quench|VBG the|the|DT unused|unused|JJ formaldehyde|formaldehyde|NN with|with|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 125|125|CD mM|mm|NN glycine|glycine|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 5|5|CD min|min|NN .|.|. The|the|DT cross-linked|cross-linked|JJ cells|cell|NNS were|be|VBD harvested|harvest|VBN and|and|CC washed|wash|VBN three|three|CD times|time|NNS with|with|IN 50|50|CD mL|ml|NN of|of|IN ice-cold|ice-cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- Tris|tris|NN Buffered|buffer|VBN Saline|saline|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT washed|wash|VBN cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ in|in|IN 0.5|0.5|CD mL|ml|NN lysis|lysis|NN buffer|buffer|NN composed|compose|VBN of|of|IN 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD ug/mL|ug/ml|NN RNaseA|rnasea|NN ,|,|, protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC 1|1|CD kU|ku|NN Ready-LyseTM|ready-lysetm|NN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT cells|cell|NNS were|be|VBD incubated|incubate|VBN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 30|30|CD min|min|NN and|and|CC then|then|RB treated|treat|VBN with|with|IN 0.5|0.5|CD mL|ml|NN of|of|IN 2XIP|2xip|NN buffer|buffer|NN with|with|IN the|the|DT protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB sonicated|sonicate|VBN four|four|CD times|time|NNS for|for|IN 20|20|CD sec|sec|NN each|each|DT in|in|IN an|a|DT ice|ice|NN bath|bath|NN to|to|TO fragment|fragment|NN the|the|DT chromatin|chromatin|NN complexes|complex|NNS using|use|VBG Misonix|Misonix|NNP sonicator|sonicator|NN 3000|3000|CD -LRB-|-lrb-|-LRB- output|output|NN level|level|NN =|=|JJ 2.5|2.5|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT range|range|NN of|of|IN the|the|DT DNA|dna|NN size|size|NN resulting|result|VBG from|from|IN the|the|DT sonication|sonication|NN procedure|procedure|NN was|be|VBD 300|300|CD --|--|: 1000|1000|CD bp|bp|NN .|.|. 6|6|CD uL|ul|NN of|of|IN mouse|mouse|NN antibody|antibody|NN -LRB-|-lrb-|-LRB- NT63|nt63|NN ,|,|, Neoclone|neoclone|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO immunoprecipitate|immunoprecipitate|NN the|the|DT chromatin|chromatin|NN complex|complex|NN of|of|IN RNA|rna|NN polymerase|polymerase|NN subunit|subunit|NN and|and|CC DNA|dna|NN .|.|. For|for|IN the|the|DT control|control|NN -LRB-|-lrb-|-LRB- mock-IP|mock-ip|NN -RRB-|-rrb-|-RRB- ,|,|, 2|2|CD ug|ug|NN of|of|IN normal|normal|JJ mouse|mouse|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Upstate|upstate|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN into|into|IN the|the|DT cell|cell|NN extract|extract|NN .|.|. IP|IP|NNP DNAs|dna|NNS were|be|VBD purified|purify|VBN with|with|IN QIAquick|qiaquick|NN PCR|pcr|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- then|then|RB amplified|amplify|VBD PCR|pcr|NN .|.|.
Cells|cell|NNS at|at|IN appropriate|appropriate|JJ cell|cell|NN density|density|NN were|be|VBD cross-linked|cross-link|VBN by|by|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 25|25|CD min|min|NN .|.|. Following|follow|VBG quenching|quench|VBG the|the|DT unused|unused|JJ formaldehyde|formaldehyde|NN with|with|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 125|125|CD mM|mm|NN glycine|glycine|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 5|5|CD min|min|NN .|.|. The|the|DT cross-linked|cross-linked|JJ cells|cell|NNS were|be|VBD harvested|harvest|VBN and|and|CC washed|wash|VBN three|three|CD times|time|NNS with|with|IN 50|50|CD mL|ml|NN of|of|IN ice-cold|ice-cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- Tris|tris|NN Buffered|buffer|VBN Saline|saline|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT washed|wash|VBN cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ in|in|IN 0.5|0.5|CD mL|ml|NN lysis|lysis|NN buffer|buffer|NN composed|compose|VBN of|of|IN 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD ug/mL|ug/ml|NN RNaseA|rnasea|NN ,|,|, protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC 1|1|CD kU|ku|NN Ready-LyseTM|ready-lysetm|NN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT cells|cell|NNS were|be|VBD incubated|incubate|VBN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 30|30|CD min|min|NN and|and|CC then|then|RB treated|treat|VBN with|with|IN 0.5|0.5|CD mL|ml|NN of|of|IN 2XIP|2xip|NN buffer|buffer|NN with|with|IN the|the|DT protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB sonicated|sonicate|VBN four|four|CD times|time|NNS for|for|IN 20|20|CD sec|sec|NN each|each|DT in|in|IN an|a|DT ice|ice|NN bath|bath|NN to|to|TO fragment|fragment|NN the|the|DT chromatin|chromatin|NN complexes|complex|NNS using|use|VBG Misonix|Misonix|NNP sonicator|sonicator|NN 3000|3000|CD -LRB-|-lrb-|-LRB- output|output|NN level|level|NN =|=|JJ 2.5|2.5|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT range|range|NN of|of|IN the|the|DT DNA|dna|NN size|size|NN resulting|result|VBG from|from|IN the|the|DT sonication|sonication|NN procedure|procedure|NN was|be|VBD 300|300|CD --|--|: 1000|1000|CD bp|bp|NN .|.|. 6|6|CD uL|ul|NN of|of|IN mouse|mouse|NN antibody|antibody|NN -LRB-|-lrb-|-LRB- NT63|nt63|NN ,|,|, Neoclone|neoclone|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO immunoprecipitate|immunoprecipitate|NN the|the|DT chromatin|chromatin|NN complex|complex|NN of|of|IN RNA|rna|NN polymerase|polymerase|NN subunit|subunit|NN -LRB-|-lrb-|-LRB- rpoB|rpob|NN -RRB-|-rrb-|-RRB- and|and|CC DNA|dna|NN .|.|. For|for|IN the|the|DT control|control|NN -LRB-|-lrb-|-LRB- mock-IP|mock-ip|NN -RRB-|-rrb-|-RRB- ,|,|, 2|2|CD ug|ug|NN of|of|IN normal|normal|JJ mouse|mouse|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Upstate|upstate|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN into|into|IN the|the|DT cell|cell|NN extract|extract|NN .|.|. IP|IP|NNP DNAs|dna|NNS were|be|VBD purified|purify|VBN with|with|IN QIAquick|qiaquick|NN PCR|pcr|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- then|then|RB amplified|amplify|VBD PCR|pcr|NN .|.|.
Cells|cell|NNS at|at|IN appropriate|appropriate|JJ cell|cell|NN density|density|NN were|be|VBD cross-linked|cross-link|VBN by|by|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 25|25|CD min|min|NN .|.|. Following|follow|VBG quenching|quench|VBG the|the|DT unused|unused|JJ formaldehyde|formaldehyde|NN with|with|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 125|125|CD mM|mm|NN glycine|glycine|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 5|5|CD min|min|NN .|.|. The|the|DT cross-linked|cross-linked|JJ cells|cell|NNS were|be|VBD harvested|harvest|VBN and|and|CC washed|wash|VBN three|three|CD times|time|NNS with|with|IN 50|50|CD mL|ml|NN of|of|IN ice-cold|ice-cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- Tris|tris|NN Buffered|buffer|VBN Saline|saline|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT washed|wash|VBN cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ in|in|IN 0.5|0.5|CD mL|ml|NN lysis|lysis|NN buffer|buffer|NN composed|compose|VBN of|of|IN 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD ug/mL|ug/ml|NN RNaseA|rnasea|NN ,|,|, protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC 1|1|CD kU|ku|NN Ready-LyseTM|ready-lysetm|NN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT cells|cell|NNS were|be|VBD incubated|incubate|VBN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 30|30|CD min|min|NN and|and|CC then|then|RB treated|treat|VBN with|with|IN 0.5|0.5|CD mL|ml|NN of|of|IN 2XIP|2xip|NN buffer|buffer|NN with|with|IN the|the|DT protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB sonicated|sonicate|VBN four|four|CD times|time|NNS for|for|IN 20|20|CD sec|sec|NN each|each|DT in|in|IN an|a|DT ice|ice|NN bath|bath|NN to|to|TO fragment|fragment|NN the|the|DT chromatin|chromatin|NN complexes|complex|NNS using|use|VBG Misonix|Misonix|NNP sonicator|sonicator|NN 3000|3000|CD -LRB-|-lrb-|-LRB- output|output|NN level|level|NN =|=|JJ 2.5|2.5|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT range|range|NN of|of|IN the|the|DT DNA|dna|NN size|size|NN resulting|result|VBG from|from|IN the|the|DT sonication|sonication|NN procedure|procedure|NN was|be|VBD 300|300|CD -|-|: 1000|1000|CD bp|bp|NN .|.|. For|for|IN the|the|DT control|control|NN -LRB-|-lrb-|-LRB- mock-IP|mock-ip|NN -RRB-|-rrb-|-RRB- ,|,|, 2|2|CD ug|ug|NN of|of|IN normal|normal|JJ mouse|mouse|NN IgG|igg|NN was|be|VBD added|add|VBN into|into|IN the|the|DT cell|cell|NN extract|extract|NN .|.|. IP|IP|NNP DNAs|dna|NNS were|be|VBD purified|purify|VBN with|with|IN QIAquick|qiaquick|NN PCR|pcr|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- then|then|RB amplified|amplify|VBD PCR|pcr|NN .|.|.
Cells|cell|NNS at|at|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN 0.5|0.5|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- 0.2|0.2|CD %|%|NN -RRB-|-rrb-|-RRB- media|media|NNS ,|,|, with|with|IN 42oC|42oc|NN heatshock|heatshock|NN for|for|IN 10|10|CD min|min|NN .|.|.
Cells|cell|NNS at|at|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN 0.5|0.5|CD -RRB-|-rrb-|-RRB- in|in|IN W2|w2|NN media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN and|and|CC 0.2|0.2|CD %|%|NN glutamine|glutamine|NN
Cells|cell|NNS at|at|IN stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN 1.5|1.5|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN glucose|glucose|NN media|media|NNS
Cells|cell|NNS corresponding|correspond|VBG to|to|TO 10|10|CD ml|ml|NN culture|culture|NN volume|volume|NN were|be|VBD harvested|harvest|VBN at|at|IN 0|0|CD hrs|hr|NNS using|use|VBG centrifugation|centrifugation|NN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD immediately|immediately|RB resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN further|further|JJ processing|processing|NN .|.|. Prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- the|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN in|in|IN cold|cold|JJ phosphate-buffered|phosphate-buffered|JJ saline|saline|NN to|to|TO remove|remove|VB RNAlater|rnalater|NN .|.|.
Cells|cell|NNS corresponding|correspond|VBG to|to|TO 10|10|CD ml|ml|NN culture|culture|NN volume|volume|NN were|be|VBD harvested|harvest|VBN at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0.1|0.1|CD mM|mm|NN IPTG|iptg|NN using|use|VBG centrifugation|centrifugation|NN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD immediately|immediately|RB resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN further|further|JJ processing|processing|NN .|.|. Prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- the|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN in|in|IN cold|cold|JJ phosphate-buffered|phosphate-buffered|JJ saline|saline|NN to|to|TO remove|remove|VB RNAlater|rnalater|NN .|.|.
Cells|cell|NNS corresponding|correspond|VBG to|to|TO 10|10|CD ml|ml|NN culture|culture|NN volume|volume|NN were|be|VBD harvested|harvest|VBN at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0|0|CD mM|mm|NN IPTG|iptg|NN using|use|VBG centrifugation|centrifugation|NN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD immediately|immediately|RB resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN further|further|JJ processing|processing|NN .|.|. Prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- the|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN in|in|IN cold|cold|JJ phosphate-buffered|phosphate-buffered|JJ saline|saline|NN to|to|TO remove|remove|VB RNAlater|rnalater|NN .|.|.
Cells|cell|NNS corresponding|correspond|VBG to|to|TO 10|10|CD ml|ml|NN culture|culture|NN volume|volume|NN were|be|VBD harvested|harvest|VBN at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 1.0|1.0|CD mM|mm|NN IPTG|iptg|NN using|use|VBG centrifugation|centrifugation|NN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD immediately|immediately|RB resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN further|further|JJ processing|processing|NN .|.|. Prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- the|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN in|in|IN cold|cold|JJ phosphate-buffered|phosphate-buffered|JJ saline|saline|NN to|to|TO remove|remove|VB RNAlater|rnalater|NN .|.|.
Cells|cell|NNS corresponding|correspond|VBG to|to|TO 10|10|CD ml|ml|NN culture|culture|NN volume|volume|NN were|be|VBD harvested|harvest|VBN at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0.1|0.1|CD mM|mm|NN IPTG|iptg|NN using|use|VBG centrifugation|centrifugation|NN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD immediately|immediately|RB resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN further|further|JJ processing|processing|NN .|.|. Prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- the|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN in|in|IN cold|cold|JJ phosphate-buffered|phosphate-buffered|JJ saline|saline|NN to|to|TO remove|remove|VB RNAlater|rnalater|NN .|.|.
Cells|cell|NNS corresponding|correspond|VBG to|to|TO 10|10|CD ml|ml|NN culture|culture|NN volume|volume|NN were|be|VBD harvested|harvest|VBN at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0|0|CD mM|mm|NN IPTG|iptg|NN using|use|VBG centrifugation|centrifugation|NN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD immediately|immediately|RB resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN further|further|JJ processing|processing|NN .|.|. Prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- the|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN in|in|IN cold|cold|JJ phosphate-buffered|phosphate-buffered|JJ saline|saline|NN to|to|TO remove|remove|VB RNAlater|rnalater|NN .|.|.
Cells|cell|NNS corresponding|correspond|VBG to|to|TO 10|10|CD ml|ml|NN culture|culture|NN volume|volume|NN were|be|VBD harvested|harvest|VBN at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 1.0|1.0|CD mM|mm|NN IPTG|iptg|NN using|use|VBG centrifugation|centrifugation|NN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD immediately|immediately|RB resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN further|further|JJ processing|processing|NN .|.|. Prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- the|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN in|in|IN cold|cold|JJ phosphate-buffered|phosphate-buffered|JJ saline|saline|NN to|to|TO remove|remove|VB RNAlater|rnalater|NN .|.|.
Cells|cell|NNS for|for|IN inoculation|inoculation|NN were|be|VBD from|from|IN overnight|overnight|JJ planktonic|planktonic|JJ culture|culture|NN in|in|IN 10|10|CD %|%|NN Luria-Bertani|luria-bertani|JJ broth|broth|NN at|at|IN 30|30|CD degree|degree|NN Celsius|Celsius|NNP .|.|. Cells|cell|NNS were|be|VBD washed|wash|VBN in|in|IN equal|equal|JJ volume|volume|NN of|of|IN fresh|fresh|JJ 10|10|CD %|%|NN LB|lb|NN broth|broth|NN before|before|IN inoculated|inoculate|VBN into|into|IN 30|30|CD ml|ml|NN 10|10|CD %|%|NN LB|lb|NN in|in|IN a|a|DT flask|flask|NN .|.|. 300|300|CD ul|ul|NN E.|e.|FW coli|coli|FW culture|culture|NN was|be|VBD inoculated|inoculate|VBN for|for|IN mono-species|mono-species|NNS pure|pure|JJ culture|culture|NN .|.|. 150|150|CD ul|ul|NN E.|e.|FW coli|coli|FW and|and|CC 60|60|CD ul|ul|NN S.|S.|NNP maltophilia|maltophilia|NNP were|be|VBD mixed|mixed|JJ and|and|CC inoculated|inoculate|VBN for|for|IN mixed-species|mixed-species|NNS cultures|culture|NNS .|.|. Flasks|flask|NNS were|be|VBD set|set|VBN on|on|IN a|a|DT shaker|shaker|NN -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- 20|20|CD C|c|NN -RRB-|-rrb-|-RRB- for|for|IN 18|18|CD h.|h.|NN
Cells|cell|NNS for|for|IN inoculation|inoculation|NN were|be|VBD from|from|IN overnight|overnight|JJ planktonic|planktonic|JJ culture|culture|NN in|in|IN 10|10|CD %|%|NN Luria-Bertani|luria-bertani|JJ broth|broth|NN at|at|IN 30|30|CD degree|degree|NN Celsius|Celsius|NNP .|.|. Cells|cell|NNS were|be|VBD washed|wash|VBN in|in|IN equal|equal|JJ volume|volume|NN of|of|IN fresh|fresh|JJ 10|10|CD %|%|NN LB|lb|NN broth|broth|NN before|before|IN inoculation|inoculation|NN and|and|CC were|be|VBD inoculated|inoculate|VBN into|into|IN 5|5|CD ml|ml|NN 10|10|CD %|%|NN LB|lb|NN in|in|IN a|a|DT disposable|disposable|JJ petri|petri|JJ dish|dish|NN -LRB-|-lrb-|-LRB- 60|60|CD mm|mm|NN x|x|CC 15|15|CD mm|mm|NN -RRB-|-rrb-|-RRB- .|.|. 50|50|CD ul|ul|NN E.|e.|FW coli|coli|FW culture|culture|NN was|be|VBD inoculated|inoculate|VBN for|for|IN mono-species|mono-species|NNS pure|pure|JJ culture|culture|NN .|.|. 50|50|CD ul|ul|NN E.|e.|FW coli|coli|FW and|and|CC 10|10|CD ul|ul|NN S.|S.|NNP maltophilia|maltophilia|NNP were|be|VBD mixed|mixed|JJ and|and|CC inoculated|inoculate|VBN for|for|IN mixed-species|mixed-species|JJ culture|culture|NN .|.|. Petri|petri|JJ dishes|dish|NNS were|be|VBD set|set|VBN static|static|JJ at|at|IN room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- 20|20|CD C|c|NN -RRB-|-rrb-|-RRB- for|for|IN 18|18|CD h|h|NN for|for|IN biofilm|biofilm|NN growth|growth|NN .|.|.
Cells|cell|NNS for|for|IN inoculation|inoculation|NN were|be|VBD from|from|IN overnight|overnight|JJ planktonic|planktonic|JJ culture|culture|NN in|in|IN 10|10|CD %|%|NN Luria-Bertani|luria-bertani|JJ broth|broth|NN at|at|IN 30|30|CD degree|degree|NN Celsius|Celsius|NNP .|.|. Cells|cell|NNS were|be|VBD washed|wash|VBN in|in|IN equal|equal|JJ volume|volume|NN of|of|IN fresh|fresh|JJ 10|10|CD %|%|NN LB|lb|NN broth|broth|NN before|before|IN inoculation|inoculation|NN .|.|. Planktonic|planktonic|JJ cultures|culture|NNS were|be|VBD conducted|conduct|VBN in|in|IN flasks|flask|NNS with|with|IN 30|30|CD ml|ml|NN 10|10|CD %|%|NN LB|lb|NN ,|,|, inoculated|inoculate|VBN with|with|IN 300|300|CD ul|ul|NN E.|e.|FW coli|coli|FW overnight|overnight|JJ culture|culture|NN .|.|. Flasks|flask|NNS were|be|VBD set|set|VBN on|on|IN a|a|DT shaker|shaker|NN -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- 20|20|CD C|c|NN -RRB-|-rrb-|-RRB- for|for|IN 18|18|CD h.|h.|NN Biofilms|biofilm|NNS were|be|VBD cultivated|cultivate|VBN in|in|IN static|static|JJ disposable|disposable|JJ petri|petri|NN dishes|dish|NNS -LRB-|-lrb-|-LRB- 60|60|CD mm|mm|NN x|x|CC 15|15|CD mm|mm|NN -RRB-|-rrb-|-RRB- with|with|IN 5|5|CD ml|ml|NN 10|10|CD %|%|NN LB|lb|NN ,|,|, inoculated|inoculate|VBN with|with|IN 50|50|CD ul|ul|NN E.|e.|FW coli|coli|FW overnight|overnight|JJ culture|culture|NN .|.|. The|the|DT petri|petri|JJ dishes|dish|NNS were|be|VBD set|set|VBN static|static|JJ at|at|IN room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- 20|20|CD C|c|NN -RRB-|-rrb-|-RRB- for|for|IN 18|18|CD h.|h.|NN
Cells|cell|NNS from|from|IN each|each|DT strain|strain|NN were|be|VBD rapidly|rapidly|RB harvested|harvest|VBN by|by|IN filtration|filtration|NN and|and|CC lysate|lysate|NN was|be|VBD produced|produce|VBN by|by|IN pulverization|pulverization|NN of|of|IN liquid|liquid|JJ nitrogen|nitrogen|NN cooled|cool|VBN samples|sample|NNS .|.|.
Cells|cell|NNS from|from|IN single|single|JJ colonies|colony|NNS were|be|VBD grown|grow|VBN on|on|IN LB|LB|NNP agar|agar|NN and|and|CC then|then|RB inoculated|inoculate|VBN into|into|IN liquid|liquid|JJ LB|lb|NN and|and|CC grown|grow|VBN to|to|TO saturation|saturation|NN .|.|. Then|then|RB 50|50|CD µl|µl|NN was|be|VBD inoculated|inoculate|VBN into|into|IN 5|5|CD ml|ml|NN of|of|IN K-medium|k-medium|NN and|and|CC grown|grow|VBN to|to|TO saturation|saturation|NN again|again|RB .|.|. The|the|DT cultures|culture|NNS were|be|VBD then|then|RB inoculated|inoculate|VBN into|into|IN the|the|DT separate|separate|JJ media|media|NNS as|as|IN follows|follow|VBZ :|:|: 25|25|CD μl|μl|NN into|into|IN K-medium|k-medium|NN ,|,|, 50|50|CD µl|µl|NN into|into|IN K-medium|k-medium|NN +|+|CC 0.3|0.3|CD M|m|NN NaCl|nacl|NN ,|,|, 75|75|CD µl|µl|NN into|into|IN K-medium|k-medium|NN +|+|CC 0.6|0.6|CD M|m|NN urea|urea|NN ;|;|: the|the|DT final|final|JJ volume|volume|NN was|be|VBD 5|5|CD ml|ml|NN in|in|IN all|all|DT cases|case|NNS .|.|. These|these|DT cultures|culture|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN in|in|IN 250|250|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flasks|flask|NNS in|in|IN the|the|DT three|three|CD media|media|NNS in|in|IN a|a|DT water|water|NN bath|bath|NN at|at|IN 30ºC|30ºC|NNP .|.|.
Cells|cell|NNS grew|grow|VBD in|in|IN MOPS|MOPS|NNP minimal|minimal|JJ medium|medium|NN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN and|and|CC 0.2|0.2|CD mM|mm|NN K2HPO4|k2hpo4|NN and|and|CC harvested|harvest|VBN at|at|IN the|the|DT OD600|od600|NN value|value|NN of|of|IN 1.0|1.0|CD .|.|.
Cells|cell|NNS grown|grow|VBN aerobically|aerobically|RB to|to|TO exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.8|0.8|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN media|media|NNS at|at|IN 37C|37c|NN were|be|VBD harvested|harvest|VBN .|.|.
Cells|cell|NNS harvested|harvest|VBN at|at|IN mid-exponential|mid-exponential|JJ phase|phase|NN ,|,|, spun|spin|VBD ,|,|, washed|wash|VBN twice|twice|RB with|with|IN M9|m9|NN medium|medium|NN and|and|CC shifted|shift|VBD to|to|TO limiting|limit|VBG or|or|CC no|no|DT thymine|thymine|NN medium|medium|NN .|.|. Samples|sample|NNS taken|take|VBN at|at|IN listed|list|VBN intervals|interval|NNS .|.|.
Cells|cell|NNS harvested|harvest|VBN at|at|IN OD450|od450|NN =|=|JJ 0.3|0.3|CD
Cells|cell|NNS in|in|IN log|log|NN phase|phase|NN under|under|IN ethanol|ethanol|NN stress|stress|NN
Cells|cell|NNS in|in|IN log|log|NN phase|phase|NN under|under|IN furfural|furfural|JJ stress|stress|NN
Cells|cell|NNS in|in|IN RNAlater|rnalater|NN were|be|VBD aliquoted|aliquote|VBN into|into|IN two|two|CD .|.|. One|one|CD served|serve|VBD as|as|IN non-sorted|non-sorted|JJ cells|cell|NNS and|and|CC kept|keep|VBD at|at|IN 4|4|CD degree|degree|NN C|c|NN .|.|. The|the|DT other|other|JJ aliquot|aliquot|NN was|be|VBD homogenized|homogenize|VBN with|with|IN OMNI|OMNI|NNP TH|th|NN homogenizer|homogenizer|NN for|for|IN 2|2|CD min|min|NN on|on|IN ice|ice|NN and|and|CC further|further|JJ aliquoted|aliquote|VBN into|into|IN small|small|JJ vials|vial|NNS .|.|. Cells|cell|NNS in|in|IN each|each|DT vial|vial|NN were|be|VBD then|then|RB re-suspended|re-suspended|JJ in|in|IN nuclease-free|nuclease-free|JJ phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN ,|,|, incubated|incubate|VBN with|with|IN anti-E|anti-e|JJ .|.|. coli|coli|NN antibody|antibody|NN and|and|CC microbeads|microbead|NNS ,|,|, followed|follow|VBN by|by|IN separation|separation|NN on|on|IN a|a|DT MACS|macs|NN separator|separator|NN -LRB-|-lrb-|-LRB- Miltenyi|Miltenyi|NNP ,|,|, Auburn|Auburn|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD degree|degree|NN C.|c.|NN Sorted|sort|VBN cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ into|into|IN RNAlater|rnalater|NN .|.|.
Cells|cell|NNS of|of|IN each|each|DT evolved|evolve|VBD colony|colony|NN type|type|NN were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 13,000|13,000|CD ×|×|CD g|g|NN for|for|IN 1|1|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN and|and|CC were|be|VBD immediately|immediately|RB used|use|VBN for|for|IN total|total|JJ RNA|rna|NN isolation|isolation|NN with|with|IN NucleoSpin|nucleospin|NN RNA|rna|NN II|ii|CD isolation|isolation|NN kit|kit|NN -LRB-|-lrb-|-LRB- Macherey|macherey|NN --|--|: Nagel|Nagel|NNP ,|,|, Biokè|Biokè|NNP ,|,|, Leiden|Leiden|NNP ,|,|, the|the|DT Netherlands|Netherlands|NNP -RRB-|-rrb-|-RRB- .|.|.
cells|cell|NNS prior|prior|RB to|to|TO treatment|treatment|NN by|by|IN norfloxacin|norfloxacin|NN
Cells|cell|NNS treated|treat|VBN during|during|IN mid-exponential|mid-exponential|JJ growth|growth|NN phase|phase|NN
Cells|cell|NNS treated|treat|VBN with|with|IN bacterial|bacterial|JJ protect|protect|VBP reagent|reagent|NN and|and|CC freeze|freeze|NN at|at|IN -70|-70|CD C|c|NN
Cells|cell|NNS used|use|VBN for|for|IN expression|expression|NN analysis|analysis|NN were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- Glansdorff|glansdorff|FW ,|,|, 1965|1965|CD -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 0.5|0.5|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- ,|,|, L-methionine|l-methionine|NN -LRB-|-lrb-|-LRB- 100|100|CD mg|mg|NN ml-1|ml-1|NN -RRB-|-rrb-|-RRB- and|and|CC with|with|IN L-arginine|l-arginine|NN -LRB-|-lrb-|-LRB- 100ug|100ug|CD ml-1|ml-1|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN expression|expression|NN analysis|analysis|NN ,|,|, cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- -LRB-|-lrb-|-LRB- OD|od|NN -RRB-|-rrb-|-RRB- 660nm|660nm|NN =|=|JJ 0.5|0.5|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT metabolism|metabolism|NN was|be|VBD quenched|quench|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|.
Cells|cell|NNS used|use|VBN for|for|IN expression|expression|NN analysis|analysis|NN were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- Glansdorff|glansdorff|FW ,|,|, 1965|1965|CD -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 0.5|0.5|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- ,|,|, L-methionine|l-methionine|NN -LRB-|-lrb-|-LRB- 100ug|100ug|CD ml-1|ml-1|NN -RRB-|-rrb-|-RRB- and|and|CC with|with|IN L-arginine|l-arginine|NN -LRB-|-lrb-|-LRB- 100ug|100ug|CD ml-1|ml-1|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN expression|expression|NN analysis|analysis|NN ,|,|, cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- -LRB-|-lrb-|-LRB- OD|od|NN -RRB-|-rrb-|-RRB- 660nm|660nm|NN =|=|JJ 0.5|0.5|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT metabolism|metabolism|NN was|be|VBD quenched|quench|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|.
Cells|cell|NNS used|use|VBN for|for|IN expression|expression|NN analysis|analysis|NN were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- Glansdorff|glansdorff|FW ,|,|, 1965|1965|CD -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 0.5|0.5|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- ,|,|, L-methionine|l-methionine|NN -LRB-|-lrb-|-LRB- 100ug|100ug|CD ml-1|ml-1|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN expression|expression|NN analysis|analysis|NN ,|,|, cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- -LRB-|-lrb-|-LRB- OD|od|NN -RRB-|-rrb-|-RRB- 660nm|660nm|NN =|=|JJ 0.5|0.5|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT metabolism|metabolism|NN was|be|VBD quenched|quench|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|.
Cell|cell|NN suspension|suspension|NN was|be|VBD ammended|ammend|VBN with|with|IN 1.25|1.25|CD M|m|NN sucrose|sucrose|NN to|to|TO an|a|DT osmotic|osmotic|JJ pressure|pressure|NN of|of|IN 2.7|2.7|CD Os|os|NNS kg-1|kg-1|NN for|for|IN 10|10|CD minutes|minute|NNS .|.|. The|the|DT biomass|biomass|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 4000|4000|CD rpm|rpm|NN and|and|CC the|the|DT pellet|pellet|NN treated|treat|VBN with|with|IN RNAProtect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
Cell|cell|NN suspension|suspension|NN was|be|VBD ammended|ammend|VBN with|with|IN 1.37|1.37|CD M|m|NN NaCl|nacl|NN to|to|TO obtain|obtain|VB an|a|DT osmotic|osmotic|JJ pressure|pressure|NN of|of|IN 2.7|2.7|CD Os|os|NNS kg-1|kg-1|NN for|for|IN 10|10|CD minutes|minute|NNS .|.|. The|the|DT biomass|biomass|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 4000|4000|CD rpm|rpm|NN and|and|CC the|the|DT pellet|pellet|NN treated|treat|VBN with|with|IN RNAProtect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
Cells|cell|NNS were|be|VBD centrifuged|centrifuge|VBN and|and|CC the|the|DT cell|cell|NN pellets|pellet|NNS were|be|VBD stored|store|VBN in|in|IN RNA|rna|NN Later|later|RB solution|solution|NN at|at|IN -80|-80|CD ºC|ºc|NN .|.|. The|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Venlo|Venlo|NNP ,|,|, Netherlands|Netherlands|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO isolate|isolate|VB total|total|JJ RNA|rna|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD then|then|RB incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN with|with|IN RNaseOut|rnaseout|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- and|and|CC DNaseI|dnasei|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacture|manufacture|NN 's|'s|POS protocol|protocol|NN for|for|IN 1|1|CD hour|hour|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD mixed|mix|VBN with|with|IN saturated|saturated|JJ phenol/chloroform|phenol/chloroform|NN -LRB-|-lrb-|-LRB- pH|ph|NN =|=|JJ 4.5|4.5|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC precipitated|precipitated|JJ with|with|IN ethanol|ethanol|NN and|and|CC 30|30|CD µL|µl|NN ,|,|, 3|3|CD M|m|NN sodium|sodium|NN acetate|acetate|NN -LRB-|-lrb-|-LRB- pH|ph|NN =|=|JJ 5.5|5.5|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- ,|,|, overnight|overnight|JJ at|at|IN -80|-80|CD ºC|ºc|NN .|.|. After|after|IN precipitation|precipitation|NN ,|,|, the|the|DT tubes|tube|NNS were|be|VBD centrifuged|centrifuge|VBN and|and|CC the|the|DT RNA|rna|NN pellet|pellet|NN was|be|VBD washed|wash|VBN twice|twice|RB with|with|IN 70|70|CD %|%|NN ethanol|ethanol|NN and|and|CC dried|dry|VBN under|under|IN vacuum|vacuum|NN .|.|.
Cells|cell|NNS were|be|VBD collected|collect|VBN as|as|IN a|a|DT function|function|NN of|of|IN time|time|NN after|after|IN rifampicin|rifampicin|NN treatment|treatment|NN at|at|IN the|the|DT specified|specify|VBN times|time|NNS .|.|. RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNAsnap|rnasnap|NN protocol|protocol|NN .|.|.
Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC washed|wash|VBN three|three|CD times|time|NNS in|in|IN ice-cold|ice-cold|JJ 1X|1x|NN PBS|PBS|NNP .|.|. The|the|DT pellet|pellet|NN was|be|VBD then|then|RB re-suspended|re-suspended|JJ in|in|IN 250|250|CD μl|μl|NN ChIP|chip|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 200|200|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 600|600|CD mM|mm|NN NaCl|nacl|NN 4|4|CD %|%|NN Triton|Triton|NNP X|X|NNP ,|,|, Complete|complete|JJ protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN EDTA-free|edta-free|NN -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. Sonication|sonication|NN of|of|IN crosslinked|crosslink|VBN samples|sample|NNS was|be|VBD performed|perform|VBN using|use|VBG the|the|DT Diagenode|Diagenode|NNP Bioruptor|Bioruptor|NNP ®|®|NN at|at|IN 30s|30s|CD intervals|interval|NNS for|for|IN 10|10|CD min|min|NN at|at|IN high|high|JJ amplitude|amplitude|NN .|.|. After|after|IN sonication|sonication|NN ,|,|, 350|350|CD μl|μl|NN of|of|IN ChIP|chip|NN buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO each|each|DT sample|sample|NN ,|,|, the|the|DT samples|sample|NNS were|be|VBD mixed|mix|VBN by|by|IN gentle|gentle|JJ pipetting|pipetting|NN and|and|CC 100|100|CD μl|μl|NN of|of|IN each|each|DT lysate|lysate|NN was|be|VBD removed|remove|VBN and|and|CC stored|store|VBN as|as|IN `|`|`` input|input|NN '|'|'' .|.|. Immunoprecipitation|immunoprecipitation|NN was|be|VBD performed|perform|VBN overnight|overnight|RB at|at|IN 4|4|CD °C|°c|NN using|use|VBG 1/100|1/100|CD anti-RecA|anti-reca|JJ antibody|antibody|NN -LRB-|-lrb-|-LRB- Abcam|abcam|NN ,|,|, ab63797|ab63797|NN -RRB-|-rrb-|-RRB- .|.|. IP|IP|NNP samples|sample|NNS were|be|VBD then|then|RB incubated|incubate|VBN with|with|IN Protein|protein|NN G|g|NN Dynabeads|dynabead|NNS ®|®|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- for|for|IN 2|2|CD h|h|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. All|all|DT samples|sample|NNS were|be|VBD washed|wash|VBN 3|3|CD times|time|NNS with|with|IN 1|1|CD X|x|NN PBS|PBS|NNP +|+|CC 0.02|0.02|CD %|%|NN Tween-20|tween-20|NN before|before|IN re-suspending|re-suspend|VBG the|the|DT Protein|protein|NN G|g|NN dynabeads|dynabead|NNS in|in|IN 200|200|CD μl|μl|NN of|of|IN TE|TE|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- +|+|CC 1|1|CD %|%|NN SDS|sds|NN .|.|. 100|100|CD μl|μl|NN of|of|IN TE|TE|NNP buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT input|input|NN samples|sample|NNS and|and|CC all|all|DT samples|sample|NNS were|be|VBD then|then|RB incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 10|10|CD h|h|NN to|to|TO reverse|reverse|VB formaldehyde|formaldehyde|NN crosslinks|crosslink|NNS .|.|. DNA|dna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT MinElute|MinElute|NNP PCR|pcr|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN was|be|VBD eluted|elute|VBN in|in|IN 50|50|CD μl|μl|NN of|of|IN TE|TE|NNP buffer|buffer|NN using|use|VBG a|a|DT 2-step|2-step|JJ elution|elution|NN .|.|. Samples|sample|NNS were|be|VBD stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD cross-linked|cross-link|VBN by|by|IN the|the|DT addition|addition|NN of|of|IN formaldehyde|formaldehyde|NN at|at|IN 1|1|CD %|%|NN final|final|JJ concentration|concentration|NN with|with|IN continued|continued|JJ shaking|shake|VBG at|at|IN 37|37|CD °C|°c|NN for|for|IN 5|5|CD min|min|NN before|before|IN quenching|quench|VBG with|with|IN glycine|glycine|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD crosslinked|crosslink|VBN in|in|IN 1|1|CD %|%|NN formadehyde|formadehyde|NN for|for|IN 25|25|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN followed|follow|VBN by|by|IN 5|5|CD minutes|minute|NNS of|of|IN quenching|quench|VBG with|with|IN glycine|glycine|NN .|.|. Cells|cell|NNS were|be|VBD washed|wash|VBN 3X|3x|NN with|with|IN ice|ice|NN cold|cold|JJ TBS|tbs|NN .|.|. Cell|cell|NN pellets|pellet|NNS were|be|VBD stored|store|VBN at|at|IN -80|-80|CD C.|C.|NNP
Cells|cell|NNS were|be|VBD cultured|culture|VBN in|in|IN LB|lb|NN medium|medium|NN containing|contain|VBG ampicillin|ampicillin|NN at|at|IN 28|28|CD ˚C|˚c|NN .|.|. The|the|DT overnight|overnight|JJ cell|cell|NN culture|culture|NN was|be|VBD inoculated|inoculate|VBN into|into|IN the|the|DT fresh|fresh|JJ medium|medium|NN at|at|IN 1/70|1/70|CD -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- and|and|CC was|be|VBD incubated|incubate|VBN for|for|IN 2|2|CD hr|hr|NN at|at|IN 28|28|CD ˚C|˚c|NN -LRB-|-lrb-|-LRB- OD600|od600|NN reached|reach|VBN 0.35|0.35|CD -RRB-|-rrb-|-RRB- and|and|CC then|then|RB for|for|IN 2|2|CD hr|hr|NN at|at|IN 42|42|CD ˚C|˚c|NN -LRB-|-lrb-|-LRB- OD600|od600|NN reached|reach|VBN 2.3|2.3|CD -RRB-|-rrb-|-RRB- to|to|TO induce|induce|VB the|the|DT PR|pr|NN promoter|promoter|NN .|.|.
Cells|cell|NNS were|be|VBD disrupted|disrupt|VBN by|by|IN sonication|sonication|NN and|and|CC NsrR|nsrr|NN bound|bind|VBD DNA|dna|NN was|be|VBD isolated|isolate|VBN with|with|IN anti-Flag|anti-flag|JJ antibody|antibody|NN .|.|.
Cells|cell|NNS were|be|VBD enyzmatically|enyzmatically|RB lysed|lyse|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN protease|protease|NN inhibitors|inhibitor|NNS prior|prior|RB to|to|TO fragmentation|fragmentation|NN using|use|VBG sonication|sonication|NN .|.|. Protein/DNA|protein/dna|NN complexes|complex|NNS were|be|VBD recovered|recover|VBN using|use|VBG an|a|DT appropriate|appropriate|JJ mouse|mouse|NN monoclonal|monoclonal|JJ antibody|antibody|NN followed|follow|VBN by|by|IN recovery|recovery|NN using|use|VBG Pan|pan|NN Mouse|mouse|NN IgG|igg|NN Dynabeads|dynabead|NNS .|.|. While|while|IN complexed|complex|VBN on|on|IN the|the|DT magnetic|magnetic|JJ bead|bead|NN ,|,|, a|a|DT series|series|NN of|of|IN enzymatic|enzymatic|JJ reactions|reaction|NNS were|be|VBD performed|perform|VBN to|to|TO 1|1|LS -RRB-|-rrb-|-RRB- end|end|VB repair|repair|NN ,|,|, fragmented|fragmented|JJ DNA|dna|NN ,|,|, 2|2|LS -RRB-|-rrb-|-RRB- ligate|ligate|NN sequencing|sequencing|NN adpator|adpator|NN 2|2|CD ,|,|, 3|3|CD -RRB-|-rrb-|-RRB- nick|nick|NN repair|repair|NN ,|,|, 4|4|LS -RRB-|-rrb-|-RRB- lambda|lambda|NN exonuclease|exonuclease|NN treatment|treatment|NN ,|,|, 5|5|CD -RRB-|-rrb-|-RRB- RecJ|recj|NN nuclease|nuclease|NN treatment|treatment|NN .|.|. This|this|DT was|be|VBD based|base|VBN on|on|IN the|the|DT method|method|NN developed|develop|VBN by|by|IN Rhee|Rhee|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- doi|doi|FW :|:|: 10.1016|10.1016|CD /|/|: j.cell|j.cell|JJ .2011.11.013|.2011.11.013|NN -RRB-|-rrb-|-RRB- .|.|. IP|IP|NNP DNA|dna|NN was|be|VBD then|then|RB rleased|rlease|VBN from|from|IN the|the|DT complex|complex|NN and|and|CC recovered|recover|VBD .|.|.
Cells|cell|NNS were|be|VBD fixed|fix|VBN in|in|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 20|20|CD min|min|NN ,|,|, quenched|quench|VBN with|with|IN glycine|glycine|NN ,|,|, and|and|CC lysed|lyse|VBN .|.|. Chromatin|chromatin|NN was|be|VBD pelleted|pelleted|JJ and|and|CC solublized|solublize|VBN by|by|IN sonication|sonication|NN .|.|.
Cells|cell|NNS were|be|VBD fixed|fix|VBN in|in|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 20|20|CD min|min|NN ,|,|, quenched|quench|VBN with|with|IN glycine|glycine|NN ,|,|, and|and|CC lysed|lyse|VBN .|.|. Chromatin|chromatin|NN was|be|VBD pelleted|pelleted|JJ and|and|CC solublized|solublize|VBN by|by|IN sonication|sonication|NN .|.|. Crosslinked|crosslink|VBN chromatin|chromatin|NN was|be|VBD then|then|RB immunoprecipitated|immunoprecipitate|VBN .|.|.
Cells|cell|NNS were|be|VBD fixed|fix|VBN in|in|IN the|the|DT required|require|VBN growth|growth|NN phase|phase|NN in|in|IN formaldehyde|formaldehyde|NN ,|,|, quenched|quench|VBN ,|,|, washed|wash|VBN and|and|CC lysed|lyse|VBN .|.|. Fragmented|fragmented|JJ DNA|dna|NN -|-|: protein|protein|NN complex|complex|NN were|be|VBD pulled|pull|VBN using|use|VBG the|the|DT monoclonal|monoclonal|JJ flag|flag|NN tag|tag|NN antibody|antibody|NN .|.|. The|the|DT complex|complex|NN was|be|VBD then|then|RB washed|wash|VBN ,|,|, reverse|reverse|VB cross-linked|cross-linked|JJ and|and|CC obtained|obtain|VBN DNA|dna|NN purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP min|min|NN elute|elute|NN PCR|pcr|NN purification|purification|NN kit|kit|NN .|.|.
Cells|cell|NNS were|be|VBD fixed|fix|VBN with|with|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN for|for|IN 5|5|CD min|min|NN before|before|IN quenching|quench|VBG with|with|IN ice-cold|ice-cold|JJ glycine|glycine|NN -LRB-|-lrb-|-LRB- 100mM|100mm|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN ,|,|, washed|wash|VBN with|with|IN ice-cold|ice-cold|JJ PBS|PBS|NNP and|and|CC flash-frozen|flash-frozen|JJ in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|. Cell|cell|NN pellets|pellet|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 500|500|CD ml|ml|NN of|of|IN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300mM|300mM|NNP NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- and|and|CC sonicated|sonicate|VBN using|use|VBG a|a|DT Misonix|Misonix|NNP sonicator|sonicator|NN -LRB-|-lrb-|-LRB- S-4000|s-4000|NN -RRB-|-rrb-|-RRB- with|with|IN a|a|DT cup|cup|NN horn|horn|NN -LRB-|-lrb-|-LRB- 431C|431c|NN -RRB-|-rrb-|-RRB- set|set|NN at|at|IN 60|60|CD %|%|NN output|output|NN ,|,|, 10|10|CD sec|sec|NN ON|ON|NNP and|and|CC 10|10|CD sec|sec|NN OFF|off|NN ,|,|, for|for|IN a|a|DT total|total|JJ sonication|sonication|NN time|time|NN of|of|IN 16|16|CD min|min|NN .|.|. Cells|cell|NNS were|be|VBD then|then|RB treated|treat|VBN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN with|with|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 2|2|CD ng/ml|ng/ml|NN ;|;|: USB|usb|JJ ,|,|, Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 20,000|20,000|CD x|x|CC g|g|NN for|for|IN 10|10|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN to|to|TO remove|remove|VB cell|cell|NN debris|debris|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB incubated|incubate|VBN with|with|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Upstate|upstate|NN ;|;|: now|now|RB Millipore|Millipore|NNP -RRB-|-rrb-|-RRB- and|and|CC protein|protein|NN G|g|NN beads|bead|NNS -LRB-|-lrb-|-LRB- GE|GE|NNP Healthcare|Healthcare|NNP -RRB-|-rrb-|-RRB- in|in|IN IP|IP|NNP buffer|buffer|NN for|for|IN 3|3|CD hours|hour|NNS at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 1000|1000|CD x|x|CC g|g|NN for|for|IN 2|2|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC antibodies|antibody|NNS were|be|VBD added|add|VBN to|to|TO the|the|DT pre-cleared|pre-cleared|JJ lysate|lysate|NN for|for|IN an|a|DT overnight|overnight|JJ incubation|incubation|NN .|.|. For|for|IN ChIP|chip|NN ,|,|, we|we|PRP used|use|VBD anti-RNAP|anti-rnap|JJ b|b|NN subunit|subunit|NN NT63|nt63|NN monoclonal|monoclonal|JJ antibodies|antibody|NNS -LRB-|-lrb-|-LRB- Neoclone|neoclone|JJ W0002|w0002|NN -RRB-|-rrb-|-RRB- ,|,|, anti-RNAP|anti-rnap|JJ s70|s70|NN subunit|subunit|NN monoclonal|monoclonal|JJ antibodies|antibody|NNS -LRB-|-lrb-|-LRB- Neoclone|neoclone|JJ W0004|w0004|NN -RRB-|-rrb-|-RRB- ,|,|, or|or|CC anti-DksA|anti-dksa|JJ rabbit|rabbit|NN polyclonal|polyclonal|JJ antisera|antisera|NNS -LRB-|-lrb-|-LRB- a|a|DT kind|kind|NN gift|gift|NN from|from|IN Diana|Diana|NNP Downs|Downs|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT next|next|JJ day|day|NN ,|,|, 30|30|CD μl|μl|NN of|of|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN Sepharose|sepharose|NN protein|protein|NN A|a|NN and|and|CC G|g|NN beads|bead|NNS in|in|IN 250|250|CD μl|μl|NN IP|IP|NNP buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT lysate|lysate|NN to|to|TO capture|capture|VB antibody-protein-DNA|antibody-protein-dna|JJ complex|complex|NN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Beads|bead|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN 1|1|CD ml|ml|NN of|of|IN 250|250|CD mM|mm|NN LiCl|licl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 2|2|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 1|1|CD ml|ml|NN 600|600|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 600|600|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 1|1|CD ml|ml|NN 300|300|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC twice|twice|RB with|with|IN 1|1|CD ml|ml|NN TE|te|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- .|.|. Elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN after|after|IN the|the|DT final|final|JJ wash|wash|NN step|step|NN ,|,|, and|and|CC beads|bead|NNS were|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO remove|remove|VB the|the|DT crosslinked|crosslink|VBN protein-DNA|protein-dna|JJ complexes|complex|NNS from|from|IN the|the|DT beads|bead|NNS .|.|. After|after|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 1000|1000|CD x|x|CC g|g|NN for|for|IN 2|2|CD min|min|NN at|at|IN 25|25|CD °C|°c|NN -RRB-|-rrb-|-RRB- to|to|TO remove|remove|VB the|the|DT beads|bead|NNS ,|,|, the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 65|65|CD °C|°c|NN to|to|TO reverse|reverse|VB the|the|DT protein-DNA|protein-dna|JJ formaldehyde|formaldehyde|NN crosslinks|crosslink|NNS .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS PCR|pcr|NN Purification|purification|NN kit|kit|NN and|and|CC eluted|elute|VBN in|in|IN a|a|DT final|final|JJ volume|volume|NN of|of|IN 65|65|CD μl|μl|NN with|with|IN 10|10|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD .|.|.
Cells|cell|NNS were|be|VBD flash|flash|NN frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN after|after|IN the|the|DT media|media|NNS was|be|VBD rapidly|rapidly|RB filtered|filter|VBN .|.|. Frozen|frozen|JJ cells|cell|NNS were|be|VBD pulverized|pulverize|VBN by|by|IN mixer|mixer|NN milling|milling|NN and|and|CC thawed|thaw|VBN in|in|IN 20|20|CD mM|mm|NN EDC|edc|NN ,|,|, pH|ph|NN 5.8|5.8|CD .|.|. The|the|DT crosslinking|crosslinking|NN reaction|reaction|NN was|be|VBD quenched|quench|VBN with|with|IN 250|250|CD mM|mm|NN glycine|glycine|NN ,|,|, 100|100|CD mM|mm|NN Tris|Tris|NNP Cl|Cl|NNP 8.0|8.0|CD ,|,|, and|and|CC 4|4|CD mM|mm|NN NaHCO3|nahco3|NN .|.|.
Cells|cell|NNS were|be|VBD flash|flash|NN frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN after|after|IN the|the|DT media|media|NNS was|be|VBD rapidly|rapidly|RB filtered|filter|VBN .|.|. Frozen|frozen|JJ cells|cell|NNS were|be|VBD pulverized|pulverize|VBN by|by|IN mixer|mixer|NN milling|milling|NN and|and|CC thawed|thaw|VBN in|in|IN 2.5|2.5|CD mM|mm|NN DSP|DSP|NNP .|.|. The|the|DT crosslinking|crosslinking|NN reaction|reaction|NN was|be|VBD quenched|quench|VBN with|with|IN 100|100|CD mM|mm|NN Tris|Tris|NNP Cl|Cl|NNP 8.3|8.3|CD .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB -LRB-|-lrb-|-LRB- 25|25|CD %|%|NN O2|o2|CD ,|,|, 70|70|CD %|%|NN N2|n2|NN and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN 0.35|0.35|CD -RRB-|-rrb-|-RRB- and|and|CC treated|treat|VBN with|with|IN 1|1|CD %|%|NN final|final|JJ volumen|voluman|NNS formaldehyde|formaldehyde|NN for|for|IN ten|ten|CD minutes|minute|NNS .|.|. Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ ,|,|, and|and|CC anaerobic|anaerobic|JJ sparging|sparging|NN was|be|VBD continued|continue|VBN for|for|IN 10|10|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN anaerobic|anaerobic|JJ sparging|sparging|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 5000|5000|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB -LRB-|-lrb-|-LRB- 70|70|CD %|%|NN N2|n2|NN ,|,|, 25|25|CD %|%|NN O2|o2|CD ,|,|, and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- or|or|CC anaerobically|anaerobically|RB -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN N2|n2|NN and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN ~|~|NN 0.3-0.35|0.3-0.35|CD -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB -LRB-|-lrb-|-LRB- 70|70|CD %|%|NN N2|n2|NN ,|,|, 25|25|CD %|%|NN O2|o2|CD ,|,|, and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- or|or|CC anaerobically|anaerobically|RB -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN N2|n2|NN and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN ~|~|NN 0.3-0.35|0.3-0.35|CD -RRB-|-rrb-|-RRB- in|in|IN MOPS|mop|NNS minimal|minimal|JJ glucose|glucose|NN media|media|NNS containing|contain|VBG 10|10|CD µM|µm|NN FeSO4|feso4|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB in|in|IN 50|50|CD ml|ml|NN LB|lb|NN medium|medium|NN until|until|IN OD600|od600|NN reached|reach|VBD ~|~|NN 1|1|CD -LRB-|-lrb-|-LRB- late|late|JJ log|log|NN phase|phase|NN -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN anaerobically|anaerobically|RB -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN N2|n2|NN and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN 0.3|0.3|CD -RRB-|-rrb-|-RRB- and|and|CC treated|treat|VBN with|with|IN 1|1|CD %|%|NN final|final|JJ volumen|voluman|NNS formaldehyde|formaldehyde|NN for|for|IN ten|ten|CD minutes|minute|NNS .|.|. Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ ,|,|, and|and|CC anaerobic|anaerobic|JJ sparging|sparging|NN was|be|VBD continued|continue|VBN for|for|IN 10|10|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN anaerobic|anaerobic|JJ sparging|sparging|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 5000|5000|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN in|in|IN LB|lb|NN medium|medium|NN to|to|TO an|a|DT OD600|od600|NN of|of|IN 0.55-0.6|0.55-0.6|CD
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.07|0.07|CD in|in|IN AB|AB|NNP glucose|glucose|NN CAA|CAA|NNP medium|medium|NN ,|,|, shifted|shift|VBD to|to|TO 39|39|CD °C|°c|NN for|for|IN 70|70|CD min|min|NN and|and|CC back|back|RB to|to|TO 30|30|CD °C|°c|NN for|for|IN 0|0|CD min|min|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.07|0.07|CD in|in|IN AB|AB|NNP glucose|glucose|NN CAA|CAA|NNP medium|medium|NN ,|,|, shifted|shift|VBD to|to|TO 39|39|CD °C|°c|NN for|for|IN 70|70|CD min|min|NN and|and|CC back|back|RB to|to|TO 30|30|CD °C|°c|NN for|for|IN 15|15|CD min|min|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.07|0.07|CD in|in|IN AB|AB|NNP glucose|glucose|NN CAA|CAA|NNP medium|medium|NN ,|,|, shifted|shift|VBD to|to|TO 39|39|CD °C|°c|NN for|for|IN 70|70|CD min|min|NN and|and|CC back|back|RB to|to|TO 30|30|CD °C|°c|NN for|for|IN 16|16|CD min|min|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.07|0.07|CD in|in|IN AB|AB|NNP glucose|glucose|NN CAA|CAA|NNP medium|medium|NN ,|,|, shifted|shift|VBD to|to|TO 39|39|CD °C|°c|NN for|for|IN 70|70|CD min|min|NN and|and|CC back|back|RB to|to|TO 30|30|CD °C|°c|NN for|for|IN 17|17|CD min|min|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.07|0.07|CD in|in|IN AB|AB|NNP glucose|glucose|NN CAA|CAA|NNP medium|medium|NN ,|,|, shifted|shift|VBD to|to|TO 39|39|CD °C|°c|NN for|for|IN 70|70|CD min|min|NN and|and|CC back|back|RB to|to|TO 30|30|CD °C|°c|NN for|for|IN 35|35|CD min|min|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.07|0.07|CD in|in|IN AB|AB|NNP glucose|glucose|NN CAA|CAA|NNP medium|medium|NN ,|,|, shifted|shift|VBD to|to|TO 39|39|CD °C|°c|NN for|for|IN 70|70|CD min|min|NN and|and|CC back|back|RB to|to|TO 30|30|CD °C|°c|NN for|for|IN 50|50|CD min|min|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.07|0.07|CD in|in|IN AB|AB|NNP glucose|glucose|NN CAA|CAA|NNP medium|medium|NN ,|,|, shifted|shift|VBD to|to|TO 39|39|CD °C|°c|NN for|for|IN 70|70|CD min|min|NN and|and|CC back|back|RB to|to|TO 30|30|CD °C|°c|NN for|for|IN 5|5|CD min|min|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN ,|,|, 200|200|CD rpm|rpm|NN in|in|IN M9|m9|NN glucose|glucose|NN ,|,|, for|for|IN 16|16|CD hours|hour|NNS -LRB-|-lrb-|-LRB- stationary|stationary|JJ phase|phase|NN -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- medium|medium|NN containing|contain|VBG 50|50|CD μg/ml|μg/ml|NN ampicillin|ampicillin|NN overnight|overnight|RB ,|,|, then|then|RB diluted|dilute|VBN at|at|IN a|a|DT ratio|ratio|NN of|of|IN 1:100|1:100|CD into|into|IN LB|lb|NN medium|medium|NN containing|contain|VBG 1.5|1.5|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- ethanol|ethanol|NN and|and|CC 50|50|CD μg/ml|μg/ml|NN ampicillin|ampicillin|NN ,|,|, and|and|CC grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- medium|medium|NN supplemented|supplement|VBN with|with|IN 50|50|CD μg/ml|μg/ml|NN ampicillin|ampicillin|NN overnight|overnight|RB ,|,|, then|then|RB inoculated|inoculate|VBN into|into|IN LB|lb|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.095|0.095|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- furfural|furfural|NN and|and|CC 50|50|CD μg/ml|μg/ml|NN ampicillin|ampicillin|NN at|at|IN an|a|DT initial|initial|JJ OD600|od600|NN value|value|NN of|of|IN 0.02|0.02|CD ,|,|, and|and|CC grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN in|in|IN M4|m4|NN minimal|minimal|JJ medium|medium|NN under|under|IN oxic|oxic|JJ and|and|CC anoxic|anoxic|JJ conditions|condition|NNS .|.|. The|the|DT minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- 1.27|1.27|CD mM|mm|NN K2HPO4|k2hpo4|NN ,|,|, 0.73|0.73|CD mM|mm|NN KH2PO4|kh2po4|NN ,|,|, 5|5|CD mM|mm|NN sodium|sodium|NN HEPES|hepes|NN ,|,|, 150|150|CD mM|mm|NN NaCl|nacl|NN ,|,|, 9|9|CD mM|mm|NN -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2SO4|2so4|NN -RRB-|-rrb-|-RRB- was|be|VBD supplemented|supplement|VBN with|with|IN 0.1|0.1|CD g/l|g/l|NN caseinhydrolysate|caseinhydrolysate|NN 1|1|CD mM|mm|NN MgSO4|mgso4|NN ,|,|, 0.1|0.1|CD mM|mm|NN CaCl2|cacl2|NN and|and|CC trace|trace|NN elements|element|NNS -LRB-|-lrb-|-LRB- 5|5|CD μM|μm|NN CoCl2|cocl2|NN ,|,|, 0.2|0.2|CD μM|μm|NN CuSO4|cuso4|NN ,|,|, 57|57|CD μM|μm|NN H3BO3|h3bo3|NN ,|,|, 5.4|5.4|CD μM|μm|NN FeCl2|fecl2|NN ,|,|, 1.3|1.3|CD μM|μm|NN MnSO4|mnso4|NN ,|,|, 67.2|67.2|CD μM|μm|NN Na2EDTA|na2edta|NN ,|,|, 3.9|3.9|CD μM|μm|NN Na2MoO4|na2moo4|NN ,|,|, 1.5|1.5|CD μM|μm|NN Na2SeO4|na2seo4|NN ,|,|, 5|5|CD μM|μm|NN NiCl2|nicl2|NN ,|,|, and|and|CC 1|1|CD μM|μm|NN ZnSO4|znso4|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT pH|ph|NN of|of|IN the|the|DT media|media|NNS was|be|VBD adjusted|adjust|VBN to|to|TO 7.2|7.2|CD .|.|. Glycerol|glycerol|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN -RRB-|-rrb-|-RRB- or|or|CC glycerol|glycerol|NN -LRB-|-lrb-|-LRB- 50mM|50mm|NN -RRB-|-rrb-|-RRB- plus|plus|CC propionate|propionate|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN -RRB-|-rrb-|-RRB- served|serve|VBD as|as|IN the|the|DT carbon|carbon|NN and|and|CC electron|electron|NN sources|source|NNS ,|,|, respectively|respectively|RB .|.|. Potassium|potassium|NN nitrate|nitrate|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN -RRB-|-rrb-|-RRB- was|be|VBD the|the|DT electron|electron|NN acceptor|acceptor|NN under|under|IN anoxic|anoxic|JJ conditions|condition|NNS .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN to|to|TO an|a|DT OD450|od450|NN of|of|IN about|about|IN 0.15|0.15|CD in|in|IN 100|100|CD ml|ml|NN AB|AB|NNP acetate|acetate|NN medium|medium|NN before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN to|to|TO an|a|DT OD600|od600|NN of|of|IN about|about|IN 0.15|0.15|CD in|in|IN 100|100|CD ml|ml|NN LB|lb|NN -LRB-|-lrb-|-LRB- +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN to|to|TO an|a|DT OD600|od600|NN of|of|IN about|about|IN 0.15|0.15|CD in|in|IN 50|50|CD ml|ml|NN LB|lb|NN -LRB-|-lrb-|-LRB- +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -RRB-|-rrb-|-RRB- before|before|IN crosslinking|crosslink|VBG .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37oC|37oc|NN without|without|IN shaking|shake|VBG in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG 5|5|CD ml|ml|NN of|of|IN the|the|DT MOPS-based|mops-based|JJ culture|culture|NN medium|medium|NN designed|design|VBN by|by|IN Neidhardt|Neidhardt|NNP .|.|. Mouse|mouse|NN cecal|cecal|JJ mucus|mucus|NN was|be|VBD prepared|prepare|VBN from|from|IN streptomycin-treated|streptomycin-treated|JJ CD-1|cd-1|NN mice|mouse|NNS -LRB-|-lrb-|-LRB- not|not|RB colonized|colonize|VBN with|with|IN E.|e.|FW coli|coli|FW -RRB-|-rrb-|-RRB- .|.|. Cultures|culture|NNS were|be|VBD grown|grow|VBN to|to|TO A600|a600|NN =|=|JJ 0.4|0.4|CD in|in|IN MOPS|MOPS|NNP medium|medium|NN containing|contain|VBG glucose|glucose|NN or|or|CC mannose|mannose|NN -LRB-|-lrb-|-LRB- 0.2|0.2|CD %|%|NN -RRB-|-rrb-|-RRB- and|and|CC also|also|RB in|in|IN 10|10|CD mg/ml|mg/ml|NN of|of|IN lyophilized|lyophilized|JJ mucus|mucus|NN at|at|IN A600|a600|NN =|=|JJ 0.2|0.2|CD -LRB-|-lrb-|-LRB- P1|p1|NN -RRB-|-rrb-|-RRB- or|or|CC 0.5|0.5|CD -LRB-|-lrb-|-LRB- P2|p2|NN -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN 65|65|CD ml|ml|NN LB|lb|NN medium|medium|NN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD600|od600|NN of|of|IN about|about|IN 0.3|0.3|CD .|.|. Subsequently|subsequently|RB 30|30|CD ml|ml|NN of|of|IN culture|culture|NN were|be|VBD transformed|transform|VBN to|to|TO a|a|DT pre|pre|JJ warmed|warm|VBN flask|flask|NN at|at|IN 43|43|CD °C|°c|NN and|and|CC the|the|DT remainder|remainder|NN kept|keep|VBD at|at|IN 30|30|CD °C|°c|NN -LRB-|-lrb-|-LRB- see|see|VB control|control|JJ sample|sample|NN -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN 65|65|CD ml|ml|NN LB|lb|NN medium|medium|NN at|at|IN 30|30|CD °C|°c|NN to|to|TO an|a|DT OD600|od600|NN of|of|IN about|about|IN 0.3|0.3|CD .|.|. Subsequently|subsequently|RB 30|30|CD ml|ml|NN of|of|IN culture|culture|NN were|be|VBD transformed|transform|VBN to|to|TO a|a|DT pre|pre|JJ warmed|warm|VBN flask|flask|NN at|at|IN 43|43|CD °C|°c|NN -LRB-|-lrb-|-LRB- see|see|VB heat|heat|NN sample|sample|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT remainder|remainder|NN kept|keep|VBD at|at|IN 30|30|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN a|a|DT 250|250|CD ml|ml|NN fermenter|fermenter|NN containing|contain|VBG 100|100|CD ml|ml|NN LB|lb|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 3|3|CD g/L|g/l|NN glucose|glucose|NN ,|,|, 0.1|0.1|CD mM|mm|NN IPTG|iptg|NN ,|,|, and|and|CC 50|50|CD μg/mL|μg/ml|NN antibiotics|antibiotic|NNS .|.|. The|the|DT fermentors|fermentor|NNS were|be|VBD operated|operate|VBN at|at|IN 37|37|CD °C|°c|NN and|and|CC 250|250|CD rpm|rpm|NN with|with|IN aeration|aeration|NN -LRB-|-lrb-|-LRB- 200|200|CD mL/min|ml/min|NN -RRB-|-rrb-|-RRB- .|.|. Flow|flow|NN rate|rate|NN was|be|VBD 1.162|1.162|CD ml/min|ml/min|NN -LRB-|-lrb-|-LRB- dilution|dilution|NN rate|rate|NN 0,7|0,7|CD /|/|: h|h|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT pellets|pellet|NNS were|be|VBD used|use|VBN for|for|IN RNA|rna|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN anaerobic|anaerobic|JJ incubator|incubator|NN for|for|IN 1h|1h|NN at|at|IN 37|37|CD ℃|℃|NN and|and|CC drugs|drug|NNS were|be|VBD added|add|VBN according|accord|VBG to|to|TO the|the|DT different|different|JJ concentrations|concentration|NNS .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN for|for|IN 30|30|CD min|min|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 22|22|CD °C|°c|NN or|or|CC 37|37|CD °C|°c|NN ,|,|, as|as|IN indicated|indicate|VBN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 37|37|CD degrees|degree|NNS celsius|celsius|NN with|with|IN shaking|shake|VBG for|for|IN 150|150|CD minutes|minute|NNS
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 37|37|CD degrees|degree|NNS celsius|celsius|NN with|with|IN shaking|shake|VBG for|for|IN 240|240|CD minutes|minute|NNS
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 37|37|CD degrees|degree|NNS celsius|celsius|NN with|with|IN shaking|shake|VBG for|for|IN 360|360|CD minutes|minute|NNS
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 37|37|CD degrees|degree|NNS celsius|celsius|NN with|with|IN shaking|shake|VBG for|for|IN 90|90|CD minutes|minute|NNS
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|LB|NNP media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN arabinose|arabinose|NN at|at|IN 37|37|CD °C|°c|NN to|to|TO and|and|CC OD600nm|od600nm|NN of|of|IN 0.2-0.25|0.2-0.25|CD
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|LB|NNP media|media|NNS with|with|IN 1mM|1mm|NN IPTG|iptg|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG for|for|IN 2|2|CD hours|hour|NNS
cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN overnight|overnight|JJ at|at|IN 37|37|CD degrees|degree|NNS celcius|celcius|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN Luria|Luria|NNP Bertani|Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- media|media|NNS at|at|IN 37C|37c|NN at|at|IN 200|200|CD rpm|rpm|NN .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD inoculated|inoculate|VBN with|with|IN single|single|JJ ,|,|, independent|independent|JJ colonies|colony|NNS in|in|IN triplicate|triplicate|NN ,|,|, incubated|incubate|VBN aerobically|aerobically|RB overnight|overnight|JJ at|at|IN 37oC|37oc|NN ,|,|, and|and|CC sub-cultured|sub-cultured|JJ to|to|TO a|a|DT starting|start|VBG OD600|od600|NN of|of|IN 0.0001|0.0001|CD .|.|. Cultures|culture|NNS were|be|VBD harvested|harvest|VBN at|at|IN OD600|od600|NN =|=|JJ 0.3|0.3|CD in|in|IN exponential|exponential|JJ phase|phase|NN and|and|CC at|at|IN OD600|od600|NN =|=|JJ 1.5|1.5|CD in|in|IN stationary|stationary|JJ phase|phase|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN M63|m63|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- 0.2|0.2|CD %|%|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ media|media|NNS at|at|IN 37oC|37oc|NN at|at|IN 200|200|CD rpm|rpm|NN .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD inoculated|inoculate|VBN with|with|IN single|single|JJ ,|,|, independent|independent|JJ colonies|colony|NNS in|in|IN triplicate|triplicate|NN ,|,|, incubated|incubate|VBN aerobically|aerobically|RB overnight|overnight|JJ at|at|IN 37oC|37oc|NN ,|,|, and|and|CC sub-cultured|sub-cultured|JJ to|to|TO a|a|DT starting|start|VBG OD600|od600|NN of|of|IN 0.0001|0.0001|CD .|.|. Cultures|culture|NNS were|be|VBD harvested|harvest|VBN at|at|IN an|a|DT OD600|od600|NN =|=|JJ 0.3|0.3|CD after|after|IN being|be|VBG maintained|maintain|VBN in|in|IN exponential|exponential|JJ phase|phase|NN for|for|IN at|at|IN least|least|JJS eight|eight|CD generations|generation|NNS .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN M63|m63|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- 0.2|0.2|CD %|%|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ media|media|NNS at|at|IN 37oC|37oc|NN at|at|IN 200|200|CD rpm|rpm|NN .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD inoculated|inoculate|VBN with|with|IN single|single|JJ ,|,|, independent|independent|JJ colonies|colony|NNS in|in|IN triplicate|triplicate|NN ,|,|, incubated|incubate|VBN aerobically|aerobically|RB overnight|overnight|JJ at|at|IN 37oC|37oc|NN ,|,|, and|and|CC sub-cultured|sub-cultured|JJ to|to|TO a|a|DT starting|start|VBG OD600|od600|NN of|of|IN 0.0001|0.0001|CD .|.|. Cultures|culture|NNS were|be|VBD harvested|harvest|VBN at|at|IN an|a|DT OD600|od600|NN =|=|JJ 1.5|1.5|CD .|.|.
cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- 0.4|0.4|CD %|%|NN w/v|w/v|NN -RRB-|-rrb-|-RRB-
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN and|and|CC 0.4|0.4|CD %|%|NN casamino|casamino|NN acid|acid|NN at|at|IN 37|37|CD ℃|℃|CD
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN casamino|casamino|NN acids|acid|NNS ,|,|, 0.5|0.5|CD %|%|NN glucose|glucose|NN 5μM|5μm|NN CaCl2|cacl2|NN and|and|CC 1mM|1mm|NN MgSO4|mgso4|NN at|at|IN 37|37|CD °C|°c|NN to|to|TO and|and|CC OD600nm|od600nm|NN of|of|IN 0.2-0.25|0.2-0.25|CD
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|mop|NNS minimal|minimal|JJ medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN at|at|IN 37|37|CD degrees|degree|NNS C|c|NN in|in|IN gas-sparged|gas-sparged|JJ Roux|Roux|NNP bottles|bottle|NNS to|to|TO mid-log|mid-log|JJ phase|phase|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|mop|NNS minimal|minimal|JJ medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN at|at|IN 37|37|CD oC|oc|NN in|in|IN gas-sparged|gas-sparged|JJ Roux|Roux|NNP bottles|bottle|NNS or|or|CC shaking|shake|VBG flasks|flask|NNS to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.3-0.4|0.3-0.4|CD -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN shake|shake|NN flasks|flask|NNS to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN under|under|IN either|either|CC aerobic|aerobic|JJ or|or|CC anaerobic|anaerobic|JJ conditions|condition|NNS depending|depend|VBG on|on|IN the|the|DT sample|sample|NN .|.|. M9|m9|NN minimal|minimal|JJ media|media|NNS supplement|supplement|NN with|with|IN either|either|CC glucose|glucose|NN ,|,|, fructose|fructose|NN ,|,|, or|or|CC glycerol|glycerol|NN as|as|IN the|the|DT sole|sole|JJ carbon|carbon|NN source|source|NN was|be|VBD used|use|VBN depending|depend|VBG on|on|IN the|the|DT sample|sample|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN TB7|tb7|NN supplemented|supplement|VBN with|with|IN 22|22|CD mM|mm|NN glucose|glucose|NN until|until|IN OD600|od600|NN ~|~|NN 1.8|1.8|CD .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN the|the|DT absence|absence|NN and|and|CC presence|presence|NN of|of|IN 0.005|0.005|CD mg/mL|mg/ml|NN 5-azacytidine|5-azacytidine|NN to|to|TO logarithmic|logarithmic|JJ phase|phase|NN -LRB-|-lrb-|-LRB- 2|2|CD hours|hour|NNS ,|,|, A600|a600|NN =|=|JJ ~|~|NN 0.45|0.45|CD -RRB-|-rrb-|-RRB- or|or|CC early|early|JJ stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- 8|8|CD hours|hour|NNS ,|,|, A600|a600|NN =|=|JJ ~|~|NN 2.7|2.7|CD -RRB-|-rrb-|-RRB-
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN the|the|DT minimal|minimal|JJ media|media|NNS ,|,|, M63|m63|NN .|.|. The|the|DT final|final|JJ cell|cell|NN concentrations|concentration|NNS were|be|VBD controlled|control|VBN ~|~|SYM 10|10|CD ^|^|SYM 8|8|CD cells/mL|cells/ml|NN within|within|IN the|the|DT exponential|exponential|JJ growth|growth|NN phase|phase|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN the|the|DT minimal|minimal|JJ media|media|NNS ,|,|, M63|m63|NN .|.|. The|the|DT final|final|JJ cell|cell|NN concentrations|concentration|NNS were|be|VBD controlled|control|VBN ~|~|NN 108|108|CD cells/mL|cells/ml|NN within|within|IN the|the|DT exponential|exponential|JJ growth|growth|NN phase|phase|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN the|the|DT minimal|minimal|JJ media|media|NNS ,|,|, modified|modify|VBN M63|m63|NN .|.|. The|the|DT final|final|JJ cell|cell|NN concentrations|concentration|NNS were|be|VBD controlled|control|VBN ~|~|SYM 10|10|CD ^|^|SYM 8|8|CD cells/mL|cells/ml|NN within|within|IN the|the|DT exponential|exponential|JJ growth|growth|NN phase|phase|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO an|a|DT OD|od|NN _|_|NN 600|600|CD of|of|IN 0.4|0.4|CD in|in|IN Luria|Luria|NNP Broth|Broth|NNP Lennox|Lennox|NNP
Cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO an|a|DT OD|od|NN of|of|IN 0.4|0.4|CD and|and|CC then|then|RB 0.5|0.5|CD mM|mm|NN IPTG|iptg|NN was|be|VBD added|add|VBN to|to|TO induce|induce|VB the|the|DT protein|protein|NN expression|expression|NN
Cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO approximately|approximately|RB mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD560|od560|NN =|=|JJ approximately|approximately|RB 0.5|0.5|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN in|in|IN Lysogeny|Lysogeny|NNP broth|broth|NN ,|,|, 37oC|37oc|NN with|with|IN shaking|shake|VBG
Cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO the|the|DT stationary|stationary|JJ phase|phase|NN at|at|IN 37ºC|37ºc|NN in|in|IN Luria-Bertani|luria-bertani|JJ medium|medium|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN with|with|IN 16|16|CD µM|µm|NN IPTG|iptg|NN and|and|CC 300|300|CD µL|µl|NN Cm20|cm20|NN anaerobically|anaerobically|RB -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN N2|n2|NN and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN 0.3|0.3|CD -RRB-|-rrb-|-RRB- and|and|CC treated|treat|VBN with|with|IN 1|1|CD %|%|NN final|final|JJ volumen|voluman|NNS formaldehyde|formaldehyde|NN for|for|IN ten|ten|CD minutes|minute|NNS .|.|. Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ ,|,|, and|and|CC anaerobic|anaerobic|JJ sparging|sparging|NN was|be|VBD continued|continue|VBN for|for|IN 10|10|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN anaerobic|anaerobic|JJ sparging|sparging|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 5000|5000|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN with|with|IN 4|4|CD µM|µm|NN IPTG|iptg|NN and|and|CC 300|300|CD µL|µl|NN Cm20|cm20|NN anaerobically|anaerobically|RB -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN N2|n2|NN and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN 0.3|0.3|CD -RRB-|-rrb-|-RRB- and|and|CC treated|treat|VBN with|with|IN 1|1|CD %|%|NN final|final|JJ volumen|voluman|NNS formaldehyde|formaldehyde|NN for|for|IN ten|ten|CD minutes|minute|NNS .|.|. Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ ,|,|, and|and|CC anaerobic|anaerobic|JJ sparging|sparging|NN was|be|VBD continued|continue|VBN for|for|IN 10|10|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN anaerobic|anaerobic|JJ sparging|sparging|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 5000|5000|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN with|with|IN 8|8|CD µM|µm|NN IPTG|iptg|NN and|and|CC 300|300|CD µL|µl|NN Cm20|cm20|NN anaerobically|anaerobically|RB -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN N2|n2|NN and|and|CC 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN 0.3|0.3|CD -RRB-|-rrb-|-RRB- and|and|CC treated|treat|VBN with|with|IN 1|1|CD %|%|NN final|final|JJ volumen|voluman|NNS formaldehyde|formaldehyde|NN for|for|IN ten|ten|CD minutes|minute|NNS .|.|. Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ ,|,|, and|and|CC anaerobic|anaerobic|JJ sparging|sparging|NN was|be|VBD continued|continue|VBN for|for|IN 10|10|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN anaerobic|anaerobic|JJ sparging|sparging|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 5000|5000|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD grown|grow|VBN with|with|IN vigorous|vigorous|JJ shaking|shake|VBG at|at|IN 37|37|CD °C|°c|NN to|to|TO mid-log|mid-log|NN -LRB-|-lrb-|-LRB- light|light|JJ scattering|scattering|NN at|at|IN 600|600|CD nm|nm|NN equivalent|equivalent|NN to|to|TO 0.4|0.4|CD OD|od|NN -RRB-|-rrb-|-RRB- .|.|. Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ ,|,|, and|and|CC shaking|shake|VBG was|be|VBD continued|continue|VBN for|for|IN 5|5|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN agitation|agitation|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 5000|5000|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD harvested|harvest|VBN after|after|IN the|the|DT addition|addition|NN of|of|IN rifampicin|rifampicin|NN -LRB-|-lrb-|-LRB- 250|250|CD μg/ml|μg/ml|NN -RRB-|-rrb-|-RRB- to|to|TO stop|stop|VB nascent|nascent|JJ transcription|transcription|NN and|and|CC quenched|quench|VBN with|with|IN stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 10|10|CD %|%|NN phenol|phenol|NN in|in|IN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT first|first|JJ timepoint|timepoint|NN was|be|VBD taken|take|VBN 3.5|3.5|CD minutes|minute|NNS after|after|IN addition|addition|NN of|of|IN the|the|DT antibiotic|antibiotic|JJ to|to|TO give|give|VB time|time|NN for|for|IN the|the|DT diffusion|diffusion|NN of|of|IN rifampicin|rifampicin|NN into|into|IN the|the|DT cells|cell|NNS and|and|CC binding|binding|NN of|of|IN the|the|DT antibiotic|antibiotic|JJ to|to|TO RNA|rna|NN polymerase|polymerase|NN .|.|. This|this|DT sample|sample|NN was|be|VBD called|call|VBN 0|0|CD minutes|minute|NNS ,|,|, and|and|CC further|further|RB samples|sample|NNS were|be|VBD taken|take|VBN at|at|IN 2.5|2.5|CD ,|,|, 5|5|CD ,|,|, 7.5|7.5|CD ,|,|, 10|10|CD ,|,|, and|and|CC 20|20|CD minutes|minute|NNS from|from|IN wild-type|wild-type|JJ E.|e.|FW coli|coli|FW and|and|CC the|the|DT RNase|rnase|NN III|iii|CD mutant|mutant|NN .|.|. A|a|DT partial|partial|JJ biological|biological|JJ replicate|replicate|VB of|of|IN wild-type|wild-type|JJ was|be|VBD taken|take|VBN -LRB-|-lrb-|-LRB- 0|0|CD ,|,|, 2.5|2.5|CD ,|,|, and|and|CC 7.5|7.5|CD minutes|minute|NNS -RRB-|-rrb-|-RRB- ,|,|, to|to|TO examine|examine|VB the|the|DT reproducibility|reproducibility|NN between|between|IN samples|sample|NNS .|.|.
Cells|cell|NNS were|be|VBD harvested|harvest|VBN and|and|CC resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN and|and|CC kept|keep|VBD in|in|IN 4C|4c|NN fridge|fridge|NN overnight|overnight|JJ .|.|. Cells|cell|NNS were|be|VBD aliquoted|aliquote|VBN into|into|IN vials|vial|NNS containing|contain|VBG around|around|IN 2x10|2x10|JJ ^|^|NN 8|8|CD cells|cell|NNS .|.|. Cells|cell|NNS in|in|IN each|each|DT vial|vial|NN were|be|VBD then|then|RB re-suspended|re-suspended|JJ in|in|IN nuclease-free|nuclease-free|JJ phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN ,|,|, incubated|incubate|VBN with|with|IN anti-E|anti-e|JJ .|.|. coli|coli|NN antibody|antibody|NN -LRB-|-lrb-|-LRB- ViroStat|virostat|NN -RRB-|-rrb-|-RRB- and|and|CC microbeads|microbead|NNS -LRB-|-lrb-|-LRB- Miltenyi|miltenyi|NN -RRB-|-rrb-|-RRB- ,|,|, followed|follow|VBN by|by|IN separation|separation|NN on|on|IN a|a|DT MACS|macs|NN separator|separator|NN -LRB-|-lrb-|-LRB- Miltenyi|Miltenyi|NNP ,|,|, Auburn|Auburn|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD degree|degree|NN C.|c.|NN Sorted|sort|VBN cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ into|into|IN RNAlater|rnalater|NN until|until|IN RNA|rna|NN extraction|extraction|NN .|.|.
Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 5,000|5,000|CD g|g|NN for|for|IN 5|5|CD min|min|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT supplier|supplier|NN 's|'s|POS protocol|protocol|NN -LRB-|-lrb-|-LRB- the|the|DT composition|composition|NN of|of|IN the|the|DT RNeasy|rneasy|NN solutions|solution|NNS are|be|VBP unknown|unknown|JJ -RRB-|-rrb-|-RRB- .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN and|and|CC 200|200|CD μl|μl|NN of|of|IN TE|TE|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|Tris|NNP ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN in|in|IN DEPC-treated|depc-treated|JJ water|water|NN ,|,|, pH|ph|NN 8|8|CD -RRB-|-rrb-|-RRB- plus|plus|CC lysosyme|lysosyme|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO resuspend|resuspend|VB the|the|DT pellet|pellet|NN .|.|. This|this|DT was|be|VBD mixed|mixed|JJ vigorously|vigorously|RB and|and|CC incubated|incubate|VBN with|with|IN intermittent|intermittent|JJ shaking|shake|VBG for|for|IN 5|5|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. Buffer|buffer|NN RLT|rlt|NN -LRB-|-lrb-|-LRB- 700|700|CD μl|μl|NN -RRB-|-rrb-|-RRB- with|with|IN β-mercaptoethanol|β-mercaptoethanol|NN -LRB-|-lrb-|-LRB- 10|10|CD μl|μl|NN of|of|IN 14.3|14.3|CD M|m|NN β-mercaptoethanol|β-mercaptoethanol|NN per|per|IN 1|1|CD ml|ml|NN RTL|rtl|NN -RRB-|-rrb-|-RRB- was|be|VBD then|then|RB added|add|VBN to|to|TO the|the|DT solution|solution|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB mixed|mix|VBN with|with|IN 500|500|CD μl|μl|NN of|of|IN absolute|absolute|JJ ethanol|ethanol|NN before|before|IN applying|apply|VBG the|the|DT solution|solution|NN to|to|TO an|a|DT RNeasy|rneasy|NN Mini|Mini|NNP column|column|NN .|.|. This|this|DT was|be|VBD then|then|RB centrifuged|centrifuge|VBN for|for|IN 15|15|CD s|s|NNS at|at|IN 8,000|8,000|CD x|x|CC g.|g.|NNP Buffer|Buffer|NNP RW1|rw1|NN -LRB-|-lrb-|-LRB- 700|700|CD μl|μl|NN -RRB-|-rrb-|-RRB- was|be|VBD applied|apply|VBN to|to|TO the|the|DT column|column|NN and|and|CC centrifuged|centrifuge|VBN to|to|TO wash|wash|VB the|the|DT RNA|rna|NN .|.|. At|at|IN this|this|DT point|point|NN an|a|DT RNase-free|rnase-free|JJ DNase|dnase|NN on-column|on-column|JJ digest|digest|VB -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- was|be|VBD carried|carry|VBN out|out|RP ,|,|, before|before|IN the|the|DT wash|wash|NN process|process|NN was|be|VBD repeated|repeat|VBN twice|twice|RB with|with|IN 500|500|CD μl|μl|NN of|of|IN RPE|rpe|NN buffer|buffer|NN .|.|. The|the|DT RNA|rna|NN was|be|VBD eluted|elute|VBN twice|twice|RB in|in|IN one|one|CD 30|30|CD μl|μl|NN volume|volume|NN of|of|IN RNase-free|rnase-free|JJ water|water|NN and|and|CC stored|store|VBD at|at|IN -70|-70|CD oC|oc|NN .|.|.
Cells|cell|NNS were|be|VBD harvested|harvest|VBN directly|directly|RB into|into|IN phenol|phenol|NN :|:|: ethanol|ethanol|NN to|to|TO stabilize|stabilize|VB RNA|rna|NN and|and|CC total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
Cells|cell|NNS were|be|VBD harvested|harvest|VBN from|from|IN aerobic|aerobic|JJ and|and|CC anaerobic|anaerobic|JJ cultures|culture|NNS of|of|IN seven|seven|CD E.|e.|FW coli|coli|FW strains|strain|NNS grown|grow|VBN to|to|TO an|a|DT OD600|od600|NN of|of|IN 0.6|0.6|CD -LRB-|-lrb-|-LRB- exponential|exponential|JJ phase|phase|NN -RRB-|-rrb-|-RRB- .|.|. Cultures|culture|NNS were|be|VBD divided|divide|VBN into|into|IN 10|10|CD ml|ml|NN aliquots|aliquot|NNS and|and|CC were|be|VBD immediately|immediately|RB mixed|mix|VBN with|with|IN 0.2|0.2|CD volumes|volume|NNS of|of|IN ice-cold|ice-cold|JJ STOP|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN ethanol|ethanol|NN ,|,|, 5|5|CD %|%|NN phenol|phenol|NN -LRB-|-lrb-|-LRB- pH|ph|NN 4.7|4.7|CD -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. After|after|IN 20|20|CD min|min|NN incubation|incubation|NN on|on|IN ice|ice|NN ,|,|, samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RP for|for|IN 10|10|CD min|min|NN at|at|IN 4|4|CD ˚C|˚c|NN and|and|CC 7000|7000|CD x|x|CC g|g|NN in|in|IN a|a|DT centrifuge|centrifuge|NN .|.|. Pellets|pellet|NNS from|from|IN one|one|CD aliquot|aliquot|NN were|be|VBD gently|gently|RB resuspended|resuspend|VBN in|in|IN RNAProtect|rnaprotect|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- to|to|TO further|further|JJ stabilize|stabilize|VB the|the|DT RNA|rna|NN .|.|. Remaining|remain|VBG samples|sample|NNS were|be|VBD mixed|mix|VBN with|with|IN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- and|and|CC placed|place|VBN at|at|IN -80|-80|CD ˚C|˚c|NN for|for|IN archival|archival|JJ storage|storage|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- and|and|CC on|on|IN column|column|NN DNase|dnase|NN treatment|treatment|NN following|follow|VBG the|the|DT manufacturers|manufacturer|NNS '|'|POS instructions|instruction|NNS .|.|. The|the|DT 23S|23s|NN and|and|CC 16S|16s|NN rRNAs|rrna|NNS were|be|VBD removed|remove|VBN by|by|IN subtractive|subtractive|JJ hybridization|hybridization|NN using|use|VBG the|the|DT MICROBExpress|microbexpress|NN kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- with|with|IN modifications|modification|NNS .|.|. Compared|compare|VBN with|with|IN the|the|DT standard|standard|JJ protocol|protocol|NN ,|,|, 50|50|CD %|%|NN more|more|JJR capture|capture|NN oligonucleotides|oligonucleotide|NNS and|and|CC magnetic|magnetic|JJ beads|bead|NNS were|be|VBD used|use|VBN .|.|. 5S|5s|NN rRNAs|rrna|NNS -LRB-|-lrb-|-LRB- 120|120|CD nt|nt|NNS in|in|IN length|length|NN -RRB-|-rrb-|-RRB- were|be|VBD removed|remove|VBN during|during|IN the|the|DT total|total|JJ RNA|rna|NN extraction|extraction|NN on|on|IN column|column|NN .|.|. Specifically|specifically|RB ,|,|, ribosomal|ribosomal|JJ depletion|depletion|NN on|on|IN total|total|JJ RNA|rna|NN isolated|isolate|VBN from|from|IN the|the|DT E.|e.|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- was|be|VBD performed|perform|VBN using|use|VBG RiboZero|RiboZero|NNP -LRB-|-lrb-|-LRB- Gram|Gram|NNP Negative|negative|JJ Bacteria|bacterium|NNS -RRB-|-rrb-|-RRB- kit|kit|NN -LRB-|-lrb-|-LRB- Epicenter|epicenter|NN ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD harvested|harvest|VBN on|on|IN days|day|NNS 1|1|CD and|and|CC 3|3|CD of|of|IN glucose|glucose|NN starvation|starvation|NN ,|,|, with|with|IN samples|sample|NNS taken|take|VBN from|from|IN the|the|DT
Cells|cell|NNS were|be|VBD harvested|harvest|VBN using|use|VBG RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- for|for|IN stabilization|stabilization|NN of|of|IN RNA|rna|NN .|.|. Stabilized|stabilize|VBN cultures|culture|NNS were|be|VBD used|use|VBN for|for|IN RNA|rna|NN isolation|isolation|NN using|use|VBG the|the|DT RNeasy|rneasy|NN MiniKit|minikit|NN system|system|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. In|in|IN brief|brief|NN ,|,|, 1|1|CD ml|ml|NN of|of|IN each|each|DT culture|culture|NN was|be|VBD used|use|VBN and|and|CC processed|process|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS including|include|VBG an|a|DT on-column|on-column|JJ DNaseI|dnasei|NN treatment|treatment|NN .|.|. RNA|rna|NN quality|quality|NN was|be|VBD assayed|assay|VBN by|by|IN denaturing|denature|VBG urea-PAGE|urea-page|NN and|and|CC by|by|IN measuring|measure|VBG the|the|DT ratio|ratio|NN of|of|IN absorption|absorption|NN at|at|IN 260/280|260/280|CD nm|nm|NN in|in|IN a|a|DT GeneQuant|GeneQuant|NNP II|II|NNP spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Amersham|amersham|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN concentration|concentration|NN was|be|VBD determined|determine|VBN by|by|IN measuring|measure|VBG UV|uv|NN light|light|NN absorption|absorption|NN at|at|IN 260|260|CD nm|nm|NN .|.|.
Cells|cell|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37C|37c|NN prior|prior|RB to|to|TO extraction|extraction|NN
Cells|cell|NNS were|be|VBD induced|induce|VBN with|with|IN arabinose|arabinose|NN or|or|CC heat|heat|NN shocked|shocked|JJ ,|,|, then|then|RB harvested|harvest|VBN and|and|CC flash|flash|VB frozen|frozen|JJ .|.|.
Cells|cell|NNS were|be|VBD inoculated|inoculate|VBN from|from|IN frozen|frozen|JJ cultures|culture|NNS into|into|IN 5|5|CD mL|ml|NN of|of|IN LB|lb|NN ,|,|, and|and|CC grown|grow|VBN .|.|. 5|5|CD µL|µl|NN of|of|IN this|this|DT overnight|overnight|JJ culture|culture|NN was|be|VBD diluted|dilute|VBN into|into|IN 5|5|CD mL|ml|NN of|of|IN LB|lb|NN with|with|IN the|the|DT appropriate|appropriate|JJ concentration|concentration|NN of|of|IN arabinose|arabinose|NN ,|,|, and|and|CC grown|grow|VBN for|for|IN 20h|20h|NN .|.|.
Cells|cell|NNS were|be|VBD inoculated|inoculate|VBN from|from|IN overnight|overnight|JJ culture|culture|NN in|in|IN rich|rich|JJ Lysogeny|lysogeny|JJ broth|broth|NN at|at|IN 37|37|CD degrees|degree|NNS in|in|IN aerobic|aerobic|JJ conditions|condition|NNS .|.|.
Cells|cell|NNS were|be|VBD inoculated|inoculate|VBN from|from|IN overnight|overnight|JJ grown|grown|JJ culture|culture|NN in|in|IN Lysogeny|Lysogeny|NNP Broth|Broth|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- and|and|CC then|then|RB harvested|harvest|VBN in|in|IN the|the|DT early|early|JJ exponential|exponential|JJ growth|growth|NN phase|phase|NN and|and|CC mid|mid|JJ exponential|exponential|JJ growth|growth|NN phase|phase|NN .|.|.
Cells|cell|NNS were|be|VBD lysed|lyse|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN ,|,|, then|then|RB samples|sample|NNS were|be|VBD taken|take|VBN for|for|IN ribosome|ribosome|NN footprint|footprint|NN extraction|extraction|NN .|.|.
Cells|cell|NNS were|be|VBD lysed|lyse|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN ,|,|, then|then|RB samples|sample|NNS were|be|VBD taken|take|VBN for|for|IN total|total|JJ RNA|rna|NN .|.|.
Cells|cell|NNS were|be|VBD lysed|lyse|VBN using|use|VBG a|a|DT bead|bead|NN beater|beater|NN -LRB-|-lrb-|-LRB- Biospec|biospec|NN -RRB-|-rrb-|-RRB- and|and|CC mRNA|mrna|NN was|be|VBD isolated|isolate|VBN using|use|VBG a|a|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
Cells|cell|NNS were|be|VBD pelleted|pelleted|JJ and|and|CC RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG a|a|DT commercially|commercially|RB available|available|JJ RNA|rna|NN extraction|extraction|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN preparations|preparation|NNS were|be|VBD then|then|RB subjected|subject|VBN to|to|TO a|a|DT DNase|dnase|NN treatment|treatment|NN to|to|TO eliminate|eliminate|VB DNA|dna|NN contamination|contamination|NN from|from|IN the|the|DT sample|sample|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. A|a|DT treatment|treatment|NN was|be|VBD also|also|RB included|include|VBN to|to|TO deplete|deplete|VB ribosomal|ribosomal|JJ RNA|rna|NN using|use|VBG a|a|DT commercially|commercially|RB available|available|JJ kit|kit|NN -LRB-|-lrb-|-LRB- MicrobExpress|MicrobExpress|NNP ,|,|, Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT two|two|CD biological|biological|JJ replicates|replicate|VBZ for|for|IN each|each|DT growth|growth|NN condition|condition|NN were|be|VBD pooled|pool|VBN for|for|IN sequencing|sequencing|NN .|.|.
Cells|cell|NNS were|be|VBD pelleted|pellete|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN RNALater|rnalater|NN -LRB-|-lrb-|-LRB- Applied|Applied|NNP Biosystems|Biosystems|NNPS -RRB-|-rrb-|-RRB- and|and|CC flash|flash|NN frozen|freeze|VBN in|in|IN ethanol-dry|ethanol-dry|JJ ice|ice|NN .|.|.
Cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN Lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10mM|10mm|NN tris|tris|NN ,|,|, 20|20|CD %|%|NN sucrose|sucrose|NN ,|,|, 50mM|50mm|NN NaCl|nacl|NN ,|,|, 10mM|10mm|NN EDTA|edta|NN ,|,|, 10mg/ml|10mg/ml|JJ lysosyme|lysosyme|NN ,|,|, 0.1|0.1|CD mg/ml|mg/ml|JJ EDTA|edta|NN ,|,|, 0.1|0.1|CD mg/ml|mg/ml|NN RNaseA|rnasea|NN -RRB-|-rrb-|-RRB- and|and|CC subsequently|subsequently|RB incubated|incubate|VBN for|for|IN 30|30|CD min|min|NN at|at|IN 37C|37c|NN .|.|. Next|next|RB ,|,|, IP|IP|NNP buffer|buffer|NN was|be|VBD added|add|VBN -LRB-|-lrb-|-LRB- 50mM|50mm|NN Hepes|hepe|NNS ,|,|, 150mM|150mm|NN NaCl|nacl|NN ,|,|, 1mM|1mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN triton|triton|NN ,|,|, 0.1|0.1|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN ,|,|, 0.1|0.1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS have|have|VBP been|be|VBN sonicated|sonicate|VBN ,|,|, centrifugated|centrifugate|VBN ,|,|, and|and|CC the|the|DT supernatent|supernatent|NN was|be|VBD used|use|VBN for|for|IN the|the|DT immunoprecipitation|immunoprecipitation|NN .|.|.
Cells|cell|NNS were|be|VBD subcultured|subculture|VBN from|from|IN overnight|overnight|JJ cultures|culture|NNS into|into|IN 20|20|CD ml|ml|NN of|of|IN LB|lb|NN media|media|NNS
Cells|cell|NNS were|be|VBD then|then|RB lysed|lyse|VBN with|with|IN 0.2|0.2|CD µM|µm|NN of|of|IN lysozyme|lysozyme|NN in|in|IN TE|TE|NNP -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-Cl|tris-cl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- for|for|IN 5|5|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN ,|,|, and|and|CC total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN contamination|contamination|NN was|be|VBD eliminated|eliminate|VBN by|by|IN treatment|treatment|NN with|with|IN TURBO|TURBO|NNP DNase|dnase|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP -RRB-|-rrb-|-RRB- .|.|. Depletion|depletion|NN of|of|IN ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD accomplished|accomplish|VBN with|with|IN the|the|DT Ribominus|Ribominus|NNP Transcriptome|Transcriptome|NNP Isolation|isolation|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP -RRB-|-rrb-|-RRB- followed|follow|VBN by|by|IN ethanol|ethanol|NN precipitation|precipitation|NN .|.|.
Cells|cell|NNS were|be|VBD then|then|RB placed|place|VBN on|on|IN ice|ice|NN and|and|CC RNAprotect|rnaprotect|NN ™|™|NN bacteria|bacterium|NNS reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO stabilize|stabilize|VB the|the|DT RNA|rna|NN .|.|. Total|total|JJ RNAs|rna|NNS of|of|IN cells|cell|NNS were|be|VBD purified|purify|VBN by|by|IN RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. Isolated|isolate|VBN RNA|rna|NN -LRB-|-lrb-|-LRB- 10|10|CD ug|ug|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN random|random|JJ primer|primer|NN cDNA|cdna|NN synthesis|synthesis|NN using|use|VBG SuperScript|SuperScript|NNP II|II|NNP reverse|reverse|JJ transcriptase|transcriptase|NN ,|,|, 18064|18064|CD --|--|: 071|071|CD -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT reaction|reaction|NN mixture|mixture|NN was|be|VBD then|then|RB subsequently|subsequently|RB treated|treat|VBN with|with|IN 1|1|CD N|n|NN NaOH|naoh|NN to|to|TO degrade|degrade|VB any|any|DT remaining|remain|VBG RNA|rna|NN and|and|CC treated|treat|VBN with|with|IN 1|1|CD N|n|NN HCl|hcl|NN to|to|TO neutralize|neutralize|VB the|the|DT NaOH|naoh|NN .|.|. Synthesized|synthesize|VBN cDNA|cdna|NN was|be|VBD then|then|RB purified|purify|VBN using|use|VBG MiniElute|MiniElute|NNP PCR|pcr|NN purification|purification|NN columns|column|NNS ,|,|, 28004|28004|CD -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. Purified|purify|VBN cDNA|cdna|NN -LRB-|-lrb-|-LRB- 3|3|CD ug|ug|NN -RRB-|-rrb-|-RRB- was|be|VBD fragmented|fragmented|JJ to|to|TO between|between|IN 50|50|CD and|and|CC 200|200|CD bps|bp|NNS by|by|IN 0.6|0.6|CD U|U|NNP /|/|: g|g|NN of|of|IN DNase|dnase|NN I|i|CD ,|,|, 27|27|CD --|--|: 0514-01|0514-01|CD -LRB-|-lrb-|-LRB- Amersham|Amersham|NNP Biosciences|Biosciences|NNP -RRB-|-rrb-|-RRB- for|for|IN 10|10|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN 1|1|CD One-Phor-All|one-phor-all|NN buffer|buffer|NN ,|,|, 27|27|CD --|--|: 0901-02|0901-02|CD -LRB-|-lrb-|-LRB- Amersham|Amersham|NNP Biosciences|Biosciences|NNP -RRB-|-rrb-|-RRB- .|.|. Heat|heat|NN inactivation|inactivation|NN of|of|IN the|the|DT DNase|dnase|NN I|i|CD enzyme|enzyme|NN was|be|VBD performed|perform|VBN at|at|IN 98|98|CD °C|°c|NN for|for|IN 10|10|CD min|min|NN .|.|.
Cells|cell|NNS were|be|VBD transferred|transfer|VBN to|to|TO the|the|DT fresh|fresh|JJ minimal|minimal|JJ media|media|NNS ,|,|, mM63|mm63|NN ,|,|, in|in|IN the|the|DT presence|presence|NN or|or|CC absence|absence|NN of|of|IN histidine|histidine|NN .|.|. The|the|DT initial|initial|JJ cell|cell|NN concentrations|concentration|NNS were|be|VBD controlled|control|VBN as|as|IN 104-105|104-105|CD cells/mL|cells/ml|NN ,|,|, and|and|CC the|the|DT final|final|JJ ones|one|NNS ~|~|VBP 108|108|CD cells/mL|cells/ml|NN within|within|IN the|the|DT exponential|exponential|JJ growth|growth|NN phase|phase|NN .|.|.
Cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN a|a|DT stop|stop|NN solution|solution|NN of|of|IN phenol|phenol|NN and|and|CC ethanol|ethanol|NN -LRB-|-lrb-|-LRB- Khodursky|Khodursky|NNP et|et|FW al|al|FW ,|,|, Methods|method|NNS in|in|IN Molecular|molecular|JJ Biology|Biology|NNP 2003|2003|CD -RRB-|-rrb-|-RRB- ,|,|, spun|spin|VBD down|down|RP ,|,|, and|and|CC flash|flash|NN frozen|frozen|JJ and|and|CC stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN a|a|DT stop|stop|NN solution|solution|NN of|of|IN Phenol|phenol|NN and|and|CC Ethanol|ethanol|NN ,|,|, spun|spin|VBD down|down|RB and|and|CC flash|flash|VB frozen|frozen|JJ and|and|CC stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN -LRB-|-lrb-|-LRB- ref|ref|NN -RRB-|-rrb-|-RRB- .|.|. Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG a|a|DT hot|hot|JJ phenol|phenol|NN method|method|NN -LRB-|-lrb-|-LRB- ref|ref|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN quality|quality|NN was|be|VBD determined|determine|VBN by|by|IN analysis|analysis|NN with|with|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD bioanalyzer|bioanalyzer|NN and|and|CC quantity|quantity|NN was|be|VBD determined|determine|VBN using|use|VBG a|a|DT NanoDrop|NanoDrop|NNP .|.|. To|to|TO enrich|enrich|VB for|for|IN mRNA|mrna|NN ,|,|, the|the|DT 23S|23s|NN and|and|CC 16S|16s|NN rRNA|rrna|NN were|be|VBD removed|remove|VBN using|use|VBG the|the|DT Ambion|Ambion|NNP MICROBExpress|MICROBExpress|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS guidelines|guideline|NNS ,|,|, except|except|IN the|the|DT total|total|JJ RNA|rna|NN was|be|VBD incubated|incubate|VBN with|with|IN the|the|DT rRNA|rrna|NN oligonucleotides|oligonucleotide|NNS for|for|IN one|one|CD hour|hour|NN instead|instead|RB of|of|IN 15|15|CD minutes|minute|NNS .|.|.
Cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN rifampicin|rifampicin|NN before|before|IN sample|sample|NN collection|collection|NN .|.|. In|in|IN some|some|DT cases|case|NNS ,|,|, kasugamycin|kasugamycin|NN was|be|VBD added|add|VBN 15|15|CD minutes|minute|NNS before|before|IN the|the|DT rifampicin|rifampicin|NN addition|addition|NN .|.|.
cell|cell|NN type|type|NN :|:|: Ancestral|ancestral|JJ I|I|PRP -|-|: cells|cell|NNS
cell|cell|NN type|type|NN :|:|: Ancestral|ancestral|JJ L|l|NN -|-|: cells|cell|NNS
cell|cell|NN type|type|NN :|:|: bacterial|bacterial|JJ cells|cell|NNS
cell|cell|NN type|type|NN :|:|: bacterial|bacterial|JJ liquid|liquid|JJ culture|culture|NN
cell|cell|NN type|type|NN :|:|: biofilm|biofilm|NN
cell|cell|NN type|type|NN :|:|: Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN
cell|cell|NN type|type|NN :|:|: Evolved|evolve|VBN I|I|PRP -|-|: cells|cell|NNS
cell|cell|NN type|type|NN :|:|: Evolved|evolve|VBN L|l|NN -|-|: cells|cell|NNS
cell|cell|NN type|type|NN :|:|: Original|original|JJ prototroph|prototroph|NN DH1|dh1|NN cells|cell|NNS
cell|cell|NN type|type|NN :|:|: Persister|persister|NN cells|cell|NNS
cell|cell|NN type|type|NN :|:|: Planktonic|planktonic|JJ cells|cell|NNS harvested|harvest|VBN at|at|IN a|a|DT turbidity|turbidity|NN of|of|IN 0.5|0.5|CD at|at|IN 600|600|CD nm|nm|NN ,|,|, adjusted|adjust|VBN to|to|TO the|the|DT turbidity|turbidity|NN at|at|IN 1|1|CD ,|,|, and|and|CC then|then|RB exposed|expose|VBN to|to|TO 20|20|CD μg/mL|μg/ml|NN ampicillin|ampicillin|NN for|for|IN 1|1|CD h.|h.|NN
Cell|cell|NN were|be|VBD grown|grow|VBN in|in|IN 3-liter|3-liter|NN stirred|stir|VBD tank|tank|NN bioreactor|bioreactor|NN anaerobically|anaerobically|RB .|.|. The|the|DT growth|growth|NN medium|medium|NN contained|contain|VBD Na2H2PO4|na2h2po4|NN -LRB-|-lrb-|-LRB- 1.1|1.1|CD g/l|g/l|NN -RRB-|-rrb-|-RRB- ,|,|, K2HPO4|k2hpo4|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD g/l|g/l|NN -RRB-|-rrb-|-RRB- ,|,|, -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2SO4|2so4|NN -LRB-|-lrb-|-LRB- 9.0|9.0|CD g/l|g/l|NN -RRB-|-rrb-|-RRB- ,|,|, Glucose|glucose|NN -LRB-|-lrb-|-LRB- 15.0|15.0|CD g/l|g/l|NN -RRB-|-rrb-|-RRB- ,|,|, CaCl2|cacl2|NN -LRB-|-lrb-|-LRB- 2.2|2.2|CD mg/l|mg/l|NN -RRB-|-rrb-|-RRB- ,|,|, MgSO4|mgso4|NN -LRB-|-lrb-|-LRB- 0.55|0.55|CD g/l|g/l|NN -RRB-|-rrb-|-RRB- ,|,|, NaH2-Citrate|nah2-citrate|NN -LRB-|-lrb-|-LRB- 234|234|CD mg/l|mg/l|NN -RRB-|-rrb-|-RRB- ,|,|, FeCl3|fecl3|NN *|*|SYM 6|6|CD H2O|h2o|NN -LRB-|-lrb-|-LRB- 25.0|25.0|CD mg/l|mg/l|NN -RRB-|-rrb-|-RRB- ,|,|, ZnSO4|znso4|NN *|*|SYM 7|7|CD H2O|h2o|NN -LRB-|-lrb-|-LRB- 0.18|0.18|CD mg/l|mg/l|NN -RRB-|-rrb-|-RRB- ,|,|, MnSO4|mnso4|NN *|*|SYM 7|7|CD H2O|h2o|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mg/l|mg/l|NN -RRB-|-rrb-|-RRB- ,|,|, CuSO4|cuso4|NN *|*|SYM 5|5|CD H2O|h2o|NN -LRB-|-lrb-|-LRB- 0.16|0.16|CD mg/l|mg/l|NN -RRB-|-rrb-|-RRB- ,|,|, CoCl2|cocl2|NN *|*|SYM 6|6|CD H2O|h2o|NN -LRB-|-lrb-|-LRB- 0.18|0.18|CD mg/l|mg/l|NN -RRB-|-rrb-|-RRB- .|.|.
CF104|cf104|NN .3.3|.3.3|CD _|_|NN u1|u1|NN
CF104|cf104|NN .3.3|.3.3|CD _|_|NN u7|u7|NN
CF104|cf104|NN .3.3|.3.3|CD _|_|NN y2|y2|NN
CF104|cf104|NN .3.3|.3.3|CD _|_|NN y9|y9|NN
CF108|cf108|NN .4|.4|NN B|b|NN _|_|CD u1|u1|NN
CF108|cf108|NN .4|.4|NN B|b|NN _|_|CD u2|u2|NN
CF108|cf108|NN .4|.4|NN B|b|NN _|_|CD y3|y3|NN
CF108|cf108|NN .4|.4|NN B|b|NN _|_|CD y8|y8|NN
CFT073|cft073|NN in|in|IN K-med|k-med|JJ
CFT073|cft073|NN in|in|IN LB|LB|NNP ,|,|, after|after|IN 5|5|CD hours|hour|NNS of|of|IN growth|growth|NN .|.|.
CFT073|cft073|NN in|in|IN LB+PAC|lb+pac|NN s|s|NNS -LRB-|-lrb-|-LRB- 100|100|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- ,|,|, after|after|IN 5|5|CD hours|hour|NNS of|of|IN growth|growth|NN .|.|.
CFT073|cft073|NN in|in|IN NaCl|nacl|NN
CFT073|cft073|NN in|in|IN urea|urea|NN
CFT073|cft073|NN K-med|k-med|JJ biological|biological|JJ rep|rep|NN 1|1|CD
CFT073|cft073|NN K-med|k-med|JJ biological|biological|JJ rep|rep|NN 2|2|CD
CFT073|cft073|NN K-med|k-med|JJ biological|biological|JJ rep|rep|NN 3|3|CD
CFT073|cft073|NN _|_|CD LB+PAC|lb+pac|NN s|s|NNS _|_|VBP rep1|rep1|NN
CFT073|cft073|NN _|_|CD LB+PAC|lb+pac|NN s|s|NNS _|_|VBP rep2|rep2|NN
CFT073|cft073|NN _|_|CD LB+PAC|lb+pac|NN s|s|NNS _|_|VBP rep3|rep3|NN
CFT073|cft073|NN _|_|CD LB|lb|NN _|_|CD rep1|rep1|NN
CFT073|cft073|NN _|_|CD LB|lb|NN _|_|CD rep2|rep2|NN
CFT073|cft073|NN _|_|CD LB|lb|NN _|_|CD rep3|rep3|NN
CFT073|cft073|NN NaCl|nacl|NN biological|biological|JJ rep|rep|NN 1|1|CD
CFT073|cft073|NN NaCl|nacl|NN biological|biological|JJ rep|rep|NN 2|2|CD
CFT073|cft073|NN NaCl|nacl|NN biological|biological|JJ rep|rep|NN 3|3|CD
CFT073|cft073|NN +|+|CC pBAD|pbad|NN rep|rep|NN 1|1|CD
CFT073|cft073|NN +|+|CC pBAD|pbad|NN rep|rep|NN 2|2|CD
CFT073|cft073|NN +|+|CC pBAD|pbad|NN rep|rep|NN 3|3|CD
CFT073|cft073|NN +|+|CC pBAD-tosR|pbad-tosr|NN rep|rep|NN 1|1|CD
CFT073|cft073|NN +|+|CC pBAD-tosR|pbad-tosr|NN rep|rep|NN 2|2|CD
CFT073|cft073|NN +|+|CC pBAD-tosR|pbad-tosr|NN rep|rep|NN 3|3|CD
CFT073|cft073|NN urea|urea|NN biological|biological|JJ rep|rep|NN 1|1|CD
CFT073|cft073|NN urea|urea|NN biological|biological|JJ rep|rep|NN 2|2|CD
CFT073|cft073|NN urea|urea|NN biological|biological|JJ rep|rep|NN 3|3|CD
Cfx|Cfx|NNP _|_|NNP IN|in|IN _|_|CD 10mkM|10mkm|NN _|_|NN 3|3|CD
Cfx|Cfx|NNP _|_|NNP IN|in|IN _|_|SYM Mu|mu|FW _|_|FW 10mkM|10mkm|NN _|_|NN 1|1|CD
Cfx|Cfx|NNP _|_|NNP IN|in|IN _|_|SYM Mu|mu|FW _|_|FW 10mkM|10mkm|NN _|_|NN 2|2|CD
Cfx|Cfx|NNP _|_|NNP IP|IP|NNP _|_|NNP 10mkM|10mkM|NNP _|_|SYM 3|3|CD
Cfx|Cfx|NNP _|_|NNP IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 10mkM|10mkm|NN _|_|NN 1|1|CD
Cfx|Cfx|NNP _|_|NNP IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 10mkM|10mkm|NN _|_|NN 2|2|CD
CGATGT-D2|cgatgt-d2|NN
CH3COOH|ch3cooh|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.9|5.9|CD ±|±|SYM 0.05|0.05|CD -RRB-|-rrb-|-RRB- ;|;|: HCl|hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 4.75|4.75|CD ±|±|SYM 0.05|0.05|CD -RRB-|-rrb-|-RRB- ;|;|: NaOH|naoh|NN -LRB-|-lrb-|-LRB- pH|ph|NN 9.6|9.6|CD ±|±|SYM 0.05|0.05|CD -RRB-|-rrb-|-RRB- ;|;|: EtOH|etoh|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN -RRB-|-rrb-|-RRB- ;|;|: NaCl|nacl|NN -LRB-|-lrb-|-LRB- 4.5|4.5|CD %|%|NN -RRB-|-rrb-|-RRB- ;|;|: Glycerol|glycerol|NN -LRB-|-lrb-|-LRB- 15|15|CD %|%|NN -RRB-|-rrb-|-RRB- ;|;|: BC|bc|NN -LRB-|-lrb-|-LRB- 7|7|CD and|and|CC 9|9|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- ;|;|: EtBr|etbr|NN -LRB-|-lrb-|-LRB- 150|150|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- ;|;|: 46|46|CD °C|°c|NN ;|;|: 15|15|CD °C|°c|NN
CH3COOH|ch3cooh|NN replicate|replicate|VBP 1|1|CD
CH3COOH|ch3cooh|NN replicate|replicate|VBP 2|2|CD
CH3COOH|ch3cooh|NN replicate|replicate|VBP 3|3|CD
channel|channel|NN 1|1|CD
Channel|Channel|NNP 1|1|CD
Chemostat|chemostat|NN 1|1|CD h|h|NN irradiated|irradiated|JJ
Chemostat|chemostat|NN 1h|1h|NN irradiated|irradiated|JJ
Chemostat|chemostat|NN 50|50|CD h|h|NN irradiated|irradiated|JJ
chemostat|chemostat|NN ,|,|, specific|specific|JJ growth|growth|NN rate|rate|NN 0.51|0.51|CD 1/h|1/h|JJ
chemostat|chemostat|NN STR|str|NN culture|culture|NN
chemostat|chemostat|NN STR|str|NN culture|culture|NN STR|str|NN reference|reference|NN 1|1|CD ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR|str|NN culture|culture|NN STR|str|NN reference|reference|NN 1|1|CD ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR|str|NN culture|culture|NN STR|str|NN reference|reference|NN 2|2|CD ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR|str|NN culture|culture|NN STR|str|NN reference|reference|NN 2|2|CD ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR|str|NN culture|culture|NN STR|str|NN reference|reference|NN 3|3|CD ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR|str|NN culture|culture|NN STR|str|NN reference|reference|NN 3|3|CD ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P1|p1|NN 120|120|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P1|p1|NN 120|120|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P1|p1|NN 25|25|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P1|p1|NN 25|25|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P1|p1|NN 28h|28h|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P1|p1|NN 28h|28h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P3|p3|NN 120|120|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P3|p3|NN 120|120|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P3|p3|NN 25|25|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P3|p3|NN 25|25|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P3|p3|NN 28h|28h|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P3|p3|NN 28h|28h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 10|10|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 10|10|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 120|120|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 120|120|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 210|210|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 210|210|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 25h|25h|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 25h|25h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 25|25|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 25|25|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 26h|26h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 28h|28h|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 28h|28h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 330|330|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 45|45|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 45|45|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 5|5|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 5|5|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN PFR|pfr|NN P5|p5|NN 75|75|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 10|10|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 10|10|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 120|120|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 120|120|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 210|210|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 210|210|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 25h|25h|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 25h|25h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 25|25|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 25|25|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 26h|26h|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 26h|26h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 28h|28h|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 28h|28h|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 330|330|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 330|330|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 45|45|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 45|45|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 5|5|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 5|5|CD min|min|NN ,|,|, rep2|rep2|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 75|75|CD min|min|NN ,|,|, rep1|rep1|NN
chemostat|chemostat|NN STR-PFR|str-pfr|NN culture|culture|NN STR|str|NN 75|75|CD min|min|NN ,|,|, rep2|rep2|NN
chilled|chill|VBN in|in|IN a|a|DT dry|dry|JJ ice/ethanol|ice/ethanol|NN .|.|. bath|bath|NN .|.|. After|after|IN homogenization|homogenization|NN with|with|IN glass|glass|NN beads|bead|NNS ,|,|, .|.|. RNA|rna|NN was|be|VBD
chip|chip|NN antibody|antibody|NN :|:|: 9E10|9e10|NN Myc|myc|NN tag|tag|NN antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-b|anti-b|JJ -LRB-|-lrb-|-LRB- RNAP|rnap|NN -RRB-|-rrb-|-RRB- NT63|nt63|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-c-myc|anti-c-myc|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-FecI|anti-feci|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-Flag|anti-flag|JJ
chip|chip|NN antibody|antibody|NN :|:|: anti-FLAG|anti-flag|JJ antibody|antibody|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Cat|Cat|NNP #|#|# :|:|: F3165-1MG|f3165-1mg|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: antiFlag|antiflag|NN M2|m2|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-Flag|anti-flag|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: Anti-FLAG|anti-flag|NN -LRB-|-lrb-|-LRB- sigma-aldrich|sigma-aldrich|JJ cat|cat|NN no|no|DT F3165|f3165|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: anti-H-NS|anti-h-ns|JJ
chip|chip|NN antibody|antibody|NN :|:|: anti-myc|anti-myc|JJ
chip|chip|NN antibody|antibody|NN :|:|: Anti-myc|anti-myc|NN -LRB-|-lrb-|-LRB- 9E10|9e10|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Santa|Santa|NNP Cruz|Cruz|NNP ,|,|, Dallas|Dallas|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: anti-myc|anti-myc|JJ -LRB-|-lrb-|-LRB- Santa|Santa|NNP Cruz|Cruz|NNP Biotech|Biotech|NNP ,|,|, sc-28207|sc-28207|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: anti-RecA|anti-reca|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-RpoB|anti-rpob|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-RpoB|anti-rpob|NN -LRB-|-lrb-|-LRB- Neoclone|Neoclone|NNP ,|,|, WP002|wp002|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: anti-rpoB|anti-rpob|NN -LRB-|-lrb-|-LRB- Santa|Santa|NNP Cruz|Cruz|NNP Biotech|Biotech|NNP ,|,|, sc-56766|sc-56766|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: anti-RpoD|anti-rpod|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-RpoF|anti-rpof|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-RpoN|anti-rpon|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-RpoS|anti-rpos|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: anti-RpoS|anti-rpos|NN -LRB-|-lrb-|-LRB- neoclone|neoclone|NN ,|,|, WP009|wp009|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: biotin|biotin|NN conjugated|conjugate|VBN anti-c-myc|anti-c-myc|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN cat|cat|NN .|.|. #|#|# :|:|: ab63797|ab63797|CD
chip|chip|NN antibody|antibody|NN cat|cat|NN .|.|. #|#|# :|:|: sc-28207|sc-28207|JJ
chip|chip|NN antibody|antibody|NN cat|cat|NN .|.|. #|#|# :|:|: W0002|w0002|NN
chip|chip|NN antibody|antibody|NN :|:|: c-Myc|c-myc|NN Antibody|antibody|NN -LRB-|-lrb-|-LRB- 9E10|9e10|NN -RRB-|-rrb-|-RRB- ,|,|, Santa|Santa|NNP Cruz|Cruz|NNP Biotech|Biotech|NNP ,|,|, sc-40|sc-40|JJ
chip|chip|NN antibody|antibody|NN :|:|: Custom|Custom|NNP anti-Fur|anti-fur|JJ polyclonal|polyclonal|JJ antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: E.|e.|FW coli|coli|FW CRP|crp|NN Monoclonal|monoclonal|JJ Antibody|antibody|NN ,|,|, Neoclone|neoclone|NN ,|,|, #N0004|#n0004|NN
chip|chip|NN antibody|antibody|NN :|:|: E.|e.|FW coli|coli|FW RNA|rna|NN Sigma|Sigma|NNP 70|70|CD Monoclonal|monoclonal|JJ Antibody|antibody|NN ,|,|, Neoclone|neoclone|NN ,|,|, #WP004|#wp004|NN
chip|chip|NN antibody|antibody|NN :|:|: FLAG|flag|NN antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: HRP-conjugated|hrp-conjugated|JJ sheep|sheep|NN anti-mouse|anti-mouse|JJ IgG|igg|NN
chip|chip|NN antibody|antibody|NN manufacturer/lot|manufacturer/lot|NN #|#|# :|:|: Sigma-Aldrich|Sigma-Aldrich|NNP ,|,|, M8823-1ML|m8823-1ml|NN ,|,|, Lot|lot|NN #|#|# SLBD7244V|slbd7244v|NN
chip|chip|NN antibody|antibody|NN manufacturer|manufacturer|NN :|:|: Upstate|upstate|JJ
chip|chip|NN antibody|antibody|NN :|:|: Monoclonal|monoclonal|JJ anti-FLAG|anti-flag|JJ antibody|antibody|NN ,|,|, Murine|murine|JJ IgG|igg|NN
chip|chip|NN antibody|antibody|NN :|:|: Monoclonal|monoclonal|JJ ANTI-FLAG|anti-flag|NN M5|m5|NN -LRB-|-lrb-|-LRB- Sigma-Aldrich|Sigma-Aldrich|NNP ,|,|, catalog|catalog|NN number|number|NN :|:|: F4042|f4042|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: none|none|NN
chip|chip|NN antibody|antibody|NN :|:|: None|none|NN
chip|chip|NN antibody|antibody|NN :|:|: none|none|NN ,|,|, input|input|NN
chip|chip|NN antibody|antibody|NN :|:|: normal|normal|JJ mouse|mouse|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Upstate|upstate|JJ -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: normal|normal|JJ rabbit|rabbit|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Upstate|upstate|JJ Biotechnology|biotechnology|NN ,|,|, Cat|cat|NN .|.|. no.|no.|RB 12-370|12-370|CD -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: RNAP|rnap|NN beta|beta|NN subunit|subunit|NN antibody|antibody|NN
chip|chip|NN antibody|antibody|NN :|:|: RNA|rna|NN polymerase|polymerase|NN subunit|subunit|NN β|β|NN
chip|chip|NN antibody|antibody|NN :|:|: RpoS|rpos|NN -LRB-|-lrb-|-LRB- Neoclone|neoclone|JJ cat|cat|NN .|.|. no|no|DT .|.|. WP009|wp009|NN -RRB-|-rrb-|-RRB-
chip|chip|NN antibody|antibody|NN :|:|: SeqA|seqa|NN
chip|chip|NN antibody|antibody|NN vendor|vendor|NN :|:|: Abcam|Abcam|NNP
chip|chip|NN antibody|antibody|NN vendor|vendor|NN :|:|: Amersham|Amersham|NNP Biosciences|Biosciences|NNP
chip|chip|NN antibody|antibody|NN vendor|vendor|NN :|:|: Neoclone|Neoclone|NNP
chip|chip|NN antibody|antibody|NN vendor|vendor|NN :|:|: Santa|Santa|NNP Cruz|Cruz|NNP Biotech|Biotech|NNP
chip|chip|NN antibody|antibody|NN vendor|vendor|NN :|:|: Santa|Santa|NNP Cruz|Cruz|NNP Biotechnology|Biotechnology|NNP
chip|chip|NN antibody|antibody|NN :|:|: σ32|σ32|NN
chip-ArcA|chip-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 1|1|CD
chip-ArcA|chip-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 2|2|CD
chip-ArcA|chip-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 3|3|CD
chip-ArcA|chip-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 1|1|CD
chip-ArcA|chip-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 2|2|CD
chip-ArcA|chip-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 3|3|CD
Chipchip|chipchip|NN BW25113/pBAD-Myc-His|bw25113/pbad-myc-his|NN C|c|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 0.5|0.5|CD %|%|NN L-arabinose|l-arabinose|JJ suspension|suspension|NN cell|cell|NN
Chipchip|chipchip|NN BW25113/pBAD-Myc-His|bw25113/pbad-myc-his|NN C-mqsA|c-mqsa|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 0.5|0.5|CD %|%|NN L-arabinose|l-arabinose|JJ suspension|suspension|NN cell|cell|NN
Chipchip|chipchip|NN BW25113/pCA24N|bw25113/pca24n|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 2|2|CD mM|mm|NN IPTG|iptg|NN biofilm|biofilm|NN cell|cell|NN
Chipchip|chipchip|NN BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 2|2|CD mM|mm|NN IPTG|iptg|NN biofilm|biofilm|NN cell|cell|NN
ChIP|chip|NN DNA|dna|NN from|from|IN MG1655|mg1655|NN _|_|CD PhoB|phob|NN _|_|CD FLAG|flag|NN
ChIP|chip|NN DNA|dna|NN from|from|IN MG1655|mg1655|NN wild|wild|JJ type|type|NN strain|strain|NN
ChIPExo-ArcA|chipexo-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 1|1|CD _|_|NN anti-myc|anti-myc|JJ
ChIPExo-ArcA|chipexo-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 2|2|CD _|_|SYM anti-myc|anti-myc|JJ
ChIPExo-ArcA|chipexo-arca|NN _|_|CD ArcA8myc|arca8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 3|3|CD _|_|NN anti-myc|anti-myc|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr1delAr2|delar1delar2|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr1delAr2|delar1delar2|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr1delAr2|delar1delar2|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr1|delar1|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr1|delar1|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr1|delar1|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr2|delar2|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr2|delar2|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delAr2|delar2|NN _|_|CD glycerol|glycerol|NN _|_|NN NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delta-crp|delta-crp|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delta-crp|delta-crp|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN delta-crp|delta-crp|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|CD anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|CD anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 4|4|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|SYM O2|o2|CD _|_|SYM 5|5|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|CD anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|CD anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|CD anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|CD anti-crp|anti-crp|JJ _|_|NN rif|rif|NN
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|CD anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|CD anti-crp|anti-crp|JJ _|_|NN rif|rif|NN
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-crp|anti-crp|JJ _|_|NN rif|rif|NN
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 4|4|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|SYM O2|o2|CD _|_|SYM 5|5|CD _|_|SYM anti-crp|anti-crp|JJ
ChIPExo-Crp|chipexo-crp|JJ _|_|NN wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 6|6|CD _|_|NN anti-crp|anti-crp|JJ
ChIPExo-Fnr|chipexo-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 1|1|CD _|_|CD anti-myc|anti-myc|JJ
ChIPExo-Fnr|chipexo-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 2|2|CD _|_|CD anti-myc|anti-myc|JJ
ChIPExo-Fnr|chipexo-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 3|3|CD _|_|NN anti-myc|anti-myc|JJ
ChIP-exo|ChIP-exo|NNP GadE|GadE|NNP pH5|ph5|NN .5|.5|CD 1|1|CD
ChIP-exo|ChIP-exo|NNP GadE|GadE|NNP pH5|ph5|NN .5|.5|CD 2|2|CD
ChIP-exo|chip-exo|JJ GadW|gadw|NN pH5|ph5|NN .5|.5|CD 1|1|CD
ChIP-exo|chip-exo|JJ GadW|gadw|NN pH5|ph5|NN .5|.5|CD 2|2|CD
ChIP-exo|chip-exo|JJ GadX|gadx|NN pH5|ph5|NN .5|.5|CD 1|1|CD
ChIP-exo|chip-exo|JJ GadX|gadx|NN pH5|ph5|NN .5|.5|CD 2|2|CD
ChIP-exo|chip-exo|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT ASM584v2|asm584v2|NN genome|genome|NN reference|reference|NN sequence|sequence|NN using|use|VBG using|use|VBG bowtie|bowtie|NN v1|v1|NN .0.0|.0.0|CD with|with|IN parameters|parameter|NNS -|-|: S|s|NN
ChIP-exo|chip-exo|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT NC|NC|NNP _|_|SYM 000913|000913|CD genome|genome|NN reference|reference|NN sequence|sequence|NN using|use|VBG using|use|VBG bowtie|bowtie|NN v1|v1|NN .0.0|.0.0|CD with|with|IN parameters|parameter|NNS -|-|: S|s|NN
ChIP-exo|chip-exo|NN reads|read|VBZ were|be|VBD aligned|align|VBN using|use|VBG BWA|bwa|NN with|with|IN default|default|NN parameters|parameter|NNS
ChIPExo-RpoD|chipexo-rpod|JJ _|_|NN wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|NN anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|SYM anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|NN anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|SYM anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD _|_|NN anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD _|_|SYM anti-rpod|anti-rpod|JJ
ChIPExo-RpoD|chipexo-rpod|NN _|_|CD wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD _|_|NN anti-rpod|anti-rpod|JJ
ChIP-exo|chip-exo|NN RpoS|rpos|NN pH5|ph5|NN .5|.5|CD 1|1|CD
ChIP-exo|chip-exo|JJ RpoS|rpos|NN pH5|ph5|NN .5|.5|CD 2|2|CD
chip-Fnr|chip-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 1|1|CD
chip-Fnr|chip-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 2|2|CD
chip-Fnr|chip-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|NN anaerobic|anaerobic|JJ _|_|NN 3|3|CD
chip-Fnr|chip-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 1|1|CD
chip-Fnr|chip-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 2|2|CD
chip-Fnr|chip-fnr|JJ _|_|NN Fnr8myc|fnr8myc|NN _|_|NN glucose|glucose|NN _|_|CD NH4CL|nh4cl|NN _|_|CD NO3|no3|NN _|_|NN 3|3|CD
ChIP|chip|NN _|_|CD hns-F|hns-f|NN _|_|SYM bcm|bcm|SYM -|-|: #|#|# 1|1|CD
ChIP|chip|NN _|_|CD hns-F|hns-f|NN _|_|CD bcm|bcm|NN +|+|CC #|#|# 1|1|CD
ChIP|chip|NN _|_|CD hns-F|hns-f|NN _|_|SYM bcm|bcm|SYM -|-|: #|#|# 2|2|CD
ChIP|chip|NN _|_|SYM hns-F|hns-f|JJ _|_|NN bcm|bcm|NN +|+|CC #|#|# 2|2|CD
ChIP-Seq|chip-seq|JJ
ChIP-seq|chip-seq|NN experiments|experiment|NNS were|be|VBD performed|perform|VBN in|in|IN duplicate|duplicate|VB using|use|VBG similar|similar|JJ growth|growth|NN condition|condition|NN and|and|CC protocols|protocol|NNS for|for|IN chromatin|chromatin|NN immunoprecipitation|immunoprecipitation|NN .|.|. The|the|DT first|first|JJ experiment|experiment|NN was|be|VBD done|do|VBN in|in|IN the|the|DT Centre|Centre|NNP for|for|IN Genomic|genomic|JJ Regulation|regulation|NN -LRB-|-lrb-|-LRB- CRG|crg|NN ,|,|, Barcelona|Barcelona|NNP ,|,|, Spain|Spain|NNP -RRB-|-rrb-|-RRB- ,|,|, while|while|IN the|the|DT second|second|JJ one|one|CD in|in|IN the|the|DT Immanuel|Immanuel|NNP Kant|Kant|NNP Baltic|Baltic|NNP Federal|Federal|NNP University|University|NNP -LRB-|-lrb-|-LRB- Kaliningrad|Kaliningrad|NNP ,|,|, Russia|Russia|NNP -RRB-|-rrb-|-RRB- .|.|. In|in|IN both|both|DT cases|case|NNS ,|,|, bacterial|bacterial|JJ cells|cell|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN until|until|IN OD600|od600|NN ~|~|NN 0.6|0.6|CD were|be|VBD treated|treat|VBN with|with|IN formaldehyde|formaldehyde|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD %|%|NN ,|,|, 20|20|CD min|min|NN incubation|incubation|NN -RRB-|-rrb-|-RRB- .|.|. Cross-linking|cross-linking|NN was|be|VBD stopped|stop|VBN with|with|IN glycine|glycine|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN of|of|IN 450|450|CD mM|mm|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN 5|5|CD minutes|minute|NNS of|of|IN incubation|incubation|NN the|the|DT cells|cell|NNS were|be|VBD pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 14,000|14,000|CD rpm|rpm|NN for|for|IN 15|15|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- +4|+4|CD °C|°c|NN -RRB-|-rrb-|-RRB- ,|,|, washed|wash|VBN twice|twice|RB with|with|IN 5|5|CD ml|ml|NN of|of|IN PBS|PBS|NNP and|and|CC resuspended|resuspend|VBN in|in|IN 1.3|1.3|CD ml|ml|NN of|of|IN ice-cold|ice-cold|JJ immunoprecipitation|immunoprecipitation|NN buffer|buffer|NN prepared|prepare|VBN from|from|IN 50|50|CD ml|ml|NN of|of|IN buffer|buffer|NN containing|contain|VBG 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.1|8.1|CD -RRB-|-rrb-|-RRB- ,|,|, 5|5|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.2|0.2|CD %|%|NN NaN3|nan3|NN ,|,|, 0.5|0.5|CD %|%|NN SDS|sds|NN ,|,|, and|and|CC 25|25|CD ml|ml|NN of|of|IN buffer|buffer|NN containing|contain|VBG 100|100|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.6|8.6|CD -RRB-|-rrb-|-RRB- ;|;|: 100|100|CD mM|mm|NN NaCl|nacl|NN ;|;|: 5|5|CD mM|mm|NN EDTA|edta|NN ;|;|: 0,2|0,2|CD %|%|NN NaN3|nan3|NN ,|,|, 5|5|CD %|%|NN Triton-X-100|triton-x-100|NN .|.|. Then|then|RB phenylmethylsulfonyl|phenylmethylsulfonyl|NN fluoride|fluoride|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB- or|or|CC 20|20|CD μl|μl|NN of|of|IN Protease|protease|NN Inhibitor|inhibitor|NN Cocktail|cocktail|NN -LRB-|-lrb-|-LRB- PIC|pic|NN ,|,|, Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- for|for|IN the|the|DT first|first|JJ and|and|CC the|the|DT second|second|JJ experiment|experiment|NN ,|,|, respectively|respectively|RB ,|,|, were|be|VBD added|add|VBN followed|follow|VBN by|by|IN incubation|incubation|NN for|for|IN 30|30|CD min|min|NN at|at|IN +4|+4|CD °C|°c|NN .|.|.
ChIP-seq|chip-seq|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS
ChIP-seq|ChIP-seq|NNP libraries|library|NNS were|be|VBD prepared|prepare|VBN from|from|IN 5-10|5-10|CD ng|ng|NN of|of|IN the|the|DT DNA|dna|NN samples|sample|NNS with|with|IN the|the|DT NebNext|NebNext|NNP ®|®|SYM Ultra|ultra|FW ™|™|FW DNA|dna|NN Library|Library|NNP Prep|Prep|NNP Kit|kit|NN for|for|IN Illumina|Illumina|NNP -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP ,|,|, MA|MA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. For|for|IN the|the|DT final|final|JJ amplification|amplification|NN of|of|IN the|the|DT library|library|NN 15|15|CD PCR|pcr|NN cycles|cycle|NNS were|be|VBD used|use|VBN .|.|. Size|size|NN distribution|distribution|NN and|and|CC concentration|concentration|NN of|of|IN the|the|DT amplicons|amplicon|NNS was|be|VBD checked|check|VBN on|on|IN the|the|DT Bioanalyzer|Bioanalyzer|NNP 2100|2100|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. In|in|IN the|the|DT first|first|JJ experiment|experiment|NN ,|,|, the|the|DT maximum|maximum|NN was|be|VBD at|at|IN about|about|IN 300|300|CD bp|bp|NN ,|,|, and|and|CC ChIP|chip|NN libraries|library|NNS were|be|VBD sequenced|sequence|VBN using|use|VBG 50|50|CD nt|nt|NNS single-end|single-end|JJ read|read|NN protocol|protocol|NN on|on|IN the|the|DT Illumina|Illumina|NNP HiSeq|hiseq|NN system|system|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- of|of|IN the|the|DT Genomics|Genomics|NNP Facility|Facility|NNP in|in|IN the|the|DT Centre|Centre|NNP for|for|IN Genomic|genomic|JJ Regulation|regulation|NN -LRB-|-lrb-|-LRB- Barcelona|Barcelona|NNP -RRB-|-rrb-|-RRB- .|.|. In|in|IN the|the|DT second|second|JJ experiment|experiment|NN ,|,|, the|the|DT maximum|maximum|NN was|be|VBD at|at|IN about|about|IN 450|450|CD bp|bp|NN ,|,|, and|and|CC samples|sample|NNS were|be|VBD sequenced|sequence|VBN using|use|VBG standard|standard|JJ paired-end|paired-end|NN 2|2|CD *|*|SYM 150|150|CD nt|nt|NNS protocol|protocol|NN on|on|IN the|the|DT MiSeq|miseq|NN system|system|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- in|in|IN the|the|DT Immanuel|Immanuel|NNP Kant|Kant|NNP Baltic|Baltic|NNP Federal|Federal|NNP University|University|NNP -LRB-|-lrb-|-LRB- Kaliningrad|Kaliningrad|NNP -RRB-|-rrb-|-RRB- .|.|.
ChIP-seq|chip-seq|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT CFT073|cft073|NN genome|genome|NN using|use|VBG bowtie|bowtie|NN -LRB-|-lrb-|-LRB- version|version|NN 0.12.8|0.12.8|CD -RRB-|-rrb-|-RRB-
ChIP-seq|chip-seq|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW NC|nc|FW _|_|SYM 000913|000913|CD genome|genome|NN using|use|VBG BWA|BWA|NNP 0.6.2|0.6.2|CD
Cholic|Cholic|NNP Acid|Acid|NNP Treatment|treatment|NN
CHP|chp|NN files|file|NNS were|be|VBD generated|generate|VBN using|use|VBG Affymetrix|Affymetrix|NNP Expression|expression|NN Control|control|NN .|.|. Downstream|downstream|JJ data|data|NN analysis|analysis|NN was|be|VBD performed|perform|VBN in|in|IN GeneSpring|GeneSpring|NNP GX|GX|NNP 12|12|CD ,|,|, CEL|CEL|NNP files|file|NNS were|be|VBD imported|import|VBN using|use|VBG RMA|RMA|NNP algorithm|algorithm|NN and|and|CC median|median|JJ normalization|normalization|NN was|be|VBD performed|perform|VBN .|.|.
Chromatin|Chromatin|NNP was|be|VBD extracted|extract|VBN and|and|CC processed|process|VBN according|accord|VBG to|to|TO Oxford|Oxford|NNP Gene|Gene|NNP Technology|Technology|NNP protocols|protocol|NNS -LRB-|-lrb-|-LRB- www.ogt.co.uk|www.ogt.co.uk|NN -RRB-|-rrb-|-RRB- .|.|.
Chromosomal|chromosomal|JJ DNA|dna|NN
CIP2G|cip2g|NN _|_|CD 00000|00000|CD
CIP2G|cip2g|NN _|_|CD 00045|00045|CD
CIP2G|cip2g|NN _|_|CD 00090|00090|CD
CIP2G|cip2g|NN _|_|CD 00135|00135|CD
CIP2G|cip2g|NN _|_|CD 00180|00180|CD
CIP4G|cip4g|NN _|_|CD 00000|00000|CD
CIP4G|cip4g|NN _|_|CD 00045|00045|CD
CIP4G|cip4g|NN _|_|CD 00090|00090|CD
CIP4G|cip4g|NN _|_|CD 00135|00135|CD
CIP4G|cip4g|NN _|_|CD 00180|00180|CD
Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 1|1|CD +|+|CC A-IP|a-ip|JJ
Ciprofloxacin|ciprofloxacin|NN Rep|Rep|NNP 1|1|CD +|+|CC A+IP|A+IP|NNP
Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 2|2|CD +|+|CC A-IP|a-ip|JJ
Ciprofloxacin|ciprofloxacin|NN Rep|Rep|NNP 2|2|CD +|+|CC A+IP|A+IP|NNP
Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 3|3|CD +|+|CC A-IP|a-ip|JJ
Ciprofloxacin|ciprofloxacin|NN Rep|Rep|NNP 3|3|CD +|+|CC A+IP|A+IP|NNP
CIPSG|CIPSG|NNP _|_|SYM 00000|00000|CD
CIPSG|cipsg|NN _|_|CD 00045|00045|CD
CIPSG|cipsg|NN _|_|CD 00090|00090|CD
CIPSG|cipsg|NN _|_|CD 00135|00135|CD
CIPSG|cipsg|NN _|_|CD 00180|00180|CD
Cirpofloxacin|cirpofloxacin|NN treated|treat|VBN fur|fur|NN mutant|mutant|JJ sample|sample|NN at|at|IN T1h|t1h|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Cirpofloxacin|cirpofloxacin|NN treated|treat|VBN fur|fur|NN mutant|mutant|JJ sample|sample|NN at|at|IN T1h|t1h|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Cirpofloxacin|cirpofloxacin|NN treated|treat|VBN WT|wt|JJ sample|sample|NN at|at|IN T1h|t1h|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Cirpofloxacin|cirpofloxacin|NN treated|treat|VBN WT|wt|JJ sample|sample|NN at|at|IN T1h|t1h|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Clarified|clarify|VBN extracts|extract|NNS were|be|VBD treated|treat|VBN with|with|IN microccocal|microccocal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- 45|45|CD enzyme|enzyme|NN units|unit|NNS per|per|IN absorbance|absorbance|NN unit|unit|NN of|of|IN lysate|lysate|NN at|at|IN 260|260|CD nm|nm|NN -RRB-|-rrb-|-RRB- ,|,|, purified|purify|VBN through|through|IN a|a|DT sucrose|sucrose|NN cushion|cushion|NN ,|,|, and|and|CC affinity|affinity|NN purified|purify|VBN via|via|IN TF|tf|NN .|.|. Ribosome-protected|ribosome-protected|JJ footprints|footprint|NNS were|be|VBD size|size|NN selected|select|VBN and|and|CC converted|convert|VBN into|into|IN a|a|DT cDNA|cdna|NN library|library|NN for|for|IN sequencing|sequencing|NN .|.|.
Clarified|clarify|VBD extracts|extract|NNS were|be|VBD treated|treat|VBN with|with|IN microccocal|microccocal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- 45|45|CD enzyme|enzyme|NN units|unit|NNS per|per|IN absorbance|absorbance|NN unit|unit|NN of|of|IN lysate|lysate|NN at|at|IN 260|260|CD nm|nm|NN -RRB-|-rrb-|-RRB- ,|,|, purified|purify|VBN through|through|IN a|a|DT sucrose|sucrose|NN gradient|gradient|NN .|.|. Ribosome-protected|ribosome-protected|JJ footprints|footprint|NNS were|be|VBD size|size|NN selected|select|VBN and|and|CC converted|convert|VBN into|into|IN a|a|DT cDNA|cdna|NN library|library|NN for|for|IN sequencing|sequencing|NN .|.|.
Clindamycin|Clindamycin|NNP _|_|NNP replicate|replicate|VB _|_|SYM 1|1|CD
Clindamycin|clindamycin|NN _|_|NN replicate|replicate|VBP _|_|NN 2|2|CD
Clindamycin|Clindamycin|NNP _|_|NNP replicate|replicate|VB _|_|SYM 3|3|CD
clinical-1|clinical-1|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
Clinical-1|clinical-1|NN vs|vs|CC Bovine-biased-1|bovine-biased-1|NN
Clinical-1|clinical-1|NN vs|vs|CC Bovine-biased-2|bovine-biased-2|NN
Clinical-1|clinical-1|NN vs|vs|CC Bovine-biased-3|bovine-biased-3|NN
Clinical-1|clinical-1|NN vs|vs|CC Bovine-biased-4|bovine-biased-4|NN
clinical-2|clinical-2|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
Clinical-2|clinical-2|NN vs|vs|CC Bovine-biased-1|bovine-biased-1|NN
Clinical-2|clinical-2|NN vs|vs|CC Bovine-biased-2|bovine-biased-2|NN
Clinical-2|clinical-2|NN vs|vs|CC Bovine-biased-3|bovine-biased-3|NN
Clinical-2|clinical-2|NN vs|vs|CC Bovine-biased-4|bovine-biased-4|NN
clinical-3|clinical-3|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
Clinical-3|clinical-3|NN vs|vs|CC Bovine-biased-1|bovine-biased-1|NN
Clinical-3|clinical-3|NN vs|vs|CC Bovine-biased-2|bovine-biased-2|NN
Clinical-3|clinical-3|NN vs|vs|CC Bovine-biased-3|bovine-biased-3|NN
Clinical-3|clinical-3|NN vs|vs|CC Bovine-biased-4|bovine-biased-4|NN
clinical-4|clinical-4|NN strain|strain|NN grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN of|of|IN growth|growth|NN
Clinical-4|clinical-4|NN vs|vs|CC Bovine-biased-1|bovine-biased-1|NN
Clinical-4|clinical-4|NN vs|vs|CC Bovine-biased-2|bovine-biased-2|NN
Clinical-4|clinical-4|NN vs|vs|CC Bovine-biased-3|bovine-biased-3|NN
Clinical-4|clinical-4|NN vs|vs|CC Bovine-biased-4|bovine-biased-4|NN
Clinical|clinical|JJ isolate|isolate|NN ,|,|, minus|minus|CC ciprofloxacin|ciprofloxacin|NN ,|,|, 0|0|CD min|min|NN
Clinical|clinical|JJ isolate|isolate|NN ,|,|, minus|minus|CC ciprofloxacin|ciprofloxacin|NN ,|,|, 30|30|CD min|min|NN
Clinical|clinical|JJ isolate|isolate|NN ,|,|, minus|minus|CC ciprofloxacin|ciprofloxacin|NN ,|,|, 90|90|CD min|min|NN
Clinical|clinical|JJ isolate|isolate|NN ,|,|, plus|plus|CC ciprofloxacin|ciprofloxacin|NN ,|,|, 0|0|CD min|min|NN
Clinical|clinical|JJ isolate|isolate|NN ,|,|, plus|plus|CC ciprofloxacin|ciprofloxacin|NN ,|,|, 30|30|CD min|min|NN
Clinical|clinical|JJ isolate|isolate|NN ,|,|, plus|plus|CC ciprofloxacin|ciprofloxacin|NN ,|,|, 90|90|CD min|min|NN
Clones|clone|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN with|with|IN 0.4|0.4|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- glucose|glucose|NN as|as|IN carbon|carbon|NN source|source|NN minimal|minimal|JJ medium|medium|NN with|with|IN 0.3|0.3|CD M|m|NN NaCl|nacl|NN -LRB-|-lrb-|-LRB- osmotic|osmotic|JJ stress|stress|NN medium|medium|NN -RRB-|-rrb-|-RRB- to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN approx.|approx.|RB 0.8|0.8|CD -RRB-|-rrb-|-RRB- .|.|.
-LSB-|-lsb-|-LRB- Clostridium|clostridium|NN -RSB-|-rsb-|-RRB- leptum|leptum|NN
-LSB-|-lsb-|-LRB- Clostridium|clostridium|NN -RSB-|-rsb-|-RRB- symbiosum|symbiosum|NN
Cluster|cluster|NN detection|detection|NN and|and|CC base|base|NN calling|calling|NN were|be|VBD performed|perform|VBN using|use|VBG RTA|RTA|NNP v1|v1|NN .13|.13|CD -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC the|the|DT quality|quality|NN of|of|IN the|the|DT reads|read|VBZ was|be|VBD assessed|assess|VBN with|with|IN CASAVA|casava|NN v1|v1|NN .8.1|.8.1|CD -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|.
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW G|g|NN 1/2|1/2|CD isolate|isolate|NN with|with|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW G|g|NN 1/2|1/2|CD isolate|isolate|NN with|with|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW G|g|NN 3/10|3/10|CD isolate|isolate|NN with|with|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW G|g|NN 4/9|4/9|CD isolate|isolate|NN with|with|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW G5|g5|NN isolate|isolate|NN with|with|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW G5|g5|NN isolate|isolate|NN with|with|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW isolate|isolate|NN G|g|NN 3/10|3/10|CD with|with|IN control|control|NN strain|strain|NN K-12|k-12|NN MG1655|mg1655|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW isolate|isolate|NN G|g|NN 4/9|4/9|CD with|with|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN with|with|IN E.|e.|FW coli|coli|FW K-12|k-12|NN M1655|m1655|NN #|#|# 1|1|CD
Co-hybridization|co-hybridization|NN of|of|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN with|with|IN E.|e.|FW coli|coli|FW K-12|k-12|NN M1655|m1655|NN #|#|# 2|2|CD
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint1|timepoint1|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint1|timepoint1|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint1|timepoint1|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint2|timepoint2|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint2|timepoint2|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint2|timepoint2|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint3|timepoint3|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint3|timepoint3|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint3|timepoint3|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint4|timepoint4|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint4|timepoint4|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint4|timepoint4|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint5|timepoint5|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint5|timepoint5|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint5|timepoint5|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint6|timepoint6|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint6|timepoint6|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint6|timepoint6|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint7|timepoint7|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint7|timepoint7|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint7|timepoint7|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN coldstress|coldstress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint1|timepoint1|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint1|timepoint1|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint1|timepoint1|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN control|control|NN _|_|SYM timepoint8|timepoint8|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN control|control|NN _|_|SYM timepoint8|timepoint8|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN control|control|NN _|_|SYM timepoint8|timepoint8|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint1|timepoint1|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint1|timepoint1|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint1|timepoint1|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint2|timepoint2|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint2|timepoint2|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint2|timepoint2|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint3|timepoint3|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint3|timepoint3|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint3|timepoint3|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint4|timepoint4|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint4|timepoint4|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint4|timepoint4|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint5|timepoint5|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint5|timepoint5|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint5|timepoint5|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint6|timepoint6|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint6|timepoint6|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint6|timepoint6|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint7|timepoint7|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint7|timepoint7|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint7|timepoint7|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN heatstress|heatstress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep3|rep3|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN lactose|lactose|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep2|rep2|NN
Coli-MDS42|coli-mds42|NN _|_|CD bcm-100mcg|bcm-100mcg|NN /|/|: ml|ml|NN _|_|NN rep1|rep1|NN
Coli-MDS42|coli-mds42|NN _|_|CD bcm-100mcg|bcm-100mcg|NN /|/|: ml|ml|NN _|_|NN rep2|rep2|NN
Coli-MDS42|coli-mds42|NN _|_|CD del-nusA|del-nusa|NN _|_|CD rep1|rep1|NN
Coli-MDS42|coli-mds42|NN _|_|CD del-nusA|del-nusa|NN _|_|CD rep2|rep2|NN
Coli-MDS42|coli-mds42|NN _|_|CD del-nusG|del-nusg|NN _|_|CD rep1|rep1|NN
Coli-MDS42|coli-mds42|NN _|_|CD del-nusG|del-nusg|NN _|_|CD rep2|rep2|NN
Coli-MDS42|coli-mds42|NN _|_|CD no-drug|no-drug|JJ _|_|NN rep1|rep1|NN
Coli-MDS42|coli-mds42|NN _|_|CD no-drug|no-drug|JJ _|_|NN rep2|rep2|NN
Coli-MG1655|coli-mg1655|NN _|_|CD bcm-100mcg|bcm-100mcg|NN /|/|: ml|ml|NN _|_|NN rep1|rep1|NN
Coli-MG1655|coli-mg1655|NN _|_|CD bcm-100mcg|bcm-100mcg|NN /|/|: ml|ml|NN _|_|NN rep2|rep2|NN
Coli-MG1655|coli-mg1655|NN _|_|CD bcm-10mcg|bcm-10mcg|NN /|/|: ml|ml|NN _|_|NN rep1|rep1|NN
Coli-MG1655|coli-mg1655|NN _|_|CD bcm-10mcg|bcm-10mcg|NN /|/|: ml|ml|NN _|_|NN rep2|rep2|NN
Coli-MG1655|coli-mg1655|NN _|_|CD bcm-25mcg|bcm-25mcg|NN /|/|: ml|ml|NN _|_|NN rep1|rep1|NN
Coli-MG1655|coli-mg1655|NN _|_|CD bcm-25mcg|bcm-25mcg|NN /|/|: ml|ml|NN _|_|NN rep2|rep2|NN
Coli-MG1655|coli-mg1655|NN _|_|CD no-drug|no-drug|JJ _|_|NN rep1|rep1|NN
Coli-MG1655|coli-mg1655|NN _|_|CD no-drug|no-drug|JJ _|_|NN rep2|rep2|NN
Coli-O157H7|coli-o157h7|NN _|_|CD bcm-100mcg|bcm-100mcg|NN /|/|: ml|ml|NN _|_|NN rep1|rep1|NN
Coli-O157H7|coli-o157h7|NN _|_|CD bcm-100mcg|bcm-100mcg|NN /|/|: ml|ml|NN _|_|NN rep2|rep2|NN
Coli-O157H7|coli-o157h7|NN _|_|CD no-drug|no-drug|JJ _|_|NN rep1|rep1|NN
Coli-O157H7|coli-o157h7|NN _|_|CD no-drug|no-drug|JJ _|_|NN rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint10|timepoint10|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint10|timepoint10|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint10|timepoint10|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint11|timepoint11|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint11|timepoint11|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint11|timepoint11|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint12|timepoint12|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint1|timepoint1|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint1|timepoint1|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint1|timepoint1|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint2|timepoint2|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint3|timepoint3|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint4|timepoint4|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint5|timepoint5|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint6|timepoint6|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint7|timepoint7|NN _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|VBP _|_|SYM timepoint8|timepoint8|CD _|_|CD rep4|rep4|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint9|timepoint9|NN _|_|CD rep1|rep1|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint9|timepoint9|NN _|_|CD rep2|rep2|NN
coli|coli|NN _|_|NN oxidativestress|oxidativestress|NN _|_|CD timepoint9|timepoint9|NN _|_|CD rep4|rep4|NN
Collected|collect|VBN cells|cell|NNS were|be|VBD lysed|lyse|VBN using|use|VBG Trizol|Trizol|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG phenol-chloroform|phenol-chloroform|JJ and|and|CC precipitated|precipitated|JJ with|with|IN ice|ice|NN cold|cold|JJ isopropanol|isopropanol|NN .|.|. Then|then|RB the|the|DT precipitations|precipitation|NNS were|be|VBD further|further|JJ washed|wash|VBN with|with|IN 70|70|CD %|%|NN ethanol|ethanol|NN and|and|CC dissolved|dissolve|VBN in|in|IN RNase-free|rnase-free|JJ water|water|NN .|.|. Genomic|genomic|JJ DNA|dna|NN was|be|VBD removed|remove|VBN using|use|VBG RNase-free|rnase-free|JJ DNase|dnase|NN I.|i.|NN RNA|rna|NN samples|sample|NNS were|be|VBD further|further|JJ purified|purify|VBN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kits|Kits|NNP -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN concentration|concentration|NN and|and|CC quality|quality|NN were|be|VBD determined|determine|VBN using|use|VBG A|a|DT Nanodrop|nanodrop|JJ ND|nd|NN 1000|1000|CD spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientific|Scientific|NNP ,|,|, Pittsburgh|Pittsburgh|NNP ,|,|, PA|pa|NN ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN .|.|. The|the|DT isolated|isolate|VBN RNA|rna|NN was|be|VBD stored|store|VBN at|at|IN −|−|CD 80|80|CD °C|°c|NN before|before|IN use|use|NN .|.|.
Collinsella|collinsella|NN aerofaciens|aerofacien|NNS ATCC|atcc|NN 25986|25986|CD
Colony|Colony|NNP Biofilm|Biofilm|NNP Replicate|replicate|VB 1|1|CD
Colony|Colony|NNP Biofilm|Biofilm|NNP Replicate|replicate|VB 2|2|CD
Colony|Colony|NNP Biofilm|Biofilm|NNP Replicate|replicate|VB 3|3|CD
Colony|Colony|NNP Biofilm|Biofilm|NNP Replicate|replicate|VB 4|4|CD
Column|Column|NNP purification|purification|NN
Combined|Combined|NNP input|input|NN
common|common|JJ reference|reference|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.5|0.5|CD -RRB-|-rrb-|-RRB-
CompA|compa|NN
Comparison|comparison|NN cya|cya|NN mutant|mutant|NN with|with|IN wt|wt|JJ under|under|IN glucose-limited|glucose-limited|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- replicate|replicate|VB 1|1|LS -RRB-|-rrb-|-RRB-
Comparison|comparison|NN cya|cya|NN mutant|mutant|NN with|with|IN wt|wt|JJ under|under|IN glucose-limited|glucose-limited|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- replicate|replicate|VB 2|2|LS -RRB-|-rrb-|-RRB-
Comparison|comparison|NN cya|cya|NN mutant|mutant|NN with|with|IN wt|wt|JJ under|under|IN glucose-limited|glucose-limited|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- replicate|replicate|VB 3|3|LS -RRB-|-rrb-|-RRB-
Comparison|comparison|NN rpoS|rpos|NN mutant|mutant|NN with|with|IN wt|wt|JJ under|under|IN glucose-limited|glucose-limited|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- replicate|replicate|VB 1|1|LS -RRB-|-rrb-|-RRB-
Comparison|comparison|NN rpoS|rpos|NN mutant|mutant|NN with|with|IN wt|wt|JJ under|under|IN glucose-limited|glucose-limited|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- replicate|replicate|VB 2|2|LS -RRB-|-rrb-|-RRB-
Comparison|comparison|NN rpoS|rpos|NN mutant|mutant|NN with|with|IN wt|wt|JJ under|under|IN glucose-limited|glucose-limited|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- replicate|replicate|VB 3|3|LS -RRB-|-rrb-|-RRB-
CompB|compb|NN
Compile|compile|VB annotated|annotated|JJ counts|count|NNS using|use|VBG custom|custom|NN Python|Python|NNP script|script|NN -LRB-|-lrb-|-LRB- ExtractMapCounts|extractmapcount|NNS from|from|IN http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN -RRB-|-rrb-|-RRB-
completely|completely|RB aerobic|aerobic|JJ conditions|condition|NNS
Computation|Computation|NNP of|of|IN genomic|genomic|JJ intervals|interval|NNS based|base|VBN on|on|IN computed|computed|JJ signal|signal|NN and|and|CC p-values|p-values|JJ
Computation|computation|NN of|of|IN summary|summary|NN statistics|statistics|NNS
CON206|con206|NN .3|.3|NN A|a|NN _|_|NN u1|u1|NN
CON206|con206|NN .3|.3|NN A|a|NN _|_|NN u2|u2|NN
CON206|con206|NN .3|.3|NN A|a|NN _|_|NN y1|y1|NN
CON206|con206|NN .3|.3|NN A|a|NN _|_|NN y2|y2|NN
CON208|con208|NN .3|.3|NN A|a|NN _|_|NN u1|u1|NN
CON208|con208|NN .3|.3|NN A|a|NN _|_|NN u8|u8|NN
CON208|con208|NN .3|.3|NN A|a|NN _|_|NN y2|y2|NN
CON208|con208|NN .3|.3|NN A|a|NN _|_|NN y6|y6|NN
concentration|concentration|NN :|:|: 0.2|0.2|CD ppm|ppm|NN
concentration|concentration|NN :|:|: 2|2|CD ppm|ppm|NN
condition|condition|NN :|:|: 37ºC|37ºc|NN
condition|condition|NN :|:|: 45ºC|45ºc|NN
condition|condition|NN :|:|: acetonitrile|acetonitrile|NN -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB-
condition|condition|NN :|:|: exponential|exponential|JJ growth|growth|NN ,|,|, 36.9|36.9|CD ºC|ºc|NN
condition|condition|NN :|:|: exponential|exponential|JJ growth|growth|NN ,|,|, 41.2|41.2|CD ºC|ºc|NN
condition|condition|NN :|:|: exponential|exponential|JJ growth|growth|NN ,|,|, 43.2|43.2|CD ºC|ºc|NN
condition|condition|NN :|:|: exponential|exponential|JJ growth|growth|NN ,|,|, 44.8|44.8|CD ºC|ºc|NN
condition|condition|NN :|:|: glucose|glucose|NN limited|limited|JJ
condition|condition|NN :|:|: heat-shocked|heat-shocked|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
condition|condition|NN :|:|: heat|heat|NN shock|shock|NN response|response|NN ,|,|, 44.8|44.8|CD ºC|ºc|NN
condition|condition|NN :|:|: histidine|histidine|NN depleted|deplete|VBD
condition|condition|NN :|:|: histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
condition|condition|NN :|:|: in|in|FW vitro|vitro|FW
condition|condition|NN :|:|: in|in|FW vivo|vivo|FW
condition|condition|NN :|:|: LB|lb|NN +3|+3|CD g/L|g/L|NNP Glc|Glc|NNP +0.1|+0.1|CD mM|mm|NN IPTG|iptg|NN
condition|condition|NN :|:|: LB|lb|NN +3|+3|CD g/L|g/L|NNP Glc|Glc|NNP +0.1|+0.1|CD mM|mm|NN IPTG|iptg|NN +|+|CC 50μg/ml|50μg/ml|JJ Amp|amp|NN
condition|condition|NN :|:|: mid-exponential|mid-exponential|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
condition|condition|NN :|:|: mid-exponential|mid-exponential|JJ condition|condition|NN with|with|IN rifampicin|rifampicin|NN treatment|treatment|NN
condition|condition|NN :|:|: myxotoxin|myxotoxin|NN
condition|condition|NN :|:|: nitrogen-limiting|nitrogen-limiting|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
condition|condition|NN :|:|: osmotic|osmotic|JJ pressure|pressure|NN
condition|condition|NN :|:|: regular|regular|JJ
condition|condition|NN :|:|: starvation|starvation|NN
condition|condition|NN :|:|: stationary|stationary|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
condition|condition|NN :|:|: temperature|temperature|NN change|change|NN
conducted|conduct|VBN by|by|IN CeGaT|cegat|NN -LRB-|-lrb-|-LRB- Tübingen|tübingen|NN ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO SOLiD|solid|JJ standard|standard|JJ protocols|protocol|NNS for|for|IN RNA-seq|rna-seq|JJ
con|con|NN _|_|CD RNAA|rnaa|NN
consensus|consensus|NN binding|binding|NN regions|region|NNS were|be|VBD obtained|obtain|VBN as|as|IN the|the|DT portion|portion|NN which|which|WDT was|be|VBD covered|cover|VBN by|by|IN replicate|replicate|VB samples|sample|NNS
contamination|contamination|NN status|status|NN :|:|: hydrocarbon|hydrocarbon|NN contaminated|contaminate|VBN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, CORM-401|corm-401|NN samples|sample|NNS or|or|CC samples|sample|NNS prior|prior|RB to|to|TO addition|addition|NN of|of|IN CORM-401|corm-401|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN for|for|IN 10|10|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN for|for|IN 10|10|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN for|for|IN 20|20|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN for|for|IN 2.5|2.5|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN for|for|IN 40|40|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN for|for|IN 5|5|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN for|for|IN 80|80|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 10|10|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 20|20|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 2.5|2.5|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 40|40|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 5|5|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 80|80|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 10|10|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 20|20|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 2.5|2.5|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 40|40|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 5|5|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 80|80|CD min|min|NN
Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, prior|prior|RB to|to|TO CORM-3|corm-3|NN addition|addition|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, CORM-401|corm-401|NN samples|sample|NNS or|or|CC samples|sample|NNS prior|prior|RB to|to|TO addition|addition|NN of|of|IN CORM-401|corm-401|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 10|10|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 20|20|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 2.5|2.5|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 40|40|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 5|5|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN for|for|IN 80|80|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 10|10|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 20|20|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 2.5|2.5|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 40|40|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 5|5|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN for|for|IN 80|80|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO CO|CO|NNP gas|gas|NN at|at|IN 0.1|0.1|CD L/min|l/min|NN for|for|IN 10|10|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO CO|CO|NNP gas|gas|NN at|at|IN 0.1|0.1|CD L/min|l/min|NN for|for|IN 20|20|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO CO|CO|NNP gas|gas|NN at|at|IN 0.1|0.1|CD L/min|l/min|NN for|for|IN 2.5|2.5|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO CO|CO|NNP gas|gas|NN at|at|IN 0.1|0.1|CD L/min|l/min|NN for|for|IN 40|40|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO CO|CO|NNP gas|gas|NN at|at|IN 0.1|0.1|CD L/min|l/min|NN for|for|IN 5|5|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO CO|CO|NNP gas|gas|NN at|at|IN 0.1|0.1|CD L/min|l/min|NN for|for|IN 80|80|CD min|min|NN
Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, prior|prior|RB to|to|TO CORM-3|corm-3|NN addition|addition|NN
control|control|NN
Control|Control|NNP
Control|Control|NNP ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN ,1.5|,1.5|CD h|h|NN ,|,|, replicate|replicate|VB 1|1|CD
Control|Control|NNP ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN ,1.5|,1.5|CD h|h|NN ,|,|, replicate|replicate|VB 2|2|CD
Control|Control|NNP ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN ,1.5|,1.5|CD h|h|NN ,|,|, replicate|replicate|VB 3|3|CD
Control|Control|NNP _|_|NNP 1|1|CD
Control109|control109|NN _|_|CD 0.8|0.8|CD %|%|NN Bu|bu|NN _|_|CD 1.5|1.5|CD h|h|NN _|_|CD rep1|rep1|NN
Control109|control109|NN _|_|CD 0.8|0.8|CD %|%|NN Bu|bu|NN _|_|CD 1.5|1.5|CD h|h|NN _|_|CD rep2|rep2|NN
Control109|control109|NN _|_|CD 0.8|0.8|CD %|%|NN Bu|bu|NN _|_|CD 1.5|1.5|CD h|h|NN _|_|CD rep3|rep3|NN
control|control|NN 12h|12h|VBP
Control-1|control-1|NN ,|,|, biological|biological|JJ rep1|rep1|NN
Control|Control|NNP _|_|NN 2|2|CD
control|control|NN 24h|24h|JJ
Control-2|control-2|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Control-3|control-3|NN ,|,|, biological|biological|JJ rep3|rep3|NN
control|control|NN 6h|6h|VBP
control|control|NN -LRB-|-lrb-|-LRB- additional|additional|JJ -RRB-|-rrb-|-RRB-
Control|Control|NNP bacteria|bacterium|NNS at|at|IN 37|37|CD °C|°c|NN -LRB-|-lrb-|-LRB- common|common|JJ reference|reference|NN -RRB-|-rrb-|-RRB- .|.|. Total|total|JJ RNA|rna|NN isolated|isolate|VBN from|from|IN 5|5|CD indepedent|indepedent|NN cultures|culture|NNS -LRB-|-lrb-|-LRB- pooled|pool|VBN after|after|IN cDNA|cdna|NN labeling|labeling|NN -RRB-|-rrb-|-RRB- .|.|.
control|control|NN ,|,|, biological|biological|JJ rep1|rep1|NN C1|c1|NN
control|control|NN ,|,|, biological|biological|JJ rep1|rep1|NN C2|c2|NN
control|control|NN ,|,|, biological|biological|JJ rep1|rep1|NN C3|c3|NN
control|control|NN ,|,|, biological|biological|JJ rep2|rep2|NN C4|c4|NN
control|control|NN ,|,|, biological|biological|JJ rep2|rep2|NN C5|c5|NN
control|control|NN ,|,|, biological|biological|JJ rep2|rep2|NN C6|c6|NN
Control|Control|NNP chemostat|chemostat|NN 1|1|CD h|h|NN not|not|RB irradiated|irradiated|JJ
Control|Control|NNP chemostat|chemostat|NN 1h|1h|NN not|not|RB irradiated|irradiated|JJ
Control|Control|NNP chemostat|chemostat|NN 50|50|CD h|h|NN not|not|RB irradiated|irradiated|JJ
Control|Control|NNP pAN1201|pan1201|NN replicate|replicate|VB 1|1|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Control|Control|NNP pAN1201|pan1201|NN replicate|replicate|VB 2|2|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Control|Control|NNP replicate|replicate|VB 1|1|CD
Control|Control|NNP replicate|replicate|VB 2|2|CD
Control|Control|NNP replicate|replicate|VB 3|3|CD
control|control|NN sample|sample|NN at|at|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep1|rep1|NN
control|control|NN sample|sample|NN at|at|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep2|rep2|NN
control|control|NN sample|sample|NN at|at|IN 60|60|CD min|min|NN ,|,|, biological|biological|JJ rep1|rep1|NN
control|control|NN sample|sample|NN at|at|IN 60|60|CD min|min|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Control|Control|NNP samples|sample|NNS -LRB-|-lrb-|-LRB- 285c/empty|285c/empty|JJ vector|vector|NN -RRB-|-rrb-|-RRB- were|be|VBD harvested|harvest|VBN via|via|IN filtration|filtration|NN and|and|CC resuspended|resuspend|VBN in|in|IN RNALater|rnalater|NN once|once|IN they|they|PRP had|have|VBD reached|reach|VBN OD|od|NN =|=|JJ 0.5|0.5|CD .|.|. Experimental|experimental|JJ samples|sample|NNS were|be|VBD harvested|harvest|VBN after|after|IN 1|1|CD hour|hour|NN of|of|IN heat|heat|NN shock|shock|NN at|at|IN 42|42|CD C|c|NN in|in|IN an|a|DT analogous|analogous|JJ procedure|procedure|NN .|.|.
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 1-1|1-1|CD
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 1-2|1-2|CD
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 2-1|2-1|CD
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 2-2|2-2|CD
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 3-1|3-1|CD
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 3-2|3-2|CD
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 4-1|4-1|CD
Control|Control|NNP _|_|NNP Step|step|VB _|_|SYM 4-2|4-2|CD
control|control|NN strain|strain|NN
Control|Control|NNP Strain|Strain|NNP at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 0h|0h|NN
Control|Control|NNP Strain|Strain|NNP at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 10h|10h|CD
Control|Control|NNP Strain|Strain|NNP at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 16h|16h|NN
Control|Control|NNP Strain|Strain|NNP at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 20h|20h|JJ
Control|Control|NNP Strain|Strain|NNP at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 6h|6h|JJ
Control|Control|NNP Strain|Strain|NNP at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 8h|8h|NN
Control|Control|NNP strain|strain|NN exponentially|exponentially|RB grown|grow|VBN in|in|IN the|the|DT absence|absence|NN of|of|IN histidine|histidine|NN
Control|Control|NNP strain|strain|NN exponentially|exponentially|RB grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN histidine|histidine|NN -LRB-|-lrb-|-LRB- 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB-
control|control|NN strain|strain|NN K-12|k-12|NN MG1655|mg1655|NN
control|control|NN strain|strain|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN
control|control|NN strain|strain|NN with|with|IN hypoxanthine|hypoxanthine|NN
control|control|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 120|120|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
control|control|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 15|15|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
control|control|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 30|30|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
control|control|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 45|45|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
control|control|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 60|60|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
Control|Control|NNP treatment|treatment|NN .|.|. Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP pH|ph|NN 7.4|7.4|CD ,|,|, 90|90|CD minutes|minute|NNS ,|,|, 37C|37c|NN ,|,|, 5|5|CD %|%|NN CO2|co2|NN ,|,|, static|static|JJ -LRB-|-lrb-|-LRB- unstressed|unstressed|JJ -RRB-|-rrb-|-RRB-
Control|Control|NNP treatment|treatment|NN .|.|. Bacteria|bacterium|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP pH|ph|NN 7.4|7.4|CD -LRB-|-lrb-|-LRB- unstressed|unstressed|JJ -RRB-|-rrb-|-RRB-
Control|Control|NNP Wild|Wild|NNP type|type|NN E.coli|e.coli|NN SE15|se15|NN vs.|vs.|CC LuxS|luxs|NN mutant|mutant|JJ E.coli|e.coli|NN SE15|se15|NN
conversion|conversion|NN :|:|: Convert|convert|VB SOLiD|solid|JJ output|output|NN to|to|TO fastq|fastq|NN -LRB-|-lrb-|-LRB- Galaxy|galaxy|NN Version|version|NN 1.0.0|1.0.0|CD -RRB-|-rrb-|-RRB- ;|;|: default|default|NN parameters|parameter|NNS .|.|.
convert|convert|VBP back|back|RB to|to|TO sorted.sam|sorted.sam|NN with|with|IN samtools|samtool|NNS
convert|convert|VBP bowtie|bowtie|NN output|output|NN .|.|. sam|sam|NN to|to|TO .|.|. bam|bam|NN with|with|IN samtools|samtool|NNS
corresponding|correspond|VBG to|to|TO the|the|DT same|same|JJ tip|tip|NN .|.|. Finally|finally|RB ,|,|, all|all|PDT the|the|DT log|log|NN ratios|ratio|NNS of|of|IN the|the|DT same|same|JJ gene|gene|NN from|from|IN each|each|DT slide|slide|NN
counting|counting|NN :|:|: countOverlaps|countoverlap|NNS of|of|IN Iranges|irange|NNS ;|;|: default|default|NN parameters|parameter|NNS
Count|count|NN reads|read|VBZ aligned|align|VBN to|to|TO each|each|DT base|base|NN IGVtools|igvtools|NN -LRB-|-lrb-|-LRB- version|version|NN 2.3.71|2.3.71|CD -RRB-|-rrb-|-RRB- ,|,|, window|window|NN size|size|NN =|=|JJ 1|1|CD
Counts|count|VBZ per|per|IN million|million|CD unique|unique|JJ reads|read|VBZ were|be|VBD calculated|calculate|VBN for|for|IN each|each|DT gene|gene|NN .|.|.
Counts|Counts|NNPS were|be|VBD depth|depth|NN normalized|normalize|VBD to|to|TO a|a|DT pseudo-reference|pseudo-reference|NN sample|sample|NN calculated|calculate|VBN from|from|IN all|all|DT samples|sample|NNS -LRB-|-lrb-|-LRB- ribozero|ribozero|NN treated|treat|VBN samples|sample|NNS -RRB-|-rrb-|-RRB- or|or|CC using|use|VBG counts|count|NNS per|per|IN million|million|CD counts|count|NNS -LRB-|-lrb-|-LRB- total|total|JJ RNA|rna|NN samples|sample|NNS -RRB-|-rrb-|-RRB- .|.|.
Coverage|Coverage|NNP calculation|calculation|NN and|and|CC normalisation|normalisation|NN -LRB-|-lrb-|-LRB- TRAPL|trapl|NN -RRB-|-rrb-|-RRB-
Coverage|Coverage|NNP calculation|calculation|NN and|and|CC normalisation|normalisation|NN -LRB-|-lrb-|-LRB- via|via|IN READemption|reademption|NN -RRB-|-rrb-|-RRB-
cpxA-ala-1|cpxa-ala-1|NN
cpxA-ala-2|cpxa-ala-2|NN
cpxA|cpxa|NN mutant|mutant|NN in|in|IN Ala|Ala|NNP media|media|NNS
cpxA|cpxa|NN mutant|mutant|NN in|in|IN Gln|gln|NN media|media|NNS
cpxR|cpxr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
cpxR|cpxr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
cpxR|cpxr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
cpxR|cpxr|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
cra-8myc|cra-8myc|NN tagged|tag|VBD strain|strain|NN _|_|NN acetate|acetate|NN
cra-8myc|cra-8myc|NN tagged|tag|VBD strain|strain|NN _|_|NN fructose|fructose|NN
cra-8myc|cra-8myc|NN tagged|tag|VBD strain|strain|NN _|_|NN glucose|glucose|NN
Cra|Cra|NNP acetate|acetate|NN 1|1|CD
Cra|Cra|NNP acetate|acetate|NN 2|2|CD
Cra|Cra|NNP fructose|fructose|NN 1|1|CD
Cra|Cra|NNP fructose|fructose|NN 2|2|CD
Cra|cra|NN glucose|glucose|NN 1|1|CD
Cra|cra|NN glucose|glucose|NN 2|2|CD
cra|cra|NN KO|ko|NN
cra|cra|NN KO|ko|NN +|+|CC L-trp|l-trp|JJ
crcB|crcb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
crcB|crcb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
crcB|crcb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
crcB|crcb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
CRE|cre|NN Multi|multi|JJ 0uM|0um|NN Rep1|rep1|NN Plasmid|plasmid|NN
CRE|cre|NN Multi|multi|JJ 0uM|0um|NN Rep2|rep2|NN Plasmid|plasmid|NN
CRE|cre|NN Multi|multi|JJ 100uM|100um|NN Rep1|rep1|NN Plasmid|plasmid|NN
CRE|cre|NN Multi|multi|JJ 100uM|100um|NN Rep2|rep2|NN Plasmid|plasmid|NN
CRE|cre|NN Single|single|JJ 100uM|100um|NN Rep1|rep1|NN Plasmid|plasmid|NN
CRE|cre|NN Single|single|JJ 100uM|100um|NN Rep2|rep2|NN Plasmid|plasmid|NN
Crooks|crook|NNS _|_|VBP aero|aero|NN
Crooks|crook|NNS _|_|VBP anaero|anaero|NN
Crosslink|Crosslink|NNP
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN ArcA-8myc|arca-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN rabbit|rabbit|NN serum|serum|NN containing|contain|VBG myc|myc|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN ArgR-8myc|argr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN 9E10|9e10|NN myc|myc|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN ArgR-8myc|argr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN rabbit|rabbit|NN serum|serum|NN containing|contain|VBG myc|myc|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN ArgR-8myc|argr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN using|use|VBG normal|normal|JJ mouse|mouse|NN IgG|igg|NN for|for|IN the|the|DT control|control|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN Fnr-8myc|fnr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN rabbit|rabbit|NN serum|serum|NN containing|contain|VBG myc|myc|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN Lrp-8myc|lrp-8myc|JJ and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN 9E10|9e10|NN myc|myc|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN Lrp-8myc|lrp-8myc|JJ and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN using|use|VBG normal|normal|JJ mouse|mouse|NN IgG|igg|NN for|for|IN the|the|DT control|control|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN PurR-8myc|purr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN 9E10|9e10|NN myc|myc|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN PurR-8myc|purr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN using|use|VBG normal|normal|JJ mouse|mouse|NN IgG|igg|NN for|for|IN the|the|DT control|control|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN RNAP|rnap|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN anti-RpoB|anti-rpob|JJ antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN RNAP|rnap|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN using|use|VBG normal|normal|JJ mouse|mouse|NN IgG|igg|NN for|for|IN the|the|DT control|control|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN RNAP|rnap|NN beta-subunit|beta-subunit|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN normal|normal|JJ mouse|mouse|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Upstate|upstate|JJ -RRB-|-rrb-|-RRB- for|for|IN the|the|DT control|control|NN -LRB-|-lrb-|-LRB- mock-IP|mock-ip|NN -RRB-|-rrb-|-RRB- .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN RNAP|rnap|NN beta-subunit|beta-subunit|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN NT63|nt63|NN mouse|mouse|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN TrpR-8myc|trpr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN 9E10|9e10|NN myc|myc|NN antibody|antibody|NN .|.|.
Cross-linked|cross-linked|JJ and|and|CC sonicated|sonicated|JJ chromatin|chromatin|NN complex|complex|NN of|of|IN TrpR-8myc|trpr-8myc|NN and|and|CC DNA|dna|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN by|by|IN using|use|VBG normal|normal|JJ mouse|mouse|NN IgG|igg|NN for|for|IN the|the|DT control|control|NN .|.|.
Cross-linked|cross-linked|JJ cells|cell|NNS were|be|VBD harvested|harvest|VBN and|and|CC washed|wash|VBN two|two|CD times|time|NNS with|with|IN ice-cold|ice-cold|JJ PBS|PBS|NNP .|.|. Cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 450μl|450μl|NN of|of|IN TES|tes|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50mM|50mm|NN Tris-HCl|tris-hcl|NN pH|ph|NN 7.5|7.5|CD ,|,|, 150mM|150mm|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- and|and|CC 20μl|20μl|NN of|of|IN lysis|lysis|NN solution|solution|NN -LRB-|-lrb-|-LRB- 13.6|13.6|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN ,|,|, 50|50|CD %|%|NN glycerol|glycerol|NN ,|,|, 50mM|50mm|NN Tris-HCl|tris-hcl|NN pH7|ph7|NN .5|.5|CD ,|,|, 100mM|100mm|NN NaCl|nacl|NN ,|,|, 1mM|1mm|NN DTT|dtt|NN ,|,|, 0.1|0.1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN -RRB-|-rrb-|-RRB- followed|follow|VBD of|of|IN a|a|DT 5|5|CD min|min|NN incubation|incubation|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. 10μl|10μl|NN of|of|IN cOmplete|complete|JJ EDTA|edta|NN free|free|JJ protease|protease|NN inhibitor|inhibitor|NN -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN and|and|CC incubated|incubate|VBN 10|10|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. 550μl|550μl|NN of|of|IN ChIP|chip|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 1.1|1.1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 1.2|1.2|CD mM|mm|NN EDTA|edta|NN ,|,|, 16.7|16.7|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, 167mM|167mm|NN NaCl|nacl|NN ,|,|, 20μl/ml|20μl/ml|NN of|of|IN cOmplete|complete|JJ EDTA|edta|NN free|free|JJ protease|protease|NN inhibitor|inhibitor|NN -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN followed|follow|VBN of|of|IN 10|10|CD min|min|NN incubation|incubation|NN at|at|IN 37ºC|37ºc|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB sonicated|sonicate|VBN -LRB-|-lrb-|-LRB- UP200S-Hielscher|up200s-hielscher|NN -RRB-|-rrb-|-RRB- to|to|TO an|a|DT average|average|JJ size|size|NN between|between|IN 300bp|300bp|JJ and|and|CC 700bp|700bp|JJ with|with|IN 5|5|CD cycles|cycle|NNS of|of|IN and|and|CC amplitude|amplitude|NN of|of|IN 55|55|CD %|%|NN ,|,|, 0.45|0.45|CD sec|sec|NN pulse|pulse|NN during|during|IN 10sec|10sec|CD and|and|CC 50sec|50sec|CD in|in|IN ice|ice|NN .|.|. Insoluble|insoluble|JJ cell|cell|NN debris|debris|NN were|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 20000g|20000g|NN for|for|IN 3|3|CD min|min|NN at|at|IN 4ºC|4ºc|NN and|and|CC the|the|DT supernatant|supernatant|JJ collected|collect|VBN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD added|add|VBN to|to|TO α-Flag-agarose|α-flag-agarose|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN at|at|IN 4ºC|4ºc|NN under|under|IN rotation|rotation|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN low|low|JJ salt|salt|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD %|%|NN SDS|sds|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 2mM|2mm|NN EDTA|edta|NN ,|,|, 20mM|20mm|NN Tris-HCl|tris-hcl|NN pH|ph|NN 8.1|8.1|CD ,|,|, 150mM|150mm|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- ,|,|, once|once|RB with|with|IN high|high|JJ salt|salt|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD %|%|NN SDS|sds|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 2mM|2mm|NN EDTA|edta|NN ,|,|, 20mM|20mm|NN Tris-HCl|tris-hcl|NN pH|ph|NN 8.1|8.1|CD ,|,|, 500mM|500mm|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- ,|,|, once|once|RB with|with|IN LiCl|licl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 250mM|250mm|NN LiCl|licl|NN ,|,|, 1|1|CD %|%|NN NP-40|np-40|NN ,|,|, 1|1|CD %|%|NN deoxycholate|deoxycholate|NN ,|,|, 1mM|1mm|NN EDTA|edta|NN ,|,|, 10mM|10mm|NN Tris-HCl|tris-hcl|NN pH|ph|NN 8.1|8.1|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC twice|twice|RB with|with|IN TE|te|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10mM|10mm|NN Tris-HCl|tris-hcl|NN pH|ph|NN 8.1|8.1|CD ,|,|, 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- .|.|. Two|two|CD washes|wash|VBZ with|with|IN 250μl|250μl|NN of|of|IN freshly|freshly|RB prepared|prepared|JJ elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN SDS|sds|NN ,|,|, 100mM|100mm|NN NaHCO3|nahco3|NN -RRB-|-rrb-|-RRB- were|be|VBD done|do|VBN followed|follow|VBN by|by|IN vortexing|vortex|VBG and|and|CC incubation|incubation|NN under|under|IN rotation|rotation|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 15|15|CD min|min|NN .|.|. To|to|TO reverse|reverse|VB the|the|DT cross-link|cross-link|NN 30μl|30μl|NN of|of|IN 5M|5m|NN NaCl|nacl|NN were|be|VBD added|add|VBN to|to|TO the|the|DT elute|elute|NN and|and|CC incubated|incubate|VBN over|over|IN night|night|NN at|at|IN 65ºC|65ºc|NN .|.|. Finally|finally|RB ,|,|, 4μl|4μl|NN of|of|IN 0.5|0.5|CD M|m|NN EDTA|edta|NN ,|,|, 20μl|20μl|NN of|of|IN 1M|1m|NN Tris-HCl|tris-hcl|NN pH|ph|NN 6.5|6.5|CD and|and|CC 2μl|2μl|CD of|of|IN 10mg/ml|10mg/ml|CD Proteinase-K|proteinase-k|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN and|and|CC the|the|DT suspension|suspension|NN incubated|incubate|VBN at|at|IN 45ºC|45ºc|NN for|for|IN 2h|2h|NN .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN and|and|CC recovered|recover|VBN by|by|IN standard|standard|JJ phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN and|and|CC ethanol|ethanol|NN precipitation|precipitation|NN with|with|IN 20μg|20μg|NN of|of|IN glycogen|glycogen|NN .|.|.
Cross-linked|cross-linked|JJ cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN ,|,|, washed|wash|VBN thrice|thrice|RB with|with|IN ice-cold|ice-cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, resuspended|resuspend|VBN in|in|IN 1|1|CD ml|ml|NN lysis|lysis|NN buffer|buffer|NN -LSB-|-lsb-|-LRB- 10|10|CD mM|mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD %|%|NN sucrose|sucrose|NN ,|,|, 50|50|CD mM|mm|NN NaCl|nacl|NN ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 20|20|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN and|and|CC 0.1|0.1|CD mg/ml|mg/ml|NN RNase|rnase|NN A|a|NN -RSB-|-rsb-|-RRB- and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD min|min|NN .|.|. After|after|IN lysis|lysis|NN ,|,|, 3|3|CD ml|ml|NN immunoprecipitation|immunoprecipitation|NN -LRB-|-lrb-|-LRB- IP|IP|NNP -RRB-|-rrb-|-RRB- buffer|buffer|NN -LSB-|-lsb-|-LRB- 50|50|CD mM|mm|NN HEPES|hepe|NNS --|--|: KOH|koh|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 150|150|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 0.1|0.1|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN ,|,|, 0.1|0.1|CD %|%|NN sodium|sodium|NN dodecyl|dodecyl|NN sulphate|sulphate|NN -LRB-|-lrb-|-LRB- SDS|sds|NN -RRB-|-rrb-|-RRB- and|and|CC PMSF|pmsf|NN -LRB-|-lrb-|-LRB- final|final|JJ 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- was|be|VBD added|add|VBN and|and|CC the|the|DT DNA|dna|NN sheared|shear|VBD to|to|TO an|a|DT average|average|JJ size|size|NN of|of|IN ~|~|NN 250|250|CD bp|bp|NN using|use|VBG a|a|DT Bioruptor|bioruptor|NN -LRB-|-lrb-|-LRB- Diagenode|diagenode|NN -RRB-|-rrb-|-RRB- .|.|. Insoluble|insoluble|JJ cellular|cellular|JJ matter|matter|NN was|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN for|for|IN 10|10|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. An|a|DT 800|800|CD μl|μl|NN aliquot|aliquot|NN was|be|VBD incubated|incubate|VBN with|with|IN 20|20|CD μl|μl|NN Protein|protein|NN A/G|a/g|NN UltraLink|UltraLink|NNP Resin|Resin|NNP -LRB-|-lrb-|-LRB- Pierce|Pierce|NNP -RRB-|-rrb-|-RRB- on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN for|for|IN 45|45|CD minutes|minute|NNS at|at|IN room|room|NN temperature|temperature|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD removed|remove|VBN and|and|CC incubated|incubate|VBN with|with|IN mouse|mouse|NN monoclonal|monoclonal|JJ antibody|antibody|NN -LRB-|-lrb-|-LRB- Neoclone|neoclone|JJ cat|cat|NN .|.|. no|no|DT .|.|. WP009|wp009|NN -RRB-|-rrb-|-RRB- and|and|CC 30|30|CD μl|μl|NN Protein|protein|NN A/G|a/g|NN UltraLink|UltraLink|NNP Resin|Resin|NNP -LRB-|-lrb-|-LRB- pre-incubated|pre-incubated|JJ with|with|IN 1mg/ml|1mg/ml|JJ BSA|bsa|NN in|in|IN TBS|tbs|NN -RRB-|-rrb-|-RRB- ,|,|, on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 90|90|CD min|min|NN .|.|. Samples|sample|NNS were|be|VBD washed|wash|VBN once|once|RB with|with|IN IP|IP|NNP buffer|buffer|NN ,|,|, twice|twice|RB with|with|IN IP|IP|NNP buffer|buffer|NN +|+|CC 500|500|CD mM|mm|NN NaCl|nacl|NN ,|,|, once|once|RB with|with|IN wash|wash|NN buffer|buffer|NN -LSB-|-lsb-|-LRB- 10|10|CD mM|mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.5|0.5|CD %|%|NN Nonidet|Nonidet|NNP P-40|P-40|NNP and|and|CC 0.5|0.5|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN -RSB-|-rsb-|-RRB- and|and|CC once|once|RB with|with|IN TE|te|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- .|.|. Immunoprecipitated|immunoprecipitate|VBN complexes|complex|NNS were|be|VBD eluted|elute|VBN in|in|IN 100|100|CD μl|μl|NN elution|elution|NN buffer|buffer|NN -LSB-|-lsb-|-LRB- 10|10|CD mM|mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN and|and|CC 1|1|CD %|%|NN SDS|sds|NN -RSB-|-rsb-|-RRB- at|at|IN 65|65|CD °C|°c|NN for|for|IN 20|20|CD min|min|NN .|.|. Immunoprecipitated|immunoprecipitate|VBN samples|sample|NNS and|and|CC the|the|DT sheared|sheared|JJ DNA|dna|NN from|from|IN the|the|DT Bioruptor|Bioruptor|NNP were|be|VBD uncrosslinked|uncrosslinked|JJ in|in|IN elution|elution|NN buffer|buffer|NN containing|contain|VBG 0.8|0.8|CD mg/ml|mg/ml|NN Pronase|Pronase|NNP at|at|IN 42|42|CD °C|°c|NN for|for|IN 2|2|CD h|h|NN followed|follow|VBN by|by|IN 65|65|CD °C|°c|NN for|for|IN 6|6|CD h.|h.|NN DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG the|the|DT phenol-chloroform|phenol-chloroform|JJ method|method|NN .|.|.
Crosslinked|crosslinked|JJ cells|cell|NNS were|be|VBD then|then|RB resuspended|resuspend|VBN in|in|IN 500|500|CD ul|ul|NN of|of|IN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- with|with|IN 40|40|CD ul|ul|NN of|of|IN protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- 50|50|CD mg|mg|NN in|in|IN 0.25|0.25|CD ml|ml|NN of|of|IN DMSO|dmso|NN and|and|CC 0.75|0.75|CD ml|ml|NN of|of|IN TDW|tdw|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD lyzed|lyze|VBN with|with|IN 1|1|CD ul|ul|NN of|of|IN lysozyme|lysozyme|NN for|for|IN 30|30|CD min|min|NN at|at|IN 37C|37c|NN on|on|IN a|a|DT rocker|rocker|NN .|.|. 0.55|0.55|CD ml|ml|NN of|of|IN 2X|2x|NN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 200|200|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO the|the|DT sample|sample|NN ,|,|, and|and|CC then|then|RB was|be|VBD sonicated|sonicate|VBN to|to|TO fragmentize|fragmentize|VB genomic|genomic|JJ DNA|dna|NN .|.|. 0.3|0.3|CD ml|ml|NN of|of|IN Wash|Wash|NNP buffer|buffer|NN I|i|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 140|140|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO make|make|VB the|the|DT volume|volume|NN up|up|IN to|to|TO 1.4|1.4|CD ml|ml|NN .|.|. Only|only|RB 0.7|0.7|CD ml|ml|NN was|be|VBD taken|take|VBN and|and|CC transfered|transfer|VBN to|to|TO a|a|DT new|new|JJ tube|tube|NN ,|,|, and|and|CC 15|15|CD ul|ul|NN of|of|IN Anti-c-myc|anti-c-myc|JJ mouse|mouse|NN antibody|antibody|NN was|be|VBD added|add|VBN ,|,|, and|and|CC the|the|DT sample|sample|NN was|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 4C|4c|NN to|to|TO make|make|VB Antibody-TF|antibody-tf|NN complex|complex|NN .|.|. 50|50|CD ul|ul|NN of|of|IN Dynabeads|Dynabeads|NNP Pan|Pan|NNP mouse|mouse|NN IgG|igg|NN were|be|VBD washed|wash|VBN 3|3|CD times|time|NNS with|with|IN bead|bead|NN washing|wash|VBG solution|solution|NN -LRB-|-lrb-|-LRB- 250|250|CD mg|mg|NN BSA|bsa|NN in|in|IN 50|50|CD ml|ml|NN of|of|IN PBS|PBS|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC were|be|VBD added|add|VBN to|to|TO the|the|DT sample|sample|NN .|.|. Cell|cell|NN lysate|lysate|NN with|with|IN beads|bead|NNS were|be|VBD incubated|incubate|VBN for|for|IN 6|6|CD hours|hour|NNS or|or|CC overnight|overnight|JJ at|at|IN 4C|4c|NN to|to|TO make|make|VB Dynabead-antibody-TF|dynabead-antibody-tf|NN complex|complex|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD pulled|pull|VBN down|down|RP on|on|IN a|a|DT magnet|magnet|NN stand|stand|NN ,|,|, and|and|CC washed|wash|VBN 2|2|CD times|time|NNS with|with|IN wash|wash|NN buffer|buffer|NN I|i|NN and|and|CC with|with|IN wash|wash|NN buffer|buffer|NN II|ii|CD -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 500|500|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, wash|wash|NN buffer|buffer|NN III|iii|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC wash|wash|NN buffer|buffer|NN IV|iv|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT bead-bound|bead-bound|JJ TF-DNA|tf-dna|NN complex|complex|NN was|be|VBD then|then|RB end-repaired|end-repaired|JJ ,|,|, dA-tailed|da-tailed|JJ ,|,|, and|and|CC ligated|ligate|VBN to|to|TO the|the|DT first|first|JJ adapter|adapter|NN .|.|. Adapter-ligated|adapter-ligated|JJ sample|sample|NN was|be|VBD then|then|RB treated|treat|VBN with|with|IN nick-repair|nick-repair|JJ reagent|reagent|NN ,|,|, and|and|CC was|be|VBD treated|treat|VBN with|with|IN lambda|lambda|NN exonuclease|exonuclease|NN and|and|CC RecJ|recj|NN exonuclease|exonuclease|NN .|.|. Then|then|RB DNA|dna|NN was|be|VBD eluted|elute|VBN away|away|RB from|from|IN Dynabeads|Dynabeads|NNPS by|by|IN incubating|incubate|VBG in|in|IN 200|200|CD ul|ul|NN of|of|IN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD %|%|NN SDS|sds|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- at|at|IN 65C|65c|CD overnight|overnight|JJ .|.|. Protein|protein|NN was|be|VBD removed|remove|VBN by|by|IN treating|treat|VBG 4|4|CD ul|ul|NN of|of|IN protease|protease|NN K|k|NN and|and|CC being|be|VBG incubated|incubate|VBN at|at|IN 55C|55c|NN for|for|IN 2|2|CD hours|hour|NNS ,|,|, and|and|CC by|by|IN Phenol-Chloroform-IAA|phenol-chloroform-iaa|NN extraction|extraction|NN .|.|. Purified|purify|VBN DNA|dna|NN was|be|VBD used|use|VBN to|to|TO bulid|bulid|VB the|the|DT second|second|JJ strand|strand|NN synthesis|synthesis|NN ,|,|, followed|follow|VBN by|by|IN another|another|DT dA-tailing|da-tailing|NN ,|,|, second|second|JJ strand|strand|NN ligation|ligation|NN ,|,|, and|and|CC 3|3|CD '|'|'' overhang|overhang|NN removal|removal|NN stpes|stpe|NNS .|.|. Then|then|RB the|the|DT sequencing|sequencing|NN library|library|NN was|be|VBD amplified|amplify|VBN with|with|IN PCR|pcr|NN enrichment|enrichment|NN .|.|.
Crosslinked|crosslinked|JJ cells|cell|NNS were|be|VBD then|then|RB resuspended|resuspend|VBN in|in|IN 500|500|CD ul|ul|NN of|of|IN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- with|with|IN 40|40|CD ul|ul|NN of|of|IN protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- 50|50|CD mg|mg|NN in|in|IN 0.25|0.25|CD ml|ml|NN of|of|IN DMSO|dmso|NN and|and|CC 0.75|0.75|CD ml|ml|NN of|of|IN TDW|tdw|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD lyzed|lyze|VBN with|with|IN 1|1|CD ul|ul|NN of|of|IN lysozyme|lysozyme|NN for|for|IN 30|30|CD min|min|NN at|at|IN 37oC|37oc|NN on|on|IN a|a|DT rocker|rocker|NN .|.|. 0.55|0.55|CD ml|ml|NN of|of|IN 2X|2x|NN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 200|200|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO the|the|DT sample|sample|NN ,|,|, and|and|CC then|then|RB was|be|VBD sonicated|sonicate|VBN to|to|TO fragmentize|fragmentize|VB genomic|genomic|JJ DNA|dna|NN .|.|. 0.3|0.3|CD ml|ml|NN of|of|IN Wash|Wash|NNP buffer|buffer|NN I|i|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 140|140|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO make|make|VB the|the|DT volume|volume|NN up|up|IN to|to|TO 1.4|1.4|CD ml|ml|NN .|.|. Only|only|RB 0.7|0.7|CD ml|ml|NN was|be|VBD taken|take|VBN and|and|CC transfered|transfer|VBN to|to|TO a|a|DT new|new|JJ tube|tube|NN ,|,|, and|and|CC 10|10|CD ul|ul|NN of|of|IN Anti-rpoB|anti-rpob|JJ mouse|mouse|NN antibody|antibody|NN was|be|VBD added|add|VBN ,|,|, and|and|CC the|the|DT sample|sample|NN was|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 4|4|CD oC|oc|NN to|to|TO make|make|VB Antibody-TF|antibody-tf|NN complex|complex|NN .|.|. 50|50|CD ul|ul|NN of|of|IN Dynabeads|Dynabeads|NNP Pan|Pan|NNP mouse|mouse|NN IgG|igg|NN were|be|VBD washed|wash|VBN 3|3|CD times|time|NNS with|with|IN bead|bead|NN washing|wash|VBG solution|solution|NN -LRB-|-lrb-|-LRB- 250|250|CD mg|mg|NN BSA|bsa|NN in|in|IN 50|50|CD ml|ml|NN of|of|IN PBS|PBS|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC were|be|VBD added|add|VBN to|to|TO the|the|DT sample|sample|NN .|.|. Cell|cell|NN lysate|lysate|NN with|with|IN beads|bead|NNS were|be|VBD incubated|incubate|VBN for|for|IN 6|6|CD hours|hour|NNS or|or|CC overnight|overnight|JJ at|at|IN 4oC|4oc|NN to|to|TO make|make|VB Dynabead-antibody-TF|dynabead-antibody-tf|NN complex|complex|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD pulled|pull|VBN down|down|RP on|on|IN a|a|DT magnet|magnet|NN stand|stand|NN ,|,|, and|and|CC washed|wash|VBN 2|2|CD times|time|NNS with|with|IN wash|wash|NN buffer|buffer|NN I|i|NN and|and|CC with|with|IN wash|wash|NN buffer|buffer|NN II|ii|CD -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 500|500|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, wash|wash|NN buffer|buffer|NN III|iii|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC wash|wash|NN buffer|buffer|NN IV|iv|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT bead-bound|bead-bound|JJ TF-DNA|tf-dna|NN complex|complex|NN was|be|VBD then|then|RB end-repaired|end-repaired|JJ ,|,|, dA-tailed|da-tailed|JJ ,|,|, and|and|CC ligated|ligate|VBN to|to|TO the|the|DT first|first|JJ adapter|adapter|NN .|.|. Adapter-ligated|adapter-ligated|JJ sample|sample|NN was|be|VBD then|then|RB treated|treat|VBN with|with|IN nick-repair|nick-repair|JJ reagent|reagent|NN ,|,|, and|and|CC was|be|VBD treated|treat|VBN with|with|IN lambda|lambda|NN exonuclease|exonuclease|NN and|and|CC RecJ|recj|NN exonuclease|exonuclease|NN .|.|. Then|then|RB DNA|dna|NN was|be|VBD eluted|elute|VBN away|away|RB from|from|IN Dynabeads|Dynabeads|NNPS by|by|IN incubating|incubate|VBG in|in|IN 200|200|CD ul|ul|NN of|of|IN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD %|%|NN SDS|sds|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- at|at|IN 65oC|65oc|NN overnight|overnight|JJ .|.|. Protein|protein|NN was|be|VBD removed|remove|VBN by|by|IN treating|treat|VBG 4|4|CD ul|ul|NN of|of|IN protease|protease|NN K|k|NN and|and|CC being|be|VBG incubated|incubate|VBN at|at|IN 55|55|CD oC|oc|NN for|for|IN 2|2|CD hours|hour|NNS ,|,|, and|and|CC by|by|IN Phenol-Chloroform-IAA|phenol-chloroform-iaa|NN extraction|extraction|NN .|.|. Purified|purify|VBN DNA|dna|NN was|be|VBD used|use|VBN to|to|TO bulid|bulid|VB the|the|DT second|second|JJ strand|strand|NN synthesis|synthesis|NN ,|,|, followed|follow|VBN by|by|IN another|another|DT dA-tailing|da-tailing|NN ,|,|, second|second|JJ strand|strand|NN ligation|ligation|NN ,|,|, and|and|CC 3|3|CD '|'|'' overhang|overhang|NN removal|removal|NN stpes|stpe|NNS .|.|. Then|then|RB the|the|DT sequencing|sequencing|NN library|library|NN was|be|VBD amplified|amplify|VBN with|with|IN PCR|pcr|NN enrichment|enrichment|NN .|.|.
Crosslinked|crosslinked|JJ cells|cell|NNS were|be|VBD then|then|RB resuspended|resuspend|VBN in|in|IN 500|500|CD ul|ul|NN of|of|IN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- with|with|IN 40|40|CD ul|ul|NN of|of|IN protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- 50|50|CD mg|mg|NN in|in|IN 0.25|0.25|CD ml|ml|NN of|of|IN DMSO|dmso|NN and|and|CC 0.75|0.75|CD ml|ml|NN of|of|IN TDW|tdw|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD lyzed|lyze|VBN with|with|IN 1|1|CD ul|ul|NN of|of|IN lysozyme|lysozyme|NN for|for|IN 30|30|CD min|min|NN at|at|IN 37oC|37oc|NN on|on|IN a|a|DT rocker|rocker|NN .|.|. 0.55|0.55|CD ml|ml|NN of|of|IN 2X|2x|NN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 200|200|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO the|the|DT sample|sample|NN ,|,|, and|and|CC then|then|RB was|be|VBD sonicated|sonicate|VBN to|to|TO fragmentize|fragmentize|VB genomic|genomic|JJ DNA|dna|NN .|.|. 0.3|0.3|CD ml|ml|NN of|of|IN Wash|Wash|NNP buffer|buffer|NN I|i|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 140|140|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO make|make|VB the|the|DT volume|volume|NN up|up|IN to|to|TO 1.4|1.4|CD ml|ml|NN .|.|. Only|only|RB 0.7|0.7|CD ml|ml|NN was|be|VBD taken|take|VBN and|and|CC transfered|transfer|VBN to|to|TO a|a|DT new|new|JJ tube|tube|NN ,|,|, and|and|CC 15|15|CD ul|ul|NN of|of|IN Anti-c-myc|anti-c-myc|JJ mouse|mouse|NN antibody|antibody|NN was|be|VBD added|add|VBN ,|,|, and|and|CC the|the|DT sample|sample|NN was|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 4|4|CD oC|oc|NN to|to|TO make|make|VB Antibody-TF|antibody-tf|NN complex|complex|NN .|.|. 50|50|CD ul|ul|NN of|of|IN Dynabeads|Dynabeads|NNP Pan|Pan|NNP mouse|mouse|NN IgG|igg|NN were|be|VBD washed|wash|VBN 3|3|CD times|time|NNS with|with|IN bead|bead|NN washing|wash|VBG solution|solution|NN -LRB-|-lrb-|-LRB- 250|250|CD mg|mg|NN BSA|bsa|NN in|in|IN 50|50|CD ml|ml|NN of|of|IN PBS|PBS|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC were|be|VBD added|add|VBN to|to|TO the|the|DT sample|sample|NN .|.|. Cell|cell|NN lysate|lysate|NN with|with|IN beads|bead|NNS were|be|VBD incubated|incubate|VBN for|for|IN 6|6|CD hours|hour|NNS or|or|CC overnight|overnight|JJ at|at|IN 4oC|4oc|NN to|to|TO make|make|VB Dynabead-antibody-TF|dynabead-antibody-tf|NN complex|complex|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD pulled|pull|VBN down|down|RP on|on|IN a|a|DT magnet|magnet|NN stand|stand|NN ,|,|, and|and|CC washed|wash|VBN 2|2|CD times|time|NNS with|with|IN wash|wash|NN buffer|buffer|NN I|i|NN and|and|CC with|with|IN wash|wash|NN buffer|buffer|NN II|ii|CD -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 500|500|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, wash|wash|NN buffer|buffer|NN III|iii|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN and|and|CC 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC wash|wash|NN buffer|buffer|NN IV|iv|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 1mM|1mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT bead-bound|bead-bound|JJ TF-DNA|tf-dna|NN complex|complex|NN was|be|VBD then|then|RB end-repaired|end-repaired|JJ ,|,|, dA-tailed|da-tailed|JJ ,|,|, and|and|CC ligated|ligate|VBN to|to|TO the|the|DT first|first|JJ adapter|adapter|NN .|.|. Adapter-ligated|adapter-ligated|JJ sample|sample|NN was|be|VBD then|then|RB treated|treat|VBN with|with|IN nick-repair|nick-repair|JJ reagent|reagent|NN ,|,|, and|and|CC was|be|VBD treated|treat|VBN with|with|IN lambda|lambda|NN exonuclease|exonuclease|NN and|and|CC RecJ|recj|NN exonuclease|exonuclease|NN .|.|. Then|then|RB DNA|dna|NN was|be|VBD eluted|elute|VBN away|away|RB from|from|IN Dynabeads|Dynabeads|NNPS by|by|IN incubating|incubate|VBG in|in|IN 200|200|CD ul|ul|NN of|of|IN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD %|%|NN SDS|sds|NN and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- at|at|IN 65oC|65oc|NN overnight|overnight|JJ .|.|. Protein|protein|NN was|be|VBD removed|remove|VBN by|by|IN treating|treat|VBG 4|4|CD ul|ul|NN of|of|IN protease|protease|NN K|k|NN and|and|CC being|be|VBG incubated|incubate|VBN at|at|IN 55|55|CD oC|oc|NN for|for|IN 2|2|CD hours|hour|NNS ,|,|, and|and|CC by|by|IN Phenol-Chloroform-IAA|phenol-chloroform-iaa|NN extraction|extraction|NN .|.|. Purified|purify|VBN DNA|dna|NN was|be|VBD used|use|VBN to|to|TO bulid|bulid|VB the|the|DT second|second|JJ strand|strand|NN synthesis|synthesis|NN ,|,|, followed|follow|VBN by|by|IN another|another|DT dA-tailing|da-tailing|NN ,|,|, second|second|JJ strand|strand|NN ligation|ligation|NN ,|,|, and|and|CC 3|3|CD '|'|'' overhang|overhang|NN removal|removal|NN stpes|stpe|NNS .|.|. Then|then|RB the|the|DT sequencing|sequencing|NN library|library|NN was|be|VBD amplified|amplify|VBN with|with|IN PCR|pcr|NN enrichment|enrichment|NN .|.|.
Crosslinked/reversed|crosslinked/reversed|VBD DNA|dna|NN
Crosslinking|crosslinking|NN was|be|VBD performed|perform|VBN using|use|VBG 1|1|CD %|%|NN of|of|IN forlmaldehyde|forlmaldehyde|NN
crp.ee.chipseq|crp.ee.chipseq|NN
crp.ee.input|crp.ee.input|JJ
crpfis.rep1.ee|crpfis.rep1.ee|NN
crpfis.rep1.me|crpfis.rep1.me|NN
crpfis.rep2.ee|crpfis.rep2.ee|NN
crpfis.rep2.me|crpfis.rep2.me|NN
crp.me.chipseq|crp.me.chipseq|NN
crp.me|crp.me|NN ,|,|, input|input|NN
crp.me.input|crp.me.input|JJ
crpmutant.fis.ee.chipseq|crpmutant.fis.ee.chipseq|NN
crpmutant.fis.ee.input|crpmutant.fis.ee.input|JJ
crpmutant.fis.me.chipseq|crpmutant.fis.me.chipseq|NN
crpmutant.fis.me.input|crpmutant.fis.me.input|JJ
crp.rep1.ee|crp.rep1.ee|NN
crp.rep1.me|crp.rep1.me|NN
crp.rep2.ee|crp.rep2.ee|NN
crp.rep2.me|crp.rep2.me|NN
crp|crp|VBP ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
crp|crp|VBP ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
crp|crp|VBP ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
crp|crp|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
CSH50|csh50|NN control|control|NN E-minimal|e-minimal|JJ medium|medium|NN 90|90|CD min|min|NN
CSH50|csh50|NN control|control|NN -LRB-|-lrb-|-LRB- mock|mock|JJ igG|igg|NN -RRB-|-rrb-|-RRB- E-minimal|e-minimal|JJ medium|medium|NN replicate|replicate|VB 1|1|CD
CSH50|csh50|NN control|control|NN -LRB-|-lrb-|-LRB- mock|mock|JJ igG|igg|NN -RRB-|-rrb-|-RRB- E-minimal|e-minimal|JJ medium|medium|NN replicate|replicate|VB 2|2|CD
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 4.5|4.5|CD 90|90|CD min|min|NN
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 4.5|4.5|CD 90|90|CD min|min|NN replicate|replicate|VBP 1|1|CD
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 4.5|4.5|CD 90|90|CD min|min|NN replicate|replicate|VBP 2|2|CD
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 4.5|4.5|CD 90|90|CD min|min|NN replicate|replicate|VBP 3|3|CD
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 7|7|CD 90|90|CD min|min|NN
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 7|7|CD 90|90|CD min|min|NN replicate|replicate|VBP 1|1|CD
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 7|7|CD 90|90|CD min|min|NN replicate|replicate|VBP 2|2|CD
CSH50|csh50|NN E-minimal|e-minimal|JJ medium|medium|NN pH|ph|NN 7|7|CD 90|90|CD min|min|NN replicate|replicate|VBP 3|3|CD
CsiR|csir|NN _|_|CD ChIPSeq|chipseq|NN
CsiR|csir|NN _|_|CD RNASeq|rnaseq|NN
cspF|cspf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
cspF|cspf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
cspF|cspf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
cspF|cspf|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
csv|csv|VBP files|file|NNS contain|contain|VBP 16|16|CD columns|column|NNS of|of|IN the|the|DT data|datum|NNS ,|,|, each|each|DT pair|pair|NN corresponds|correspond|VBZ to|to|TO the|the|DT counts|count|NNS from|from|IN the|the|DT top|top|NN -LRB-|-lrb-|-LRB- odd|odd|JJ numbers|number|NNS -RRB-|-rrb-|-RRB- and|and|CC bottom|bottom|NN -LRB-|-lrb-|-LRB- even|even|RB numbers|number|NNS -RRB-|-rrb-|-RRB- strand|strand|NN .|.|. The|the|DT first|first|JJ pair|pair|NN corresponds|correspond|VBZ to|to|TO counts|count|NNS collected|collect|VBN at|at|IN 0|0|CD minutes|minute|NNS after|after|IN rifampicin|rifampicin|NN addition|addition|NN .|.|. Similarly|similarly|RB ,|,|, the|the|DT second|second|JJ ,|,|, third|third|JJ ,|,|, fourth|fourth|JJ ,|,|, fifth|fifth|JJ ,|,|, sixth|sixth|JJ ,|,|, seventh|seventh|JJ ,|,|, and|and|CC eigth|eigth|NN pairs|pair|NNS correspond|correspond|VBP to|to|TO counts|count|NNS collected|collect|VBN at|at|IN 2|2|CD ,|,|, 4|4|CD ,|,|, 6|6|CD ,|,|, 8|8|CD ,|,|, 10|10|CD ,|,|, 15|15|CD ,|,|, and|and|CC 20|20|CD minutes|minute|NNS after|after|IN rifampicin|rifampicin|NN addition|addition|NN .|.|. The|the|DT ith|ith|NN row|row|NN in|in|IN each|each|DT column|column|NN corresponds|correspond|VBZ to|to|TO the|the|DT number|number|NN of|of|IN alignments|alignment|NNS at|at|IN the|the|DT ith|ith|NN base|base|NN in|in|IN NC|NC|NNP _|_|SYM 000913.2|000913.2|CD .|.|.
ctrl1|ctrl1|NN
ctrl2|ctrl2|NN
ctrl3|ctrl3|NN
cultivation|cultivation|NN :|:|: continuous|continuous|JJ cultivation|cultivation|NN ,|,|, A-stat|a-stat|JJ
cultivation|cultivation|NN :|:|: continuous|continuous|JJ cultivation|cultivation|NN ,|,|, chemostat|chemostat|NN
culture|culture|NN :|:|: 18|18|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN
Culture|culture|NN cells|cell|NNS
culture|culture|NN condition|condition|NN :|:|: Aerobic|aerobic|JJ cultures|culture|NNS
culture|culture|NN condition|condition|NN :|:|: Anaerobic|anaerobic|JJ cultures|culture|NNS
culture|culture|NN condition|condition|NN :|:|: Anaerobic|anaerobic|JJ Cultures|culture|NNS
culture|culture|NN condition|condition|NN :|:|: anaerobic|anaerobic|JJ fermentive|fermentive|JJ condition|condition|NN
culture|culture|NN condition|condition|NN :|:|: nitrate|nitrate|VB respiratory|respiratory|JJ condition|condition|NN
Culture|culture|NN conditions|condition|NNS :|:|: 37|37|CD C|c|NN with|with|IN shaking|shake|VBG at|at|IN 220|220|CD RPM|rpm|NN
culture|culture|NN conditions|condition|NNS :|:|: aerobic|aerobic|JJ
culture|culture|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ
Cultured|culture|VBN cells|cell|NNS
Cultured|culture|VBN cells|cell|NNS -LRB-|-lrb-|-LRB- 50|50|CD mL|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD cross-linked|cross-link|VBN with|with|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 30|30|CD min|min|NN and|and|CC added|add|VBD 2|2|CD mL|ml|NN of|of|IN 2.5|2.5|CD M|m|NN glycine|glycine|NN to|to|TO quench|quench|VB the|the|DT unused|unused|JJ formaldehyde|formaldehyde|NN .|.|. After|after|IN washing|wash|VBG three|three|CD times|time|NNS with|with|IN 50|50|CD mL|ml|NN of|of|IN ice-cold|ice-cold|JJ Tris-buffered|tris-buffered|JJ saline|saline|NN -LRB-|-lrb-|-LRB- TBS|tbs|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT washed|washed|JJ cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 0.5|0.5|CD mL|ml|NN of|of|IN lysis|lysis|NN buffer|buffer|NN composed|compose|VBN of|of|IN 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD μg/mL|μg/ml|NN RNaseA|rnasea|NN ,|,|, protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN and|and|CC 1|1|CD kU|ku|NN Ready-Lyse|ready-lyse|NN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN at|at|IN 37oC|37oc|NN for|for|IN 30|30|CD min|min|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD then|then|RB treated|treat|VBN with|with|IN 0.5|0.5|CD mL|ml|NN of|of|IN 2|2|CD ×|×|CD IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 2|2|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- Triton|Triton|NNP X-100|x-100|NN ,|,|, and|and|CC protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -RRB-|-rrb-|-RRB- ,|,|, followed|follow|VBN by|by|IN incubation|incubation|NN on|on|IN ice|ice|NN for|for|IN 30|30|CD min|min|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB sonicated|sonicate|VBN in|in|IN an|a|DT ice|ice|NN bath|bath|NN using|use|VBG Sonic|Sonic|NNP Dismembrator|Dismembrator|NNP Model|Model|NNP 500|500|CD -LRB-|-lrb-|-LRB- four|four|CD times|time|NNS for|for|IN 20|20|CD s|s|NNS each|each|DT ,|,|, output|output|NN level|level|NN ,|,|, 2.5|2.5|CD -RRB-|-rrb-|-RRB- .|.|. Size|size|NN distribution|distribution|NN of|of|IN the|the|DT fragmented|fragmented|JJ DNAs|dna|NNS was|be|VBD confirmed|confirm|VBN using|use|VBG agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN -LRB-|-lrb-|-LRB- 200-400|200-400|CD bp|bp|NN -RRB-|-rrb-|-RRB- after|after|IN removing|remove|VBG cell|cell|NN debris|debris|NN by|by|IN centrifugation|centrifugation|NN .|.|.
culture|culture|NN denity|denity|NN :|:|: OD600|od600|NN =|=|JJ 0.55-0.6|0.55-0.6|CD culture|culture|NN
cultured|culture|VBN in|in|IN :|:|: M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN 0.2|0.2|CD %|%|NN acetate|acetate|NN
cultured|culture|VBN in|in|IN :|:|: M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN 0.2|0.2|CD %|%|NN fructose|fructose|NN
cultured|culture|VBN in|in|IN :|:|: M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN
Culture|culture|NN grown|grow|VBN in|in|IN 14|14|CD ml|ml|NN tube|tube|NN
Culture|culture|NN grown|grow|VBN in|in|IN 250|250|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flask|flask|NN
culture/growth|culture/growth|NN condition|condition|NN :|:|: Heatshock|Heatshock|NNP 15|15|CD min|min|NN
culture/growth|culture/growth|NN condition|condition|NN :|:|: Heatshock|heatshock|NN 30|30|CD min|min|NN
culture/growth|culture/growth|NN condition|condition|NN :|:|: Heatshock|heatshock|NN 60|60|CD min|min|NN
culture/growth|culture/growth|NN condition|condition|NN :|:|: LB|lb|NN -LRB-|-lrb-|-LRB- OD|od|NN =|=|JJ 0.87|0.87|CD -RRB-|-rrb-|-RRB-
culture/growth|culture/growth|NN condition|condition|NN :|:|: MOPS-P|mops-p|NN 0h|0h|NN
culture/growth|culture/growth|NN condition|condition|NN :|:|: MOPS-P|mops-p|NN 2h|2h|JJ
culture/growth|culture/growth|NN condition|condition|NN :|:|: MOPS-P|mops-p|NN 4h|4h|NN
culture|culture|NN media|media|NNS :|:|: 10|10|CD %|%|NN Luria|Luria|NNP broth|broth|NN
culture|culture|NN media|media|NNS :|:|: LB|lb|NN
culture|culture|NN media|media|NNS :|:|: LB|lb|NN with|with|IN 2.5|2.5|CD mM|mm|NN Fumaric|fumaric|JJ acid|acid|NN
Culture|culture|NN of|of|IN bacterial|bacterial|JJ strains|strain|NNS -LRB-|-lrb-|-LRB- 10|10|CD mL|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD centrifuged|centrifuge|VBN 20|20|CD min|min|NN at|at|IN 10,000|10,000|CD g|g|NN and|and|CC bacterial|bacterial|JJ pellets|pellet|NNS were|be|VBD washed|wash|VBN 3|3|CD times|time|NNS with|with|IN 2|2|CD mL|ml|NN of|of|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN -LRB-|-lrb-|-LRB- PBS|PBS|NNP -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN extraction|extraction|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT EasyDNA|easydna|NN kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN instructions|instruction|NNS slightly|slightly|RB modified|modify|VBN .|.|. Briefly|briefly|RB ,|,|, the|the|DT bacterial|bacterial|JJ pellet|pellet|NN was|be|VBD incubated|incubate|VBN 5|5|CD min|min|NN in|in|IN 200|200|CD μL|μl|NN of|of|IN PBS|PBS|NNP and|and|CC 1|1|CD μL|μl|NN of|of|IN protéinase|protéinase|NN K|k|NN -LRB-|-lrb-|-LRB- 20|20|CD mg/mL|mg/ml|NN ,|,|, Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- .|.|. Then|then|RB ,|,|, bacteria|bacterium|NNS were|be|VBD grinded|grind|VBN 3|3|CD min|min|NN with|with|IN ~|~|NN 100|100|CD mg|mg|NN of|of|IN 0.1|0.1|CD mm|mm|NN zirconia|zirconia|NN beads|bead|NNS -LRB-|-lrb-|-LRB- BioSpec|BioSpec|NNP Products|Products|NNPS -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT model|model|NN MM2000|mm2000|NN BeadBeater|beadbeater|NN instrument|instrument|NN -LRB-|-lrb-|-LRB- Retsch|retsch|NN -RRB-|-rrb-|-RRB- .|.|. Concentration|concentration|NN and|and|CC quality|quality|NN of|of|IN isolated|isolate|VBN gDNA|gdna|NN were|be|VBD checked|check|VBN with|with|IN the|the|DT spectrophotometer|spectrophotometer|NN Nanodrop|Nanodrop|NNP 1000|1000|CD -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- .|.|. Their|they|PRP$ integrity|integrity|NN was|be|VBD verified|verify|VBN by|by|IN 1|1|CD %|%|NN agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN .|.|. gDNA|gdna|NN were|be|VBD kept|keep|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|.
Cultures|culture|NNS -LRB-|-lrb-|-LRB- +|+|CC A|a|DT and|and|CC -|-|: A|a|NN -RRB-|-rrb-|-RRB- were|be|VBD incubated|incubate|VBN at|at|IN 32|32|CD °C|°c|NN with|with|IN shaking|shake|VBG for|for|IN additional|additional|JJ 15|15|CD min|min|NN ,|,|, then|then|RB cells|cell|NNS were|be|VBD pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 10|10|CD °C|°c|NN -LRB-|-lrb-|-LRB- 4500xg|4500xg|NN -RRB-|-rrb-|-RRB- and|and|CC resuspended|resuspend|VBN in|in|IN 10|10|CD ml|ml|NN of|of|IN TES|tes|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-Cl|tris-cl|NN pH7|ph7|NN .5|.5|CD ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 250|250|CD mM|mm|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- .|.|. Washing|wash|VBG procedure|procedure|NN was|be|VBD repeated|repeat|VBN twice|twice|RB to|to|TO remove|remove|VB culture|culture|NN liquid|liquid|NN and|and|CC excess|excess|NN of|of|IN gyrase|gyrase|NN poison|poison|NN .|.|.
Culture|culture|NN samples|sample|NNS for|for|IN microarray|microarray|NN analysis|analysis|NN were|be|VBD added|add|VBN to|to|TO ice-cold|ice-cold|JJ 5|5|CD %|%|NN water-saturated|water-saturated|JJ phenol|phenol|NN in|in|IN ethanol|ethanol|NN solution|solution|NN ,|,|, centrifuged|centrifuge|VBN at|at|IN 6,600|6,600|CD g|g|NN and|and|CC the|the|DT cell|cell|NN pellets|pellet|NNS flash|flash|VBP frozen|freeze|VBN in|in|IN liquid|liquid|JJ N2|n2|NN before|before|IN storing|store|VBG at|at|IN -80|-80|CD degrees|degree|NNS C|c|NN until|until|IN required|require|VBN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN the|the|DT stored|store|VBN cell|cell|NN pellets|pellet|NNS using|use|VBG the|the|DT hot|hot|JJ phenol|phenol|NN method|method|NN ,|,|, and|and|CC labeled|label|VBN Cy3|cy3|NN and|and|CC Cy5|cy5|NN cDNA|cdna|NN was|be|VBD prepared|prepare|VBN from|from|IN 16|16|CD ug|ug|NN total|total|JJ RNA|rna|NN with|with|IN 10|10|CD ug|ug|NN random|random|JJ hexamer|hexamer|NN -LRB-|-lrb-|-LRB- Integrated|Integrated|NNP DNA|DNA|NNP Technologies|Technologies|NNPS ,|,|, Inc.|Inc.|NNP ,|,|, Coralville|Coralville|NNP ,|,|, IA|IA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
Culture|culture|NN samples|sample|NNS frozen|freeze|VBN in|in|IN liquid|liquid|JJ methanol|methanol|NN
Culture|culture|NN samples|sample|NNS were|be|VBD transferred|transfer|VBN directly|directly|RB into|into|IN an|a|DT ice-cold|ice-cold|JJ ethanol/phenol|ethanol/phenol|NN stop|stop|VB solution|solution|NN ,|,|, then|then|RB collected|collect|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN until|until|IN RNA|rna|NN extraction|extraction|NN .|.|.
Cultures|culture|NNS for|for|IN samples|sample|NNS 1|1|CD and|and|CC 2|2|CD were|be|VBD incubated|incubate|VBN at|at|IN 44|44|CD °C|°c|NN for|for|IN 45|45|CD min|min|NN after|after|IN growth|growth|NN .|.|.
Cultures|culture|NNS grown|grow|VBN in|in|IN MOPS|mop|NNS minimal|minimal|JJ glucose|glucose|NN media|media|NNS containing|contain|VBG 10|10|CD µM|µm|NN FeSO4|feso4|NN
Cultures|culture|NNS of|of|IN both|both|DT strains|strain|NNS were|be|VBD started|start|VBN with|with|IN a|a|DT 2|2|CD %|%|NN overnight|overnight|JJ inoculum|inoculum|NN in|in|IN LB|LB|NNP media|media|NNS containing|contain|VBG 35ug/ml|35ug/ml|JJ chloramphenicol|chloramphenicol|NN .|.|.
Cultures|culture|NNS of|of|IN Caulobacter|caulobacter|NN -LRB-|-lrb-|-LRB- TLS1631-TLS1633|tls1631-tls1633|NN -RRB-|-rrb-|-RRB- were|be|VBD grown|grow|VBN at|at|IN 30oC|30oC|NNP in|in|IN PYE|PYE|NNP and|and|CC supplemented|supplement|VBN with|with|IN antibiotics|antibiotic|NNS ,|,|, as|as|RB necessary|necessary|JJ ,|,|, at|at|IN appropriate|appropriate|JJ concentrations|concentration|NNS .|.|. To|to|TO deplete|deplete|VB wild-type|wild-type|JJ non-tagged|non-tagged|JJ ParB|parb|NN ,|,|, exponential-phase|exponential-phase|NN cells|cell|NNS were|be|VBD washed|wash|VBN off|off|RP xylose|xylose|NN and|and|CC re-introduced|re-introduced|JJ to|to|TO PYE|PYE|NNP +0.2|+0.2|CD %|%|NN glucose|glucose|NN for|for|IN an|a|DT additional|additional|JJ 5|5|CD hours|hour|NNS .|.|. After|after|IN 4|4|CD hours|hour|NNS ,|,|, vanillate|vanillate|NN was|be|VBD added|add|VBN to|to|TO induce|induce|VB the|the|DT expression|expression|NN of|of|IN flag-parB|flag-parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- or|or|CC flag-parB|flag-parb|NN -LRB-|-lrb-|-LRB- G101S/R104A|g101s/r104a|NN -RRB-|-rrb-|-RRB- for|for|IN an|a|DT hour|hour|NN .|.|. Cultures|culture|NNS of|of|IN Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- TLS1637-TLS1650|tls1637-tls1650|NN -RRB-|-rrb-|-RRB- were|be|VBD grown|grow|VBN at|at|IN 30oC|30oC|NNP in|in|IN LB|LB|NNP and|and|CC supplemented|supplement|VBN with|with|IN antibiotics|antibiotic|NNS ,|,|, as|as|RB necessary|necessary|JJ ,|,|, at|at|IN appropriate|appropriate|JJ concentrations|concentration|NNS .|.|. IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mM|mm|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO induce|induce|VB the|the|DT production|production|NN of|of|IN T18-ParB|t18-parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- or|or|CC T18-ParB|t18-parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN an|a|DT hour|hour|NN ,|,|, formadehyde|formadehyde|NN -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO fix|fix|VB cells|cell|NNS for|for|IN ChIP-seq|ChIP-seq|NNP .|.|.
Cultures|culture|NNS of|of|IN E.|e.|FW coli|coli|FW CFT073|cft073|NN were|be|VBD maintained|maintain|VBN at|at|IN --|--|: 80ºC|80ºc|NN in|in|IN Luria-Bertani|luria-bertani|JJ broth|broth|NN with|with|IN 15|15|CD %|%|NN glycerol|glycerol|NN .|.|. Cultures|culture|NNS were|be|VBD streaked|streak|VBN onto|onto|IN LB|LB|NNP agar|agar|NN plates|plate|NNS and|and|CC incubated|incubate|VBN -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN ,|,|, 24|24|CD h|h|NN -RRB-|-rrb-|-RRB- .|.|. A|a|DT single|single|JJ colony|colony|NN was|be|VBD inoculated|inoculate|VBN into|into|IN 150|150|CD mL|ml|NN of|of|IN LB|lb|NN broth|broth|NN -LRB-|-lrb-|-LRB- in|in|IN a|a|DT 500|500|CD mL|ml|NN baffled|baffle|VBN flask|flask|NN -RRB-|-rrb-|-RRB- .|.|. Three|three|CD inoculated|inoculate|VBN flasks|flask|NNS contained|contain|VBD LB|lb|NN broth|broth|NN alone|alone|RB -LRB-|-lrb-|-LRB- controls|control|NNS -RRB-|-rrb-|-RRB- ,|,|, and|and|CC three|three|CD inoculated|inoculate|VBN flasks|flask|NNS were|be|VBD supplemented|supplement|VBN with|with|IN cranberry|cranberry|NN derived|derive|VBN PAC|PAC|NNP extract|extract|NN -LRB-|-lrb-|-LRB- 100|100|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- .|.|. Bacteria|bacterium|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN ,|,|, 5|5|CD h|h|NN ,|,|, 200|200|CD rpm|rpm|NN to|to|TO mid-log|mid-log|JJ growth|growth|NN phase|phase|NN .|.|.
Cultures|culture|NNS of|of|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN and|and|CC its|its|PRP$ derivates|derivate|NNS were|be|VBD cross|cross|JJ linked|link|VBN by|by|IN addition|addition|NN of|of|IN 27|27|CD µl|µl|NN of|of|IN formaldehyde|formaldehyde|NN -LRB-|-lrb-|-LRB- 37|37|CD %|%|NN -RRB-|-rrb-|-RRB- per|per|IN ml|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN 1|1|CD %|%|NN -RRB-|-rrb-|-RRB- .|.|. Crosslinking|crosslinking|NN was|be|VBD performed|perform|VBN at|at|IN slow|slow|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 100|100|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- for|for|IN 20|20|CD min|min|NN followed|follow|VBN by|by|IN quenching|quench|VBG with|with|IN 0.2|0.2|CD ml|ml|NN of|of|IN 2.5|2.5|CD M|m|NN glycine|glycine|NN per|per|IN ml|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN 0.5|0.5|CD M|m|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC washed|wash|VBN twice|twice|RB with|with|IN cold|cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- pH7|ph7|NN .5|.5|CD -RRB-|-rrb-|-RRB- .|.|. After|after|IN resuspension|resuspension|NN in|in|IN 1|1|CD ml|ml|NN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10mM|10mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD %|%|NN sucrose|sucrose|NN ,|,|, 50mM|50mm|NN NaCl|nacl|NN ,|,|, 10mM|10mm|NN EDTA|edta|NN ,|,|, 10|10|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN -RRB-|-rrb-|-RRB- and|and|CC incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD min|min|NN C|c|NN followed|follow|VBN by|by|IN addition|addition|NN of|of|IN 4|4|CD ml|ml|NN IP|IP|NNP buffer|buffer|NN cells|cell|NNS were|be|VBD sonicated|sonicate|VBN on|on|IN ice|ice|NN with|with|IN 12|12|CD times|time|NNS 30|30|CD sec|sec|NN and|and|CC 30|30|CD sec|sec|NN breaks|break|NNS at|at|IN an|a|DT UP|up|NN 400s|400s|CD Ultrasonic|ultrasonic|JJ processor|processor|NN -LRB-|-lrb-|-LRB- Dr.|Dr.|NNP Hielscher|Hielscher|NNP GmbH|gmbh|NN -RRB-|-rrb-|-RRB- with|with|IN 100|100|CD %|%|NN power|power|NN .|.|. After|after|IN centrifugation|centrifugation|NN for|for|IN 10|10|CD min|min|NN at|at|IN 9000|9000|CD g|g|NN ,|,|, 800|800|CD µl|µl|NN aliquotes|aliquote|NNS of|of|IN the|the|DT supernatant|supernatant|NN were|be|VBD stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|. 800|800|CD µl|µl|NN of|of|IN sonicated|sonicated|JJ cell|cell|NN extract|extract|NN -LRB-|-lrb-|-LRB- see|see|VB above|above|IN -RRB-|-rrb-|-RRB- were|be|VBD incubated|incubate|VBN with|with|IN 20|20|CD µl|µl|NN protein|protein|NN A/G|a/g|NN agarose|agarose|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Ultralink|ultralink|NN -RRB-|-rrb-|-RRB- and|and|CC antibody|antibody|NN rotating|rotate|VBG at|at|IN 4|4|CD °C|°c|NN .|.|. Washing|wash|VBG was|be|VBD done|do|VBN with|with|IN 500|500|CD µl|µl|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 2|2|CD x|x|CC 500|500|CD µl|µl|NN IP|IP|NNP buffer|buffer|NN -LSB-|-lsb-|-LRB- 50|50|CD mM|mm|NN HEPES-KOH|hepes-koh|NN pH|ph|NN 7.5|7.5|CD ,|,|, 150|150|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X|X|NNP 100|100|CD ,|,|, 0.1|0.1|CD %|%|NN Sodium|sodium|NN deoxycholate|deoxycholate|NN ,|,|, 0.1|0.1|CD %|%|NN SDS|sds|NN -RSB-|-rsb-|-RRB- ,|,|, 1|1|CD x|x|CC IP|IP|NNP buffer|buffer|NN with|with|IN 500mM|500mm|NN NaCl|nacl|NN ,|,|, 1|1|CD x|x|NN wash|wash|NN buffer|buffer|NN -LSB-|-lsb-|-LRB- 10mM|10mm|NN Tris|Tris|NNP pH|ph|NN 8.0|8.0|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.5|0.5|CD %|%|NN Nonidet-P40|nonidet-p40|NN ,|,|, 0.5|0.5|CD %|%|NN Sodium|sodium|NN deoxycholate|deoxycholate|NN -RSB-|-rsb-|-RRB- and|and|CC 1|1|CD x|x|CC TE|TE|NNP -RRB-|-rrb-|-RRB- followed|follow|VBN by|by|IN rotation|rotation|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN three|three|CD minutes|minute|NNS with|with|IN subsequent|subsequent|JJ collection|collection|NN of|of|IN the|the|DT beads|bead|NNS by|by|IN centrifugation|centrifugation|NN .|.|. For|for|IN elution|elution|NN ,|,|, 100|100|CD µl|µl|NN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT beads|bead|NNS ,|,|, incubated|incubate|VBN in|in|IN a|a|DT 65|65|CD °C|°c|NN water|water|NN bath|bath|NN for|for|IN 10|10|CD min|min|NN and|and|CC centrifuged|centrifuge|VBN as|as|IN above|above|JJ .|.|. After|after|IN reversion|reversion|NN of|of|IN crosslink|crosslink|NNP the|the|DT DNA|dna|NN was|be|VBD purified|purify|VBN with|with|IN phenol/chloroform|phenol/chloroform|NN .|.|.
Cultures|culture|NNS of|of|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN and|and|CC its|its|PRP$ derivates|derivate|NNS were|be|VBD cross|cross|JJ linked|link|VBN by|by|IN addition|addition|NN of|of|IN 27|27|CD µl|µl|NN of|of|IN formaldehyde|formaldehyde|NN -LRB-|-lrb-|-LRB- 37|37|CD %|%|NN -RRB-|-rrb-|-RRB- per|per|IN ml|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN 1|1|CD %|%|NN -RRB-|-rrb-|-RRB- .|.|. Crosslinking|crosslinking|NN was|be|VBD performed|perform|VBN at|at|IN slow|slow|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 100|100|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- for|for|IN 20|20|CD min|min|NN followed|follow|VBN by|by|IN quenching|quench|VBG with|with|IN 0.2|0.2|CD ml|ml|NN of|of|IN 2.5|2.5|CD M|m|NN glycine|glycine|NN per|per|IN ml|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN 0.5|0.5|CD M|m|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC washed|wash|VBN twice|twice|RB with|with|IN cold|cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- pH7|ph7|NN .5|.5|CD -RRB-|-rrb-|-RRB- .|.|. After|after|IN resuspension|resuspension|NN in|in|IN 1|1|CD ml|ml|NN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10mM|10mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD %|%|NN sucrose|sucrose|NN ,|,|, 50mM|50mm|NN NaCl|nacl|NN ,|,|, 10mM|10mm|NN EDTA|edta|NN ,|,|, 10|10|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN -RRB-|-rrb-|-RRB- and|and|CC incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD min|min|NN C|c|NN followed|follow|VBN by|by|IN addition|addition|NN of|of|IN 4|4|CD ml|ml|NN IP|IP|NNP buffer|buffer|NN cells|cell|NNS were|be|VBD sonicated|sonicate|VBN on|on|IN ice|ice|NN with|with|IN 12|12|CD times|time|NNS 30|30|CD sec|sec|NN and|and|CC 30|30|CD sec|sec|NN breaks|break|NNS at|at|IN an|a|DT UP|up|NN 400s|400s|CD Ultrasonic|ultrasonic|JJ processor|processor|NN -LRB-|-lrb-|-LRB- Dr.|Dr.|NNP Hielscher|Hielscher|NNP GmbH|gmbh|NN -RRB-|-rrb-|-RRB- with|with|IN 100|100|CD %|%|NN power|power|NN .|.|. After|after|IN centrifugation|centrifugation|NN for|for|IN 10|10|CD min|min|NN at|at|IN 9000|9000|CD g|g|NN ,|,|, 800|800|CD µl|µl|NN aliquotes|aliquote|NNS of|of|IN the|the|DT supernatant|supernatant|NN were|be|VBD stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|. 800|800|CD µl|µl|NN of|of|IN sonicated|sonicated|JJ cell|cell|NN extract|extract|NN -LRB-|-lrb-|-LRB- see|see|VB above|above|IN -RRB-|-rrb-|-RRB- were|be|VBD incubated|incubate|VBN with|with|IN 20|20|CD µl|µl|NN protein|protein|NN A/G|a/g|NN agarose|agarose|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Ultralink|ultralink|NN -RRB-|-rrb-|-RRB- and|and|CC antibody|antibody|NN rotating|rotate|VBG at|at|IN 4|4|CD °C|°c|NN .|.|. Washing|wash|VBG was|be|VBD done|do|VBN with|with|IN 500|500|CD µl|µl|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 2|2|CD x|x|CC 500|500|CD µl|µl|NN IP|IP|NNP buffer|buffer|NN -LSB-|-lsb-|-LRB- 50|50|CD mM|mm|NN HEPES-KOH|hepes-koh|NN pH|ph|NN 7.5|7.5|CD ,|,|, 150|150|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X|X|NNP 100|100|CD ,|,|, 0.1|0.1|CD %|%|NN Sodium|sodium|NN deoxycholate|deoxycholate|NN ,|,|, 0.1|0.1|CD %|%|NN SDS|sds|NN -RSB-|-rsb-|-RRB- ,|,|, 1|1|CD x|x|CC IP|IP|NNP buffer|buffer|NN with|with|IN 500mM|500mm|NN NaCl|nacl|NN ,|,|, 1|1|CD x|x|NN wash|wash|NN buffer|buffer|NN -LSB-|-lsb-|-LRB- 10mM|10mm|NN Tris|Tris|NNP pH|ph|NN 8.0|8.0|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.5|0.5|CD %|%|NN Nonidet-P40|nonidet-p40|NN ,|,|, 0.5|0.5|CD %|%|NN Sodium|sodium|NN deoxycholate|deoxycholate|NN -RSB-|-rsb-|-RRB- and|and|CC 1|1|CD x|x|CC TE|TE|NNP -RRB-|-rrb-|-RRB- followed|follow|VBN by|by|IN rotation|rotation|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN three|three|CD minutes|minute|NNS with|with|IN subsequent|subsequent|JJ collection|collection|NN of|of|IN the|the|DT beads|bead|NNS by|by|IN centrifugation|centrifugation|NN .|.|. For|for|IN elution|elution|NN ,|,|, 100|100|CD µl|µl|NN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT beads|bead|NNS ,|,|, incubated|incubate|VBN in|in|IN a|a|DT 65|65|CD °C|°c|NN water|water|NN bath|bath|NN for|for|IN 10|10|CD min|min|NN and|and|CC centrifuged|centrifuge|VBN as|as|IN above|above|JJ .|.|. After|after|IN reversion|reversion|NN of|of|IN crosslink|crosslink|NNP the|the|DT DNA|dna|NN was|be|VBD purified|purify|VBN with|with|IN phenol/chloroform|phenol/chloroform|NN .|.|. METHOD|method|NN DETAILS|detail|NNS are|be|VBP given|give|VBN and|and|CC are|be|VBP important|important|JJ for|for|IN the|the|DT different|different|JJ arrays|array|NNS .|.|. METHOD|method|NN DETAILS|detail|NNS :|:|: For|for|IN RNAP|rnap|NN old|old|JJ ,|,|, SeqA|seqa|NN old|old|JJ and|and|CC SeqA|seqa|NN old|old|JJ deltaSeqA|deltaseqa|NN :|:|: Cell|cell|NN extracts|extract|NNS were|be|VBD incubated|incubate|VBN with|with|IN agarose|agarose|NN beads|bead|NNS and|and|CC antibody|antibody|NN over|over|IN night|night|NN .|.|. Samples|sample|NNS were|be|VBD transferred|transfer|VBN to|to|TO a|a|DT Spin-X|spin-x|NN centrifuge|centrifuge|NN column|column|NN -LRB-|-lrb-|-LRB- Costar|costar|NN -RRB-|-rrb-|-RRB- ,|,|, centrifuged|centrifuge|VBN for|for|IN 2|2|CD min|min|NN at|at|IN 4.000|4.000|CD rpm|rpm|NN to|to|TO collect|collect|VB the|the|DT beads|bead|NNS on|on|IN the|the|DT column|column|NN .|.|. The|the|DT flow|flow|NN through|through|IN was|be|VBD removed|remove|VBN .|.|. Washing|wash|VBG was|be|VBD by|by|IN adding|add|VBG the|the|DT described|describe|VBN buffers|buffer|NNS to|to|TO the|the|DT beads|bead|NNS on|on|IN the|the|DT spin|spin|NN column|column|NN and|and|CC rotation|rotation|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN three|three|CD minutes|minute|NNS with|with|IN subsequent|subsequent|JJ collection|collection|NN of|of|IN the|the|DT beads|bead|NNS by|by|IN centrifugation|centrifugation|NN as|as|IN above|above|JJ .|.|. For|for|IN elution|elution|NN ,|,|, 100|100|CD µl|µl|NN elution|elution|NN buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT column|column|NN with|with|IN the|the|DT beads|bead|NNS ,|,|, incubated|incubate|VBN in|in|IN a|a|DT 65|65|CD °C|°c|NN water|water|NN bath|bath|NN for|for|IN 10|10|CD min|min|NN and|and|CC centrifuged|centrifuge|VBN as|as|IN above|above|JJ .|.|. To|to|TO prepare|prepare|VB the|the|DT control|control|NN DNA|dna|NN ,|,|, 800|800|CD µl|µl|NN of|of|IN sonicated|sonicated|JJ cell|cell|NN extract|extract|NN was|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN over|over|IN night|night|NN followed|follow|VBN by|by|IN 30|30|CD min|min|NN after|after|IN addition|addition|NN of|of|IN 1|1|CD µl|µl|NN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 20|20|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC extraction|extraction|NN with|with|IN phenol/chloroform|phenol/chloroform|NN .|.|. For|for|IN SeqA|seqa|NN new|new|JJ ,|,|, SeqA|seqa|NN new|new|JJ deltaSeqA|deltaseqa|NN ,|,|, sigma32|sigma32|NN 30|30|CD °C|°c|NN and|and|CC sigma|sigma|NN 32|32|CD 43|43|CD °C|°c|NN :|:|: The|the|DT ChIP|chip|NN protocol|protocol|NN as|as|IN described|describe|VBN above|above|IN resulted|result|VBN in|in|IN the|the|DT high|high|JJ background|background|NN signal|signal|NN .|.|. The|the|DT following|follow|VBG modifications|modification|NNS were|be|VBD applied|apply|VBN .|.|. First|first|RB ,|,|, agarose|agarose|NN beads|bead|NNS were|be|VBD not|not|RB collected|collect|VBN on|on|IN a|a|DT spin|spin|NN column|column|NN but|but|CC instead|instead|RB at|at|IN the|the|DT bottom|bottom|NN of|of|IN a|a|DT usual|usual|JJ 1.5|1.5|CD ml|ml|NN reaction|reaction|NN tube|tube|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD than|than|IN removed|remove|VBN by|by|IN pipetting|pipetting|NN .|.|. Second|second|RB ,|,|, the|the|DT control|control|NN DNA|dna|NN was|be|VBD taken|take|VBN from|from|IN the|the|DT supernatant|supernatant|JJ resulting|result|VBG from|from|IN centrifugation|centrifugation|NN of|of|IN the|the|DT precipitated|precipitated|JJ chromatin|chromatin|NN beads|bead|NNS processed|process|VBN further|further|RB as|as|IN the|the|DT immuno|immuno|NN precipitated|precipitated|JJ DNA|dna|NN after|after|IN elution|elution|NN .|.|. Third|Third|NNP ,|,|, before|before|IN addition|addition|NN of|of|IN proteinase|proteinase|NN K|k|NN sample|sample|NN and|and|CC control|control|NN DNA|dna|NN were|be|VBD incubated|incubate|VBN with|with|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 50|50|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- for|for|IN at|at|IN least|least|JJS 90|90|CD min|min|NN at|at|IN 42|42|CD °C|°c|NN .|.|. Incubation|incubation|NN of|of|IN 800|800|CD µl|µl|NN cell|cell|NN extract|extract|NN with|with|IN σ32|σ32|NN -|-|: or|or|CC SeqA|seqa|NN antiserum|antiserum|NN was|be|VBD for|for|IN 1|1|CD h|h|NN at|at|IN 4|4|CD °C|°c|NN .|.|. For|for|IN sigma32|sigma32|CD 30|30|CD °C|°c|NN short|short|JJ RNase|rnase|NN and|and|CC sigma32|sigma32|NN 30|30|CD °C|°c|NN short|short|JJ RNase|rnase|NN :|:|: The|the|DT ChIP|chip|NN protocol|protocol|NN was|be|VBD as|as|IN described|describe|VBN for|for|IN sigma|sigma|NN 32|32|CD 30|30|CD °C|°c|NN and|and|CC sigma|sigma|NN 32|32|CD 43|43|CD °C|°c|NN but|but|CC with|with|IN a|a|DT shorter|shorter|JJR RNase|rnase|NN A|a|DT incubation|incubation|NN for|for|IN only|only|RB 30|30|CD instead|instead|RB of|of|IN 90|90|CD min|min|NN .|.|.
Cultures|culture|NNS were|be|VBD diluted|dilute|VBN into|into|IN DNA-RNA|DNA-RNA|NNP Protect|Protect|NNP -LRB-|-lrb-|-LRB- Sierra|Sierra|NNP Diagnostics|Diagnostics|NNPS -RRB-|-rrb-|-RRB- to|to|TO inhibit|inhibit|VB RNA|rna|NN degradation|degradation|NN and|and|CC the|the|DT RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG RNeasy|rneasy|NN minkits|minkit|NNS with|with|IN the|the|DT optional|optional|JJ DNase|dnase|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
Cultures|culture|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN 1|1|CD L|l|NN volumes|volume|NNS of|of|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN ,|,|, supplemented|supplement|VBN with|with|IN MgSO4|mgso4|NN -LRB-|-lrb-|-LRB- 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, CaCl2|cacl2|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC glucose|glucose|NN -LRB-|-lrb-|-LRB- 10|10|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- in|in|IN vigorously|vigorously|RB shaken|shake|VBN -LRB-|-lrb-|-LRB- 225|225|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- Fernbach|fernbach|NN flasks|flask|NNS .|.|.
Cultures|culture|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN .|.|.
Cultures|culture|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN .|.|. Cells|cell|NNS were|be|VBD cultured|culture|VBN with|with|IN 25|25|CD ug/ml|ug/ml|JJ chloramphenicol|chloramphenicol|NN to|to|TO maintain|maintain|VB selection|selection|NN .|.|. However|however|RB ,|,|, this|this|DT genomic|genomic|JJ mutation|mutation|NN is|be|VBZ stable|stable|JJ and|and|CC RNA|rna|NN was|be|VBD prepared|prepare|VBN from|from|IN non-selectively|non-selectively|JJ grown|grown|JJ cultures|culture|NNS inoculated|inoculate|VBN with|with|IN overnight|overnight|JJ stocks|stock|NNS -LRB-|-lrb-|-LRB- grown|grow|VBN with|with|IN selection|selection|NN -RRB-|-rrb-|-RRB- to|to|TO eliminate|eliminate|VB any|any|DT unrelated|unrelated|JJ effects|effect|NNS of|of|IN exogenous|exogenous|JJ drugs|drug|NNS on|on|IN gene|gene|NN expression|expression|NN .|.|.
Cultures|culture|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN .|.|. Cells|cell|NNS were|be|VBD cultured|culture|VBN with|with|IN 25|25|CD ug/ml|ug/ml|NN kanamycin|kanamycin|NN to|to|TO maintain|maintain|VB selection|selection|NN .|.|. However|however|RB ,|,|, this|this|DT genomic|genomic|JJ mutation|mutation|NN is|be|VBZ stable|stable|JJ and|and|CC RNA|rna|NN was|be|VBD prepared|prepare|VBN from|from|IN non-selectively|non-selectively|JJ grown|grown|JJ cultures|culture|NNS inoculated|inoculate|VBN with|with|IN overnight|overnight|JJ stocks|stock|NNS -LRB-|-lrb-|-LRB- grown|grow|VBN with|with|IN selection|selection|NN -RRB-|-rrb-|-RRB- to|to|TO eliminate|eliminate|VB any|any|DT unrelated|unrelated|JJ effects|effect|NNS of|of|IN exogenous|exogenous|JJ drugs|drug|NNS on|on|IN gene|gene|NN expression|expression|NN .|.|.
Cultures|culture|NNS were|be|VBD grown|grow|VBN to|to|TO the|the|DT OD600|od600|NN value|value|NN of|of|IN 1.0|1.0|CD and|and|CC treated|treat|VBN with|with|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN for|for|IN 10|10|CD min|min|NN .|.|. To|to|TO quench|quench|VB the|the|DT reaction|reaction|NN ,|,|, glycine|glycine|NN was|be|VBD added|add|VBN at|at|IN the|the|DT final|final|JJ concentration|concentration|NN of|of|IN 0.125|0.125|CD M|m|NN for|for|IN 5|5|CD min|min|NN .|.|. Cells|cell|NNS were|be|VBD washed|wash|VBN twice|twice|RB with|with|IN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- ,|,|, 0.1|0.1|CD M|m|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN and|and|CC 0.5|0.5|CD %|%|NN Tween-20|tween-20|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT washed|wash|VBN cells|cell|NNS were|be|VBD then|then|RB lysed|lyse|VBN with|with|IN the|the|DT lysis|lysis|NN buffer|buffer|NN containing|contain|VBG 8|8|CD KU/ml|ku/ml|NN lysozyme|lysozyme|NN ,|,|, 1|1|CD mM|mm|NN PMSF|pmsf|NN and|and|CC protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD min|min|NN at|at|IN 4|4|CD ℃|℃|NN .|.|. The|the|DT lysates|lysate|NNS were|be|VBD sonicated|sonicate|VBN by|by|IN a|a|DT sonicator|sonicator|NN -LRB-|-lrb-|-LRB- Bioruptor|bioruptor|NN -RRB-|-rrb-|-RRB- and|and|CC this|this|DT sonication|sonication|NN resulted|result|VBD in|in|IN the|the|DT size|size|NN of|of|IN DNA|dna|NN ranged|range|VBD from|from|IN 100|100|CD bps|bp|NNS to|to|TO 1000|1000|CD bps|bp|NNS with|with|IN the|the|DT average|average|JJ size|size|NN of|of|IN 500|500|CD bps|bp|NNS .|.|. After|after|IN sonication|sonication|NN ,|,|, the|the|DT lysates|lysate|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 12,000|12,000|CD g|g|NN for|for|IN 20|20|CD min|min|NN at|at|IN 4|4|CD ℃|℃|NN and|and|CC the|the|DT resulting|result|VBG supernatant|supernatant|NN was|be|VBD used|use|VBN for|for|IN immunoprecipitation|immunoprecipitation|NN .|.|. Before|before|IN immunoprecipitation|immunoprecipitation|NN ,|,|, the|the|DT magnetic|magnetic|JJ beads|bead|NNS coated|coat|VBN with|with|IN Dynabeads|Dynabeads|NNPS Protein|protein|NN G|g|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- were|be|VBD pre-incubated|pre-incubated|JJ with|with|IN 0.05|0.05|CD mg/ml|mg/ml|NN anti-FLAG|anti-flag|JJ antibody|antibody|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT lysates|lysate|NNS were|be|VBD also|also|RB pre-cleared|pre-clear|VBN by|by|IN incubating|incubate|VBG with|with|IN the|the|DT beads|bead|NNS only|only|RB .|.|. To|to|TO immunoprecipitate|immunoprecipitate|NN the|the|DT PhoB-FLAG-DNA|phob-flag-dna|JJ complex|complex|NN ,|,|, beads|bead|NNS pre-incubated|pre-incubated|JJ with|with|IN antibody|antibody|NN were|be|VBD added|add|VBN in|in|IN both|both|CC lysates|lysate|NNS of|of|IN MG1655|mg1655|NN _|_|CD PhoB|phob|NN _|_|CD FLAG|flag|NN and|and|CC MG1655|mg1655|NN strains|strain|NNS at|at|IN 4|4|CD ℃|℃|CD overnight|overnight|JJ .|.|. The|the|DT beads|bead|NNS were|be|VBD washed|wash|VBN once|once|RB with|with|IN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- ,|,|, 0.1|0.1|CD M|m|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, and|and|CC 0.05|0.05|CD %|%|NN -LSB-|-lsb-|-LRB- v/v|v/v|NN -RSB-|-rsb-|-RRB- Tween-20|tween-20|NN and|and|CC 1|1|CD mM|mm|NN fresh|fresh|JJ PMSF|pmsf|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN ChIP|chip|NN wash|wash|NN buffer|buffer|NN I|i|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|Tris|NNP HCl|hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.1|0.1|CD %|%|NN Tween-20|tween-20|NN and|and|CC 1|1|CD mM|mm|NN fresh|fresh|JJ PMSF|pmsf|NN -RRB-|-rrb-|-RRB- ,|,|, three|three|CD times|time|NNS with|with|IN ChIP|chip|NN wash|wash|NN buffer|buffer|NN II|ii|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- ,|,|, 500|500|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.1|0.1|CD %|%|NN -LSB-|-lsb-|-LRB- v/v|v/v|NN -RSB-|-rsb-|-RRB- Tween-20|tween-20|NN and|and|CC 1|1|CD mM|mm|NN fresh|fresh|JJ PMSF|pmsf|NN -RRB-|-rrb-|-RRB- ,|,|, once|once|RB with|with|IN ChIP|chip|NN wash|wash|NN buffer|buffer|NN III|iii|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.1|0.1|CD %|%|NN -LSB-|-lsb-|-LRB- v/v|v/v|NN -RSB-|-rsb-|-RRB- Tween-20|tween-20|NN and|and|CC 1|1|CD mM|mm|NN fresh|fresh|JJ PMSF|pmsf|NN -RRB-|-rrb-|-RRB- and|and|CC once|once|RB with|with|IN TE|te|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN removing|remove|VBG the|the|DT TE|TE|NNP buffer|buffer|NN ,|,|, beads|bead|NNS were|be|VBD incubated|incubate|VBN with|with|IN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.4|7.4|CD -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN and|and|CC 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- at|at|IN 65|65|CD ℃|℃|NN for|for|IN 15|15|CD min|min|NN twice|twice|RB and|and|CC then|then|RB the|the|DT resulting|result|VBG eluted|elute|VBN solutions|solution|NNS combined|combine|VBN .|.|. After|after|IN incubating|incubate|VBG with|with|IN the|the|DT final|final|JJ concentration|concentration|NN of|of|IN 10.5|10.5|CD U/ml|u/ml|NN proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- at|at|IN 42|42|CD ℃|℃|NN for|for|IN 2|2|CD hours|hour|NNS ,|,|, the|the|DT reverse|reverse|JJ cross-link|cross-link|NN procedure|procedure|NN was|be|VBD performed|perform|VBN by|by|IN incubating|incubate|VBG at|at|IN 65|65|CD ℃|℃|CD overnight|overnight|JJ .|.|. Samples|sample|NNS were|be|VBD then|then|RB treated|treat|VBN with|with|IN the|the|DT final|final|JJ concentration|concentration|NN of|of|IN 26|26|CD μg/ml|μg/ml|NN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT PCR|pcr|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO purify|purify|VB DNA|dna|NN from|from|IN the|the|DT RNase|rnase|NN A-treated|a-treated|JJ samples|sample|NNS .|.|.
Cultures|culture|NNS were|be|VBD inoculated|inoculate|VBN from|from|IN a|a|DT single|single|JJ colony|colony|NN ,|,|, incubated|incubate|VBN overnight|overnight|RB ,|,|, sub-cultured|sub-cultured|JJ with|with|IN a|a|DT 1|1|CD %|%|NN inoculum|inoculum|NN ,|,|, and|and|CC grown|grow|VBN to|to|TO the|the|DT late|late|JJ exponential|exponential|JJ growth|growth|NN phase|phase|NN ,|,|, corresponding|correspond|VBG to|to|TO an|a|DT OD600|od600|NN nm|nm|NN of|of|IN 0.6|0.6|CD --|--|: 0.7|0.7|CD .|.|.
Cultures|culture|NNS were|be|VBD maintained|maintain|VBN on|on|IN tryptic|tryptic|JJ soy|soy|NN agar|agar|NN -LRB-|-lrb-|-LRB- TSA|tsa|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Becton|Becton|NNP Dickinson|Dickinson|NNP ,|,|, Le|Le|NNP Pont|Pont|NNP Claix|Claix|NNP ,|,|, France|France|NNP -RRB-|-rrb-|-RRB- .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD grown|grow|VBN in|in|IN Difco|Difco|NNP Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- broth|broth|NN -LRB-|-lrb-|-LRB- Lennox|lennox|NN ;|;|: Franklin|Franklin|NNP Lakes|Lakes|NNP ,|,|, NJ|NJ|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN aerobically|aerobically|RB on|on|IN a|a|DT shaker|shaker|NN at|at|IN 200|200|CD rpm|rpm|NN .|.|. Bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- picked|pick|VBN from|from|IN 5-10|5-10|CD colonies|colony|NNS -RRB-|-rrb-|-RRB- were|be|VBD suspended|suspend|VBN in|in|IN 1|1|CD ml|ml|NN of|of|IN PBS|PBS|NNP ,|,|, yielding|yield|VBG a|a|DT suspension|suspension|NN corresponding|correspond|VBG to|to|TO the|the|DT turbidity|turbidity|NN of|of|IN McFarland|McFarland|NNP 0.5|0.5|CD ,|,|, and|and|CC diluted|dilute|VBN 1:100|1:100|CD in|in|IN minimal|minimal|JJ salt|salt|NN -LRB-|-lrb-|-LRB- MS|ms|NN -RRB-|-rrb-|-RRB- -|-|: medium|medium|NN -LRB-|-lrb-|-LRB- ~|~|NN 106|106|CD CFU/ml|cfu/ml|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT suspension|suspension|NN was|be|VBD exposed|expose|VBN to|to|TO CORM-2|corm-2|NN -LRB-|-lrb-|-LRB- 250|250|CD µM|µm|NN -RRB-|-rrb-|-RRB- or|or|CC vehicle|vehicle|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD %|%|NN DMSO|dmso|NN -RRB-|-rrb-|-RRB- for|for|IN 4|4|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN .|.|. A|a|DT volume|volume|NN -LRB-|-lrb-|-LRB- 10|10|CD µl|µl|NN -RRB-|-rrb-|-RRB- was|be|VBD spread|spread|VBN onto|onto|IN TSA-agar|tsa-agar|JJ plates|plate|NNS and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN overnight|overnight|JJ .|.|. This|this|DT procedure|procedure|NN was|be|VBD repeated|repeat|VBN 10|10|CD times|time|NNS -LRB-|-lrb-|-LRB- 10x|10x|CD ,|,|, ~|~|CD 45|45|CD generations|generation|NNS -RRB-|-rrb-|-RRB- or|or|CC 20|20|CD times|time|NNS -LRB-|-lrb-|-LRB- 20x|20x|NN ,|,|, ~|~|NN 90|90|CD generations|generation|NNS -RRB-|-rrb-|-RRB- .|.|.
cultures|culture|NNS were|be|VBD split|split|VBN into|into|IN two|two|CD 10|10|CD ml|ml|NN cultures|culture|NNS .|.|. One|one|CD half|half|NN was|be|VBD treated|treat|VBN with|with|IN 2|2|CD mM|mm|NN NaN3|nan3|NN for|for|IN 10|10|CD minutes|minute|NNS and|and|CC the|the|DT other|other|JJ half|half|NN was|be|VBD left|leave|VBN untreated|untreated|JJ
Cultures|culture|NNS were|be|VBD spun|spin|VBN down|down|RP at|at|IN 4|4|CD °C|°c|NN ,|,|, 15,000|15,000|CD ×|×|CD g|g|NN for|for|IN 3|3|CD minutes|minute|NNS .|.|. Supernatants|supernatant|NNS were|be|VBD discarded|discard|VBN after|after|IN centrifugation|centrifugation|NN and|and|CC cell|cell|NN pellets|pellet|NNS were|be|VBD flash|flash|NN frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN for|for|IN storage|storage|NN at|at|IN -80|-80|CD °C|°c|NN .|.|. Cells|cell|NNS were|be|VBD lysed|lyse|VBN with|with|IN 1|1|CD mg|mg|NN of|of|IN lysozme|lysozme|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP L6871|L6871|NNP -RRB-|-rrb-|-RRB- in|in|IN 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- USB|usb|JJ 75825|75825|CD -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 0.1|0.1|CD mM|mm|NN EDTA|edta|NN -LRB-|-lrb-|-LRB- USB|usb|JJ 15694|15694|CD -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD extracted|extract|VBN with|with|IN PureLink|purelink|NN RNA|rna|NN Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC further|further|JJ purified|purify|VBN and|and|CC concentrated|concentrate|VBN with|with|IN RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator-5|Concentrator-5|NNP -LRB-|-lrb-|-LRB- Zymo|Zymo|NNP Research|Research|NNP -RRB-|-rrb-|-RRB- to|to|TO assure|assure|VB sample|sample|NN quality|quality|NN .|.|. The|the|DT purified|purify|VBN RNA|rna|NN samples|sample|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG a|a|DT Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- and|and|CC Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN for|for|IN bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO deplete|deplete|VB rRNA|rrna|NN from|from|IN the|the|DT samples|sample|NNS .|.|.
Cultures|culture|NNS were|be|VBD transferred|transfer|VBN directly|directly|RB into|into|IN an|a|DT ice-cold|ice-cold|JJ ethanol/phenol|ethanol/phenol|NN stop|stop|VB solution|solution|NN ,|,|, which|which|WDT immediately|immediately|RB inactivated|inactivate|VBD cellular|cellular|JJ RNases|rnase|NNS .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD oC|oc|NN until|until|IN RNA|rna|NN extraction|extraction|NN .|.|.
culture|culture|NN system|system|NN :|:|: BACTEC|bactec|NN
culture|culture|NN system|system|NN :|:|: flask|flask|NN with|with|IN continous|continous|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB-
culture|culture|NN system|system|NN :|:|: flask|flask|NN with|with|IN continuous|continuous|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB-
culture|culture|NN system|system|NN :|:|: static|static|JJ petri|petri|JJ dish|dish|NN -LRB-|-lrb-|-LRB- disposable|disposable|JJ -RRB-|-rrb-|-RRB-
culture|culture|NN temperature|temperature|NN :|:|: 30|30|CD °C|°c|NN for|for|IN 60|60|CD min|min|NN
culture|culture|NN temperature|temperature|NN :|:|: 37|37|CD °C|°c|NN
culture|culture|NN temperature|temperature|NN :|:|: 42|42|CD °C|°c|NN
culture|culture|NN temperature|temperature|NN :|:|: 42|42|CD °C|°c|NN for|for|IN 60|60|CD min|min|NN
culture|culture|NN temperature|temperature|NN :|:|: room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- 20|20|CD C|c|NN -RRB-|-rrb-|-RRB-
culture|culture|NN time|time|NN :|:|: 18|18|CD h|h|NN
culture|culture|NN type|type|NN :|:|: Ancestor|Ancestor|NNP
culture|culture|NN type|type|NN :|:|: coculture|coculture|NN
culture|culture|NN type|type|NN :|:|: evolved|evolve|VBD
culture|culture|NN type|type|NN :|:|: monoculture|monoculture|NN
Custom|Custom|NNP anti-Fur|anti-fur|JJ antibodies|antibody|NNS were|be|VBD purified|purify|VBN over|over|IN a|a|DT His6-Fur|his6-fur|NN bound|bind|VBD HiTrap|HiTrap|NNP NHS-activated|NHS-activated|NNP HP|HP|NNP column|column|NN -LRB-|-lrb-|-LRB- GE|GE|NNP Healthcare|Healthcare|NNP -RRB-|-rrb-|-RRB- as|as|IN previously|previously|RB described|describe|VBN -LRB-|-lrb-|-LRB- PMID|pmid|NN :|:|: 21478858|21478858|CD -RRB-|-rrb-|-RRB- .|.|. Western|western|NN blot|blot|NN analyses|analysis|NNS showed|show|VBD that|that|IN the|the|DT purified|purify|VBN antibody|antibody|NN was|be|VBD specific|specific|JJ for|for|IN Fur|Fur|NNP .|.|.
CV108|cv108|NN _|_|CD minus|minus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 1|1|CD
CV108|cv108|NN _|_|CD minus|minus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 2|2|CD
CV108|cv108|NN _|_|CD minus|minus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 3|3|CD
CV108|cv108|NN _|_|NN plus|plus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 1|1|CD
CV108|cv108|NN _|_|NN plus|plus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 2|2|CD
CV108|cv108|NN _|_|NN plus|plus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 3|3|CD
Cy3|cy3|NN and|and|CC Cy5|cy5|NN intensities|intensity|NNS were|be|VBD normalized|normalize|VBN by|by|IN scaling|scale|VBG so|so|RB that|that|IN the|the|DT 75th|75th|JJ percentile|percentile|NN in|in|IN the|the|DT Cy3|cy3|NN and|and|CC Cy5|cy5|NN channels|channel|NNS were|be|VBD equal|equal|JJ .|.|.
Cy3|cy3|NN labeled|label|VBN EHEC|EHEC|NNP grown|grow|VBN in|in|IN DMEM|DMEM|NNP pH|ph|NN 7.4|7.4|CD
Cy3|cy3|NN labeled|label|VBN EHEC|EHEC|NNP grown|grow|VBN in|in|IN DMEM|DMEM|NNP pH|ph|NN 7.4|7.4|CD ,|,|, 15|15|CD minutes|minute|NNS
Cy3|cy3|NN labeled|label|VBN EHEC|EHEC|NNP grown|grow|VBN in|in|IN DMEM|DMEM|NNP pH|ph|NN 7.4|7.4|CD ,|,|, 90|90|CD minutes|minute|NNS
Cy5|cy5|NN labeled|label|VBN EHEC|ehec|NN acid-adapted|acid-adapted|JJ in|in|IN DMEM|DMEM|NNP pH|ph|NN 5|5|CD ,|,|, followed|follow|VBN by|by|IN 30|30|CD minutes|minute|NNS pH|ph|NN 3|3|CD
Cy5|cy5|NN labeled|label|VBN EHEC|EHEC|NNP acid-stressed|acid-stressed|JJ in|in|IN DMEM|DMEM|NNP pH|ph|NN 3|3|CD ,|,|, 15|15|CD minutes|minute|NNS
Cy5|cy5|NN labeled|label|VBN EHEC|EHEC|NNP acid-stressed|acid-stressed|JJ in|in|IN DMEM|DMEM|NNP pH|ph|NN 3|3|CD ,|,|, 30minutes|30minutes|CD
Cy5|cy5|NN labeled|label|VBN EHEC|EHEC|NNP bile|bile|NN salt-stressed|salt-stressed|JJ in|in|IN DMEM|DMEM|NNP ,|,|, 90|90|CD minutes|minute|NNS
cy|cy|NN _|_|CD a4|a4|NN
cya|cya|NN mutant|mutant|JJ
cya.rep1.ee|cya.rep1.ee|NN
cya.rep1.me|cya.rep1.me|NN
cya.rep2.ee|cya.rep2.ee|NN
cya.rep2.me|cya.rep2.me|NN
cy|cy|NN _|_|CD b4|b4|NN
cyc1|cyc1|NN
cyc2|cyc2|NN
cyc3|cyc3|NN
cyc4|cyc4|NN
cyd1|cyd1|NN
cyd2|cyd2|NN
cyd3|cyd3|NN
cyd4|cyd4|NN
cysA|cysa|NN KO|ko|NN rep1|rep1|NN
cysA|cysa|NN KO|ko|NN rep2|rep2|NN
cysA|cysa|NN KO|ko|NN rep3|rep3|NN
cysG|cysg|NN KO|ko|NN LB|lb|NN rep1|rep1|NN
cysG|cysg|NN KO|ko|NN LB|lb|NN rep2|rep2|NN
cysH|cysh|NN KO|ko|NN LB|lb|NN rep1|rep1|NN
cysH|cysh|NN KO|ko|NN LB|lb|NN rep2|rep2|NN
cysQ-gln-1|cysq-gln-1|NN
cysQ-gln-2|cysq-gln-2|NN
cysQ|cysq|NN mutantin|mutantin|NN Ala|ala|NN media|media|NNS
cysQ|cysq|NN mutantin|mutantin|NN Gln|gln|NN media|media|NNS
Cysteine|cysteine|NN addition|addition|NN
Cytidine|cytidine|NN addition|addition|NN
D1-ae10|d1-ae10|NN
D1-ae11|d1-ae11|NN
D1-ae12|d1-ae12|NN
D1|d1|NN +|+|CC ae7|ae7|NN
D1|d1|NN +|+|CC ae8|ae8|NN
D1|d1|NN +|+|CC ae9|ae9|NN
D1|d1|NN +|+|CC AN|a|DT
D1|d1|NN +|+|CC AN2|an2|NN
D1|d1|NN +|+|CC AN3|an3|NN
D1-AN4|d1-an4|NN
D1-AN5|d1-an5|NN
D1-AN6|d1-an6|NN
D2|d2|NN _|_|CD 14|14|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|SYM m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|SYM m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|SYM m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 14|14|CD _|_|NN m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 1|1|CD _|_|CD m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 2|2|CD _|_|CD m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|SYM m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|SYM m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|SYM m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 4|4|CD _|_|CD m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D2|d2|NN _|_|NN 7|7|CD _|_|NN m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 10|10|CD _|_|SYM m1|m1|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m10|m10|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m11|m11|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m12|m12|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m13|m13|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m2|m2|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m3|m3|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m4|m4|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m5|m5|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m6|m6|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m7|m7|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m8|m8|NN
D3|d3|NN _|_|CD 10|10|CD _|_|NN m9|m9|NN
D3|d3|NN _|_|CD 14|14|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|SYM m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|SYM m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|SYM m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 14|14|CD _|_|NN m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 2|2|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|SYM m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|SYM m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|SYM m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 4|4|CD _|_|CD m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN _|_|NN 7|7|CD _|_|NN m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D3|d3|NN +|+|CC ae19|ae19|NN
D3|d3|NN +|+|CC ae20|ae20|NN
D3|d3|NN +|+|CC ae21|ae21|NN
D3-ae22|d3-ae22|NN
D3-ae23|d3-ae23|NN
D3-ae24|d3-ae24|NN
D3|d3|NN +|+|CC AN13|an13|NN
D3|d3|NN +|+|CC AN14|an14|NN
D3|d3|NN +|+|CC AN15|an15|NN
D3-AN16|d3-an16|NN
D3-AN17|d3-an17|NN
D3-AN18|d3-an18|NN
D4|d4|NN _|_|CD 10|10|CD _|_|SYM m1|m1|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m10|m10|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m11|m11|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m12|m12|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m13|m13|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m2|m2|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m3|m3|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m4|m4|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m5|m5|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m6|m6|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m7|m7|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m8|m8|NN
D4|d4|NN _|_|CD 10|10|CD _|_|NN m9|m9|NN
D4|d4|NN _|_|CD 14|14|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|SYM m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|SYM m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|SYM m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 14|14|CD _|_|NN m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 1|1|CD _|_|CD m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 1|1|CD _|_|CD m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 1|1|CD _|_|CD m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 1|1|CD _|_|CD m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 1|1|CD _|_|CD m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m11|m11|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 2|2|CD _|_|CD m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|NN m10|m10|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|SYM m12|m12|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|SYM m13|m13|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 4|4|CD _|_|CD m9|m9|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
D4|d4|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
dam|dam|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
dam|dam|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r2|r2|NN
dam|dam|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r3|r3|NN
dam|dam|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
∆|∆|CD dapF|dapf|NN parent|parent|NN Sample|sample|NN 28|28|CD
∆|∆|CD dapF|dapf|NN parent|parent|NN Sample|sample|NN 47|47|CD
∆|∆|CD dapF|dapf|NN parent|parent|NN Sample|Sample|NNP 9|9|CD
dapF|dapf|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 10|10|CD
dapF|dapf|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 29|29|CD
dapF|dapf|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 48|48|CD
dapF|dapf|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|Sample|NNP 11|11|CD
dapF|dapf|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|Sample|NNP 30|30|CD
dapF|dapf|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|Sample|NNP 49|49|CD
Data|Data|NNP analysis|analysis|NN was|be|VBD carried|carry|VBN out|out|RP using|use|VBG the|the|DT Agilent|Agilent|NNP GeneSpring|GeneSpring|NNP GX|GX|NNP .|.|. Robust|robust|JJ Multi-array|multi-array|JJ Average|average|JJ -LRB-|-lrb-|-LRB- RMA|rma|NN -RRB-|-rrb-|-RRB- normalization|normalization|NN performed|perform|VBN using|use|VBG of|of|IN signal|signal|NN intensity|intensity|NN spot|spot|NN data|datum|NNS which|which|WDT obtained|obtain|VBN by|by|IN scanning|scanning|NN process|process|NN and|and|CC it|it|PRP is|be|VBZ indicated|indicate|VBN as|as|IN a|a|DT scatter|scatter|NN plot|plot|NN data|datum|NNS .|.|. Distribution|distribution|NN of|of|IN all|all|DT genes|gene|NNS which|which|WDT obtained|obtain|VBD result|result|NN of|of|IN the|the|DT experiment|experiment|NN is|be|VBZ indicated|indicate|VBN as|as|IN a|a|DT histogram|histogram|NN .|.|. Accuracy|accuracy|NN of|of|IN the|the|DT results|result|NNS of|of|IN the|the|DT experiment|experiment|NN was|be|VBD determined|determine|VBN through|through|IN comparison|comparison|NN of|of|IN the|the|DT histogram|histogram|NN with|with|IN the|the|DT scatter|scatter|NN plot|plot|NN data|datum|NNS .|.|.
Data|Data|NNP analysis|analysis|NN was|be|VBD done|do|VBN using|use|VBG R|r|NN language|language|NN and|and|CC environment|environment|NN for|for|IN a|a|DT statistical|statistical|JJ computing|computing|NN and|and|CC Bioconductor|bioconductor|NN .|.|. Array|array|NN data|datum|NNS were|be|VBD normalized|normalize|VBN with|with|IN gcRMA|gcrma|NN method|method|NN .|.|.
Data|Data|NNP collapsed|collapse|VBD using|use|VBG fastx|fastx|NN collapser|collapser|NN to|to|TO remove|remove|VB identical|identical|JJ sequencing|sequencing|NN reads|read|VBZ -LRB-|-lrb-|-LRB- http://hannonlab.cshl.edu/fastx_toolkit/index.html|http://hannonlab.cshl.edu/fastx_toolkit/index.html|NN -RRB-|-rrb-|-RRB- -|-|: Example|example|NN :|:|: fastx|fastx|NN _|_|NN collapser|collapser|NN -|-|: i|i|FW DL4900|dl4900|FW _|_|SYM clipped.fasta|clipped.fasta|SYM -|-|: o|o|NN DL4900|dl4900|NN _|_|CD clip|clip|NN _|_|SYM clp.fasta|clp.fasta|FW
Data|Data|NNP extraction|extraction|NN from|from|IN Images|image|NNS was|be|VBD done|do|VBN using|use|VBG Feature|Feature|NNP Extraction|Extraction|NNP software|software|NN v|v|LS 9.5.1|9.5.1|CD of|of|IN Agilent|Agilent|NNP .|.|. Feature|feature|NN extracted|extract|VBN raw|raw|JJ data|datum|NNS was|be|VBD analyzed|analyze|VBN using|use|VBG GeneSpring|GeneSpring|NNP GX|GX|NNP V|V|NNP 7.3.1|7.3.1|CD software|software|NN from|from|IN Agilent|Agilent|NNP .|.|. Normalization|normalization|NN of|of|IN the|the|DT data|datum|NNS was|be|VBD done|do|VBN in|in|IN GeneSpring|GeneSpring|NNP GX|GX|NNP using|use|VBG the|the|DT recommended|recommend|VBN one|one|CD color|color|NN Per|per|IN Chip|chip|NN and|and|CC Per|per|IN Gene|Gene|NNP Data|Data|NNP Transformation|transformation|NN :|:|: Set|set|VB measurements|measurement|NNS less|less|JJR than|than|IN 0.01|0.01|CD to|to|TO 0.01|0.01|CD ,|,|, Per|per|IN Chip|chip|NN :|:|: Normalize|normalize|VB to|to|TO 50th|50th|JJ percentile|percentile|NN ,|,|, Per|per|IN Gene|gene|NN :|:|: Normalize|normalize|VB to|to|TO Specific|specific|JJ Samples|sample|NNS .|.|. Significant|significant|JJ genes|gene|NNS up|up|RB and|and|CC down|down|RB regulated|regulate|VBN showing|show|VBG one|one|CD fold|fold|NN and|and|CC above|above|IN among|among|IN the|the|DT samples|sample|NNS was|be|VBD identified|identify|VBN .|.|.
Data|Data|NNP filtered|filter|VBD for|for|IN PCR|pcr|NN success|success|NN ,|,|, >|>|JJR 3x|3x|NN local|local|JJ background|background|NN and|and|CC spot|spot|NN quality|quality|NN -LRB-|-lrb-|-LRB- GenePix|GenePix|NNP Flag|Flag|NNP -RRB-|-rrb-|-RRB- .|.|. Normalized|normalize|VBN using|use|VBG Lowess|Lowess|NNP smoothing|smooth|VBG from|from|IN MA|MA|NNP plot|plot|NN
Data|Data|NNP filtering|filter|VBG was|be|VBD done|do|VBN with|with|IN in-house|in-house|JJ script|script|NN with|with|IN the|the|DT set|set|VBN value|value|NN as|as|IN follows|follow|VBZ :|:|: Removal|removal|NN if|if|IN %|%|NN of|of|IN N|n|NN nucleotide|nucleotide|NN is|be|VBZ more|more|JJR than|than|IN 10|10|CD %|%|NN ,|,|, if|if|IN more|more|JJR than|than|IN 40|40|CD %|%|NN of|of|IN the|the|DT nucleotide|nucleotide|NN is|be|VBZ Q20|q20|NN or|or|CC less|less|JJR ,|,|, if|if|IN average|average|JJ quality|quality|NN of|of|IN the|the|DT reads|read|VBZ is|be|VBZ less|less|JJR than|than|IN Q20|q20|NN .|.|.
Data|Data|NNP from|from|IN two|two|CD independent|independent|JJ experiments|experiment|NNS were|be|VBD normalized|normalize|VBN and|and|CC then|then|RB analyzed|analyze|VBN using|use|VBG the|the|DT GenePix|GenePix|NNP Pro|pro|FW 3.0|3.0|CD software|software|NN -LRB-|-lrb-|-LRB- Axon|Axon|NNP Instruments|Instruments|NNP -RRB-|-rrb-|-RRB- .|.|.
Data|Data|NNP has|have|VBZ not|not|RB been|be|VBN processed|process|VBN other|other|JJ than|than|IN those|those|DT protocols|protocol|NNS within|within|IN GCOSv1|gcosv1|NN .4|.4|CD
Data|datum|NNS included|include|VBD in|in|IN file|file|NN has|have|VBZ not|not|RB been|be|VBN processed|process|VBN other|other|JJ than|than|IN those|those|DT protocols|protocol|NNS within|within|IN GCOSv1|gcosv1|NN .4|.4|CD
Data|Data|NNP obtained|obtain|VBN from|from|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN microarrays|microarray|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT Ratio-based|ratio-based|JJ and|and|CC Lowess|lowess|JJ methods|method|NNS in|in|IN Acuity|acuity|NN 3.1|3.1|CD -LRB-|-lrb-|-LRB- Axon|axon|NN instruments|instrument|NNS -RRB-|-rrb-|-RRB- before|before|IN analysis|analysis|NN .|.|. The|the|DT normalized|normalize|VBN data|datum|NNS for|for|IN all|all|DT strains|strain|NNS were|be|VBD converted|convert|VBN into|into|IN log2|log2|NN -LRB-|-lrb-|-LRB- Fluor|Fluor|NNP 647/Fluor|647/Fluor|NNP 546|546|CD -RRB-|-rrb-|-RRB- in|in|IN Acuity|acuity|NN 3.1|3.1|CD and|and|CC subsequently|subsequently|RB analyzed|analyze|VBN in|in|IN Microsoft|Microsoft|NNP Excel|Excel|NNP .|.|. Control|control|NN ,|,|, blank|blank|JJ ,|,|, and|and|CC test|test|NN spots|spot|NNS with|with|IN a|a|DT mean|mean|JJ intensity|intensity|NN below|below|IN that|that|DT of|of|IN the|the|DT mean|mean|NN of|of|IN all|all|DT negative|negative|JJ controls|control|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT analysis|analysis|NN .|.|. The|the|DT arithmetic|arithmetic|NN mean|mean|NN of|of|IN the|the|DT remaining|remain|VBG spots|spot|NNS across|across|IN the|the|DT duplicates|duplicate|NNS was|be|VBD taken|take|VBN to|to|TO construct|construct|VB the|the|DT dataset|dataset|NN .|.|. GACK|gack|NN -LRB-|-lrb-|-LRB- Genomotyping|genomotyping|JJ Analysis|analysis|NN by|by|IN Charles|Charles|NNP Kim|Kim|NNP -RRB-|-rrb-|-RRB- ,|,|, was|be|VBD used|use|VBN to|to|TO generate|generate|VB a|a|DT cut|cut|NN off|off|IN value|value|NN determining|determine|VBG the|the|DT presence|presence|NN or|or|CC absence|absence|NN of|of|IN genes|gene|NNS ,|,|, and|and|CC a|a|DT dendrogram|dendrogram|NN using|use|VBG the|the|DT Euclidean|euclidean|JJ distance|distance|NN metric|metric|JJ with|with|IN average|average|JJ linkage|linkage|NN was|be|VBD created|create|VBN with|with|IN tMEV|tmev|NN v4|v4|NN .1|.1|NN .|.|.
Data|Data|NNP processed|process|VBN with|with|IN FeatureExtraction|FeatureExtraction|NNP v9|v9|NN .5.1|.5.1|NN and|and|CC quantile|quantile|NN normalized|normalize|VBD using|use|VBG R2|r2|NN .6.1|.6.1|CD statistical|statistical|JJ software|software|NN
Data|Data|NNP quantification|quantification|NN was|be|VBD performed|perform|VBN using|use|VBG Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP software|software|NN 9.3.2.1|9.3.2.1|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technology|Technology|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT average|average|JJ fluorescence|fluorescence|NN intensity|intensity|NN for|for|IN each|each|DT spot|spot|NN was|be|VBD calculated|calculate|VBN and|and|CC local|local|JJ background|background|NN was|be|VBD subtracted|subtract|VBN .|.|. All|all|DT data|datum|NNS normalization|normalization|NN and|and|CC selection|selection|NN of|of|IN fold-changed|fold-changed|JJ genes|gene|NNS were|be|VBD performed|perform|VBN using|use|VBG GeneSpringGX|GeneSpringGX|NNP 7.3.1|7.3.1|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technology|Technology|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. Normalization|normalization|NN for|for|IN Agilent|Agilent|NNP one-color|one-color|JJ method|method|NN was|be|VBD performed|perform|VBN ,|,|, which|which|WDT is|be|VBZ Data|Data|NNP transformation|transformation|NN .|.|. Set|set|VB measurements|measurement|NNS less|less|JJR than|than|IN 5.0|5.0|CD to|to|TO 5.0|5.0|CD and|and|CC Per|per|IN Chip|chip|NN :|:|: Normalize|normalize|VB to|to|TO 50th|50th|JJ percentage|percentage|NN .|.|. Reliable|reliable|JJ genes|gene|NNS were|be|VBD filtered|filter|VBN by|by|IN flag|flag|NN as|as|IN following|follow|VBG the|the|DT Agilent|Agilent|NNP manual|manual|NN .|.|.
Data|Data|NNP =|=|JJ read.madata|read.madata|NN -LRB-|-lrb-|-LRB- \|\|CD
Data|Data|NNP selection|selection|NN
Datasets|dataset|NNS were|be|VBD normalized|normalize|VBN using|use|VBG locally|locally|RB weighted|weighted|JJ linear|linear|JJ regression|regression|NN -LRB-|-lrb-|-LRB- LOWESS|lowess|NN -RRB-|-rrb-|-RRB- normalization|normalization|NN on|on|IN raw|raw|JJ Cy3|cy3|NN and|and|CC Cy5|cy5|NN signals|signal|NNS to|to|TO correct|correct|VB for|for|IN intensity-dependent|intensity-dependent|JJ dye|dye|VB effects|effect|NNS within|within|IN each|each|DT array|array|NN using|use|VBG the|the|DT ``|``|`` normalizeWithinArrays|normalizewithinarrays|NN ''|''|'' function|function|NN in|in|IN the|the|DT limma|limma|NN package|package|NN for|for|IN the|the|DT statistical|statistical|JJ program|program|NN R|r|NN -LRB-|-lrb-|-LRB- v.|v.|CC 2.14.2|2.14.2|CD -RRB-|-rrb-|-RRB- .|.|.
Data|Data|NNP was|be|VBD analysed|analyse|VBN using|use|VBG GeneSpring|GeneSpring|NNP
Data|Data|NNP was|be|VBD analyzed|analyze|VBN in|in|IN the|the|DT Affymetrix|Affymetrix|NNP GenomeChipOperating|GenomeChipOperating|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- GCOS|GCOS|NNP -RRB-|-rrb-|-RRB- .|.|.
Data|Data|NNP was|be|VBD analyzed|analyze|VBN in|in|IN the|the|DT software|software|NN Acuity|acuity|NN 4.0|4.0|CD -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Devices|Devices|NNPS ,|,|, Sunnyvale|Sunnyvale|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. Hybridized|hybridize|VBN spots|spot|NNS for|for|IN E.|e.|FW coli|coli|FW K12|k12|NN having|have|VBG a|a|DT high|high|JJ QC|qc|NN -LRB-|-lrb-|-LRB- quality|quality|NN control|control|NN -RRB-|-rrb-|-RRB- value|value|NN >|>|JJR 0.1|0.1|CD ,|,|, good|good|JJ flag|flag|NN tags|tag|NNS -LRB-|-lrb-|-LRB- A|a|NN ,|,|, B|b|NN and|and|CC C|c|NN -RRB-|-rrb-|-RRB- in|in|IN both|both|CC Cy3/Cy5|cy3/cy5|NN channels|channel|NNS were|be|VBD chosen|choose|VBN for|for|IN analysis|analysis|NN .|.|. LOWESS|lowess|NN normalization|normalization|NN was|be|VBD performed|perform|VBN with|with|IN three|three|CD iterations|iteration|NNS using|use|VBG a|a|DT smoothing|smoothing|NN factor|factor|NN of|of|IN 0.4|0.4|CD .|.|. One|one|CD sample|sample|NN t-tests|t-test|NNS were|be|VBD performed|perform|VBN across|across|IN replicates|replicate|VBZ .|.|. P-value|p-value|NN of|of|IN 0.05|0.05|CD was|be|VBD chosen|choose|VBN as|as|IN the|the|DT significant|significant|JJ level|level|NN .|.|.
Data|Data|NNP was|be|VBD analyzed|analyze|VBN in|in|IN the|the|DT software|software|NN Acuity|acuity|NN 4.0|4.0|CD -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Devices|Devices|NNPS ,|,|, Sunnyvale|Sunnyvale|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. LOWESS|lowess|NN normalization|normalization|NN was|be|VBD performed|perform|VBN with|with|IN three|three|CD iterations|iteration|NNS using|use|VBG a|a|DT smoothing|smoothing|NN factor|factor|NN of|of|IN 0.4|0.4|CD .|.|. Hybridized|hybridize|VBN spots|spot|NNS having|have|VBG a|a|DT high|high|JJ QC|qc|NN -LRB-|-lrb-|-LRB- quality|quality|NN control|control|NN -RRB-|-rrb-|-RRB- value|value|NN >|>|JJR 0.1|0.1|CD ,|,|, good|good|JJ flag|flag|NN tags|tag|NNS -LRB-|-lrb-|-LRB- A|a|NN ,|,|, B|b|NN and|and|CC C|c|NN -RRB-|-rrb-|-RRB- in|in|IN both|both|CC Cy3/Cy5|cy3/cy5|NN channels|channel|NNS were|be|VBD chosen|choose|VBN for|for|IN further|further|JJ analysis|analysis|NN .|.|. One|one|CD sample|sample|NN t-tests|t-test|NNS were|be|VBD performed|perform|VBN across|across|IN replicates|replicate|VBZ .|.|. Step-down|step-down|JJ Bonferroni-Holm|Bonferroni-Holm|NNP was|be|VBD used|use|VBN for|for|IN the|the|DT correction|correction|NN of|of|IN multiple|multiple|JJ hypotheses|hypothesis|NNS testing|testing|NN .|.|. Only|only|RB oligonucleotides|oligonucleotide|NNS for|for|IN E.|e.|FW coli|coli|FW K12|k12|NN were|be|VBD choosen|choosen|VBN to|to|TO draw|draw|VB conclusion|conclusion|NN .|.|.
Data|Data|NNP was|be|VBD analyzed|analyze|VBN with|with|IN RMA|rma|NN using|use|VBG the|the|DT program|program|NN Partek|Partek|NNP 6.6|6.6|CD
Data|Data|NNP was|be|VBD extracted|extract|VBN with|with|IN Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP software|software|NN 10.7|10.7|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- using|use|VBG default|default|NN parameters|parameter|NNS -LRB-|-lrb-|-LRB- protocol|protocol|NN GE1-v1|ge1-v1|NN _|_|CD 91|91|CD -RRB-|-rrb-|-RRB- to|to|TO obtain|obtain|VB background|background|NN subtracted|subtract|VBN and|and|CC spatially|spatially|RB detrended|detrend|VBD Processed|processed|JJ Signal|signal|NN intensities|intensity|NNS .|.|. Features|feature|NNS flagged|flag|VBD in|in|IN Feature|Feature|NNP Extraction|Extraction|NNP as|as|IN Feature|Feature|NNP Non-uniform|non-uniform|JJ outliers|outlier|NNS were|be|VBD excluded|exclude|VBN .|.|.
Data|Data|NNP was|be|VBD obtained|obtain|VBN using|use|VBG the|the|DT GeneChip|GeneChip|NNP ®|®|NNP Command|command|NN Console|console|NN and|and|CC Expression|expression|NN Console|Console|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- AGCC|AGCC|NNP ;|;|: Version|Version|NNP 3.2|3.2|CD and|and|CC Expression|expression|NN Console|console|NN ;|;|: Version|Version|NNP 1.2|1.2|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT MAS5|mas5|NN algorithm|algorithm|NN to|to|TO generate|generate|VB .|.|. CHP|chp|NN files|file|NNS .|.|.
Data|Data|NNP was|be|VBD processed|process|VBN by|by|IN MATLAB|MATLAB|NNP to|to|TO median|median|JJ normalize|normalize|VB each|each|DT channel|channel|NN and|and|CC lowess|lowess|NN normalize|normalize|VBP the|the|DT sample|sample|NN set|set|NN .|.|.
Data|Data|NNP were|be|VBD analyzed|analyze|VBN by|by|IN Feature|Feature|NNP Extraction|Extraction|NNP V.|V.|NNP 11.5.1.1|11.5.1.1|CD .|.|. RNA|rna|NN
Data|datum|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG custom|custom|NN software|software|NN based|base|VBN on|on|IN the|the|DT R|r|NN programming|programming|NN environment|environment|NN and|and|CC BioConductor|BioConductor|NNP packages|package|NNS .|.|. Each|each|DT probe|probe|NN was|be|VBD randomly|randomly|RB spotted|spot|VBN in|in|IN three|three|CD to|to|TO five|five|CD replicates|replicate|VBZ to|to|TO control|control|VB for|for|IN positional|positional|JJ effects|effect|NNS on|on|IN the|the|DT array|array|NN .|.|. Data|datum|NNS from|from|IN replicate|replicate|VBP probes|probe|NNS were|be|VBD summarized|summarize|VBN by|by|IN the|the|DT median|median|NN of|of|IN the|the|DT log2-transformed|log2-transformed|JJ intensities|intensity|NNS .|.|. No|no|DT normalization|normalization|NN or|or|CC background|background|NN correction|correction|NN was|be|VBD performed|perform|VBN .|.|.
Data|Data|NNP were|be|VBD analyzed|analyze|VBN using|use|VBG GeneChip|GeneChip|NNP Operating|Operating|NNP Software|Software|NNP Version|Version|NNP 1.4|1.4|CD -LRB-|-lrb-|-LRB- Affymetrix|Affymetrix|NNP -RRB-|-rrb-|-RRB-
Data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN RMA|rma|NN -LRB-|-lrb-|-LRB- Robust|robust|JJ Multiarray|Multiarray|NNP Analysis|analysis|NN -RRB-|-rrb-|-RRB- using|use|VBG Affymetrix|Affymetrix|NNP default|default|NN analysis|analysis|NN settings|setting|NNS and|and|CC global|global|JJ scaling|scaling|NN as|as|IN normalization|normalization|NN method|method|NN .|.|.
Data|Data|NNP were|be|VBD extracted|extract|VBN in|in|IN GenePix|GenePix|NNP 4100A|4100a|CD scanning|scanning|NN software|software|NN and|and|CC normalized|normalize|VBD using|use|VBG the|the|DT lowess|lowess|NN method|method|NN implemented|implement|VBN in|in|IN TM4|tm4|NN MIDAS|midas|NN
Data|Data|NNP were|be|VBD extracted|extract|VBN with|with|IN Feature|feature|NN Extraction|extraction|NN software|software|NN 10.7|10.7|CD -LRB-|-lrb-|-LRB- Agilent|agilent|JJ technologies|technology|NNS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP ,|,|, US|US|NNP -RRB-|-rrb-|-RRB- .|.|. Raw|raw|NN data|datum|NNS were|be|VBD normalized|normalize|VBN by|by|IN Quantile|quantile|JJ algorithm|algorithm|NN ,|,|, GeneSpring|GeneSpring|NNP Software|Software|NNP 11.0|11.0|CD -LRB-|-lrb-|-LRB- Agilent|agilent|JJ technologies|technology|NNS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP ,|,|, US|US|NNP -RRB-|-rrb-|-RRB- .|.|.
Data|Data|NNP were|be|VBD normalized|normalize|VBN using|use|VBG LOWESS|lowess|NN -LRB-|-lrb-|-LRB- MIDAS|midas|NN -RRB-|-rrb-|-RRB- and|and|CC analyzed|analyze|VBN for|for|IN statistical|statistical|JJ significance|significance|NN using|use|VBG the|the|DT Rank|Rank|NNP Product|Product|NNP method|method|NN in|in|IN the|the|DT MultiExperimentViewer|MultiExperimentViewer|NNP
Data|Data|NNP were|be|VBD normalized|normalize|VBN using|use|VBG RMA|RMA|NNP algorithm|algorithm|NN from|from|IN R/Bioconductor/XPS|r/bioconductor/xps|NN package|package|NN .|.|.
Data|Data|NNP were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT LOWESS|LOWESS|NNP algorithm|algorithm|NN and|and|CC analyzed|analyze|VBN for|for|IN statistical|statistical|JJ significance|significance|NN using|use|VBG the|the|DT MeV|mev|NN package|package|NN
Data|Data|NNP were|be|VBD processed|process|VBN using|use|VBG Affymetrix|Affymetrix|NNP apt-probeset-summarize|apt-probeset-summarize|JJ software|software|NN version|version|NN 1.10|1.10|CD and|and|CC RMA|RMA|NNP algorithm|algorithm|NN .|.|. Samples|sample|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT standard|standard|JJ normalization|normalization|NN probes|probe|NNS present|present|JJ on|on|IN the|the|DT Affymetrix|Affymetrix|NNP GeneChip|GeneChip|NNP .|.|.
Data|Data|NNP were|be|VBD processed|process|VBN using|use|VBG the|the|DT robust|robust|JJ multiarray|multiarray|JJ average|average|JJ algorithm|algorithm|NN -LRB-|-lrb-|-LRB- RMA|rma|NN -RRB-|-rrb-|-RRB- for|for|IN normalization|normalization|NN ,|,|, background|background|NN correction|correction|NN and|and|CC expression|expression|NN value|value|NN calculation|calculation|NN .|.|. The|the|DT EB|EB|NNP -LRB-|-lrb-|-LRB- Wright|Wright|NNP and|and|CC Simon|Simon|NNP -RRB-|-rrb-|-RRB- test|test|NN was|be|VBD used|use|VBN for|for|IN the|the|DT fold|fold|JJ change|change|NN and|and|CC the|the|DT pvalue|pvalue|NN calculation|calculation|NN ,|,|,
Data|Data|NNP were|be|VBD visualized|visualize|VBN in|in|IN the|the|DT Rockhopper|Rockhopper|NNP IGV|igv|NN genome|genome|NN browser|browser|NN -LRB-|-lrb-|-LRB- McClure|McClure|NNP et|et|FW al.|al.|FW ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- and|and|CC TreeView|TreeView|NNP 3.0|3.0|CD -LRB-|-lrb-|-LRB- Saldana|Saldana|NNP et|et|FW al.|al.|FW ,|,|, 2004|2004|CD -RRB-|-rrb-|-RRB- .|.|.
day|day|NN :|:|: .|.|. strain|strain|NN :|:|: .|.|. oxygen|oxygen|NN :|:|: .|.|.
dcd|dcd|VBD KO|KO|NNP LB|LB|NNP rep1|rep1|NN
dcd|dcd|NN KO|KO|NNP LB|LB|NNP rep2|rep2|NN
dcd|dcd|NN KO|ko|NN M9|m9|NN rep1|rep1|NN
dcd|dcd|NN KO|ko|NN M9|m9|NN rep2|rep2|NN
DdksA|ddksa|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, leucine|leucine|NN ,|,|, isoleucine|isoleucine|NN ,|,|, valine|valine|NN ,|,|, glycine|glycine|NN ,|,|, phenylalanine|phenylalanine|NN ,|,|, threonine|threonine|NN -LRB-|-lrb-|-LRB- 40|40|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC uracil|uracil|NN -LRB-|-lrb-|-LRB- 50|50|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN and|and|CC treated|treat|VBN with|with|IN 0.5|0.5|CD mg/ml|mg/ml|NN serine|serine|NN hydroxamate|hydroxamate|NN -LRB-|-lrb-|-LRB- SHX|shx|NN -RRB-|-rrb-|-RRB- for|for|IN 20|20|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN vigorous|vigorous|JJ shaking|shake|VBG .|.|.
DdksA|ddksa|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, leucine|leucine|NN ,|,|, isoleucine|isoleucine|NN ,|,|, valine|valine|NN ,|,|, glycine|glycine|NN ,|,|, phenylalanine|phenylalanine|NN ,|,|, threonine|threonine|NN -LRB-|-lrb-|-LRB- 40|40|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC uracil|uracil|NN -LRB-|-lrb-|-LRB- 50|50|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN vigorous|vigorous|JJ shaking|shake|VBG .|.|.
DdksA|ddksa|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, leucine|leucine|NN ,|,|, isoleucine|isoleucine|NN ,|,|, valine|valine|NN ,|,|, glycine|glycine|NN ,|,|, phenylalanine|phenylalanine|NN ,|,|, threonine|threonine|NN -LRB-|-lrb-|-LRB- 40|40|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC uracil|uracil|NN -LRB-|-lrb-|-LRB- 50|50|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.4|0.4|CD -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN with|with|IN vigorous|vigorous|JJ shaking|shake|VBG .|.|.
Deconvolute|deconvolute|JJ peaks|peak|NNS in|in|IN close|close|JJ proximity|proximity|NN ,|,|, dPeak|dpeak|NN
Deer|deer|NNS feces|fece|NNS isolate|isolate|VBP D1|d1|NN
Deer|deer|NNS feces|fece|NNS isolate|isolate|NN D3|d3|NN
Deer|deer|NNS feces|fece|NNS isolate|isolate|VBP W6A|w6a|NN
Deer|deer|NNS III|iii|CD versus|versus|CC MG1655|mg1655|CD technical|technical|JJ replicate|replicate|VB 1|1|CD
Deer|deer|NNS III|iii|CD versus|versus|CC MG1655|mg1655|CD technical|technical|JJ replicate|replicate|VB 2|2|CD
Deer|deer|NNS II|ii|CD versus|versus|CC MG1655|mg1655|CD technical|technical|JJ replicate|replicate|VB 1|1|CD
Deer|deer|NNS II|ii|CD versus|versus|CC MG1655|mg1655|CD technical|technical|JJ replicate|replicate|VB 2|2|CD
Deer|deer|NNS I|I|PRP versus|versus|CC MG1655|mg1655|NN technical|technical|JJ replicate|replicate|VB 1|1|CD
Deer|deer|NNS I|I|PRP versus|versus|CC MG1655|mg1655|NN technical|technical|JJ replicate|replicate|VB 2|2|CD
Delta|Delta|NNP dksA|dksA|NNP Cells|cell|NNS
Delta|Delta|NNP dksA|dksA|NNP Cells|cell|NNS Replicate|replicate|VB 1|1|CD
Delta|Delta|NNP dksA|dksA|NNP Cells|cell|NNS Replicate|replicate|VB 2|2|CD
Delta|Delta|NNP dksA|dksA|NNP Cells|cell|NNS Replicate|replicate|VB 3|3|CD
delta|delta|NN hfq|hfq|NN
Delta|delta|NN hfq|hfq|NN
deltamatP|deltamatp|NN 22|22|CD °C|°c|NN
delta-rnr|delta-rnr|JJ mutant|mutant|JJ _|_|NN anoxic|anoxic|JJ -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB- _|_|SYM glycerol|glycerol|NN
delta-rnr|delta-rnr|JJ mutant|mutant|JJ _|_|NN anoxic|anoxic|JJ -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB- _|_|SYM glycerol|glycerol|NN +|+|CC propionate|propionate|NN
delta-rnr|delta-rnr|JJ mutant|mutant|JJ _|_|NN oxic|oxic|JJ _|_|NN glycerol|glycerol|NN
delta-rnr|delta-rnr|JJ mutant|mutant|JJ _|_|NN oxic|oxic|JJ _|_|NN glycerol|glycerol|NN +|+|CC propionate|propionate|NN
Delta|Delta|NNP rseA|rseA|NNP
Demultiplexing|Demultiplexing|NNP
Depletion|depletion|NN of|of|IN ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD accomplished|accomplish|VBN with|with|IN the|the|DT Ribominus|Ribominus|NNP Transcriptome|Transcriptome|NNP Isolation|isolation|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP -RRB-|-rrb-|-RRB- followed|follow|VBN by|by|IN ethanol|ethanol|NN precipitation|precipitation|NN .|.|. A|a|DT stranded|stranded|JJ library|library|NN was|be|VBD prepared|prepare|VBN using|use|VBG a|a|DT ScriptSeq|ScriptSeq|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- using|use|VBG manufacturer|manufacturer|NN 's|'s|POS recommended|recommend|VBN protocols|protocol|NNS .|.|. Each|each|DT sample|sample|NN was|be|VBD tagged|tag|VBN with|with|IN a|a|DT six|six|CD nucleotide|nucleotide|NN barcode|barcode|NN unique|unique|JJ to|to|TO each|each|DT sample|sample|NN to|to|TO allow|allow|VB multiplexing|multiplexing|NN .|.|. The|the|DT products|product|NNS are|be|VBP purified|purify|VBN and|and|CC enriched|enrich|VBN by|by|IN PCR|pcr|NN to|to|TO create|create|VB the|the|DT final|final|JJ cDNA|cdna|NN library|library|NN .|.|. Final|final|JJ libraries|library|NNS were|be|VBD checked|check|VBN for|for|IN quality|quality|NN and|and|CC quantity|quantity|NN by|by|IN TapeStation|TapeStation|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- and|and|CC qPCR|qpcr|NN using|use|VBG Kapa|Kapa|NNP 's|'s|POS library|library|NN quantification|quantification|NN kit|kit|NN for|for|IN Illumina|Illumina|NNP Sequencing|sequencing|NN platforms|platform|NNS -LRB-|-lrb-|-LRB- Kapa|Kapa|NNP Biosystems|Biosystems|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS recommended|recommend|VBN protocols|protocol|NNS .|.|. Six|six|CD samples|sample|NNS were|be|VBD sequenced|sequence|VBN per|per|IN lane|lane|NN on|on|IN a|a|DT 50|50|CD cycle|cycle|NN single|single|JJ end|end|NN run|run|NN on|on|IN a|a|DT HiSeq|hiseq|JJ 2500|2500|CD -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- in|in|IN high|high|JJ output|output|NN mode|mode|NN using|use|VBG version|version|NN 4|4|CD reagents|reagent|NNS .|.|.
Desulfovibrio|desulfovibrio|NN piger|piger|NN GOR1|gor1|NN
Detailed|detailed|JJ parameters|parameter|NNS for|for|IN reads|read|VBZ mapping|mapping|NN :|:|: bowtie2|bowtie2|NN -|-|: x|x|CC ATCC8739|atcc8739|NN -1|-1|CD X|x|NN _|_|NN 1|1|CD .|.|. fq|fq|NN -2|-2|CD X|x|NN _|_|NN 2|2|CD .|.|. fq|fq|NN --|--|: no-mixed|no-mixed|JJ -|-|: p|p|NN 2|2|CD -|-|: S|s|NN X.sam|x.sam|NN
developmental|developmental|JJ stage|stage|NN :|:|: mixed|mixed|JJ population|population|NN ,|,|, exponential|exponential|JJ phase|phase|NN
DGE|dge|NN analysis|analysis|NN used|use|VBD a|a|DT false-discovery|false-discovery|JJ rate|rate|NN -LRB-|-lrb-|-LRB- FDR|FDR|NNP -RRB-|-rrb-|-RRB- of|of|IN 0.10|0.10|CD .|.|.
∆|∆|SYM dgk|dgk|FW parent|parent|NN Sample|sample|NN 16|16|CD
∆|∆|CD dgk|dgk|NN parent|parent|NN Sample|sample|NN 35|35|CD
∆|∆|CD dgk|dgk|NN parent|parent|NN Sample|sample|NN 54|54|CD
dgk|dgk|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 17|17|CD
dgk|dgk|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 36|36|CD
dgk|dgk|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 55|55|CD
dgk|dgk|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 18|18|CD
dgk|dgk|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 37|37|CD
dgk|dgk|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 56|56|CD
dgk|dgk|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 19|19|CD
dgk|dgk|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 38|38|CD
dgk|dgk|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 57|57|CD
DH1-log|dh1-log|JJ
DH1-log-tr|dh1-log-tr|JJ
DicF|dicf|NN rep1|rep1|NN
DicF|dicf|NN rep2|rep2|NN
DicF|dicf|NN rep3|rep3|NN
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR APPLE|APPLE|NNP :|:|: 250|250|CD ,|,|, OAT|oat|NN :|:|: 250|250|CD ,|,|, RICE|RICE|NNP :|:|: 250|250|CD ,|,|, BEEF|beef|NN :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR APPLE|APPLE|NNP :|:|: 250|250|CD ,|,|, RICE|RICE|NNP :|:|: 250|250|CD ,|,|, OAT|oat|NN :|:|: 250|250|CD ,|,|, BEEF|beef|NN :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR APPLE|APPLE|NNP :|:|: 250|250|CD ,|,|, RICE|RICE|NNP :|:|: 250|250|CD ,|,|, PEACH|PEACH|NNP :|:|: 250|250|CD ,|,|, CHICK|CHICK|NNP :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR APPLE|APPLE|NNP :|:|: 666.7|666.7|CD ,|,|, BEEF|beef|NN :|:|: 222.2|222.2|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD ,|,|, PEACH|PEACH|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR APPLE|APPLE|NNP :|:|: 666.7|666.7|CD ,|,|, OAT|oat|NN :|:|: 222.2|222.2|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR APPLE|APPLE|NNP :|:|: 666.7|666.7|CD ,|,|, PEACH|PEACH|NNP :|:|: 222.2|222.2|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD ,|,|, RICE|RICE|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR APPLE|APPLE|NNP :|:|: 666.7|666.7|CD ,|,|, PEACH|PEACH|NNP :|:|: 222.2|222.2|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR BEEF|beef|NN :|:|: 250|250|CD ,|,|, PEA|PEA|NNP :|:|: 250|250|CD ,|,|, CHICK|CHICK|NNP :|:|: 250|250|CD ,|,|, OAT|oat|NN :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR BEEF|beef|NN :|:|: 666.7|666.7|CD ,|,|, PEACH|PEACH|NNP :|:|: 222.2|222.2|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD ,|,|, RICE|RICE|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR BEEF|beef|NN :|:|: 666.7|666.7|CD ,|,|, RICE|RICE|NNP :|:|: 222.2|222.2|CD ,|,|, PEA|PEA|NNP :|:|: 55.6|55.6|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR CHICK|chick|NN :|:|: 421.1|421.1|CD ,|,|, BEEF|beef|NN :|:|: 421.1|421.1|CD ,|,|, PEA|PEA|NNP :|:|: 105.3|105.3|CD ,|,|, APPLE|APPLE|NNP :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR CHICK|chick|NN :|:|: 666.7|666.7|CD ,|,|, PEACH|PEACH|NNP :|:|: 222.2|222.2|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD ,|,|, RICE|RICE|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR CHICK|chick|NN :|:|: 666.7|666.7|CD ,|,|, PEACH|PEACH|NNP :|:|: 222.2|222.2|CD ,|,|, RICE|RICE|NNP :|:|: 55.6|55.6|CD ,|,|, OAT|oat|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR CHICK|chick|NN :|:|: 666.7|666.7|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 222.2|222.2|CD ,|,|, RICE|RICE|NNP :|:|: 55.6|55.6|CD ,|,|, OAT|oat|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR OAT|oat|NN :|:|: 421.1|421.1|CD ,|,|, APPLE|APPLE|NNP :|:|: 421.1|421.1|CD ,|,|, BEEF|beef|NN :|:|: 105.3|105.3|CD ,|,|, RICE|RICE|NNP :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR OAT|oat|NN :|:|: 421.1|421.1|CD ,|,|, RICE|RICE|NNP :|:|: 421.1|421.1|CD ,|,|, CHICK|CHICK|NNP :|:|: 105.3|105.3|CD :|:|: APPLE|APPLE|NNP :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR OAT|oat|NN :|:|: 666.7|666.7|CD ,|,|, RICE|RICE|NNP :|:|: 222.2|222.2|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEA|pea|NN :|:|: 250|250|CD ,|,|, OAT|oat|NN :|:|: 250|250|CD ,|,|, BEEF|beef|NN :|:|: 250|250|CD ,|,|, CHICK|CHICK|NNP :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEA|pea|NN :|:|: 421.1|421.1|CD ,|,|, CHICK|CHICK|NNP :|:|: 421.1|421.1|CD ,|,|, RICE|RICE|NNP :|:|: 105.3|105.3|CD ,|,|, PEACH|PEACH|NNP :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEA|pea|NN :|:|: 666.7|666.7|CD ,|,|, APPLE|APPLE|NNP :|:|: 222.2|222.2|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD ,|,|, PEACH|PEACH|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEA|pea|NN :|:|: 666.7|666.7|CD ,|,|, CHICK|CHICK|NNP :|:|: 222.2|222.2|CD ,|,|, OAT|oat|NN :|:|: 55.6|55.6|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEA|pea|NN :|:|: 666.7|666.7|CD ,|,|, PEACH|PEACH|NNP :|:|: 222.2|222.2|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD ,|,|, OAT|oat|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEA|pea|NN :|:|: 666.7|666.7|CD ,|,|, RICE|RICE|NNP :|:|: 222.2|222.2|CD ,|,|, APPLE|APPLE|NNP :|:|: 55.6|55.6|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEA|pea|NN :|:|: 666.7|666.7|CD ,|,|, RICE|RICE|NNP :|:|: 222.2|222.2|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD ,|,|, PEACH|PEACH|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEACH|peach|NN :|:|: 250|250|CD ,|,|, OAT|oat|NN :|:|: 250|250|CD ,|,|, RICE|RICE|NNP :|:|: 250|250|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEACH|peach|NN :|:|: 421.1|421.1|CD ,|,|, BEEF|beef|NN :|:|: 421.1|421.1|CD ,|,|, OAT|oat|NN :|:|: 105.3|105.3|CD ,|,|, RICE|RICE|NNP :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEACH|peach|NN :|:|: 421.1|421.1|CD ,|,|, OAT|oat|NN :|:|: 421.1|421.1|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 105.3|105.3|CD ,|,|, BEEF|beef|NN :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEACH|peach|NN :|:|: 666.7|666.7|CD ,|,|, OAT|oat|NN :|:|: 222.2|222.2|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEACH|peach|NN :|:|: 666.7|666.7|CD ,|,|, PEA|PEA|NNP :|:|: 222.2|222.2|CD ,|,|, APPLE|APPLE|NNP :|:|: 55.6|55.6|CD ,|,|, CHICK|CHICK|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEACH|peach|NN :|:|: 666.7|666.7|CD ,|,|, PEA|PEA|NNP :|:|: 222.2|222.2|CD ,|,|, OAT|oat|NN :|:|: 55.6|55.6|CD ,|,|, RICE|RICE|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR PEACH|peach|NN :|:|: 666.7|666.7|CD ,|,|, PEA|PEA|NNP :|:|: 222.2|222.2|CD ,|,|, RICE|RICE|NNP :|:|: 55.6|55.6|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR RICE|rice|NN :|:|: 666.7|666.7|CD ,|,|, APPLE|APPLE|NNP :|:|: 222.2|222.2|CD ,|,|, SWEET|SWEET|NNP _|_|NNP POTATO|POTATO|NNP :|:|: 55.6|55.6|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 250|250|CD ,|,|, APPLE|APPLE|NNP :|:|: 250|250|CD ,|,|, PEACH|PEACH|NNP :|:|: 250|250|CD ,|,|, BEEF|beef|NN :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 250|250|CD ,|,|, BEEF|beef|NN :|:|: 250|250|CD ,|,|, PEACH|PEACH|NNP :|:|: 250|250|CD ,|,|, RICE|RICE|NNP :|:|: 250|250|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 421.1|421.1|CD ,|,|, OAT|oat|NN :|:|: 421.1|421.1|CD ,|,|, CHICK|CHICK|NNP :|:|: 105.3|105.3|CD ,|,|, RICE|RICE|NNP :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 421.1|421.1|CD ,|,|, RICE|RICE|NNP :|:|: 421.1|421.1|CD ,|,|, CHICK|CHICK|NNP :|:|: 105.3|105.3|CD ,|,|, PEA|PEA|NNP :|:|: 52.6|52.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 666.7|666.7|CD ,|,|, APPLE|APPLE|NNP :|:|: 222.2|222.2|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD ,|,|, PEACH|PEACH|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 666.7|666.7|CD ,|,|, CHICK|CHICK|NNP :|:|: 222.2|222.2|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD ,|,|, PEA|PEA|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 666.7|666.7|CD ,|,|, OAT|oat|NN :|:|: 222.2|222.2|CD ,|,|, PEACH|PEACH|NNP :|:|: 55.6|55.6|CD ,|,|, PEA|PEA|NNP :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN a|a|DT meal|meal|NN of|of|IN human|human|JJ pureed|pureed|NN food|food|NN in|in|IN the|the|DT following|follow|VBG concentrations|concentration|NNS -LRB-|-lrb-|-LRB- g/kg|g/kg|NN -RRB-|-rrb-|-RRB- =|=|JJ >|>|JJR SWEET|sweet|JJ _|_|NN POTATO|potato|NN :|:|: 666.7|666.7|CD ,|,|, RICE|RICE|NNP :|:|: 222.2|222.2|CD ,|,|, PEACH|PEACH|NNP :|:|: 55.6|55.6|CD ,|,|, BEEF|beef|NN :|:|: 55.6|55.6|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09049|.09049|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09050|.09050|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09051|.09051|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09052|.09052|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09053|.09053|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09054|.09054|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09055|.09055|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09055|.09055|CD .|.|.
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09056|.09056|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09057|.09057|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09057|.09057|CD .|.|.
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09058|.09058|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09059|.09059|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09620|.09620|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09621|.09621|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09622|.09622|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09623|.09623|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09624|.09624|CD
diet|diet|NN :|:|: Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09625|.09625|CD
Differential|differential|JJ expression|expression|NN analysis|analysis|NN was|be|VBD carried|carry|VBN out|out|RP using|use|VBG cuffdiff|cuffdiff|JJ v.|v.|CC 2.0.2|2.0.2|CD with|with|IN upper-quartile|upper-quartile|JJ normalization|normalization|NN and|and|CC fr-firststrand|fr-firststrand|NN for|for|IN library|library|NN type|type|NN
Differential|differential|JJ expression|expression|NN analysis|analysis|NN was|be|VBD performed|perform|VBN with|with|IN R|r|NN -LRB-|-lrb-|-LRB- version|version|NN 3.1.1|3.1.1|CD -RRB-|-rrb-|-RRB- and|and|CC edgeR|edger|NN -LRB-|-lrb-|-LRB- version|version|NN 3.8.5|3.8.5|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Bioconductor|bioconductor|NN -RRB-|-rrb-|-RRB- .|.|.
Differential|differential|JJ expression|expression|NN analysis|analysis|NN with|with|IN DESeq|deseq|NN -LRB-|-lrb-|-LRB- Anders|Anders|NNP and|and|CC Huber|Huber|NNP 2010|2010|CD -RRB-|-rrb-|-RRB- with|with|IN the|the|DT default|default|NN setting|set|VBG
Differential|differential|JJ expression|expression|NN between|between|IN aerobic|aerobic|JJ and|and|CC anaerobic|anaerobic|JJ environments|environment|NNS was|be|VBD identified|identify|VBN by|by|IN using|use|VBG DESeq2|deseq2|NN -LRB-|-lrb-|-LRB- Love|love|NN M|m|NN ,|,|, Huber|Huber|NNP W|W|NNP and|and|CC Anders|Anders|NNP S|s|NN ,|,|, 2014|2014|CD -RRB-|-rrb-|-RRB-
differential|differential|JJ expression|expression|NN :|:|: Bioconductor|Bioconductor|NNP package|package|NN edgeR|edger|NN -LRB-|-lrb-|-LRB- version|version|NN 3.2.3|3.2.3|CD -RRB-|-rrb-|-RRB- ;|;|: default|default|NN parameters|parameter|NNS
Differential|differential|JJ expression|expression|NN testing|testing|NN between|between|IN sample|sample|NN groups|group|NNS was|be|VBD performed|perform|VBN in|in|IN Rstudio|Rstudio|NNP -LRB-|-lrb-|-LRB- v.|v.|CC 1.0.36|1.0.36|CD -RRB-|-rrb-|-RRB- using|use|VBG DESeq2|deseq2|NN -LRB-|-lrb-|-LRB- v.|v.|CC 1.14.1|1.14.1|CD -RRB-|-rrb-|-RRB-
Differential|differential|JJ gene|gene|NN expression|expression|NN -LRB-|-lrb-|-LRB- DGE|dge|NN -RRB-|-rrb-|-RRB- was|be|VBD then|then|RB performed|perform|VBN on|on|IN fragments|fragment|NNS per|per|IN kilobase|kilobase|NN mapped|map|VBN -LRB-|-lrb-|-LRB- FPKM|fpkm|NN -RRB-|-rrb-|-RRB- values|value|NNS in|in|IN Cufflinks|Cufflinks|NNP '|'|POS Cuffdiff|cuffdiff|JJ package|package|NN -LRB-|-lrb-|-LRB- version|version|NN 0.0.7|0.0.7|CD -RRB-|-rrb-|-RRB- .|.|.
Differentially|differentially|RB expressed|express|VBD -LRB-|-lrb-|-LRB- DE|de|NN -RRB-|-rrb-|-RRB- genes|gene|NNS in|in|IN all|all|DT stress|stress|NN evolved|evolve|VBD strains|strain|NNS were|be|VBD found|find|VBN relative|relative|JJ to|to|TO the|the|DT expression|expression|NN levels|level|NNS in|in|IN the|the|DT reference|reference|NN G500|g500|NN strain|strain|NN using|use|VBG the|the|DT edgeR|edger|NN R|r|NN package|package|NN .|.|.
Differentially|differentially|RB expressed|express|VBD genes|gene|NNS were|be|VBD identified|identify|VBN by|by|IN processing|process|VBG raw|raw|JJ counts|count|NNS of|of|IN mapped|map|VBN reads|read|VBZ with|with|IN edgeR|edger|NN R|r|NN library|library|NN version|version|NN 2.6.9|2.6.9|CD .|.|. Normalized|normalize|VBN counts|count|NNS for|for|IN each|each|DT biological|biological|JJ replicate|replicate|VB were|be|VBD averaged|average|VBN between|between|IN two|two|CD technical|technical|JJ replicates|replicate|VBZ .|.|.
Dilution|Dilution|NNP rate|rate|NN =|=|JJ 0.14|0.14|CD /|/|: h|h|NN
dinI|dini|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r1|r1|NN
dinI|dini|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r2|r2|FW
dinI|dini|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
dinI|dini|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
dinP|dinp|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r1|r1|FW
dinP|dinp|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r2|r2|FW
dinP|dinp|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
dinP|dinp|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
Direct|Direct|NNP testing|testing|NN of|of|IN culture|culture|NN broth|broth|NN -LRB-|-lrb-|-LRB- Standard|standard|JJ -RRB-|-rrb-|-RRB- or|or|CC after|after|IN centrifugation|centrifugation|NN of|of|IN culture|culture|NN broth|broth|NN -LRB-|-lrb-|-LRB- Supernatant|supernatant|NN -RRB-|-rrb-|-RRB-
disease|disease|NN state|state|NN :|:|: control|control|NN
disease|disease|NN state|state|NN :|:|: cystic|cystic|JJ fibrosis|fibrosis|NN
Dividing|divide|VBG t|t|NN =|=|JJ 2|2|CD hours|hour|NNS
DksA|dksa|NN ChIP|chip|NN DNA|dna|NN from|from|IN DdksA|ddksa|NN cells|cell|NNS
DksA|dksa|NN ChIP|chip|NN DNA|dna|NN from|from|IN wt|wt|JJ cells|cell|NNS
DksA|dksa|NN _|_|CD DdksA|ddksa|NN _|_|NN untreated|untreated|JJ
DksA|dksa|NN _|_|CD wt|wt|JJ _|_|NN untreated|untreated|JJ _|_|NN rep1|rep1|NN
DksA|dksa|NN _|_|CD wt|wt|JJ _|_|NN untreated|untreated|JJ _|_|NN rep2|rep2|NN
DL4184|dl4184|NN biological|biological|JJ repeat|repeat|NN 1|1|CD RecA|reca|NN ChIP|chip|NN
DL4184|dl4184|NN biological|biological|JJ repeat|repeat|NN 2|2|CD RecA|reca|NN ChIP|chip|NN _|_|NN reanalyzed|reanalyze|VBN
DL4184C|dl4184c|NN _|_|CD ChIP-seq|ChIP-seq|NNP
DL4201|dl4201|NN biological|biological|JJ repeat|repeat|NN 1|1|CD RecA|reca|NN ChIP|chip|NN
DL4201|dl4201|NN biological|biological|JJ repeat|repeat|NN 2|2|CD RecA|reca|NN ChIP|chip|NN _|_|NN reanalyzed|reanalyze|VBN
DL4201C|dl4201c|NN _|_|CD ChIP-seq|ChIP-seq|NNP
DL4311C|DL4311C|NNP _|_|SYM ChIP-seq|ChIP-seq|NNP
DL4312C|DL4312C|NNP _|_|SYM ChIP-seq|ChIP-seq|NNP
DL4899|dl4899|NN
DL4900|dl4900|NN
DL4900|dl4900|NN _|_|NN input|input|NN
DL5215|dl5215|NN
DL5322|dl5322|NN
DL5324|dl5324|NN
DL5326|dl5326|NN
DL5328|dl5328|NN
DL5330|dl5330|NN
DL5699|dl5699|NN biological|biological|JJ repeat|repeat|NN 1|1|CD RecA|reca|NN ChIP|chip|NN
DL5699|dl5699|NN biological|biological|JJ repeat|repeat|NN 2|2|CD RecA|reca|NN ChIP|chip|NN
DL6204|dl6204|NN biological|biological|JJ repeat|repeat|NN 1|1|CD RecA|reca|NN ChIP|chip|NN
DL6204|dl6204|NN biological|biological|JJ repeat|repeat|NN 2|2|CD RecA|reca|NN ChIP|chip|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN ,|,|, rep1|rep1|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN ,|,|, rep2|rep2|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN ,|,|, rep|rep|NN 3|3|CD
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN ,|,|, rep|rep|NN 4|4|CD
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN with|with|IN 0.025|0.025|CD mM|mm|NN CspA|cspa|NN protein|protein|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN with|with|IN 0.05|0.05|CD mM|mm|NN CspA|cspa|NN protein|protein|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN with|with|IN 0.1|0.1|CD mM|mm|NN CspA|cspa|NN protein|protein|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN with|with|IN 0.1|0.1|CD mM|mm|NN CspA|cspa|NN protein|protein|NN ,|,|, rep1|rep1|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN with|with|IN 0.1|0.1|CD mM|mm|NN CspA|cspa|NN protein|protein|NN ,|,|, rep|rep|NN 2|2|CD
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN with|with|IN 0.1|0.1|CD mM|mm|NN CspA|cspa|NN protein|protein|NN ,|,|, rep|rep|NN 3|3|CD
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 10|10|CD °C|°c|NN with|with|IN 0.1|0.1|CD mM|mm|NN CspA|cspa|NN protein|protein|NN ,|,|, rep|rep|NN 4|4|CD
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 37|37|CD °C|°c|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 37|37|CD °C|°c|NN ,|,|, rep1|rep1|NN
DMS-MaPSeq|dms-mapseq|NN of|of|IN purified|purify|VBN cspA|cspa|NN mRNA|mrna|NN at|at|IN 37|37|CD °C|°c|NN ,|,|, rep|rep|NN 2|2|CD
DMSO|dmso|NN _|_|VBD 0|0|CD min|min|NN _|_|CD rep1|rep1|NN
DMSO|dmso|NN _|_|VBD 0|0|CD min|min|NN _|_|CD rep2|rep2|NN
DMSO|dmso|NN _|_|VBD 0|0|CD min|min|NN _|_|CD rep3|rep3|NN
DMSO|dmso|NN _|_|SYM 60|60|CD min|min|NN _|_|CD rep1|rep1|NN
DMSO|dmso|NN _|_|SYM 60|60|CD min|min|NN _|_|CD rep2|rep2|NN
DMSO|dmso|NN _|_|SYM 60|60|CD min|min|NN _|_|CD rep3|rep3|NN
DMSO|dmso|NN _|_|SYM 60|60|CD min|min|NN _|_|CD rep4|rep4|NN
DMSO-Only|dmso-only|JJ Treatment|treatment|NN
DMSO|dmso|NN treatment|treatment|NN ,|,|, 0|0|CD min|min|NN ,|,|, replicate|replicate|VB 1|1|CD
DMSO|dmso|NN treatment|treatment|NN ,|,|, 0|0|CD min|min|NN ,|,|, replicate|replicate|VB 2|2|CD
DMSO|dmso|NN treatment|treatment|NN ,|,|, 0|0|CD min|min|NN ,|,|, replicate|replicate|VB 3|3|CD
DMSO|dmso|NN treatment|treatment|NN ,|,|, 60|60|CD min|min|NN ,|,|, replicate|replicate|VB 1|1|CD
DMSO|dmso|NN treatment|treatment|NN ,|,|, 60|60|CD min|min|NN ,|,|, replicate|replicate|VB 2|2|CD
DMSO|dmso|NN treatment|treatment|NN ,|,|, 60|60|CD min|min|NN ,|,|, replicate|replicate|VB 3|3|CD
DMSO|dmso|NN treatment|treatment|NN ,|,|, 60|60|CD min|min|NN ,|,|, replicate|replicate|VB 4|4|CD
DMS-seq|dms-seq|JJ 30|30|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
DMS-seq|dms-seq|NN 6|6|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
DMS-seq|dms-seq|NN 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD cspABEG|cspabeg|NN cells|cell|NNS
DMS-seq|dms-seq|NN 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD cspBG|cspbg|NN cells|cell|NNS
DMS-seq|dms-seq|NN 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
DMS-seq|dms-seq|NN of|of|IN purified|purify|VBN mRNA|mrna|NN in|in|FW vitro|vitro|FW at|at|IN 10|10|CD °C|°c|NN ,|,|, rep1|rep1|NN
DMS-seq|dms-seq|NN of|of|IN purified|purify|VBN mRNA|mrna|NN in|in|FW vitro|vitro|FW at|at|IN 10|10|CD °C|°c|NN ,|,|, rep2|rep2|NN
DMS-seq|dms-seq|NN of|of|IN WT|wt|JJ cells|cell|NNS after|after|IN kasugamycin|kasugamycin|NN treatment|treatment|NN at|at|IN 10|10|CD °C|°c|NN
DMS-seq|dms-seq|NN -LRB-|-lrb-|-LRB- Ribo|Ribo|NNP -|-|: RNA|rna|NN -RRB-|-rrb-|-RRB-
DMS-seq|dms-seq|NN -LRB-|-lrb-|-LRB- Total|total|JJ RNA|rna|NN -RRB-|-rrb-|-RRB-
dnaA|dnaa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
dnaA|dnaa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
dnaA|dnaa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
dnaA|dnaa|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
dnaB-Ts|dnab-t|NNS _|_|VBP 30|30|CD °C|°c|NN
dnaB-Ts|dnab-t|NNS _|_|VBP 42|42|CD °C|°c|NN
dnaB-Ts|dnab-t|NNS Î|î|NN ''|''|'' ahpC|ahpc|NN _|_|CD 30|30|CD °C|°c|NN
dnaB-Ts|dnab-t|NNS Î|î|NN ''|''|'' ahpC|ahpc|NN _|_|CD 42|42|CD °C|°c|NN
dnaC2|dnac2|NN 30|30|CD '|'|'' at|at|IN 30|30|CD deg|deg|NN ,|,|, 2|2|CD ug|ug|NN gen|gen|NN DNA|dna|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
dnaC2|dnac2|NN 90|90|CD '|'|'' at|at|IN 42|42|CD deg|deg|NN ,|,|, 2|2|CD ug|ug|NN gen|gen|NN DNA|dna|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
dnaC2|dnac2|NN synchrony|synchrony|NN 30|30|CD '|'|'' after|after|IN shift|shift|NN ,|,|, print|print|NN 7|7|CD array|array|NN
dnaC|dnac|NN fully|fully|RB replicated|replicate|VBN ,|,|, 2|2|CD ug|ug|NN Sau3AI|sau3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
dnaC|dnac|NN fully|fully|RB replicated|replicate|VBN ,|,|, 2|2|CD ug|ug|NN Say3AI|say3ai|NN ,|,|, pdN6|pdn6|NN RT|rt|NN
dnaC|dnac|NN genomic|genomic|JJ DNA|dna|NN ,|,|, Sau3A|sau3a|NN ,|,|, 2|2|CD ug|ug|NN
DNA|dna|NN detected|detect|VBN with|with|IN GyrA|gyra|NN immunoglobulin|immunoglobulin|NN
DNA|dna|NN extraction|extraction|NN :|:|: Genomic|genomic|JJ DNA|dna|NN was|be|VBD isolated|isolate|VBN and|and|CC purified|purify|VBN according|accord|VBG to|to|TO standard|standard|JJ procedures|procedure|NNS -LRB-|-lrb-|-LRB- Ausubel|Ausubel|NNP et|et|FW al.|al.|FW 1994|1994|CD -RRB-|-rrb-|-RRB- .|.|. Genomic|genomic|JJ DNA|dna|NN was|be|VBD fragmented|fragment|VBN by|by|IN nebulization|nebulization|NN as|as|IN described|describe|VBN by|by|IN Girgis|Girgis|NNP et|et|FW al.|al.|FW .|.|. PLoS|PLoS|NNP Genetics|Genetics|NNP 3|3|CD -LRB-|-lrb-|-LRB- 9|9|CD -RRB-|-rrb-|-RRB- :|:|: e154|e154|NN -LRB-|-lrb-|-LRB- 2007|2007|CD -RRB-|-rrb-|-RRB- and|and|CC purified|purify|VBN by|by|IN phenol/chloroform|phenol/chloroform|NN extraction|extraction|NN and|and|CC ethanol|ethanol|NN precipitated|precipitate|VBD .|.|.
DNA|dna|NN fragments|fragment|NNS were|be|VBD treated|treat|VBN with|with|IN Epicentre|Epicentre|NNP End-It|end-it|JJ DNA|dna|NN End|end|NN Repair|Repair|NNP Kit|kit|NN and|and|CC 3|3|CD '|'|'' A|a|DT overhangs|overhang|NNS were|be|VBD added|add|VBN with|with|IN DNA|dna|NN polymerase|polymerase|NN I|i|NN -LRB-|-lrb-|-LRB- Klenow|klenow|NN fragment|fragment|NN -RRB-|-rrb-|-RRB- .|.|. Adapters|adapter|NNS from|from|IN the|the|DT IlluminaTruSeq|illuminatruseq|NN DNA|dna|NN sample|sample|NN preparation|preparation|NN kit|kit|NN were|be|VBD ligated|ligate|VBN using|use|VBG LigFast|LigFast|NNP -LRB-|-lrb-|-LRB- Promega|Promega|NNP -RRB-|-rrb-|-RRB- and|and|CC DNAs|dna|NNS were|be|VBD amplified|amplify|VBN by|by|IN PCR|pcr|NN using|use|VBG primers|primer|NNS provided|provide|VBN in|in|IN the|the|DT IlluminaTruSeq|illuminatruseq|NN DNA|dna|NN sample|sample|NN preparation|preparation|NN kit|kit|NN and|and|CC Phusion|phusion|NN DNA|dna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- .|.|. Products|Products|NNPS of|of|IN the|the|DT ligation|ligation|NN reaction|reaction|NN and|and|CC PCR|pcr|NN amplification|amplification|NN in|in|IN the|the|DT range|range|NN 300-400|300-400|CD bp|bp|NN were|be|VBD purified|purify|VBN by|by|IN 2|2|CD %|%|NN agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN .|.|. DNA|dna|NN concentrations|concentration|NNS were|be|VBD measured|measure|VBN using|use|VBG Qubit|Qubit|NNP ™|™|SYM dsDNA|dsdna|NN HS|hs|NN Assay|assay|NN Kits|kit|NNS -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- .|.|.
dnaJ-ala-1|dnaj-ala-1|NN
dnaJ-ala-2|dnaj-ala-2|NN
dnaJ-gln-1|dnaj-gln-1|NN
dnaJ-gln-2|dnaj-gln-2|NN
dnaJ|dnaj|NN mutant|mutant|NN in|in|IN Ala|Ala|NNP media|media|NNS
dnaJ|dnaj|NN mutant|mutant|NN in|in|IN Gln|gln|NN media|media|NNS
DnaK|dnak|NN deletant|deletant|JJ _|_|NN 37C|37c|NN
DNA|dna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS by|by|IN FASTERIS|FASTERIS|NNP SA|SA|NNP ,|,|, Switzerland|Switzerland|NNP
dnaN|dnaN|NNP __|__|VBD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
dnaN|dnan|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
dnaN|dnan|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
dnaN|dnan|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
DNA|dna|NN samples|sample|NNS were|be|VBD submitted|submit|VBN to|to|TO the|the|DT University|University|NNP of|of|IN Wisconsin-Madison|Wisconsin-Madison|NNP DNA|DNA|NNP Sequencing|sequencing|NN Facility|facility|NN for|for|IN ChIP-seq|ChIP-seq|NNP library|library|NN preparation|preparation|NN .|.|. All|all|DT libraries|library|NNS were|be|VBD generated|generate|VBN using|use|VBG reagents|reagent|NNS from|from|IN the|the|DT Illumina|Illumina|NNP Paired|Paired|NNP End|End|NNP Sample|Sample|NNP Preparation|Preparation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT Illumina|Illumina|NNP protocol|protocol|NN ``|``|`` Preparing|prepare|VBG Samples|sample|NNS for|for|IN ChIP|chip|NN Sequencing|sequencing|NN of|of|IN DNA|dna|NN ''|''|'' -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP part|part|NN #|#|# 11257047|11257047|CD RevA|reva|NN -RRB-|-rrb-|-RRB- as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS ,|,|, except|except|IN products|product|NNS of|of|IN the|the|DT ligation|ligation|NN reaction|reaction|NN were|be|VBD purified|purify|VBN by|by|IN gel|gel|NN electrophoresis|electrophoresis|NN using|use|VBG 2|2|CD %|%|NN SizeSelect|sizeselect|NN agarose|agarose|NN gels|gel|NNS -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- targeting|target|VBG 50|50|CD bp|bp|NN fragments|fragment|NNS .|.|. After|after|IN library|library|NN construction|construction|NN and|and|CC amplification|amplification|NN ,|,|, quality|quality|NN and|and|CC quantity|quantity|NN were|be|VBD assessed|assess|VBN using|use|VBG an|a|DT Agilent|agilent|JJ DNA|dna|NN 1000|1000|CD series|series|NN chip|chip|NN assay|assay|NN -LRB-|-lrb-|-LRB- Agilent|agilent|NN -RRB-|-rrb-|-RRB- and|and|CC QuantIT|quantit|NN PicoGreen|picogreen|NN dsDNA|dsdna|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB ,|,|, and|and|CC libraries|library|NNS were|be|VBD standardized|standardized|JJ to|to|TO 10μM|10μm|NN .|.|. Cluster|cluster|NN generation|generation|NN was|be|VBD performed|perform|VBN using|use|VBG a|a|DT cBot|cBot|NNP Single|single|JJ Read|Read|NNP Cluster|Cluster|NNP Generation|Generation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC placed|place|VBN on|on|IN the|the|DT Illumina|Illumina|NNP cBot|cBot|NNP .|.|. For|for|IN aerobic|aerobic|JJ and|and|CC anaerobic|anaerobic|JJ replicates|replicate|VBZ A|a|NN ,|,|, a|a|DT single|single|JJ read|read|NN ,|,|, 50|50|CD bp|bp|NN run|run|NN was|be|VBD performed|perform|VBN ,|,|, using|use|VBG standard|standard|JJ SBS|SBS|NNP kits|kit|NNS -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC SCS|scs|NN 2.6|2.6|CD on|on|IN an|a|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP IIx|IIx|NNP .|.|. For|for|IN aerobic|aerobic|JJ and|and|CC anaerobic|anaerobic|JJ replicates|replicate|VBZ B|b|NN and|and|CC C|c|NN ,|,|, the|the|DT input|input|NN ,|,|, and|and|CC the|the|DT anaerobic|anaerobic|JJ ,|,|, iron|iron|NN deficient|deficient|JJ samples|sample|NNS ,|,|, a|a|DT single|single|JJ read|read|NN ,|,|, 50|50|CD bp|bp|NN run|run|NN was|be|VBD performed|perform|VBN ,|,|, using|use|VBG standard|standard|JJ SBS|SBS|NNP kits|kit|NNS -LRB-|-lrb-|-LRB- v3|v3|NN -RRB-|-rrb-|-RRB- and|and|CC SCS|scs|NN 1.8.2|1.8.2|CD on|on|IN an|a|DT Illumina|Illumina|NNP HiSeq2000|hiseq2000|NN .|.|.
dnaT|dnat|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
dnaT|dnat|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
dnaT|dnat|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
dnaT|dnat|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
DNA|dna|NN was|be|VBD extracted|extract|VBN from|from|IN resulting|result|VBG supernatant|supernatant|JJ with|with|IN phenol/chlorophorm|phenol/chlorophorm|NN method|method|NN followed|follow|VBN by|by|IN ethanol|ethanol|NN precipitation|precipitation|NN .|.|. Mock|mock|JJ controls|control|NNS -LRB-|-lrb-|-LRB- -|-|: IP|IP|NNP -RRB-|-rrb-|-RRB- were|be|VBD made|make|VBN both|both|DT for|for|IN +|+|CC A|a|DT and|and|CC for|for|IN -|-|: A|a|NN :|:|: 100|100|CD μl|μl|NN aliquots|aliquot|NNS of|of|IN lysates|lysate|NNS obtained|obtain|VBN after|after|IN sonication|sonication|NN were|be|VBD deproteinized|deproteinize|VBN and|and|CC DNA|dna|NN was|be|VBD purified|purify|VBN as|as|IN described|describe|VBN earlier|earlier|RBR .|.|. The|the|DT procedure|procedure|NN described|describe|VBD gives|give|VBZ a|a|DT quartet|quartet|NN of|of|IN samples|sample|NNS -LRB-|-lrb-|-LRB- +|+|CC A+IP|a+ip|NN ,|,|, +|+|CC A-IP|a-ip|NN ,|,|, -|-|: A+IP|a+ip|NN ,|,|, -|-|: A-IP|a-ip|NN -RRB-|-rrb-|-RRB- ,|,|, where|where|WRB +|+|CC A-IP|a-ip|NN ,|,|, -|-|: A+IP|a+ip|NN ,|,|, and|and|CC -|-|: A-IP|a-ip|NN serves|serve|VBZ as|as|IN controls|control|NNS for|for|IN gyrase|gyrase|NN poison|poison|NN action|action|NN and|and|CC immunoprecipitation|immunoprecipitation|NN .|.|.
DNA|dna|NN was|be|VBD extracted|extract|VBN in|in|IN the|the|DT same|same|JJ manner|manner|NN as|as|IN described|describe|VBN by|by|IN McNulty|McNulty|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- PMID|pmid|NN :|:|: 22030749|22030749|CD -RRB-|-rrb-|-RRB- .|.|.
DNA|dna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT Qiagen|Qiagen|NNP Cell|cell|NN Lysis|lysis|NN and|and|CC Protein|protein|NN Precipitation|precipitation|NN solutions|solution|NNS .|.|. Detailed|detailed|JJ protocols|protocol|NNS are|be|VBP listed|list|VBN in|in|IN the|the|DT Supplementary|Supplementary|NNP Materials|Materials|NNPS
DNA|dna|NN was|be|VBD removed|remove|VBN with|with|IN Dnase|Dnase|NNP I.|I.|NNP rRNA|rrna|NN was|be|VBD removed|remove|VBN with|with|IN the|the|DT gram-negative|gram-negative|JJ RiboZero|RiboZero|NNP kit|kit|NN .|.|. Libraries|library|NNS were|be|VBD prepared|prepare|VBN with|with|IN the|the|DT RNAUltra|rnaultra|NN directional|directional|JJ kit|kit|NN from|from|IN New|New|NNP England|England|NNP Biolabs|Biolabs|NNP for|for|IN total|total|JJ RNA|rna|NN sequencing|sequencing|NN .|.|. For|for|IN signal|signal|NN peptide|peptide|NN fusions|fusion|NNS ,|,|, cDNA|cdna|NN was|be|VBD constructed|construct|VBN using|use|VBG primers|primer|NNS that|that|WDT target|target|VBP the|the|DT signal-peptide-coding/barcode|signal-peptide-coding/barcode|JJ region|region|NN of|of|IN the|the|DT fusion|fusion|NN RNAs|rna|NNS .|.|.
DNA|dna|NN were|be|VBD extracted|extract|VBN and|and|CC purified|purify|VBN as|as|IN described|describe|VBN by|by|IN Muniesa|Muniesa|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- 2003|2003|CD -RRB-|-rrb-|-RRB- .|.|. Shiga|shiga|NN toxin|toxin|NN 2-converting|2-converting|JJ bacteriophages|bacteriophage|NNS associated|associate|VBN with|with|IN clonal|clonal|JJ variability|variability|NN in|in|IN Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN strains|strain|NNS of|of|IN human|human|JJ origin|origin|NN isolated|isolate|VBN from|from|IN a|a|DT single|single|JJ outbreak|outbreak|NN .|.|. Infect|infect|VB Immun|Immun|NNP 71|71|CD ,|,|, 4554-4562|4554-4562|CD .|.|.
DNA|dna|NN were|be|VBD submitted|submit|VBN to|to|TO the|the|DT Joint|Joint|NNP Genome|Genome|NNP Institute|Institute|NNP for|for|IN ChIP-seq|ChIP-seq|NNP library|library|NN preparation|preparation|NN .|.|. Samples|sample|NNS were|be|VBD sheared|shear|VBN to|to|TO 200-500|200-500|CD nt|nt|NNS during|during|IN the|the|DT IP|IP|NNP process|process|NN to|to|TO facilitate|facilitate|VB library|library|NN preparation|preparation|NN .|.|. All|all|DT libraries|library|NNS were|be|VBD generated|generate|VBN using|use|VBG reagents|reagent|NNS from|from|IN the|the|DT Illumina|Illumina|NNP Paired|Paired|NNP End|End|NNP Sample|Sample|NNP Preparation|Preparation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT Illumina|Illumina|NNP protocol|protocol|NN ``|``|`` Preparing|prepare|VBG Samples|sample|NNS for|for|IN ChIP|chip|NN Sequencing|sequencing|NN of|of|IN DNA|dna|NN ''|''|'' -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP part|part|NN #|#|# 11257047|11257047|CD RevA|reva|NN -RRB-|-rrb-|-RRB- as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS ,|,|, except|except|IN products|product|NNS of|of|IN the|the|DT ligation|ligation|NN reaction|reaction|NN were|be|VBD purified|purify|VBN by|by|IN gel|gel|NN electrophoresis|electrophoresis|NN using|use|VBG 2|2|CD %|%|NN SizeSelect|sizeselect|NN agarose|agarose|NN gels|gel|NNS -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- targeting|target|VBG either|either|CC 275|275|CD bp|bp|NN fragments|fragment|NNS -LRB-|-lrb-|-LRB- s70|s70|NN libraries|library|NNS -RRB-|-rrb-|-RRB- .|.|. After|after|IN library|library|NN construction|construction|NN and|and|CC amplification|amplification|NN ,|,|, quality|quality|NN and|and|CC quantity|quantity|NN were|be|VBD assessed|assess|VBN using|use|VBG an|a|DT Agilent|agilent|JJ DNA|dna|NN 1000|1000|CD series|series|NN chip|chip|NN assay|assay|NN -LRB-|-lrb-|-LRB- Agilent|agilent|NN -RRB-|-rrb-|-RRB- and|and|CC QuantIT|quantit|NN PicoGreen|picogreen|NN dsDNA|dsdna|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB ,|,|, and|and|CC libraries|library|NNS were|be|VBD standardized|standardized|JJ to|to|TO 10μM|10μm|NN .|.|. Cluster|cluster|NN generation|generation|NN was|be|VBD performed|perform|VBN using|use|VBG a|a|DT cBot|cBot|NNP Single|single|JJ Read|Read|NNP Cluster|Cluster|NNP Generation|Generation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC placed|place|VBN on|on|IN the|the|DT Illumina|Illumina|NNP cBot|cBot|NNP .|.|. A|a|DT single|single|JJ read|read|NN ,|,|, 36|36|CD bp|bp|NN run|run|NN was|be|VBD performed|perform|VBN ,|,|, using|use|VBG standard|standard|JJ SBS|SBS|NNP kits|kit|NNS -LRB-|-lrb-|-LRB- v4|v4|NN -RRB-|-rrb-|-RRB- and|and|CC SCS|scs|NN 2.6|2.6|CD on|on|IN an|a|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP IIx|IIx|NNP .|.|. Basecalling|basecall|VBG was|be|VBD performed|perform|VBN using|use|VBG the|the|DT standard|standard|JJ Illumina|Illumina|NNP Pipeline|Pipeline|NNP version|version|NN 1.6|1.6|CD .|.|.
DNeasy|dneasy|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB-
Donor|donor|NN was|be|VBD transformed|transform|VBN with|with|IN a|a|DT random|random|JJ genomic|genomic|JJ library|library|NN made|make|VBN from|from|IN E.|e.|FW coli|coli|FW and|and|CC stored|store|VBN as|as|IN glycerol|glycerol|NN stocks|stock|NNS .|.|. The|the|DT library|library|NN was|be|VBD revived|revive|VBN and|and|CC transferred|transfer|VBN to|to|TO four|four|CD recipient|recipient|JJ strains|strain|NNS using|use|VBG conjugation|conjugation|NN ;|;|: the|the|DT donor|donor|NN was|be|VBD miniprepped|miniprepp|VBN at|at|IN this|this|DT time|time|NN ,|,|, and|and|CC the|the|DT recipients|recipient|NNS were|be|VBD miniprepped|miniprepp|VBN after|after|IN outgrowth|outgrowth|NN under|under|IN dual|dual|JJ selection|selection|NN .|.|. Two|two|CD recipient|recipient|JJ libraries|library|NNS in|in|IN BWG|bwg|NN and|and|CC BWY|bwy|NN were|be|VBD propagated|propagate|VBN under|under|IN n-butanol|n-butanol|JJ stress|stress|NN for|for|IN three|three|CD days|day|NNS ,|,|, and|and|CC then|then|RB miniprepped|miniprepp|VBD as|as|RB well|well|RB .|.|.
double|double|JJ mutant|mutant|JJ -LRB-|-lrb-|-LRB- PPK1|ppk1|NN and|and|CC PPX|ppx|NN -RRB-|-rrb-|-RRB-
Double|double|JJ stranded|strand|VBN cDNA|cdna|NN was|be|VBD generated|generate|VBN using|use|VBG Superscript|Superscript|NNP II|II|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- to|to|TO generate|generate|VB the|the|DT first|first|JJ strand|strand|NN followed|follow|VBN by|by|IN E.|e.|FW coli|coli|FW DNA|dna|NN polymerase|polymerase|NN ,|,|, RNaseH|rnaseh|NN ,|,|, and|and|CC E.coli|e.coli|NN DNA|dna|NN ligase|ligase|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- to|to|TO generate|generate|VB the|the|DT second|second|JJ strand|strand|NN .|.|.
Double|double|JJ stranded|strand|VBN cDNA|cdna|NN was|be|VBD generated|generate|VBN using|use|VBG Superscript|Superscript|NNP II|II|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- to|to|TO generate|generate|VB the|the|DT first|first|JJ strand|strand|NN followed|follow|VBN by|by|IN E.|e.|FW coli|coli|FW DNA|dna|NN polymerase|polymerase|NN ,|,|, RNaseH|rnaseh|NN ,|,|, and|and|CC E.coli|e.coli|NN DNA|dna|NN ligase|ligase|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- to|to|TO generate|generate|VB the|the|DT second|second|JJ strand.isoamyl|strand.isoamyl|JJ alcohol|alcohol|NN -LRB-|-lrb-|-LRB- 25:24:1|25:24:1|CD ,|,|, pH|ph|NN 8.0|8.0|CD ;|;|: Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- and|and|CC lysed|lyse|VBN by|by|IN using|use|VBG a|a|DT bead|bead|NN beater|beater|NN -LRB-|-lrb-|-LRB- BioSpec|BioSpec|NNP Products|Products|NNPS -RRB-|-rrb-|-RRB- .|.|. Cellular|cellular|JJ debris|debris|NN was|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 8,000|8,000|CD g|g|NN ;|;|: 3|3|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT nucleic|nucleic|JJ acids|acid|NNS were|be|VBD precipitated|precipitate|VBN with|with|IN isopropanol|isopropanol|NN and|and|CC sodium|sodium|NN acetate|acetate|NN and|and|CC resuspended|resuspend|VBN in|in|IN 100|100|CD ul|ul|NN TE|TE|NNP .|.|. The|the|DT resuspension|resuspension|NN was|be|VBD further|further|JJ purified|purify|VBN with|with|IN a|a|DT Qiagen|Qiagen|NNP PCR|pcr|NN column|column|NN and|and|CC eluted|elute|VBN into|into|IN 30|30|CD ul|ul|NN of|of|IN EB|EB|NNP buffer|buffer|NN .|.|.
dpiA|dpia|NN 2x|2x|NN Overexpression|overexpression|NN pHI1429|phi1429|NN in|in|IN LB|lb|NN at|at|IN 37|37|CD Mid|Mid|NNP Log|Log|NNP Phase|phase|NN
dpiAoverexpressor|dpiaoverexpressor|NN
d|d|NN _|_|CD rnr|rnr|NN NO3|no3|NN 1|1|CD
d|d|NN _|_|CD rnr|rnr|NN NO3|no3|NN 2|2|CD
d|d|NN _|_|CD rnr|rnr|NN NO3|no3|NN w/propionate|w/propionate|NN 1|1|CD
d|d|NN _|_|CD rnr|rnr|NN NO3|no3|NN w/propionate|w/propionate|NN 2|2|CD
d|d|NN _|_|CD rnr|rnr|NN O2|o2|CD 1|1|CD
d|d|NN _|_|CD rnr|rnr|NN O2|o2|CD 2|2|CD
d|d|NN _|_|CD rnr|rnr|NN O2|o2|CD w/propionate|w/propionate|NN 1|1|CD
d|d|NN _|_|CD rnr|rnr|NN O2|o2|CD w/propionate|w/propionate|NN 2|2|CD
Drug|Drug|NNP :|:|: bicyclomycin|bicyclomycin|NN
Drug|drug|NN :|:|: none|none|NN
DSP1|dsp1|NN _|_|CD AP|ap|NN
DSP1|dsp1|NN _|_|CD Total|total|JJ
DSP2|dsp2|NN _|_|CD AP|ap|NN
DSP2|dsp2|NN _|_|CD Total|total|JJ
DSP3|dsp3|NN _|_|CD AP|ap|NN
DSP3|dsp3|NN _|_|CD Total|total|JJ
Duplicate|duplicate|VB O/N|o/n|NN cultures|culture|NNS in|in|IN LB|lb|NN with|with|IN 15|15|CD mg/L|mg/l|NN chloramphenicol|chloramphenicol|NN each|each|DT of|of|IN strains|strain|NNS pCA24N,-gfp|pca24n,-gfp|NN /|/|: DA4201|da4201|NN ,|,|, Svi3-3|svi3-3|NN comp|comp|NN .|.|. -LRB-|-lrb-|-LRB- recoded|recode|VBN Svi3-3|svi3-3|NN -RRB-|-rrb-|-RRB- /|/|: DA4201|da4201|NN and|and|CC pORF1/DA4201|porf1/da4201|NN were|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN two|two|CD ,|,|, four|four|CD and|and|CC four|four|CD cultures|culture|NNS of|of|IN 20|20|CD mL|ml|NN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN with|with|IN 5|5|CD μg/mL|μg/ml|NN chloramphenicol|chloramphenicol|NN .|.|. The|the|DT pCA24N,-gfp|pca24n,-gfp|NN /|/|: DA4201|da4201|NN cultures|culture|NNS and|and|CC two|two|CD cultures|culture|NNS each|each|DT of|of|IN Svi3-3|svi3-3|NN comp|comp|NN .|.|. -LRB-|-lrb-|-LRB- recoded|recode|VBN Svi3-3|svi3-3|NN -RRB-|-rrb-|-RRB- /|/|: DA4201|da4201|NN and|and|CC pORF1/DA4201|porf1/da4201|NN were|be|VBD supplemented|supplement|VBN by|by|IN 50|50|CD μM|μm|NN IPTG|iptg|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO OD|od|NN 0.15-0.2|0.15-0.2|CD and|and|CC cells|cell|NNS were|be|VBD withdrawn|withdraw|VBN for|for|IN RNA|rna|NN extraction|extraction|NN and|and|CC whole|whole|JJ cell|cell|NN proteomics|proteomic|NNS .|.|.
E058|e058|NN in|in|FW vitro|vitro|FW ,|,|, biological|biological|JJ rep1|rep1|NN
E058|e058|NN in|in|FW vitro|vitro|FW ,|,|, biological|biological|JJ rep2|rep2|NN
E058|e058|NN in|in|FW vivo|vivo|FW ,|,|, biological|biological|JJ rep1|rep1|NN
E058|e058|NN in|in|FW vivo|vivo|FW ,|,|, biological|biological|JJ rep2|rep2|NN
E058|e058|NN in|in|FW vivo|vivo|FW ,|,|, biological|biological|JJ rep3|rep3|NN
E058ΔrstAB|e058δrstab|NN in|in|FW vivo|vivo|FW ,|,|, biological|biological|JJ rep1|rep1|NN
E058ΔrstAB|e058δrstab|NN in|in|FW vivo|vivo|FW ,|,|, biological|biological|JJ rep2|rep2|NN
E058ΔrstAB|e058δrstab|NN in|in|FW vivo|vivo|FW ,|,|, biological|biological|JJ rep3|rep3|NN
E0-E1|e0-e1|NN _|_|CD rep1|rep1|NN _|_|VBD a|a|DT
E0-E1|e0-e1|NN _|_|CD rep1|rep1|NN _|_|NN b|b|NN
E0-E1|e0-e1|NN _|_|CD rep2|rep2|NN _|_|VBD a|a|DT
E0-E1|e0-e1|NN _|_|CD rep2|rep2|NN _|_|NN b|b|NN
E0-E1|e0-e1|NN _|_|CD rep3|rep3|NN _|_|VBD a|a|DT
E0-E1|e0-e1|NN _|_|CD rep3|rep3|NN _|_|NN b|b|NN
E11|e11|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|SYM m1|m1|NN
E1|e1|NN _|_|VBD 14|14|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m2|m2|NN
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m3|m3|NN
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m4|m4|NN
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m8|m8|NN
E1|e1|NN _|_|VBD 14|14|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 6|6|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 6|6|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 6|6|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|CD 6|6|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E11|e11|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 2|2|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 6|6|CD _|_|NN m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 6|6|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|CD 6|6|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E13|e13|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|VBD 4|4|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|SYM 6|6|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 6|6|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 6|6|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 6|6|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 6|6|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 6|6|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E15|e15|CD _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 6|6|CD _|_|NN m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 6|6|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 6|6|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 6|6|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 6|6|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 6|6|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|CD 6|6|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E17|e17|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E1|e1|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|CD 6|6|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E19|e19|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|SYM m1|m1|NN
E2|e2|NN _|_|CD 14|14|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|NN m3|m3|NN
E2|e2|NN _|_|CD 14|14|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|NN m4|m4|NN
E2|e2|NN _|_|CD 14|14|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|NN m6|m6|NN
E2|e2|NN _|_|CD 14|14|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 14|14|CD _|_|NN m8|m8|NN
E2|e2|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E22|e22|NN
E2|e2|NN _|_|NN 2|2|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 2|2|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 2|2|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 2|2|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 2|2|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 2|2|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 2|2|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 2|2|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E2|e2|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 14|14|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 14|14|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 14|14|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 14|14|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 14|14|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 14|14|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 14|14|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 2|2|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E3|e3|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E4|e4|NN -|-|: O2|o2|CD 1|1|CD
E4|e4|NN +|+|CC O2|o2|CD 1|1|CD
E4|e4|NN -|-|: O2|o2|CD 2|2|CD
E4|e4|NN +|+|CC O2|o2|CD 2|2|CD
E4|e4|NN -|-|: O2|o2|CD 3|3|CD
E4|e4|NN +|+|CC O2|o2|CD 3|3|CD
E9|e9|NN _|_|NN 1|1|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 1|1|CD _|_|CD m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 1|1|CD _|_|CD m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 1|1|CD _|_|CD m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 1|1|CD _|_|CD m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 1|1|CD _|_|CD m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 1|1|CD _|_|CD m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 1|1|CD _|_|CD m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|SYM m1|m1|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 4|4|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 6|6|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 6|6|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 6|6|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 6|6|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|CD 6|6|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 7|7|CD _|_|NN m2|m2|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 7|7|CD _|_|NN m3|m3|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 7|7|CD _|_|NN m4|m4|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 7|7|CD _|_|NN m5|m5|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 7|7|CD _|_|NN m6|m6|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 7|7|CD _|_|NN m7|m7|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
E9|e9|NN _|_|NN 7|7|CD _|_|NN m8|m8|NN -LSB-|-lsb-|-LRB- COPRO-Seq|copro-seq|NN -RSB-|-rsb-|-RRB-
Each|each|DT bacteria|bacterium|NNS pellet|pellet|NN from|from|IN a|a|DT 25|25|CD ml|ml|NN culture|culture|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.3|0.3|CD -RRB-|-rrb-|-RRB- was|be|VBD homogeneously|homogeneously|RB resuspended|resuspend|VBN in|in|IN 200|200|CD µl|µl|NN of|of|IN Buffer|Buffer|NNP A|A|NNP -LSB-|-lsb-|-LRB- 10|10|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8.0|8.0|CD ;|;|: 20|20|CD %|%|NN Sucrose|sucrose|NN ;|;|: 100|100|CD mM|mm|NN NaCl|nacl|NN -RSB-|-rsb-|-RRB- supplemented|supplement|VBN with|with|IN 200|200|CD U|U|NNP SUPERase|SUPERase|NNP •|•|SYM In|in|IN ™|™|CD RNase|rnase|NN Inhibitor|inhibitor|NN ,|,|, by|by|IN pipetting|pipetting|NN .|.|. 50|50|CD µl|µl|NN of|of|IN Buffer|buffer|NN B|b|NN -LSB-|-lsb-|-LRB- 50|50|CD mM|mm|NN EDTA|edta|NN ;|;|: 120|120|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8.0|8.0|CD -RSB-|-rsb-|-RRB- supplemented|supplement|VBN with|with|IN 1|1|CD µl|µl|NN Ready-Lyse|ready-lyse|NN ™|™|CD Lysozyme|Lysozyme|NNP Solution|solution|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, cat|cat|NN .|.|. R1810M|r1810m|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN dropwise|dropwise|NN ,|,|, and|and|CC the|the|DT vial|vial|NN was|be|VBD gently|gently|RB tilted|tilted|JJ 5|5|CD times|time|NNS to|to|TO ensure|ensure|VB homogenous|homogenous|JJ mixing|mix|VBG .|.|. The|the|DT sample|sample|NN was|be|VBD then|then|RB incubated|incubate|VBN 1|1|CD minute|minute|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. 250|250|CD µl|µl|NN of|of|IN Buffer|buffer|NN C|c|NN -LSB-|-lsb-|-LRB- 0.5|0.5|CD %|%|NN Tween-20|tween-20|NN :|:|: 0.4|0.4|CD %|%|NN NaDOC|nadoc|NN ;|;|: 2|2|CD M|m|NN NaCl|nacl|NN ;|;|: 10|10|CD mM|mm|NN EDTA|edta|NN -RSB-|-rsb-|-RRB- were|be|VBD immediately|immediately|RB added|add|VBN dropwise|dropwise|NN .|.|. The|the|DT sample|sample|NN was|be|VBD then|then|RB incubated|incubate|VBN 5|5|CD minutes|minute|NNS at|at|IN room|room|NN temperature|temperature|NN .|.|. At|at|IN this|this|DT stage|stage|NN the|the|DT solution|solution|NN clears|clear|VBZ considerably|considerably|RB without|without|IN increasing|increase|VBG its|its|PRP$ viscosity|viscosity|NN ,|,|, and|and|CC nucleoid|nucleoid|JJ becomes|become|VBZ visible|visible|JJ .|.|. Using|use|VBG a|a|DT cut|cut|NN P1000|p1000|NN pipette|pipette|NN tip|tip|NN ,|,|, the|the|DT whole|whole|JJ sample|sample|NN was|be|VBD gently|gently|RB layered|layer|VBN on|on|IN the|the|DT top|top|NN of|of|IN a|a|DT 5-30|5-30|CD %|%|NN w/v|w/v|NN sucrose|sucrose|NN gradient|gradient|NN -LSB-|-lsb-|-LRB- 10|10|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8.0|8.0|CD ;|;|: 1|1|CD M|m|NN NaCl|nacl|NN ;|;|: 1|1|CD mM|mm|NN EDTA|edta|NN ;|;|: 1|1|CD mM|mm|NN DTT|dtt|NN -RSB-|-rsb-|-RRB- ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 17,000|17,000|CD RPM|rpm|NN in|in|IN a|a|DT SW55Ti|sw55ti|NN rotor|rotor|NN -LRB-|-lrb-|-LRB- Beckman|Beckman|NNP Coulter|Coulter|NNP ,|,|, cat|cat|NN .|.|. 342194|342194|CD -RRB-|-rrb-|-RRB- for|for|IN 9|9|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN centrifugation|centrifugation|NN ,|,|, the|the|DT nucleoid|nucleoid|JJ fraction|fraction|NN was|be|VBD collected|collect|VBN using|use|VBG a|a|DT syringe|syringe|NN with|with|IN a|a|DT 18G|18g|NN blunt|blunt|JJ fill|fill|NN needle|needle|NN ,|,|, and|and|CC transferred|transfer|VBN to|to|TO a|a|DT new|new|JJ centrifuge|centrifuge|NN tube|tube|NN .|.|. The|the|DT remaining|remain|VBG gradient|gradient|NN was|be|VBD assumed|assume|VBN to|to|TO represent|represent|VB the|the|DT cytosolic|cytosolic|JJ fraction|fraction|NN .|.|. The|the|DT nucleoid|nucleoid|NN was|be|VBD then|then|RB resuspended|resuspend|VBN in|in|IN 2.5|2.5|CD ml|ml|NN Wash|Wash|NNP &|&|CC Resuspension|Resuspension|NNP buffer|buffer|NN -LSB-|-lsb-|-LRB- 40|40|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 7.5|7.5|CD ;|;|: 150|150|CD mM|mm|NN KCl|kcl|NN ;|;|: 10|10|CD mM|mm|NN MgCl2|mgcl2|NN ;|;|: 1|1|CD mM|mm|NN DTT|dtt|NN ;|;|: 0.01|0.01|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN -RSB-|-rsb-|-RRB- supplemented|supplement|VBN with|with|IN 200|200|CD U|U|NNP SUPERase|SUPERase|NNP •|•|SYM In|in|IN ™|™|CD RNase|rnase|NN Inhibitor|inhibitor|NN ,|,|, pulse|pulse|NN vortexed|vortex|VBD for|for|IN 5|5|CD seconds|seconds|NNS ,|,|, and|and|CC then|then|RB centrifuged|centrifuge|VBD at|at|IN 28,000|28,000|CD RPM|rpm|NN in|in|IN a|a|DT SW55Ti|sw55ti|NN rotor|rotor|NN for|for|IN 30|30|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- 0|0|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN centrifugation|centrifugation|NN the|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT nucleoid|nucleoid|JJ pellet|pellet|NN was|be|VBD washed|wash|VBN twice|twice|RB with|with|IN 2|2|CD ml|ml|NN of|of|IN Wash|Wash|NNP &|&|CC Resuspension|Resuspension|NNP buffer|buffer|NN ,|,|, taking|take|VBG care|care|NN not|not|RB to|to|TO disturb|disturb|VB it|it|PRP .|.|. The|the|DT nucleoid|nucleoid|NN was|be|VBD then|then|RB resuspended|resuspend|VBN in|in|IN 500|500|CD µl|µl|NN Wash|Wash|NNP &|&|CC Resuspension|Resuspension|NNP buffer|buffer|NN ,|,|, and|and|CC solubilized|solubilize|VBN by|by|IN addition|addition|NN of|of|IN 0.1|0.1|CD gr|gr|NN acid-washed|acid-washed|JJ glass|glass|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP ,|,|, cat|cat|NN .|.|. G1145|g1145|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC shaking|shake|VBG for|for|IN 5|5|CD minutes|minute|NNS in|in|IN a|a|DT TissueLyser|TissueLyser|NNP -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP -RRB-|-rrb-|-RRB- .|.|. For|for|IN each|each|DT 100|100|CD µl|µl|NN of|of|IN purified|purify|VBN nucleoids|nucleoid|NNS -LRB-|-lrb-|-LRB- or|or|CC cytosolic|cytosolic|JJ fraction|fraction|NN -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD ml|ml|NN of|of|IN TRIzol|trizol|NN ®|®|CD Reagent|Reagent|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, cat|cat|NN .|.|. 15596-018|15596-018|CD -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN ,|,|, and|and|CC RNA|rna|NN was|be|VBD extracted|extract|VBN following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. RNA|rna|NN was|be|VBD analyzed|analyze|VBN on|on|IN a|a|DT 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- .|.|. In|in|IN all|all|DT experiments|experiment|NNS ,|,|, RNA|rna|NN from|from|IN cytosolic|cytosolic|JJ fraction|fraction|NN -LRB-|-lrb-|-LRB- corresponding|correspond|VBG to|to|TO mature|mature|JJ RNA|rna|NN species|species|NNS -RRB-|-rrb-|-RRB- had|have|VBD RIN|RIN|NNP >|>|JJR 9.5|9.5|CD .|.|. Total|total|JJ RNA|rna|NN yield|yield|NN from|from|IN nucleoid|nucleoid|JJ fraction|fraction|NN was|be|VBD ~|~|CD 6|6|CD %|%|NN of|of|IN the|the|DT total|total|JJ RNA|rna|NN content|content|NN .|.|.
Each|each|DT dataset|dataset|NN was|be|VBD normalized|normalize|VBN to|to|TO reads|read|VBZ per|per|IN million|million|CD per|per|IN position|position|NN prior|prior|RB to|to|TO further|further|JJ analysis|analysis|NN .|.|.
Each|each|DT strain|strain|NN was|be|VBD inoculated|inoculate|VBN from|from|IN the|the|DT frozen|frozen|JJ stock|stock|NN into|into|IN 10|10|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN for|for|IN preculture|preculture|NN .|.|. Five-microliter|five-microliter|NN aliquots|aliquot|NNS of|of|IN preculture|preculture|JJ medium|medium|NN cells|cell|NNS were|be|VBD inoculated|inoculate|VBN into|into|IN the|the|DT fresh|fresh|JJ minimal|minimal|JJ media|media|NNS ,|,|, M9|m9|NN with|with|IN 5|5|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- ethanol|ethanol|NN in|in|IN 10|10|CD mL|ml|NN test|test|NN tube|tube|NN with|with|IN screw|screw|NN cap|cap|NN and|and|CC cultured|culture|VBN for|for|IN 10|10|CD generations|generation|NNS .|.|. When|when|WRB OD600nm|od600nm|NN reached|reach|VBD 0.05|0.05|CD within|within|IN the|the|DT exponential|exponential|JJ growth|growth|NN phase|phase|NN ,|,|, cell|cell|NN were|be|VBD collected|collect|VBN .|.|.
Each|each|DT tube|tube|NN of|of|IN the|the|DT cell|cell|NN pellet|pellet|NN stored|store|VBD at|at|IN -80|-80|CD ˚C|˚c|NN was|be|VBD resuspended|resuspend|VBN in|in|IN 650|650|CD ml|ml|NN TES|tes|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 7.5|7.5|CD ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 0.1|0.1|CD %|%|NN TritonX|tritonx|NN 100|100|CD ,|,|, 0.3|0.3|CD mM|mm|NN PMSF|pmsf|NN -RRB-|-rrb-|-RRB- at|at|IN room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- RT|rt|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT cell|cell|NN suspension|suspension|NN was|be|VBD mixed|mix|VBN with|with|IN 100|100|CD kU|ku|NN Ready-Lyse|Ready-Lyse|NNP Lysozyme|Lysozyme|NNP -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- and|and|CC 50|50|CD µg|µg|NN RNaseA|rnasea|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN for|for|IN 5|5|CD min|min|NN ,|,|, allowing|allow|VBG rapid|rapid|JJ cell|cell|NN lysis|lysis|NN .|.|. To|to|TO digest|digest|VB the|the|DT nucleoide|nucleoide|NN ,|,|, 62.5|62.5|CD U|U|NNP DNaseI|dnasei|NN -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- and|and|CC 250|250|CD µg/ml|µg/ml|JJ heparin|heparin|NN at|at|IN the|the|DT final|final|JJ concentrations|concentration|NNS as|as|RB well|well|RB as|as|IN 74|74|CD ml|ml|NN DNaseI|dnasei|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN MnCl2|mncl2|NN 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO the|the|DT mixture|mixture|NN and|and|CC incubated|incubate|VBN for|for|IN 10|10|CD min|min|NN at|at|IN RT.|RT.|NNP .|.|. To|to|TO remove|remove|VB cell|cell|NN debris|debris|NN ,|,|, the|the|DT mixture|mixture|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 20,000|20,000|CD x|x|CC g|g|NN for|for|IN 3|3|CD min|min|NN at|at|IN 4|4|CD ˚C|˚c|NN and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD collected|collect|VBN into|into|IN a|a|DT new|new|JJ 1.5|1.5|CD ml|ml|NN tube|tube|NN .|.|. The|the|DT supernatant|supernatant|JJ including|include|VBG RNAPs|rnap|NNS that|that|WDT form|form|VBP ternary|ternary|JJ complexes|complex|NNS with|with|IN RNA/DNA|rna/dna|NN were|be|VBD immobilized|immobilize|VBN on|on|IN ~|~|NN 155|155|CD µl|µl|NN Ni-NTA|ni-nta|NN agarose|agarose|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- pre-equilibrated|pre-equilibrated|JJ with|with|IN the|the|DT binding|binding|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD M|m|NN NaCl|nacl|NN ,|,|, 5|5|CD mM|mm|NN imidazole|imidazole|NN ,|,|, 5|5|CD %|%|NN glycerol|glycerol|NN ,|,|, 20|20|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH7|ph7|NN .9|.9|NN ,|,|, 1|1|CD mM|mm|NN 2-mercaptoethanol|2-mercaptoethanol|NN -RRB-|-rrb-|-RRB- with|with|IN shaking|shake|VBG for|for|IN 10|10|CD min|min|NN at|at|IN 4|4|CD ˚C|˚c|NN .|.|. The|the|DT immobilized|immobilize|VBN ternary|ternary|JJ complexes|complex|NNS were|be|VBD washed|wash|VBN five|five|CD times|time|NNS with|with|IN the|the|DT wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 1M|1m|NN NaCl|nacl|NN ,|,|, 15|15|CD mM|mm|NN imidazole|imidazole|NN ,|,|, 5|5|CD %|%|NN glycerol|glycerol|NN ,|,|, pH7|ph7|NN .9|.9|NN ,|,|, 1|1|CD mM|mm|NN 2-mercaptoethanol|2-mercaptoethanol|NN -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD ˚C|˚c|NN ,|,|, washed|wash|VBN twice|twice|RB with|with|IN the|the|DT nuclease|nuclease|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 40|40|CD mM|mm|NN KCl|kcl|NN ,|,|, 15|15|CD mM|mm|NN imidazole|imidazole|NN ,|,|, 20|20|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 7.9|7.9|CD ,|,|, 0.3|0.3|CD mM|mm|NN MgCl2|mgcl2|NN 5|5|CD %|%|NN glycerol|glycerol|NN ,|,|, 1|1|CD mM|mm|NN 2-mercaptoethanol|2-mercaptoethanol|NN -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD ˚C|˚c|NN .|.|. The|the|DT RNA|rna|NN transcript|transcript|NN and|and|CC DNA|dna|NN unprotected|unprotected|JJ by|by|IN RNAP|rnap|NN were|be|VBD cleaved|cleave|VBN by|by|IN the|the|DT additions|addition|NNS of|of|IN 0.4|0.4|CD U|U|NNP RNase|rnase|NN V1|v1|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, 0.7|0.7|CD U|U|NNP RNase|rnase|NN T1|t1|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC 5|5|CD U|U|NNP DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Takara|Takara|NNP Bio|Bio|NNP -RRB-|-rrb-|-RRB- to|to|TO the|the|DT immobilized|immobilize|VBN complexes|complex|NNS and|and|CC incubation|incubation|NN for|for|IN 7|7|CD min|min|NN at|at|IN RT.|RT.|NNP .|.|. The|the|DT nuclease-treated|nuclease-treated|JJ complexes|complex|NNS were|be|VBD washed|wash|VBN twice|twice|RB with|with|IN the|the|DT wash|wash|NN buffer|buffer|NN ,|,|, twice|twice|RB with|with|IN the|the|DT MnCl2-free|mncl2-free|NN nuclease|nuclease|NN buffer|buffer|NN at|at|IN 4|4|CD ˚C|˚c|NN ,|,|, and|and|CC eluted|elute|VBN by|by|IN increasing|increase|VBG the|the|DT concentration|concentration|NN of|of|IN imidazole|imidazole|NN to|to|TO 100|100|CD mM|mm|NN followed|follow|VBN by|by|IN shaking|shake|VBG for|for|IN 10|10|CD min|min|NN at|at|IN 4|4|CD ˚C|˚c|NN in|in|IN the|the|DT presence|presence|NN of|of|IN 30|30|CD U|U|NNP SUPERase|SUPERase|NNP RNase|rnase|NN inhibitor|inhibitor|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|.
Each|each|DT type|type|NN of|of|IN error|error|NN rates|rate|NNS per|per|IN position|position|NN was|be|VBD determined|determine|VBN as|as|IN the|the|DT number|number|NN of|of|IN sequence|sequence|NN reads|read|VBZ with|with|IN a|a|DT particular|particular|JJ type|type|NN of|of|IN base-substitution|base-substitution|NN divided|divide|VBN by|by|IN the|the|DT number|number|NN of|of|IN the|the|DT reads|read|VBZ with|with|IN the|the|DT reference|reference|NN base|base|NN in|in|IN each|each|DT DNA|dna|NN position|position|NN .|.|.
early|early|JJ stationary|stationary|JJ phase|phase|NN 1|1|CD
early|early|JJ stationary|stationary|JJ phase|phase|NN 2|2|CD
early|early|JJ stationary|stationary|JJ phase|phase|NN 3|3|CD
early|early|JJ stationary|stationary|JJ phase|phase|NN 4|4|CD
early|early|JJ stationary|stationary|JJ phase|phase|NN 5|5|CD
EC12n090|ec12n090|NN RpoE|rpoe|NN 2.5|2.5|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC12n091|ec12n091|NN RpoE|rpoe|NN 5|5|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC12n092a|ec12n092a|NN RpoE|rpoe|NN 10|10|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC12n093|ec12n093|NN RpoE|rpoe|NN 20|20|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC12n094|ec12n094|NN RpoE|rpoe|NN 30|30|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC12n095|ec12n095|NN RpoE|rpoe|NN 60|60|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC12n096|ec12n096|NN RpoE|rpoe|NN 0|0|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC12n097|ec12n097|NN delta|delta|NN rseA|rsea|NN
EC12n098|ec12n098|NN delta|delta|NN rseA|rsea|NN
EC12n099|ec12n099|NN delta|delta|NN rseA|rsea|NN
EC12n101|ec12n101|NN RpoE|rpoe|NN 0|0|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC18n018|ec18n018|NN hfq|hfq|NN +|+|CC rpoE|rpoe|NN overexpression|overexpression|NN 20|20|CD min|min|NN
EC18n019|ec18n019|NN hfq|hfq|NN -|-|: rpoE|rpoe|NN overexpression|overexpression|NN 20|20|CD min|min|NN
EC18n035|ec18n035|NN delta|delta|NN rseA|rsea|NN
EC18n036|ec18n036|NN delta|delta|NN rseA|rsea|NN
EC18n037|ec18n037|NN delta|delta|NN hfq|hfq|NN
EC18n038|ec18n038|NN delta|delta|NN hfq|hfq|NN
EC18n039|ec18n039|NN delta|delta|NN hfq|hfq|NN
EC18n040|ec18n040|NN delta|delta|NN hfq|hfq|NN
EC18n122|ec18n122|NN RpoH|rpoh|NN 10|10|CD min|min|NN Time|Time|NNP course|course|NN 4|4|CD
EC18n136|ec18n136|NN hfq|hfq|NN +|+|CC rpoE|rpoe|NN overexpression|overexpression|NN 20|20|CD min|min|NN
Ec18n137|ec18n137|NN hfq|hfq|NN -|-|: rpoE|rpoe|NN overexpression|overexpression|NN 20|20|CD min|min|NN
EC18n139|ec18n139|NN hfq|hfq|NN +|+|CC rpoE|rpoe|NN overexpression|overexpression|NN 20|20|CD min|min|NN
EC18n140|ec18n140|NN hfq|hfq|NN -|-|: rpoE|rpoe|NN overexpression|overexpression|NN 20|20|CD min|min|NN
EC18n167|ec18n167|NN RpoH|rpoh|NN 0|0|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC18n168|ec18n168|NN RpoH|rpoh|NN 2.5|2.5|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC18n169|ec18n169|NN RpoH|rpoh|NN 5|5|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC18n170|ec18n170|NN RpoH|rpoh|NN 10|10|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC18n171|ec18n171|NN RpoH|rpoh|NN 20|20|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC18n177|ec18n177|NN RpoH|rpoh|NN 0|0|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC18n178|ec18n178|NN RpoH|rpoh|NN 2.5|2.5|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC18n179|ec18n179|NN RpoH|rpoh|NN 5|5|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC18n180|ec18n180|NN RpoH|rpoh|NN 10|10|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC18n181|ec18n181|NN RpoH|rpoh|NN 20|20|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC18n182|ec18n182|NN RpoH|rpoh|NN 0|0|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC18n183|ec18n183|NN RpoH|rpoh|NN 2.5|2.5|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC18n184|ec18n184|NN RpoH|rpoh|NN 5|5|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC18n185|ec18n185|NN RpoH|rpoh|NN 10|10|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC18n186|ec18n186|NN RpoH|rpoh|NN 20|20|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC19n075|ec19n075|NN delta|delta|NN hfq|hfq|NN
EC19n076|ec19n076|NN delta|delta|NN hfq|hfq|NN
EC19n098|ec19n098|NN delta|delta|NN hfq|hfq|NN
EC19n099|ec19n099|NN delta|delta|NN hfq|hfq|NN
EC19n100|ec19n100|NN delta|delta|NN rseA|rsea|NN
EC19n101|ec19n101|NN delta|delta|NN rseA|rsea|NN
EC7n018|ec7n018|NN RpoE|rpoe|NN 5|5|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC7n019|ec7n019|NN RpoE|rpoe|NN 15|15|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC7n065|ec7n065|NN RpoE|rpoe|NN 5|5|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC7n066|ec7n066|NN RpoE|rpoe|NN 15|15|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC7n067|ec7n067|NN RpoE|rpoe|NN 30|30|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC7n068|ec7n068|NN RpoE|rpoe|NN 60|60|CD min|min|NN Time|Time|NNP course|course|NN 2|2|CD
EC7n071|ec7n071|NN RpoE|rpoe|NN 60|60|CD min|min|NN Time|Time|NNP course|course|NN 1|1|CD
EC8n021|ec8n021|NN RpoE|rpoe|NN 2.5|2.5|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC8n022|ec8n022|NN RpoE|rpoe|NN 5|5|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC8n050|ec8n050|NN RpoE|rpoe|NN 10|10|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC8n051|ec8n051|NN RpoE|rpoe|NN 20|20|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC8n052|ec8n052|NN RpoE|rpoe|NN 30|30|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC8n053|ec8n053|NN RpoE|rpoe|NN 60|60|CD min|min|NN Time|Time|NNP course|course|NN 3|3|CD
EC|EC|NNP _|_|VBD Cont1|cont1|NN _|_|NN DNA|dna|NN
EC|ec|NN _|_|CD Cont1|cont1|NN _|_|NN RNA|rna|NN
EC|ec|NN _|_|CD Cont2|cont2|NN _|_|NN DNA|dna|NN
EC|ec|NN _|_|CD Cont2|cont2|NN _|_|NN RNA|rna|NN
ecd3-c-0081429|ecd3-c-0081429|NN wt|wt|JJ vs|vs|CC dpiAoverexpressor|dpiaoverexpressor|JJ
ecd3-c-0101429|ecd3-c-0101429|NN wt|wt|JJ vs|vs|CC dpiAoverexpressor|dpiaoverexpressor|JJ
ECDH5|ecdh5|NN _|_|CD GD|gd|NN _|_|CD RP1|rp1|NN
EcJR-8|ecjr-8|NN grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 0.5|0.5|CD in|in|IN DMEM-MOPS|dmem-mops|NN 0.4|0.4|CD %|%|NN glucose|glucose|NN at|at|IN a|a|DT 10:1|10:1|CD flask-to-media|flask-to-media|NN volume|volume|NN in|in|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 180|180|CD RPM|rpm|NN -RRB-|-rrb-|-RRB- .|.|.
EcJR-8|ecjr-8|NN grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.8|1.8|CD in|in|IN DMEM-MOPS|dmem-mops|NN 0.4|0.4|CD %|%|NN glucose|glucose|NN at|at|IN a|a|DT 10:1|10:1|CD flask-to-media|flask-to-media|NN volume|volume|NN in|in|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 180|180|CD RPM|rpm|NN -RRB-|-rrb-|-RRB- .|.|.
eco|eco|VBP _|_|SYM 0.21|0.21|CD _|_|SYM 0.11|0.11|CD
eco|eco|NN _|_|CD 0.26|0.26|CD _|_|SYM 0.11|0.11|CD
eco|eco|NN _|_|CD 0.31|0.31|CD _|_|SYM 0.11|0.11|CD
eco|eco|NN _|_|CD 0.36|0.36|CD _|_|SYM 0.11|0.11|CD
eco|eco|NN _|_|CD 0.40|0.40|CD _|_|SYM 0.11|0.11|CD
eco|eco|NN _|_|CD 0.48|0.48|CD _|_|SYM 0.11|0.11|CD
Eco|Eco|NNP 50ng|50ng|SYM -|-|: 0|0|CD %|%|NN
Eco|eco|NN 50ng|50ng|SYM -|-|: 10|10|CD %|%|NN
Eco|eco|NN 50ng|50ng|SYM -|-|: 15|15|CD %|%|NN
Eco|eco|NN 50ng|50ng|SYM -|-|: 20|20|CD %|%|NN
Eco|eco|NN 50ng|50ng|SYM -|-|: 25|25|CD %|%|NN
Eco|eco|NN 50ng|50ng|SYM -|-|: 32.5|32.5|CD %|%|NN
Eco|eco|NN 50ng|50ng|SYM -|-|: 45|45|CD %|%|NN
Eco|eco|NN 50ng|50ng|SYM -|-|: 5|5|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 0|0|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 10|10|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 15|15|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 20|20|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 25|25|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 32.5|32.5|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 45|45|CD %|%|NN
Eco|eco|NN 5ng|5ng|SYM -|-|: 5|5|CD %|%|NN
E.|e.|FW coli|coli|FW
E.|e.|FW coli|coli|FW 042|042|CD WT|wt|JJ
E|e|NN coli|coli|NN ,|,|, 0|0|CD min|min|NN
E.|E.|NNP coli|coli|NN -|-|: 0|0|CD min|min|NN before|before|IN nutrient|nutrient|NN shift|shift|NN
E.|E.|NNP coli|coli|NN 0|0|CD mins|min|NNS
E.coli|e.coli|NN 0|0|CD minutes|minute|NNS after|after|IN BRP|brp|NN induction|induction|NN
E.coli|e.coli|NNS _|_|VBP 0|0|CD %|%|NN tannin|tannin|NN _|_|NN #|#|# 2|2|CD
E.coli|e.coli|NNS _|_|VBP 0|0|CD %|%|NN tannin|tannin|NN _|_|NN #|#|# 8|8|CD
E.|E.|NNP coli|coli|NN 10|10|CD mins|min|NNS
E.coli|e.coli|NN -10|-10|CD minutes|minute|NNS after|after|IN BRP|brp|NN induction|induction|NN
E.coli|e.coli|NN 10|10|CD minutes|minute|NNS after|after|IN BRP|BRP|NNP induction|induction|NN
E|e|NN coli|coli|NN ,|,|, 15|15|CD min|min|NN
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD AE|ae|NN _|_|NN 1|1|CD
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD AE|ae|NN _|_|NN 2|2|CD
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD aerobic|aerobic|JJ
E.|E.|NNP coli|coli|NN -|-|: 15|15|CD min|min|NN after|after|IN shift|shift|NN to|to|TO limiting|limit|VBG medium|medium|NN
E.|E.|NNP coli|coli|NN -|-|: 15|15|CD min|min|NN after|after|IN shift|shift|NN to|to|TO thymineless|thymineless|JJ medium|medium|NN
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD ANA|ANA|NNP _|_|SYM 1|1|CD
E.|e.|FW coli|coli|FW _|_|SYM 15|15|CD min|min|NN _|_|CD ANA|ANA|NNP _|_|NN 2|2|CD
E.|e.|FW coli|coli|FW _|_|SYM 15|15|CD min|min|NN _|_|NN anaerobic|anaerobic|JJ
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|NN anaerobic|anaerobic|JJ
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD CORM-2|corm-2|NN treated|treat|VBN _|_|SYM aerobic|aerobic|JJ
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD CORM-2|corm-2|NN treated|treat|VBN _|_|SYM anaerobic|anaerobic|JJ
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD CORM|CORM|NNP _|_|CD AE|AE|NNP _|_|SYM 1|1|CD
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD CORM|CORM|NNP _|_|CD AE|AE|NNP _|_|NN 2|2|CD
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD CORM|CORM|NNP _|_|NNP ANA|ANA|NNP _|_|SYM 1|1|CD
E.coli|e.coli|NNS _|_|VBP 15|15|CD min|min|NN _|_|CD CORM|CORM|NNP _|_|NNP ANA|ANA|NNP _|_|NN 2|2|CD
E.|E.|NNP coli|coli|NN 15|15|CD minute|minute|NN 5|5|CD µM|µm|NN cadmium|cadmium|NN dye|dye|VB swap|swap|NN treatment|treatment|NN
E.|E.|NNP coli|coli|NN 15|15|CD minute|minute|NN 5|5|CD µM|µm|NN cadmium|cadmium|NN treatment|treatment|NN
E.|E.|NNP coli|coli|NN 15|15|CD minute|minute|NN pH|ph|NN only|only|RB dye|dye|VB swap|swap|NN treatment|treatment|NN
E.|E.|NNP coli|coli|NN 15|15|CD minute|minute|NN pH|ph|NN only|only|RB treatment|treatment|NN
E.|E.|NNP coli|coli|NN ,|,|, 15|15|CD minutes|minute|NNS ,|,|, 5|5|CD µM|µm|NN cadmium|cadmium|NN ,|,|, pH|ph|NN 5|5|CD
E.|E.|NNP coli|coli|NN ,|,|, 15|15|CD minutes|minute|NNS ,|,|, 5|5|CD µM|µm|NN cadmium|cadmium|NN ,|,|, pH|ph|NN 7|7|CD
E.|E.|NNP coli|coli|NN ,|,|, 15|15|CD minutes|minute|NNS ,|,|, no|no|DT cadmium|cadmium|NN ,|,|, pH|ph|NN 5|5|CD
E.|E.|NNP coli|coli|NN ,|,|, 15|15|CD minutes|minute|NNS ,|,|, no|no|DT cadmium|cadmium|NN ,|,|, pH|ph|NN 7|7|CD
E.|E.|NNP coli|coli|NN ,|,|, 1-h|1-h|NN ,|,|, serine|serine|NN hydroxamate|hydroxamate|NN
E.coli|e.coli|NNS _|_|VBP 1|1|CD %|%|NN tannin|tannin|NN _|_|NN #|#|# 3|3|CD
e.coli|e.coli|NNS _|_|VBP 1|1|CD %|%|NN tannin|tannin|NN _|_|NN #|#|# 5|5|CD
E.coli-1x|e.coli-1x|NN CORM2-rep1|corm2-rep1|NN
E.coli-1x|e.coli-1x|NN CORM2-rep2|corm2-rep2|NN
E.coli-1x|e.coli-1x|NN CORM2-rep3|corm2-rep3|NN
E.coli-1x|e.coli-1x|NN CORM2-rep4|corm2-rep4|NN
E.coli-1x|e.coli-1x|NN vehicle-rep1|vehicle-rep1|NN
E.coli-1x|e.coli-1x|NN vehicle-rep2|vehicle-rep2|NN
E.coli-1x|e.coli-1x|NN vehicle-rep3|vehicle-rep3|NN
E.coli-1x|e.coli-1x|NN vehicle-rep4|vehicle-rep4|NN
E.coli|e.coli|NN 20|20|CD minutes|minute|NNS after|after|IN BRP|brp|NN induction|induction|NN
E.coli-20x|e.coli-20x|NN CORM2-rep1|corm2-rep1|NN
E.coli-20x|e.coli-20x|NN CORM2-rep2|corm2-rep2|NN
E.coli-20x|e.coli-20x|NN CORM2-rep3|corm2-rep3|NN
E.coli-20x|e.coli-20x|NN CORM2-rep4|corm2-rep4|NN
E.coli-20x|e.coli-20x|NN vehicle-rep1|vehicle-rep1|NN
E.coli-20x|e.coli-20x|NN vehicle-rep2|vehicle-rep2|NN
E.coli-20x|e.coli-20x|NN vehicle-rep3|vehicle-rep3|NN
E.coli-20x|e.coli-20x|NN vehicle-rep4|vehicle-rep4|NN
E|e|NN coli|coli|NN ,|,|, 25|25|CD min|min|NN
E|e|NN coli|coli|NN ,|,|, 25|25|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
E.|e.|FW coli|coli|FW 2.5|2.5|CD mins|min|NNS
Ecoli|Ecoli|NNP ,|,|, 2|2|CD min|min|NN
E|e|NN coli|coli|NN ,|,|, 2|2|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
E.coli|e.coli|NN 2|2|CD minutes|minute|NNS after|after|IN BRP|BRP|NNP induction|induction|NN
E.|E.|NNP coli|coli|NN 2|2|CD %|%|NN NaCl|nacl|NN
E.|E.|NNP coli|coli|NN -|-|: 30|30|CD min|min|NN after|after|IN shift|shift|NN to|to|TO limiting|limit|VBG medium|medium|NN
E.|E.|NNP coli|coli|NN -|-|: 30|30|CD min|min|NN after|after|IN shift|shift|NN to|to|TO thymineless|thymineless|JJ medium|medium|NN
E.|E.|NNP coli|coli|NN 30|30|CD mins|min|NNS
E.coli|e.coli|NN 30|30|CD minutes|minute|NNS after|after|IN BRP|BRP|NNP induction|induction|NN
E.|E.|NNP coli|coli|NN 3538|3538|CD #|#|# 1|1|CD
E.|E.|NNP coli|coli|NN 3538|3538|CD #|#|# 2|2|CD
ecoli|ecolus|NNS _|_|VBP 3538|3538|CD _|_|SYM 2x|2x|FW _|_|FW v2|v2|FW
E.|e.|FW coli|coli|FW 3538|3538|CD #|#|# 3|3|CD
ecoli|ecolus|NNS _|_|VBP 3538|3538|CD _|_|SYM 3x|3x|FW _|_|FW v2|v2|FW
ecoli|ecolus|NNS _|_|VBP 3538|3538|CD _|_|SYM 4x|4x|FW _|_|FW v2|v2|FW
E|e|NN coli|coli|NN ,|,|, 35|35|CD min|min|NN
E|e|NN coli|coli|NN ,|,|, 35|35|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
E.|e.|FW coli|coli|FW 3.5|3.5|CD %|%|NN NaCl|nacl|NN ,|,|, replicate|replicate|VB 1|1|CD
E.|E.|NNP coli|coli|NN 3.5|3.5|CD %|%|NN NaCl|nacl|NN ,|,|, replicate|replicate|VB 2|2|CD
e.coli|e.coli|NNS ,|,|, 37|37|CD °C|°c|NN ,|,|, 60|60|CD min|min|NN
E.coli|e.coli|NNS ,|,|, 37|37|CD °C|°c|NN ,|,|, 60|60|CD min|min|NN
E.coli|e.coli|NN ,37|,37|CD °C|°c|NN ,|,|, 60|60|CD min|min|NN
E.coli|e.coli|NN ，|，|NN 37|37|CD °C|°c|NN ，|，|CD 60|60|CD min|min|NN
E.|E.|NNP coli|coli|NN 37L|37l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 37L|37l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 37L|37l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|E.|NNP coli|coli|NN 3|3|CD '|'|'' RACE|race|NN Rep1|rep1|JJ
E.|e.|FW coli|coli|FW 3|3|CD '|'|'' RACE|race|NN Rep2|rep2|JJ
E.|e.|FW coli|coli|FW 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 41ºC|41ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 41ºC|41ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 41ºC|41ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 41B|41b|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 41B|41b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 43ºC|43ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 43ºC|43ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 43ºC|43ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 43B|43b|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 43B|43b|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 2|2|CD
e.coli|e.coli|NNS ,|,|, 43|43|CD °C|°c|NN ,|,|, 60|60|CD min|min|NN
E.coli|e.coli|NNS ,|,|, 43|43|CD °C|°c|NN ,|,|, 60|60|CD min|min|NN
E.coli|e.coli|NN ,43|,43|CD °C|°c|NN ,|,|, 60|60|CD min|min|NN
E.coli|e.coli|NN ，|，|CD 43|43|CD °C|°c|NN ，|，|CD 60|60|CD min|min|NN
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, evolutionary|evolutionary|JJ temperature|temperature|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN evolved|evolve|VBD strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW 45L|45l|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN 45L|45l|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 2|2|CD
E|e|NN coli|coli|NN ,|,|, 45|45|CD min|min|NN
E.|E.|NNP coli|coli|NN -|-|: 45|45|CD min|min|NN after|after|IN shift|shift|NN to|to|TO limiting|limit|VBG medium|medium|NN
E.|E.|NNP coli|coli|NN -|-|: 45|45|CD min|min|NN after|after|IN shift|shift|NN to|to|TO thymineless|thymineless|JJ medium|medium|NN
E|e|NN coli|coli|NN ,|,|, 45|45|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
E.coli|e.coli|NN 45|45|CD minutes|minute|NNS after|after|IN BRP|BRP|NNP induction|induction|NN
E.|E.|NNP coli|coli|NN 4.5|4.5|CD %|%|NN NaCl|nacl|NN
E|e|NN coli|coli|NN ,|,|, 55|55|CD min|min|NN
E.|E.|NNP coli|coli|NN 5.5|5.5|CD %|%|NN NaCl|nacl|NN
E|e|NN coli|coli|NN ,|,|, 5|5|CD min|min|NN
Ecoli|Ecoli|NNP ,|,|, 5|5|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
E|e|NN coli|coli|NN ,|,|, 5|5|CD min|min|NN after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN first|first|RB replicate|replicate|VB
E.|e.|FW coli|coli|FW 5|5|CD minute|minute|NN 5|5|CD µM|µm|NN cadmium|cadmium|NN dye|dye|VB swap|swap|NN treatment|treatment|NN
E.|E.|NNP coli|coli|NN 5|5|CD minute|minute|NN 5|5|CD µM|µm|NN cadmium|cadmium|NN treatment|treatment|NN
E.|E.|NNP coli|coli|NN 5|5|CD minute|minute|NN pH|ph|NN only|only|RB dye|dye|VB swap|swap|NN treatment|treatment|NN
E.|E.|NNP coli|coli|NN 5|5|CD minute|minute|NN pH|ph|NN only|only|RB treatment|treatment|NN
E.|E.|NNP coli|coli|NN ,|,|, 5|5|CD minutes|minute|NNS ,|,|, 5|5|CD µM|µm|NN cadmium|cadmium|NN ,|,|, pH|ph|NN 5|5|CD
E.|E.|NNP coli|coli|NN ,|,|, 5|5|CD minutes|minute|NNS ,|,|, 5|5|CD µM|µm|NN cadmium|cadmium|NN ,|,|, pH|ph|NN 7|7|CD
E.coli|e.coli|NNS 5|5|CD minutes|minute|NNS after|after|IN BRP|BRP|NNP induction|induction|NN
E.|E.|NNP coli|coli|NN ,|,|, 5|5|CD minutes|minute|NNS ,|,|, no|no|DT cadmium|cadmium|NN ,|,|, pH|ph|NN 5|5|CD
E.|E.|NNP coli|coli|NN ,|,|, 5|5|CD minutes|minute|NNS ,|,|, no|no|DT cadmium|cadmium|NN ,|,|, pH|ph|NN 7|7|CD
E.|e.|FW coli|coli|FW 5|5|CD %|%|NN NaCl|nacl|NN
E.|E.|NNP coli|coli|NN -|-|: 60|60|CD min|min|NN after|after|IN shift|shift|NN to|to|TO limiting|limit|VBG medium|medium|NN
E.|E.|NNP coli|coli|NN -|-|: 60|60|CD min|min|NN after|after|IN shift|shift|NN to|to|TO thymineless|thymineless|JJ medium|medium|NN
E.coli|e.coli|NN 60|60|CD minutes|minute|NNS after|after|IN BRP|BRP|NNP induction|induction|NN
E.|E.|NNP coli|coli|NN 7|7|CD mins|min|NNS
E.|e.|FW coli|coli|FW 8624|8624|CD
E.|E.|NNP coli|coli|NN 8624|8624|CD qseF|qsef|NN deletion|deletion|NN mutant|mutant|JJ
E.|e.|FW coli|coli|FW 8624|8624|CD WT|WT|NNP
E.|E.|NNP coli|coli|NN -|-|: 90|90|CD min|min|NN after|after|IN shift|shift|NN to|to|TO limiting|limit|VBG medium|medium|NN
E.|E.|NNP coli|coli|NN -|-|: 90|90|CD min|min|NN after|after|IN shift|shift|NN to|to|TO thymineless|thymineless|JJ medium|medium|NN
E.|E.|NNP coli|coli|NN AcrA|AcrA|NNP Multidrug|Multidrug|NNP Efflux|Efflux|NNP Mutant|mutant|JJ
E.|e.|FW coli|coli|FW AcrB|acrb|NN and|and|CC EmrAB|EmrAB|NNP Multidrug|Multidrug|NNP Efflux|Efflux|NNP Double|double|JJ Mutant|mutant|JJ
E.|e.|FW coli|coli|FW AcrB|acrb|NN Multidrug|multidrug|JJ Efflux|efflux|NN Mutant|mutant|JJ
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 0|0|CD min|min|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 15|15|CD min|min|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 25|25|CD min|min|NN _|_|CD rep1|rep1|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 25|25|CD min|min|NN _|_|CD rep2|rep2|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 2|2|CD min|min|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 35|35|CD min|min|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 45|45|CD min|min|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 55|55|CD min|min|NN _|_|CD rep1|rep1|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 55|55|CD min|min|NN _|_|CD rep2|rep2|NN
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 5|5|CD min|min|NN _|_|SYM Rep1|rep1|JJ
ecoli|ecolus|NNS _|_|VBP aerobicanaerobic|aerobicanaerobic|JJ _|_|NN 5|5|CD min|min|NN _|_|CD rep2|rep2|NN
Ecoli|ecolus|NNS _|_|VBP Ag0|ag0|NN .0|.0|CD _|_|NN rep1|rep1|NN
Ecoli|ecolus|NNS _|_|VBP Ag0|ag0|NN .0|.0|CD _|_|NN rep2|rep2|NN
Ecoli|ecolus|NNS _|_|VBP Ag0|ag0|NN .0|.0|CD _|_|NN rep3|rep3|NN
Ecoli|ecolus|NNS _|_|VBP Ag5|ag5|NN .0|.0|CD _|_|NN rep1|rep1|NN
Ecoli|ecolus|NNS _|_|VBP Ag5|ag5|NN .0|.0|CD _|_|NN rep2|rep2|NN
Ecoli|ecolus|NNS _|_|VBP Ag5|ag5|NN .0|.0|CD _|_|NN rep3|rep3|NN
Ecoli|ecolus|NNS _|_|VBP Ag6|ag6|NN .5|.5|CD _|_|NN rep1|rep1|NN
Ecoli|ecolus|NNS _|_|VBP Ag6|ag6|NN .5|.5|CD _|_|NN rep2|rep2|NN
Ecoli|ecolus|NNS _|_|VBP Ag6|ag6|NN .5|.5|CD _|_|NN rep3|rep3|NN
Ecoli|ecolus|NNS _|_|VBP Ag8|ag8|NN .5|.5|CD _|_|NN rep1|rep1|NN
Ecoli|ecolus|NNS _|_|VBP Ag8|ag8|NN .5|.5|CD _|_|NN rep2|rep2|NN
Ecoli|ecolus|NNS _|_|VBP Ag8|ag8|NN .5|.5|CD _|_|SYM rep3|rep3|CD
Ecoli|Ecoli|NNP _|_|NNP Ampicillin|Ampicillin|NNP treatment|treatment|NN T1|t1|NN
Ecoli|Ecoli|NNP _|_|NNP Ampicillin|Ampicillin|NNP treatment|treatment|NN T2|t2|NN
Ecoli|Ecoli|NNP _|_|NNP Ampicillin|Ampicillin|NNP treatment|treatment|NN T3|t3|NN
Ecoli|Ecoli|NNP _|_|NNP Ampicillin|Ampicillin|NNP treatment|treatment|NN T4|t4|NN
Ecoli|Ecoli|NNP _|_|NNP Ampicillin|Ampicillin|NNP treatment|treatment|NN T5|t5|NN
Ecoli|Ecoli|NNP _|_|NNP Ampicillin|Ampicillin|NNP treatment|treatment|NN T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, reference|reference|NN Genomic|genomic|JJ DNA|dna|NN T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN vs|vs|CC Aerobic|aerobic|JJ OD|od|NN 0.4|0.4|CD T6|t6|NN
E.|E.|NNP coli|coli|NN ancestor|ancestor|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN ancestor|ancestor|NN strain|strain|NN ,|,|, 30|30|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN ancestor|ancestor|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN ancestor|ancestor|NN strain|strain|NN ,|,|, 5|5|CD min|min|NN heat|heat|NN shock|shock|NN at|at|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN ancestor|ancestor|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN ancestor|ancestor|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN ancestor|ancestor|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW Anc|anc|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 1|1|CD
E.|e.|FW coli|coli|FW Anc|anc|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, long|long|RB ,|,|, rep|rep|NN 2|2|CD
E.|e.|FW coli|coli|FW Anc|anc|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 1|1|CD
E.|e.|FW coli|coli|FW Anc|anc|NN strain|strain|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, rep|rep|NN 2|2|CD
E.|e.|FW coli|coli|FW Anc|anc|NN strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 1|1|CD
E.|e.|FW coli|coli|FW Anc|anc|NN strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 2|2|CD
E.|e.|FW coli|coli|FW Anc|anc|NN strain|strain|NN ,|,|, regular|regular|JJ temperature|temperature|NN ,|,|, rep|rep|NN 3|3|CD
E.|E.|NNP coli|coli|NN and|and|CC S.|S.|NNP Typhimurium|Typhimurium|NNP cells|cell|NNS -LRB-|-lrb-|-LRB- at|at|IN mid-exponential|mid-exponential|JJ growth|growth|NN phase|phase|NN -RRB-|-rrb-|-RRB- were|be|VBD fixed|fix|VBN with|with|IN formaldehyde|formaldehyde|NN -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB- for|for|IN 20|20|CD min|min|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG .|.|. The|the|DT crosslinking|crosslinking|NN reaction|reaction|NN was|be|VBD then|then|RB quenched|quench|VBN by|by|IN the|the|DT addition|addition|NN of|of|IN glycine|glycine|NN -LRB-|-lrb-|-LRB- 0.33|0.33|CD M|m|NN final|final|JJ concentrationg|concentrationg|NN -RRB-|-rrb-|-RRB- for|for|IN 5|5|CD minutes|minute|NNS at|at|IN room|room|NN temperature|temperature|NN with|with|IN gentle|gentle|JJ mixing|mix|VBG .|.|. Cells|cell|NNS where|where|WRB then|then|RB lysed|lyse|VBN on|on|IN ice|ice|NN with|with|IN lysozyme|lysozyme|NN and|and|CC sonication|sonication|NN .|.|.
E.|E.|NNP Coli|Coli|NNP ArcA-8myc|ArcA-8myc|NNP ChIP|chip|NN DNA|dna|NN Mock|mock|NN antibody|antibody|NN anaerobic|anaerobic|JJ
E.|E.|NNP Coli|Coli|NNP ArcA-8myc|ArcA-8myc|NNP ChIP|chip|NN DNA|dna|NN Mock|mock|NN antibody|antibody|NN NO3|no3|NN
E.|E.|NNP Coli|Coli|NNP ArcA|ArcA|NNP ChIP|chip|NN DNA|dna|NN anaerobic|anaerobic|JJ
E.|E.|NNP Coli|Coli|NNP ArcA|ArcA|NNP ChIP|chip|NN DNA|dna|NN NO3|no3|NN
E.|E.|NNP Coli|Coli|NNP ArgR|argr|NN ChIP|chip|NN DNA|dna|NN Arginine|arginine|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP ArgR|argr|NN ChIP|chip|NN DNA|dna|NN Arginine|arginine|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP ArgR|argr|NN ChIP|chip|NN DNA|dna|NN NH4Cl|nh4cl|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP ArgR|argr|NN ChIP|chip|NN DNA|dna|NN NH4Cl|nh4cl|NN 2|2|CD
E.|E.|NNP coli|coli|NN ATCC|atcc|NN 25922|25922|CD marR|marr|NN deletion|deletion|NN +|+|CC QnrS|qnrs|NN replicate|replicate|VBP 1|1|CD
E.|E.|NNP coli|coli|NN ATCC|atcc|NN 25922|25922|CD marR|marr|NN deletion|deletion|NN +|+|CC QnrS|qnrs|NN replicate|replicate|VBP 2|2|CD
E.|E.|NNP coli|coli|NN ATCC|atcc|NN 25922|25922|CD QnrS|qnrs|NN replicate|replicate|VBP 1|1|CD
E.|E.|NNP coli|coli|NN ATCC|atcc|NN 25922|25922|CD QnrS|qnrs|NN replicate|replicate|VBP 2|2|CD
E.|E.|NNP coli|coli|NN ATCC|atcc|NN 25922|25922|CD Ser83Leu|ser83leu|NN +|+|CC QnrS|qnrs|NN replicate|replicate|VBP 1|1|CD
E.|E.|NNP coli|coli|NN ATCC|atcc|NN 25922|25922|CD Ser83Leu|ser83leu|NN +|+|CC QnrS|qnrs|NN replicate|replicate|VBP 2|2|CD
E.|E.|NNP coli|coli|NN ATCC|atcc|NN 25922|25922|CD -LRB-|-lrb-|-LRB- wild-type|wild-type|JJ -RRB-|-rrb-|-RRB- and|and|CC EC14|ec14|NN ,|,|, EC19|ec19|NN ,|,|, EC24|ec24|NN -LRB-|-lrb-|-LRB- LLQR|llqr|NN -RRB-|-rrb-|-RRB- isogenic|isogenic|JJ strains|strain|NNS were|be|VBD tested|test|VBN to|to|TO evaluate|evaluate|VB the|the|DT global|global|JJ response|response|NN to|to|TO relevant|relevant|JJ fix|fix|NN concentration|concentration|NN of|of|IN ciprofloxacin|ciprofloxacin|NN -LRB-|-lrb-|-LRB- 1|1|CD mg/L|mg/l|NN ,|,|, breakpoint|breakpoint|NN for|for|IN reduced|reduce|VBN susceptibility|susceptibility|NN according|accord|VBG to|to|TO CLSI|clsi|NN -RRB-|-rrb-|-RRB- .|.|. All|all|DT of|of|IN them|they|PRP were|be|VBD susceptible|susceptible|JJ to|to|TO quinolones|quinolone|NNS according|accord|VBG to|to|TO CLSI|CLSI|NNP breakpoints|breakpoint|NNS .|.|. -LRB-|-lrb-|-LRB- CLSI|clsi|NN ,|,|, n.d.|n.d.|NN -RRB-|-rrb-|-RRB- Cultures|culture|NNS were|be|VBD started|start|VBN from|from|IN single|single|JJ colonies|colony|NNS and|and|CC grown|grow|VBN overnight|overnight|JJ in|in|IN 25|25|CD ml|ml|NN of|of|IN LB|lb|NN .|.|. These|these|DT cell|cell|NN were|be|VBD diluted|dilute|VBN 1:100|1:100|CD and|and|CC growth|growth|NN to|to|TO cell|cell|NN concentration|concentration|NN of|of|IN 4x108|4x108|CD cells/ml|cells/ml|NNS -LRB-|-lrb-|-LRB- OD600|od600|CD nm|nm|NN =|=|JJ 0.4|0.4|CD ,|,|, exponential|exponential|JJ phase|phase|NN -RRB-|-rrb-|-RRB- for|for|IN treatment|treatment|NN .|.|. Three|three|CD biological|biological|JJ replicates|replicate|VBZ per|per|IN genotype|genotype|NN were|be|VBD incubated|incubate|VBN at|at|IN 1|1|CD mg/L|mg/l|NN of|of|IN ciprofloxacin|ciprofloxacin|NN during|during|IN 60|60|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- that|that|WDT means|mean|VBZ 250xMIC|250xmic|NN for|for|IN E.|e.|FW coli|coli|FW ATCC|atcc|NN 25922|25922|CD ,|,|, 8xMIC|8xmic|NN for|for|IN EC14|ec14|NN ,|,|, 2xMIC|2xmic|NN for|for|IN EC19|ec19|NN and|and|CC 1xMIC|1xmic|NN for|for|IN EC24|ec24|NN -RRB-|-rrb-|-RRB- .|.|. Approximately|approximately|RB 109|109|CD cells|cell|NNS -LRB-|-lrb-|-LRB- 2|2|CD ml|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD taken|take|VBN for|for|IN RNA|rna|NN isolation|isolation|NN .|.|.
E.|E.|NNP coli|coli|NN B178|b178|NN groESL|groesl|NN -LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- expressing|express|VBG human|human|JJ Hsp60|hsp60|NN and|and|CC Hsp10|hsp10|NN
E.|e.|FW coli|coli|FW B178|b178|NN groESL|groesl|NN -LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- expressing|express|VBG human|human|JJ wt|wt|JJ and|and|CC Val98Ile|val98ile|NN Hsp60|hsp60|NN and|and|CC Hsp10|hsp10|NN
E.|e.|FW coli|coli|FW batch|batch|NN culture|culture|NN without|without|IN TAP|tap|NN
E.|e.|FW coli|coli|FW batch|batch|NN culture|culture|NN with|with|IN TAP|tap|NN
E.|e.|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- cells|cell|NNS expressing|express|VBG catalytically|catalytically|RB inactive|inactive|JJ mutant|mutant|NN of|of|IN M.HpyAVIB|m.hpyavib|NN
E.|e.|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- cells|cell|NNS expressing|express|VBG wild-type|wild-type|JJ M.HpyAVIB|m.hpyavib|NN
E.|e.|FW coli|coli|FW BW25113|bw25113|NN were|be|VBD maintained|maintain|VBN in|in|IN Luria-Bertani|luria-bertani|JJ medium|medium|NN at|at|IN 37ºC|37ºc|NN for|for|IN about|about|RB 14|14|CD h|h|NN until|until|IN they|they|PRP reached|reach|VBD the|the|DT stationary|stationary|JJ phase|phase|NN of|of|IN cell|cell|NN growth|growth|NN before|before|IN treatment|treatment|NN .|.|.
Ecoli|Ecoli|NNP _|_|SYM CaCl2|cacl2|NN wash|wash|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP CaCl2|cacl2|NN wash|wash|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP CaCl2|cacl2|NN wash|wash|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP CaCl2|cacl2|NN wash|wash|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP CaCl2|cacl2|NN wash|wash|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP CaCl2|cacl2|NN wash|wash|NN T6|t6|NN
E.|e.|FW coli|coli|FW CC72|cc72|NN was|be|VBD grown|grow|VBN in|in|IN water|water|NN bath|bath|NN to|to|TO early-exponential|early-exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN 0.2|0.2|CD -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN in|in|IN LB|lb|NN medium|medium|NN .|.|.
E.|E.|NNP coli|coli|NN _|_|CD CCCP|CCCP|NNP _|_|SYM 15|15|CD min|min|NN
E.|E.|NNP coli|coli|NN cell|cell|NN
E.|E.|NNP coli|coli|NN cell|cell|NN cultures|culture|NNS
E|e|NN coli|coli|NN cells|cell|NNS
E.coli|e.coli|NN cells|cell|NNS
E.|E.|NNP coli|coli|NN cells|cell|NNS 0|0|CD min|min|NN before|before|IN perturbation|perturbation|NN
E.|E.|NNP coli|coli|NN cells|cell|NNS 10|10|CD min|min|NN after|after|IN specific|specific|JJ perturbation|perturbation|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0.1|0.1|CD mM|mm|NN IPTG|iptg|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0|0|CD mM|mm|NN IPTG|iptg|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 1.5|1.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 1.0|1.0|CD mM|mm|NN IPTG|iptg|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN high|high|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 1.0|1.0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN low|low|JJ IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN addition|addition|NN of|of|IN no|no|DT IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0|0|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0.1|0.1|CD mM|mm|NN IPTG|iptg|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 0|0|CD mM|mm|NN IPTG|iptg|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN 3.5|3.5|CD hrs|hr|NNS after|after|IN induction|induction|NN with|with|IN 1.0|1.0|CD mM|mm|NN IPTG|iptg|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN the|the|DT time|time|NN of|of|IN IPTG|iptg|NN induction|induction|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN the|the|DT time|time|NN of|of|IN IPTG|iptg|NN induction|induction|NN -LRB-|-lrb-|-LRB- T|t|NN =|=|JJ 0|0|CD hrs|hr|NNS -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN the|the|DT time|time|NN of|of|IN IPTG|iptg|NN induction|induction|NN -LRB-|-lrb-|-LRB- T|t|NN =|=|JJ 0|0|CD hrs|hr|NNS -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep1|rep1|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.coli|e.coli|NN cells|cell|NNS at|at|IN the|the|DT time|time|NN of|of|IN IPTG|iptg|NN induction|induction|NN -LRB-|-lrb-|-LRB- T|t|NN =|=|JJ 0|0|CD hrs|hr|NNS -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep|rep|NN 1|1|CD
E.coli|e.coli|NN cells|cell|NNS at|at|IN the|the|DT time|time|NN of|of|IN IPTG|iptg|NN induction|induction|NN -LRB-|-lrb-|-LRB- T|t|NN =|=|JJ 0|0|CD hrs|hr|NNS -RRB-|-rrb-|-RRB- ,|,|, biological|biological|JJ rep2|rep2|NN ,|,|, technical|technical|JJ rep2|rep2|NN
E.|E.|NNP coli|coli|NN cells|cell|NNS containing|contain|VBG a|a|DT pBAD18|pbad18|NN vector|vector|NN encoding|encode|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP exposed|expose|VBN to|to|TO arabinose|arabinose|VB inducer|inducer|NN for|for|IN 0.5|0.5|CD h.|h.|NN RNA|rna|NN extracted|extract|VBN with|with|IN Invitrogen|Invitrogen|NNP PureLink|PureLink|NNP kit|kit|NN .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS from|from|IN biofilm|biofilm|NN 1|1|CD
E.|E.|NNP coli|coli|NN cells|cell|NNS from|from|IN biofilm|biofilm|NN 2|2|CD
E.|E.|NNP coli|coli|NN cells|cell|NNS from|from|IN planktonic|planktonic|JJ culture|culture|NN 1|1|CD
E.|E.|NNP coli|coli|NN cells|cell|NNS from|from|IN planktonic|planktonic|JJ culture|culture|NN 2|2|CD
E.|E.|NNP coli|coli|NN cells|cell|NNS grown|grow|VBN to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN after|after|IN 6-8|6-8|CD generations|generation|NNS after|after|IN stationary|stationary|JJ phase|phase|NN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN +|+|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|.
E.coli|e.coli|NN cells|cell|NNS grown|grow|VBN with|with|IN aeration|aeration|NN in|in|IN LB|LB|NNP media|media|NNS at|at|IN 37º|37º|CD C|c|NN until|until|IN early|early|JJ log|log|NN phase|phase|NN -LRB-|-lrb-|-LRB- 0.4|0.4|CD -RRB-|-rrb-|-RRB- and|and|CC were|be|VBD treated|treat|VBN with/without|with/without|NN 200|200|CD mM|mm|NN glyphosate|glyphosate|NN for|for|IN 1|1|CD h|h|NN ,|,|, after|after|IN that|that|IN the|the|DT cells|cell|NNS were|be|VBD harvested|harvest|VBN to|to|TO extract|extract|NN RNA|rna|NN .|.|. LB|lb|NN medium|medium|NN recipe|recipe|NN is|be|VBZ as|as|IN follow|follow|VB :|:|: 10g|10g|CD tryptone|tryptone|NN ,|,|, 5g|5g|NN yeast|yeast|NN extract|extract|NN ,|,|, 10g|10g|CD NaCl|nacl|NN per|per|IN 1|1|CD liter|liter|NN .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS _|_|VBP HS15min|hs15min|NN
E.|e.|FW coli|coli|FW cells|cell|NNS _|_|VBP HS30min|hs30min|NN
E.|e.|FW coli|coli|FW cells|cell|NNS _|_|VBP HS60min|hs60min|NN
E.|e.|FW coli|coli|FW cells|cell|NNS _|_|VBP LB|lb|NN -LRB-|-lrb-|-LRB- OD|od|NN =|=|JJ 0.87|0.87|CD -RRB-|-rrb-|-RRB-
E.|E.|NNP coli|coli|NN cells|cell|NNS _|_|VBP M-P0h|m-p0h|JJ
E.|E.|NNP coli|coli|NN cells|cell|NNS _|_|VBP M-P2h|m-p2h|JJ
E.|E.|NNP coli|coli|NN cells|cell|NNS _|_|VBP M-P4h|m-p4h|JJ
E.|e.|FW coli|coli|FW cells|cell|NNS were|be|VBD crosslinked|crosslink|VBN in|in|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN for|for|IN 25|25|CD minutes|minute|NNS at|at|IN RT|rt|NN on|on|IN a|a|DT rocker|rocker|NN ,|,|, then|then|RB washed|wash|VBN 3|3|CD times|time|NNS with|with|IN 50|50|CD ml|ml|NN of|of|IN ice-cold|ice-cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- Tris|tris|NN buffered|buffer|VBN saline|saline|NN -RRB-|-rrb-|-RRB- each|each|DT time|time|NN .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 22|22|CD °C|°c|NN ,|,|, 30|30|CD °C|°c|NN and|and|CC 37|37|CD °C|°c|NN in|in|IN either|either|CC Lennox|Lennox|NNP Broth|Broth|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- or|or|CC liquid|liquid|JJ minimal|minimal|JJ medium|medium|NN A|a|DT supplemented|supplement|VBN with|with|IN 0.12|0.12|CD %|%|NN casamino|casamino|NN acids|acid|NNS and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 0.2|0.2|CD -LRB-|-lrb-|-LRB- early|early|JJ exponential|exponential|JJ -RRB-|-rrb-|-RRB- or|or|CC 2|2|CD -LRB-|-lrb-|-LRB- stationary|stationary|JJ phase|phase|NN -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN annular|annular|JJ reactor|reactor|NN -LRB-|-lrb-|-LRB- BioSurface|BioSurface|NNP Technologies|Technologies|NNPS ,|,|, Bozeman|Bozeman|NNP ,|,|, MT|MT|NNP -RRB-|-rrb-|-RRB- inoculated|inoculate|VBN with|with|IN 1|1|CD ml|ml|NN overnight|overnight|JJ cultures|culture|NNS and|and|CC supplied|supply|VBN with|with|IN fresh|fresh|JJ 10-fold|10-fold|JJ diluted|diluted|JJ Luria|Luria|NNP broth|broth|NN at|at|IN 100|100|CD ml/h|ml/h|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 7-days|7-day|NNS .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN onto|onto|IN membrane|membrane|NN filters|filter|NNS -LRB-|-lrb-|-LRB- pore|pore|NN size|size|NN 0.45|0.45|CD micrometer|micrometer|NN -RRB-|-rrb-|-RRB- after|after|IN pre-filtering|pre-filter|VBG out|out|RP aggregates|aggregate|NNS larger|larger|JJR than|than|IN 5|5|CD micrometer|micrometer|NN from|from|IN planktonic|planktonic|JJ cultures|culture|NNS in|in|IN the|the|DT reactor|reactor|NN .|.|. Cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ in|in|IN RNAlater|rnalater|NN after|after|IN harvest|harvest|NN and|and|CC stored|store|VBD at|at|IN 4|4|CD degree|degree|NN C|c|NN overnight|overnight|JJ .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN Kornberg|Kornberg|NNP medium|medium|NN -LRB-|-lrb-|-LRB- 1.1|1.1|CD %|%|NN -LSB-|-lsb-|-LRB- wt/vol|wt/vol|NN -RSB-|-rsb-|-RRB- K2HPO4|k2hpo4|NN ,|,|, 0.85|0.85|CD %|%|NN -LSB-|-lsb-|-LRB- wt/vol|wt/vol|NN -RSB-|-rsb-|-RRB- KH2PO4|kh2po4|NN ,|,|, 0.6|0.6|CD %|%|NN -LSB-|-lsb-|-LRB- wt/vol|wt/vol|NN -RSB-|-rsb-|-RRB- yeast|yeast|NN extract|extract|NN containing|contain|VBG 0.5|0.5|CD %|%|NN -LSB-|-lsb-|-LRB- wt/vol|wt/vol|NN -RSB-|-rsb-|-RRB- glucose|glucose|NN -RRB-|-rrb-|-RRB- to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ ~|~|NN 0.6|0.6|CD -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN and|and|CC shaking|shake|VBG 250rpm|250rpm|JJ
E.|e.|FW coli|coli|FW cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN Luria|Luria|NNP Broth|Broth|NNP supplemented|supplement|VBN with|with|IN 100ug/ml|100ug/ml|JJ ampicillin|ampicillin|NN to|to|TO retain|retain|VB the|the|DT plasmids|plasmid|NNS .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS were|be|VBD grown|grow|VBN until|until|IN mid-exponential|mid-exponential|JJ phase|phase|NN and|and|CC treated|treat|VBN with|with|IN 0.5|0.5|CD mM|mm|NN isopropyl-β-d-thiogalactopyranoside|isopropyl-β-d-thiogalactopyranoside|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN -RRB-|-rrb-|-RRB- to|to|TO induce|induce|VB expression|expression|NN of|of|IN the|the|DT empty|empty|JJ vector|vector|NN or|or|CC the|the|DT small|small|JJ RNA|rna|NN .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS with|with|IN construct|construct|NN and|and|CC control|control|NN plasmids|plasmid|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN overnight|overnight|JJ with|with|IN aeration|aeration|NN in|in|IN a|a|DT shaking|shake|VBG incubator|incubator|NN in|in|IN 5|5|CD ml|ml|NN of|of|IN defined|define|VBN supplemented|supplement|VBN M9|m9|NN medium|medium|NN with|with|IN the|the|DT appropriate|appropriate|JJ antibiotic|antibiotic|JJ .|.|. In|in|IN the|the|DT morning|morning|NN ,|,|, 60|60|CD μl|μl|NN of|of|IN each|each|DT sample|sample|NN were|be|VBD diluted|dilute|VBN into|into|IN 3|3|CD ml|ml|NN of|of|IN fresh|fresh|JJ medium|medium|NN and|and|CC grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG for|for|IN another|another|DT hour|hour|NN -LRB-|-lrb-|-LRB- outgrowth|outgrowth|NN -RRB-|-rrb-|-RRB- .|.|. 200|200|CD μl|μl|NN of|of|IN each|each|DT sample|sample|NN were|be|VBD then|then|RB transferred|transfer|VBN in|in|IN 8|8|CD wells|well|NNS of|of|IN a|a|DT 96-well|96-well|JJ plate|plate|NN -LRB-|-lrb-|-LRB- Costar|costar|NN -RRB-|-rrb-|-RRB- at|at|IN approximately|approximately|RB 0.1|0.1|CD OD|od|NN -LRB-|-lrb-|-LRB- 600|600|CD nm|nm|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT samples|sample|NNS were|be|VBD placed|place|VBN in|in|IN a|a|DT Synergy|synergy|NN HT|ht|NN Microplate|Microplate|NNP Reader|Reader|NNP -LRB-|-lrb-|-LRB- BioTek|BioTek|NNP -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN orbital|orbital|JJ shaking|shake|VBG at|at|IN 1,000|1,000|CD rpm|rpm|NN for|for|IN 1|1|CD h|h|NN ,|,|, performing|perform|VBG measurements|measurement|NNS of|of|IN GFP|gfp|NN -LRB-|-lrb-|-LRB- excitation|excitation|NN -LRB-|-lrb-|-LRB- ex|ex|FW .|.|. -RRB-|-rrb-|-RRB- ,|,|, 485|485|CD nm|nm|NN ;|;|: emission|emission|NN -LRB-|-lrb-|-LRB- em|em|NN .|.|. -RRB-|-rrb-|-RRB- ,|,|, 528|528|CD nm|nm|NN -RRB-|-rrb-|-RRB- and|and|CC OD|od|NN -LRB-|-lrb-|-LRB- 600|600|CD nm|nm|NN -RRB-|-rrb-|-RRB- every|every|DT 15|15|CD minutes|minute|NNS .|.|.
E.|E.|NNP coli|coli|NN cells|cell|NNS with|with|IN or|or|CC without|without|IN BnTR1|bntr1|NN were|be|VBD transferred|transfer|VBN and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN and|and|CC 42|42|CD °C|°c|NN for|for|IN 1|1|CD hour|hour|NN ,|,|, respectively|respectively|RB
E.|E.|NNP coli|coli|NN CFT073|cft073|NN carrying|carry|VBG either|either|CC pBAD|pbad|NN or|or|CC pBAD-tosR-his6|pbad-tosr-his6|NN were|be|VBD cultured|culture|VBN overnight|overnight|JJ in|in|IN biological|biological|JJ triplicates|triplicate|NNS in|in|IN LB|lb|NN medium|medium|NN containing|contain|VBG ampicillin|ampicillin|NN -LRB-|-lrb-|-LRB- 100|100|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- .|.|. Cultures|culture|NNS were|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN containing|contain|VBG 10|10|CD mM|mm|NN L-arabinose|l-arabinose|NN and|and|CC ampicillin|ampicillin|NN and|and|CC cultured|culture|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN aeration|aeration|NN .|.|. A|a|DT 400|400|CD µL|µl|NN sample|sample|NN was|be|VBD collected|collect|VBN between|between|IN OD600|od600|CD 0.46-0.96|0.46-0.96|CD ,|,|, and|and|CC stabilized|stabilize|VBN by|by|IN the|the|DT immediate|immediate|JJ addition|addition|NN of|of|IN 800|800|CD µl|µl|NN of|of|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
E.coli|e.coli|NN CFT073|cft073|NN genomic|genomic|JJ DNA|dna|NN
E.coli|e.coli|NN CFT073|cft073|NN genomic|genomic|JJ DNA|dna|NN hybridization|hybridization|NN to|to|TO LLNL|llnl|NN virulence|virulence|NN mechanism|mechanism|NN array|array|NN v2A|v2a|NN
E.|E.|NNP coli|coli|NN Cholic|Cholic|NNP Acid|Acid|NNP Treatment|treatment|NN
E.|E.|NNP coli|coli|NN CMA540|cma540|NN -LRB-|-lrb-|-LRB- MG1693|mg1693|NN ∆|∆|CD hfq|hfq|NN :|:|: :|:|: cat|cat|NN -RRB-|-rrb-|-RRB-
Ecoli|ecolus|NNS ,|,|, completely|completely|RB aerobic|aerobic|JJ conditions|condition|NNS
E.|e.|FW coli|coli|FW _|_|FW control|control|NN _|_|SYM 30|30|CD min|min|NN
Ecoli|Ecoli|NNP _|_|NN control|control|NN _|_|CD 5h|5h|NN _|_|CD rep1|rep1|NN
Ecoli|ecoli|JJ _|_|NN control|control|NN _|_|CD 5h|5h|NN _|_|CD rep2|rep2|NN
Ecoli|ecoli|JJ _|_|NN control|control|NN _|_|CD 5h|5h|NN _|_|CD rep3|rep3|NN
Ecoli|ecoli|JJ _|_|NN control|control|NN _|_|CD 5h|5h|JJ _|_|NN rep4|rep4|NN
E.|e.|FW coli|coli|FW control|control|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
E.|E.|NNP coli|coli|NN control|control|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 2|2|LS -RRB-|-rrb-|-RRB-
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN ,|,|, replicate|replicate|VB 1|1|CD
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN ,|,|, replicate|replicate|VB 2|2|CD
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN ,|,|, replicate|replicate|VB 3|3|CD
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN ,|,|, replicate|replicate|VB 4|4|CD
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, control|control|JJ culture|culture|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|JJ _|_|NN control|control|NN _|_|CD repA|repa|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repA|repa|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repA|repa|NN _|_|CD t3|t3|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repB|repb|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repB|repb|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repB|repb|NN _|_|CD t3|t3|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repC|repc|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repC|repc|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP control|control|NN _|_|CD repC|repc|NN _|_|CD t3|t3|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN N|n|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN Q|Q|NNP strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN _|_|NN glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW CRP|crp|NN R|r|NN strain|strain|NN grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW culture|culture|NN
e.coli|e.coli|JJ culture|culture|NN protocol|protocol|NN :|:|: conditioned|condition|VBN Caco-2|caco-2|NN cell|cell|NN medium|medium|NN
e.coli|e.coli|JJ culture|culture|NN protocol|protocol|NN :|:|: fresh|fresh|JJ medium|medium|NN
E.|E.|NNP coli|coli|NN cultures|culture|NNS
E.|e.|FW coli|coli|FW cultures|culture|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN glucose|glucose|NN as|as|IN the|the|DT primary|primary|JJ carbon|carbon|NN source|source|NN and|and|CC harvested|harvest|VBN at|at|IN mid|mid|JJ exponetial|exponetial|JJ phase|phase|NN .|.|. Aerobic|aerobic|JJ E.|e.|FW coli|coli|FW conditions|condition|NNS were|be|VBD grown|grow|VBN in|in|IN shake|shake|NN flasks|flask|NNS and|and|CC anaerobic|anaerobic|JJ conditions|condition|NNS were|be|VBD grown|grow|VBN in|in|IN anoxic|anoxic|JJ serum|serum|NN bottles|bottle|NNS .|.|. Condition|condition|NN specific|specific|JJ media|media|NNS supplementation|supplementation|NN was|be|VBD added|add|VBN as|as|IN described|describe|VBN else|else|RB where|where|WRB .|.|.
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN ,|,|, replicate|replicate|VB C|c|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB A|a|DT
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB B|b|NN
E.coli|e.coli|NNS ,|,|, culture|culture|NN with|with|IN VWPE|vwpe|NN extract|extract|NN diluted|dilute|VBN in|in|IN ethanol|ethanol|NN 20|20|CD %|%|NN ,|,|, at|at|IN the|the|DT time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, replicate|replicate|VB C|c|NN
E.|e.|FW coli|coli|FW cultutures|cultuture|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN media|media|NNS using|use|VBG standard|standard|JJ protocol|protocol|NN ,|,|, to|to|TO log|log|VB phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN of|of|IN 0.7-0.8|0.7-0.8|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW D1|d1|NN #|#|# 1|1|CD
E.|E.|NNP coli|coli|NN D1|d1|NN #|#|# 2|2|CD
ecoli|ecolus|NNS _|_|VBP D1|d1|NN _|_|SYM 2x|2x|FW _|_|FW v2|v2|FW
E.|e.|FW coli|coli|FW D1|d1|NN #|#|# 3|3|CD
ecoli|ecolus|NNS _|_|VBP D1|d1|NN _|_|SYM 3x|3x|FW _|_|FW v2|v2|FW
ecoli|ecolus|NNS _|_|VBP D1|d1|NN _|_|SYM 4x|4x|FW _|_|FW v2|v2|FW
Ecoli|ecolus|NNS _|_|VBP dFNR|dfnr|NN _|_|CD rep1|rep1|NN _|_|NN anaerobic|anaerobic|JJ
Ecoli|ecolus|NNS _|_|VBP dFNR|dfnr|NN _|_|CD rep2|rep2|NN _|_|CD anaerobic|anaerobic|JJ
Ecoli|Ecoli|NNP _|_|NNP Early|Early|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T1|t1|NN
Ecoli|Ecoli|NNP _|_|NNP Early|Early|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T2|t2|NN
Ecoli|Ecoli|NNP _|_|NNP Early|Early|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T3|t3|NN
Ecoli|Ecoli|NNP _|_|NNP Early|Early|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T4|t4|NN
Ecoli|Ecoli|NNP _|_|NNP Early|Early|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T5|T5|NNP
Ecoli|Ecoli|NNP _|_|NNP Early|Early|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T6|T6|NNP
Ecoli|Ecoli|NNP _|_|NNP Early|Early|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T7|T7|NNP
E.|E.|NNP coli|coli|NN EDL933|edl933|NN #|#|# 1|1|CD
E.|E.|NNP coli|coli|NN EDL933|edl933|NN #|#|# 2|2|CD
ecoli|ecolus|NNS _|_|VBP EDL933|edl933|NN _|_|SYM 2x|2x|FW _|_|FW v2|v2|FW
E.|e.|FW coli|coli|FW EDL933|edl933|NN #|#|# 3|3|CD
ecoli|ecolus|NNS _|_|VBP EDL933|edl933|NN _|_|SYM 3x|3x|FW _|_|FW v2|v2|FW
ecoli|ecolus|NNS _|_|VBP EDL933|edl933|NN _|_|SYM 4x|4x|FW _|_|FW v2|v2|FW
E.|e.|FW coli|coli|FW Estradiol|estradiol|NN Treatment|treatment|NN
E.coli|e.coli|NN ethanologen|ethanologen|NN strain|strain|NN GLBRCE1|glbrce1|NN or|or|CC GLBRCE1|glbrce1|NN lacking|lack|VBG the|the|DT plasmid-borne|plasmid-borne|JJ PET|pet|NN cassette|cassette|NN -LRB-|-lrb-|-LRB- GLBRCE1|glbrce1|NN _|_|CD pBBR|pbbr|NN -RRB-|-rrb-|-RRB- was|be|VBD grown|grow|VBN in|in|IN AFEX|AFEX|NNP corn|corn|NN stover|stover|NN hydrolysate|hydrolysate|NN -LRB-|-lrb-|-LRB- ACSH|acsh|NN -RRB-|-rrb-|-RRB- .|.|. Fermentations|fermentation|NNS were|be|VBD carried|carry|VBN out|out|RP in|in|IN 3|3|CD L|l|NN bioreactors|bioreactor|NNS -LRB-|-lrb-|-LRB- Applikon|Applikon|NNP Biotechnology|Biotechnology|NNP -RRB-|-rrb-|-RRB- containing|contain|VBG 2.45|2.45|CD L|l|NN of|of|IN ACSH|acsh|NN and|and|CC cultures|culture|NNS were|be|VBD diluted|dilute|VBN into|into|IN ACSH|acsh|NN with|with|IN initial|initial|JJ OD|od|NN at|at|IN 0.2|0.2|CD ,|,|, grown|grow|VBN anaerobically|anaerobically|RB overnight|overnight|RB ,|,|, and|and|CC then|then|RB inoculated|inoculate|VBN into|into|IN bioreactors|bioreactor|NNS to|to|TO a|a|DT starting|start|VBG OD600|od600|NN of|of|IN 0.2|0.2|CD .|.|. One|one|CD biological|biological|JJ replicate|replicate|VBP was|be|VBD grown|grow|VBN in|in|IN each|each|DT medium|medium|NN .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD obtained|obtain|VBN at|at|IN 3|3|CD time|time|NN points|point|NNS ,|,|, corresponding|correspond|VBG to|to|TO mid-exponential|mid-exponential|JJ -LRB-|-lrb-|-LRB- Exp|exp|NN -RRB-|-rrb-|-RRB- ,|,|, transitional|transitional|JJ -LRB-|-lrb-|-LRB- Trans|Trans|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC stationary|stationary|JJ -LRB-|-lrb-|-LRB- Stat|stat|NN -RRB-|-rrb-|-RRB- growth|growth|NN phases|phase|NNS .|.|.
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repA|repa|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repA|repa|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repA|repa|NN _|_|CD t3|t3|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repB|repb|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repB|repb|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repB|repb|NN _|_|CD t3|t3|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repC|repc|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repC|repc|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP ethanol|ethanol|NN _|_|NN repC|repc|NN _|_|CD t3|t3|NN
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP FecI|FecI|NNP ChIP|ChIP|NNP DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP FecI|FecI|NNP ChIP|ChIP|NNP DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP FecI|FecI|NNP ChIP|ChIP|NNP DNA|DNA|NNP 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP FecI|FecI|NNP ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP FecI|FecI|NNP ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP FecI|FecI|NNP ChIP|chip|NN DNA|dna|NN Mock|mock|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN DelN|deln|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN DelN|deln|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN DelN|deln|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoD|rpod|NN DelN|deln|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoF|rpof|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoF|rpof|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoF|rpof|NN ChIP|chip|NN DNA|dna|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoF|rpof|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoF|rpof|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoF|rpof|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Exponential|Exponential|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP coli|coli|NN expressing|express|VBG dr1558|dr1558|NN replicate|replicate|VB 1|1|CD
E.|E.|NNP coli|coli|NN expressing|express|VBG dr1558|dr1558|NN replicate|replicate|VB 2|2|CD
E.|E.|NNP coli|coli|NN expressing|express|VBG dr1558|dr1558|NN replicate|replicate|VB 3|3|CD
E.|E.|NNP coli|coli|NN flhD|flhd|NN ,|,|, A600|a600|NN =|=|JJ 0.2|0.2|CD on|on|IN mucus|mucus|NN
E.|E.|NNP coli|coli|NN flhD|flhd|NN ,|,|, A600|a600|NN =|=|JJ 0.4|0.4|CD on|on|IN glucose|glucose|NN
E.|e.|FW coli|coli|FW flhD|flhd|NN ,|,|, A600|a600|NN =|=|JJ 0.4|0.4|CD on|on|IN mannose|mannose|NN
E.|e.|FW coli|coli|FW flhD|flhd|NN ,|,|, A600|a600|NN =|=|JJ 0.5|0.5|CD on|on|IN mucus|mucus|NN
E.|E.|NNP Coli|Coli|NNP Fnr-8myc|fnr-8myc|JJ ChIP|chip|NN DNA|dna|NN Mock|mock|NN antibody|antibody|NN anaerobic|anaerobic|JJ
E.|E.|NNP Coli|Coli|NNP Fnr-8myc|fnr-8myc|JJ ChIP|chip|NN DNA|dna|NN Mock|mock|NN antibody|antibody|NN NO3|no3|NN
E.|E.|NNP Coli|Coli|NNP Fnr|Fnr|NNP ChIP|ChIP|NNP DNA|DNA|NNP anaerobic|anaerobic|JJ
E.|E.|NNP Coli|Coli|NNP Fnr|Fnr|NNP ChIP|ChIP|NNP DNA|DNA|NNP NO3|no3|NN
E.|E.|NNP coli|coli|NN Frag1|frag1|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 2|2|LS -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW Frag1|frag1|NN -LRB-|-lrb-|-LRB- control|control|NN sample|sample|NN 1|1|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW Frag1|frag1|NN ,|,|, hyperosmotic|hyperosmotic|JJ NaCl|nacl|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 1|1|LS -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW Frag1|frag1|NN ,|,|, NaCl|nacl|NN hyperosmotic|hyperosmotic|JJ treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 2|2|LS -RRB-|-rrb-|-RRB-
E.coli|e.coli|NN Frag1|frag1|NN ,|,|, sucrose|sucrose|NN hyperosmotic|hyperosmotic|JJ treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 1|1|LS -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW Frag1|frag1|NN ,|,|, sucrose|sucrose|NN hyperosmotic|hyperosmotic|JJ treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 2|2|LS -RRB-|-rrb-|-RRB-
E.|E.|NNP coli|coli|NN G|g|NN 1/2|1/2|CD
E.|E.|NNP coli|coli|NN G4/9|g4/9|NN
E.|e.|FW coli|coli|FW G5|g5|NN
E.|e.|FW coli|coli|FW galT|galt|NN mutant|mutant|JJ cells|cell|NNS were|be|VBD cultivated|cultivate|VBN in|in|IN 125-mL|125-ml|NN corning|corning|NN flasks|flask|NNS containing|contain|VBG 30|30|CD mL|ml|NN of|of|IN M63|m63|NN minimal|minimal|JJ medium|medium|NN plus|plus|CC glycerol|glycerol|NN -LRB-|-lrb-|-LRB- final|final|JJ 0.3|0.3|CD %|%|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN .|.|.
E.|E.|NNP coli|coli|NN galT|galt|NN mutant|mutant|NN with|with|IN galactose|galactose|NN
E.|E.|NNP coli|coli|NN galT|galt|NN mutant|mutant|NN without|without|IN galactose|galactose|NN
Ecoli|Ecoli|NNP _|_|NNP Gamma|Gamma|NNP treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Gamma|gamma|NN treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Gamma|gamma|NN treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Gamma|gamma|NN treatment|treatment|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Gamma|gamma|NN treatment|treatment|NN T5|t5|NN
E.coli|e.coli|NN gene|gene|NN expression|expression|NN data|datum|NNS in|in|IN deletion|deletion|NN of|of|IN chaperone|chaperone|NN DnaK|dnak|NN
E.|e.|FW coli|coli|FW _|_|FW gentamicin|gentamicin|NN _|_|SYM 30|30|CD min|min|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 110|110|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 170|170|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 230|230|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 30|30|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 350|350|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 50|50|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, acetate|acetate|NN concentration|concentration|NN ≤|≤|CD 0.35|0.35|CD gL-1|gl-1|NN
E.|E.|NNP coli|coli|NN ,|,|, glucose|glucose|NN limitation|limitation|NN -LRB-|-lrb-|-LRB- glucose|glucose|NN concentration|concentration|NN <|<|JJR 0.05|0.05|CD gL-1|gl-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW ,|,|, glucose|glucose|NN limitation|limitation|NN -LRB-|-lrb-|-LRB- glucose|glucose|NN concentration|concentration|NN <|<|JJR 0.05|0.05|CD gL-1|gl-1|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch|fed-batch|JJ
E.|e.|FW coli|coli|FW glutamine|glutamine|NN 1|1|CD
E.|E.|NNP coli|coli|NN glutamine|glutamine|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Glutamine|Glutamine|NNP RpoN|rpon|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP coli|coli|NN grow|grow|VB in|in|IN LB|lb|NN rich|rich|JJ medium|medium|NN to|to|TO OD600|od600|NN =|=|JJ 2.4|2.4|CD
E.coli|e.coli|NNS ,|,|, grown|grow|VBN in|in|IN LB|lb|NN +|+|CC glycerol|glycerol|NN to0|to0|NN .8|.8|CD OD|od|NN
E.coli|e.coli|NNS ,|,|, grown|grow|VBN in|in|IN LB|lb|NN +|+|CC glycerol|glycerol|NN to|to|TO 0.8|0.8|CD OD|od|NN
E.coli|e.coli|NNS ,|,|, grown|grow|VBN in|in|IN LB|lb|NN to|to|TO 0.8|0.8|CD OD|od|NN
E.coli|e.coli|NNS ,|,|, grown|grow|VBN in|in|IN LB|lb|NN to0|to0|NN .8|.8|CD OD|od|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP gyrArparCr|gyrarparcr|NN _|_|CD Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T5|t5|NN
E.|e.|FW coli|coli|FW harboring|harboring|NN pRadGro|pradgro|NN replicate|replicate|VBP 1|1|CD
E.|E.|NNP coli|coli|NN harboring|harboring|NN pRadGro|pradgro|NN replicate|replicate|VBP 2|2|CD
E.|E.|NNP coli|coli|NN harboring|harboring|NN pRadGro|pradgro|NN replicate|replicate|VBP 3|3|CD
E.|E.|NNP coli|coli|NN HB101|hb101|NN grown|grow|VBN in|in|IN Terrific|Terrific|NNP broth|broth|NN media|media|NNS for|for|IN 12|12|CD hours|hour|NNS were|be|VBD washed|wash|VBN three|three|CD times|time|NNS in|in|IN sdH2O|sdh2o|NN and|and|CC re-suspended|re-suspended|JJ in|in|IN S-Basal|s-basal|JJ complete|complete|JJ medium|medium|NN .|.|.
E.coli|e.coli|NNS _|_|VBP heat|heat|NN _|_|NN dynamic|dynamic|JJ _|_|NN 1|1|CD
E.coli|e.coli|NNS _|_|VBP heat|heat|NN _|_|NN dynamic|dynamic|JJ _|_|NN 2|2|CD
E.|E.|NNP coli|coli|NN heatshock|heatshock|NN 1|1|CD
E.|E.|NNP coli|coli|NN heatshock|heatshock|NN 2|2|CD
E.|E.|NNP coli|coli|NN heat|heat|NN shock|shock|NN gene|gene|NN expression|expression|NN data|datum|NNS using|use|VBG direct|direct|JJ labeling|labeling|NN method|method|NN -LRB-|-lrb-|-LRB- replicate-1|replicate-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW heat|heat|NN shock|shock|NN gene|gene|NN expression|expression|NN data|datum|NNS using|use|VBG direct|direct|JJ labeling|labeling|NN method|method|NN -LRB-|-lrb-|-LRB- replicate-2|replicate-2|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW heat|heat|NN shock|shock|NN gene|gene|NN expression|expression|NN data|datum|NNS using|use|VBG PAOD|paod|NN method|method|NN -LRB-|-lrb-|-LRB- replicate-1|replicate-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW heat|heat|NN shock|shock|NN gene|gene|NN expression|expression|NN data|datum|NNS using|use|VBG PAOD|paod|NN method|method|NN -LRB-|-lrb-|-LRB- replicate-2|replicate-2|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW heat|heat|NN shock|shock|NN gene|gene|NN expression|expression|NN data|datum|NNS using|use|VBG random|random|JJ priming|priming|NN method|method|NN -LRB-|-lrb-|-LRB- replicate-1|replicate-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW heat|heat|NN shock|shock|NN gene|gene|NN expression|expression|NN data|datum|NNS using|use|VBG random|random|JJ priming|priming|NN method|method|NN -LRB-|-lrb-|-LRB- replicate-2|replicate-2|NN -RRB-|-rrb-|-RRB-
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Heatshock|Heatshock|NNP RpoH|rpoh|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 3|3|CD
E.|e.|FW coli|coli|FW hhahha2|hhahha2|NN
E.|e.|FW coli|coli|FW hns|hns|FW
E.|e.|FW coli|coli|FW hns2|hns2|NN
E.|e.|FW coli|coli|FW hnshns2|hnshns2|NN
E.coli|e.coli|NN /|/|: Hsp60-wt/VAL98Ile|hsp60-wt/val98ile|NN -LRB-|-lrb-|-LRB- -|-|: /|/|: +|+|CC -RRB-|-rrb-|-RRB-
E.coli|e.coli|NN /|/|: Hsp60-wt/wt|hsp60-wt/wt|NN -LRB-|-lrb-|-LRB- -|-|: /|/|: +|+|CC -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW Hydrocortisone|hydrocortisone|NN Treatment|treatment|NN
E|e|NN coli|coli|NN ,|,|, immediately|immediately|RB after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
E.|e.|FW coli|coli|FW imp|imp|FW fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- -LSB-|-lsb-|-LRB- control|control|NN -RSB-|-rsb-|-RRB-
E.|e.|FW coli|coli|FW imp|imp|FW fabI|fabi|NN -LRB-|-lrb-|-LRB- G94V|g94v|NN -RRB-|-rrb-|-RRB- -LSB-|-lsb-|-LRB- control|control|NN -RSB-|-rsb-|-RRB-
E.|e.|FW coli|coli|FW incubated|incubate|VBN with|with|IN GST-fused|gst-fused|JJ Drosophila|drosophila|NN immune|immune|JJ proteins|protein|NNS for|for|IN 10|10|CD min|min|NN
E.|E.|NNP coli|coli|NN incubated|incubate|VBN with|with|IN GST-fused|gst-fused|JJ Drosophila|drosophila|NN immune|immune|JJ proteins|protein|NNS for|for|IN 10|10|CD min|min|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW incubated|incubate|VBN with|with|IN GST-fused|gst-fused|JJ Drosophila|drosophila|NN immune|immune|JJ proteins|protein|NNS for|for|IN 10|10|CD min|min|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW incubated|incubate|VBN with|with|IN GST-fused|gst-fused|JJ Drosophila|drosophila|NN immune|immune|JJ proteins|protein|NNS for|for|IN 10|10|CD min|min|NN ,|,|, biological|biological|JJ rep3|rep3|NN
E.|e.|FW coli|coli|FW incubated|incubate|VBN with|with|IN GST|gst|NN protein|protein|NN alone|alone|RB for|for|IN 10|10|CD min|min|NN
E.|E.|NNP coli|coli|NN incubated|incubate|VBN with|with|IN GST|gst|NN protein|protein|NN for|for|IN 10|10|CD min|min|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW incubated|incubate|VBN with|with|IN GST|gst|NN protein|protein|NN for|for|IN 10|10|CD min|min|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW incubated|incubate|VBN with|with|IN GST|gst|NN protein|protein|NN for|for|IN 10|10|CD min|min|NN ,|,|, biological|biological|JJ rep3|rep3|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T4|t4|NN
E.|E.|NNP Coli|Coli|NNP Iron|Iron|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Iron|Iron|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Iron|Iron|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Iron|Iron|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP coli|coli|NN isolate|isolate|NN G|g|NN 1/2|1/2|CD
E.|E.|NNP coli|coli|NN isolate|isolate|NN G|g|NN 3/10|3/10|CD
E.|E.|NNP coli|coli|NN isolate|isolate|NN G3/10|g3/10|NN
E.|E.|NNP coli|coli|NN isolate|isolate|NN G4/9|g4/9|NN
E.|E.|NNP coli|coli|NN isolate|isolate|NN G5|g5|NN
E.coli|e.coli|NNS _|_|VBP IVT-RNA|ivt-rna|NN _|_|CD sigma70-1|sigma70-1|NN
E.coli|e.coli|NNS _|_|VBP IVT-RNA|ivt-rna|NN _|_|CD sigma70-2|sigma70-2|NN
E.coli|e.coli|NNS _|_|VBP IVT-RNA|ivt-rna|NN _|_|CD sigmaS|sigmas|NN
E.coli|e.coli|NNS _|_|VBP IVT-RNA|ivt-rna|NN _|_|CD sigmaS-2|sigmas-2|NN
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 10|10|CD min|min|NN _|_|NN f|f|FW _|_|FW 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 10|10|CD min|min|NN _|_|NN f|f|FW _|_|FW 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 10|10|CD min|min|NN _|_|NN f|f|FW _|_|FW 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 10|10|CD min|min|NN _|_|NN m|m|NN _|_|NN 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 10|10|CD min|min|NN _|_|NN m|m|NN _|_|NN 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 10|10|CD min|min|NN _|_|NN m|m|NN _|_|NN 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 20|20|CD min|min|NN _|_|NN f|f|FW _|_|FW 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 20|20|CD min|min|NN _|_|NN f|f|FW _|_|FW 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 20|20|CD min|min|NN _|_|NN f|f|FW _|_|FW 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 20|20|CD min|min|NN _|_|NN m|m|NN _|_|NN 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 20|20|CD min|min|NN _|_|NN m|m|NN _|_|NN 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM 42C|42c|CD _|_|SYM 20|20|CD min|min|NN _|_|NN m|m|NN _|_|SYM 3|3|CD
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN mqsR|mqsr|NN mutant|mutant|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pBAD-Myc-His|bw25113/pbad-myc-his|NN C|c|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 0.5|0.5|CD %|%|NN L-arabinose|l-arabinose|JJ suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pBAD-Myc-His|bw25113/pbad-myc-his|NN C-mqsA|c-mqsa|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 0.5|0.5|CD %|%|NN L-arabinose|l-arabinose|JJ suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N|bw25113/pca24n|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN 2|2|CD mM|mm|NN IPTG|iptg|NN suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N|bw25113/pca24n|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN then|then|RB 2|2|CD mM|mm|NN IPTG|iptg|NN for|for|IN 15|15|CD min|min|NN short|short|JJ time|time|NN suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N|bw25113/pca24n|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 2|2|CD mM|mm|NN IPTG|iptg|NN biofilm|biofilm|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN 2|2|CD mM|mm|NN IPTG|iptg|NN suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN then|then|RB 2|2|CD mM|mm|NN IPTG|iptg|NN for|for|IN 15|15|CD min|min|NN short|short|JJ time|time|NN suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN in|in|IN LB|lb|NN for|for|IN 24|24|CD h|h|NN 37oC|37oc|NN with|with|IN 2|2|CD mM|mm|NN IPTG|iptg|NN biofilm|biofilm|NN cell|cell|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN wt|wt|JJ at|at|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD LB|lb|NN 37C|37c|NN suspension|suspension|NN cell|cell|NN
E.|e.|FW coli|coli|FW K12|k12|NN cells|cell|NNS ,|,|, M9|m9|NN ,|,|, 8|8|CD h|h|NN
E.|E.|NNP coli|coli|NN K12|k12|NN grown|grow|VBN in|in|IN M63|m63|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- 0.2|0.2|CD %|%|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ media|media|NNS ,|,|, sampled|sample|VBN in|in|IN exponential|exponential|JJ phase|phase|NN OD600|od600|NN =|=|JJ 0.3|0.3|CD
E.|E.|NNP coli|coli|NN K12|k12|NN grown|grow|VBN in|in|IN M63|m63|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- 0.2|0.2|CD %|%|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ media|media|NNS ,|,|, sampled|sample|VBN in|in|IN stationary|stationary|JJ phase|phase|NN OD600|od600|NN =|=|JJ 1.5|1.5|CD
E.|E.|NNP coli|coli|NN K12|k12|NN grown|grow|VBN in|in|IN minimal|minimal|JJ medium|medium|NN with|with|IN added|add|VBN 5|5|CD μM|μm|NN TPEN|tpen|NN
E.|e.|FW coli|coli|FW K12|k12|NN grown|grow|VBN in|in|IN minimal|minimal|JJ medium|medium|NN without|without|IN added|add|VBN TPEN|tpen|NN
E.|e.|FW coli|coli|FW K12|k12|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN rep1|rep1|NN
E.|e.|FW coli|coli|FW K12|k12|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN rep2|rep2|NN
E.|e.|FW coli|coli|FW K12|k12|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN rep3|rep3|NN
E.|e.|FW coli|coli|FW K12|k12|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN rep4|rep4|NN
E.|e.|FW coli|coli|FW K12|k12|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN rep5|rep5|NN
E.|e.|FW coli|coli|FW K12|k12|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN rep6|rep6|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN
E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cra-8myc|cra-8myc|NN tagged|tag|VBD strains|strain|NNS was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, fructose|fructose|NN and|and|CC acetate|acetate|NN .|.|.
E.|E.|NNP coli|coli|NN -LSB-|-lsb-|-LRB- K-12|k-12|NN MG1655|mg1655|NN strain|strain|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- was|be|VBD grown|grow|VBN overnight|overnight|RB at|at|IN 30|30|CD °C|°c|NN in|in|IN LB|lb|NN medium|medium|NN .|.|. The|the|DT resulting|result|VBG culture|culture|NN was|be|VBD diluted|dilute|VBN 500-fold|500-fold|JJ in|in|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN and|and|CC grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN for|for|IN 3.5|3.5|CD hours|hour|NNS such|such|JJ that|that|IN O.D.|O.D.|NNP at|at|IN 600|600|CD nm|nm|NN became|become|VBD 0.30-0.35|0.30-0.35|CD .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG|mg|NN 1655|1655|CD was|be|VBD grown|grow|VBN in|in|IN LB-Miller|lb-miller|NN broth|broth|NN at|at|IN 37|37|CD °C|°c|NN ,160|,160|CD rpm|rpm|NN to|to|TO an|a|DT O.D.|o.d.|NN 600|600|CD nm|nm|NN of|of|IN 0|0|CD .|.|. 7|7|CD
E.|E.|NNP coli|coli|NN K12|k12|NN MG1655|mg1655|NN was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- O.D.|o.d.|NN 600nm|600nm|CD 0.5|0.5|CD -RRB-|-rrb-|-RRB- or|or|CC to|to|TO stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- O.D.|o.d.|NN 600nm|600nm|CD 1.5|1.5|CD -RRB-|-rrb-|-RRB- aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN or|or|CC W2|w2|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN and|and|CC 0.2|0.2|CD %|%|NN glutamine|glutamine|NN .|.|. For|for|IN heatshock|heatshock|NN conditions|condition|NNS ,|,|, cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN and|and|CC incubated|incubate|VBN at|at|IN 42oC|42oc|NN for|for|IN 10|10|CD min|min|NN .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN WT|wt|NN and|and|CC Fur-8-myc|fur-8-myc|NN tagged|tag|VBD strains|strain|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN .|.|. For|for|IN iron|iron|NN treated|treat|VBN cells|cell|NNS ,|,|, 0.1|0.1|CD mM|mm|NN of|of|IN FeCl2|fecl2|NN were|be|VBD treated|treat|VBN from|from|IN the|the|DT beginning|beginning|NN of|of|IN culture|culture|NN ,|,|, and|and|CC for|for|IN DPD|dpd|NN treated|treat|VBN cells|cell|NNS ,|,|, 0.2|0.2|CD mM|mm|NN of|of|IN DPD|dpd|NN were|be|VBD added|add|VBN at|at|IN early-log|early-log|JJ phase|phase|NN and|and|CC continued|continue|VBD to|to|TO culture|culture|NN for|for|IN additional|additional|JJ 2h|2h|NN .|.|. For|for|IN the|the|DT rifampicin-treated|rifampicin-treated|JJ cultures|culture|NNS ,|,|, the|the|DT rifampicin|rifampicin|NN dissolved|dissolve|VBN in|in|IN methanol|methanol|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 150|150|CD mg/mL|mg/ml|NN at|at|IN mid-log|mid-log|JJ phase|phase|NN and|and|CC stirred|stir|VBD for|for|IN 20|20|CD min|min|NN .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN WT|WT|NNP ,|,|, and|and|CC Δcra|Δcra|NNP were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, fructose|fructose|NN and|and|CC acetate|acetate|NN .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN WT|wt|NN and|and|CC Δfur|δfur|NN were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN .|.|. For|for|IN iron|iron|NN treated|treat|VBN cells|cell|NNS ,|,|, 0.1|0.1|CD mM|mm|NN of|of|IN FeCl2|fecl2|NN were|be|VBD treated|treat|VBN from|from|IN the|the|DT beginning|beginning|NN of|of|IN culture|culture|NN ,|,|, and|and|CC for|for|IN DPD|dpd|NN treated|treat|VBN cells|cell|NNS ,|,|, 0.2|0.2|CD mM|mm|NN of|of|IN DPD|dpd|NN were|be|VBD added|add|VBN at|at|IN early-log|early-log|JJ phase|phase|NN and|and|CC continued|continue|VBD to|to|TO culture|culture|NN for|for|IN additional|additional|JJ 2h|2h|NN .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN WT|wt|NN and|and|CC ΔompR|δompr|NN were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN .|.|. Then|then|RB cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN 0.3|0.3|CD M|m|NN of|of|IN NaCl|nacl|NN at|at|IN mid-log|mid-log|JJ pahse|pahse|NN for|for|IN 30|30|CD min|min|NN with|with|IN agitation|agitation|NN .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN WT|WT|NNP ,|,|, GadE-8-myc|gade-8-myc|NN ,|,|, GadW-8-myc|gadw-8-myc|NN ,|,|, and|and|CC GadX-8-myc|gadx-8-myc|NN tagged|tag|VBD strains|strain|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.3|0.3|CD -RRB-|-rrb-|-RRB- aerobically|aerobically|RB -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN at|at|IN pH|ph|NN 5.5|5.5|CD .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN WT|wt|NN ,|,|, gadE|gade|NN ,|,|, gadW|gadw|NN and|and|CC gadX|gadx|NN mutant|mutant|JJ cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.3|0.3|CD -RRB-|-rrb-|-RRB- aerobically|aerobically|RB -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN at|at|IN pH|ph|NN 5.5|5.5|CD .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN WT|wt|NN ,|,|, ΔoxyR|δoxyr|NN ,|,|, ΔsoxR|δsoxr|NN ,|,|, and|and|CC ΔsoxS|δsoxs|NN were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN aerobically|aerobically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN .|.|. Then|then|RB cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN 250|250|CD uM|um|NN of|of|IN paraquat|paraquat|NN at|at|IN mid-log|mid-log|JJ pahse|pahse|NN for|for|IN 20|20|CD min|min|NN with|with|IN agitation|agitation|NN .|.|.
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM pBAD|pbad|FW _|_|FW 30C|30c|FW _|_|FW f|f|FW _|_|SYM 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM pBad|pbad|FW _|_|FW 30C|30c|FW _|_|FW f|f|FW _|_|SYM 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM pBAD|pbad|FW _|_|FW 30C|30c|FW _|_|FW f|f|FW _|_|SYM 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|SYM pBAD|pbad|FW _|_|FW 30C|30c|FW _|_|FW f|f|FW _|_|SYM 4|4|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBAD|pbad|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBAD|pbad|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBAD|pbad|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBAD|pbad|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 4|4|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32I54N|pbadsigma32i54n|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32I54N|pbadsigma32i54n|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32I54N|pbadsigma32i54n|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32I54N|pbadsigma32i54n|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32wt|pbadsigma32wt|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32wt|pbadsigma32wt|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32wt|pbadsigma32wt|NN _|_|SYM 30C|30c|FW _|_|FW f|f|FW _|_|SYM 3|3|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32wt|pbadsigma32wt|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 1|1|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32wt|pbadsigma32wt|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|NN 2|2|CD
ecoli|ecolus|NNS _|_|VBP k12|k12|NN _|_|CD pBADsigma32wt|pbadsigma32wt|NN _|_|SYM 30C|30c|CD _|_|NN m|m|NN _|_|SYM 3|3|CD
E.|e.|FW coli|coli|FW K-12|k-12|NN strain|strain|NN BW25113|bw25113|NN was|be|VBD evolved|evolve|VBN in|in|IN chemostats|chemostat|NNS .|.|. The|the|DT cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS -LRB-|-lrb-|-LRB- 5|5|CD g/L|g/l|NN glucose|glucose|NN -RRB-|-rrb-|-RRB- with|with|IN increasing|increase|VBG concentrations|concentration|NNS of|of|IN n-butanol|n-butanol|NN .|.|.
E.|E.|NNP coli|coli|NN K12|k12|NN strain|strain|NN JM109|jm109|NN
E.|e.|FW coli|coli|FW K12|k12|NN substrain|substrain|NN W3110|w3110|NN was|be|VBD used|use|VBN in|in|IN this|this|DT study|study|NN .|.|. Bioreactor|Bioreactor|NNP cultivations|cultivation|NNS were|be|VBD performed|perform|VBN using|use|VBG a|a|DT two-compartment|two-compartment|JJ bioreactor|bioreactor|NN system|system|NN consisting|consist|VBG of|of|IN an|a|DT STR|str|NN -LRB-|-lrb-|-LRB- 3L|3l|NN -RRB-|-rrb-|-RRB- with|with|IN a|a|DT recycle|recycle|VB loop|loop|NN -LRB-|-lrb-|-LRB- PFR|pfr|NN -RRB-|-rrb-|-RRB- in|in|IN defined|define|VBN medium|medium|NN at|at|IN pH7|ph7|NN and|and|CC 37|37|CD °C|°c|NN .|.|. Bioreactor|Bioreactor|NNP cultivations|cultivation|NNS were|be|VBD carried|carry|VBN out|out|RP with|with|IN a|a|DT minimal|minimal|JJ medium|medium|NN containing|contain|VBG -LRB-|-lrb-|-LRB- per|per|IN liter|liter|NN -RRB-|-rrb-|-RRB- 19.0|19.0|CD g|g|NN glucose|glucose|NN ,|,|, 1.0|1.0|CD g|g|NN NaH2PO4|nah2po4|NN .|.|. ·|·|NN 2|2|CD H2O|h2o|NN ,|,|, 2.6|2.6|CD g|g|NN K2HPO4|k2hpo4|NN ,|,|, 3.8|3.8|CD g|g|NN -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2SO4|2so4|NN ,|,|, and|and|CC a|a|DT trace|trace|NN element|element|NN solution|solution|NN -LRB-|-lrb-|-LRB- 0.11|0.11|CD g|g|NN Na3C6H5O7|na3c6h5o7|NN ,|,|, 0.00835|0.00835|CD g|g|NN FeCl3|fecl3|NN ·|·|NN 6|6|CD H2O|h2o|NN ,|,|, 0.00009|0.00009|CD g|g|NN ZnSO4|znso4|NN ·|·|NN 7|7|CD H2O|h2o|NN ,|,|, 0.00005|0.00005|CD g|g|NN MnSO4|mnso4|NN ·|·|NN H2O|h2o|NN ,|,|, 0.0008|0.0008|CD g|g|NN CuSO4|cuso4|NN ·|·|NN 5|5|CD H2O|h2o|NN ,|,|, 0.00009|0.00009|CD g|g|NN CoCl2|cocl2|NN ·|·|NN 6|6|CD H2O|h2o|NN ,|,|, 0.0044|0.0044|CD g|g|NN CaCl2|cacl2|NN ·|·|NN 2|2|CD H2O|h2o|NN ,|,|, 0.1|0.1|CD g|g|NN MgSO4|mgso4|NN ·|·|NN 7|7|CD H2O|h2o|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT STR-PFR|str-pfr|NN was|be|VBD operated|operate|VBN as|as|IN a|a|DT chemostat|chemostat|NN with|with|IN ammonia|ammonia|NN as|as|IN the|the|DT growth-limiting|growth-limiting|JJ substrate|substrate|NN .|.|. First|first|RB ,|,|, a|a|DT reference|reference|NN steady|steady|JJ state|state|NN -LRB-|-lrb-|-LRB- µ|µ|NN =|=|JJ 0.2|0.2|CD h|h|NN −|−|NN 1|1|CD -RRB-|-rrb-|-RRB- was|be|VBD established|establish|VBN in|in|IN the|the|DT STR|str|NN and|and|CC sampled|sample|VBD three|three|CD times|time|NNS during|during|IN a|a|DT 16|16|CD h|h|NN period|period|NN following|follow|VBG establishment|establishment|NN of|of|IN the|the|DT steady|steady|JJ state|state|NN .|.|. Then|then|RB ,|,|, the|the|DT PFR|pfr|NN was|be|VBD added|add|VBN and|and|CC samples|sample|NNS for|for|IN RNA-sequencing|rna-sequencing|NN were|be|VBD aquired|aquire|VBN .|.|.
E.|E.|NNP coli|coli|NN K-12|k-12|NN untreated|untreated|JJ -LRB-|-lrb-|-LRB- reference|reference|NN sample|sample|NN -RRB-|-rrb-|-RRB- _|_|SYM rep|rep|NN #|#|# 1|1|CD
E.|E.|NNP coli|coli|NN K-12|k-12|NN untreated|untreated|JJ -LRB-|-lrb-|-LRB- reference|reference|NN sample|sample|NN -RRB-|-rrb-|-RRB- _|_|SYM rep|rep|NN #|#|# 2|2|CD
E.|E.|NNP coli|coli|NN K-12|k-12|NN untreated|untreated|JJ -LRB-|-lrb-|-LRB- reference|reference|NN sample|sample|NN -RRB-|-rrb-|-RRB- _|_|SYM rep|rep|NN #|#|# 3|3|CD
E.|e.|FW coli|coli|FW K-12|k-12|NN W3110|w3110|NN #|#|# 1|1|CD
E.|e.|FW coli|coli|FW K-12|k-12|NN W3110|w3110|NN #|#|# 2|2|CD
E.|e.|FW coli|coli|FW K-12|k-12|NN W3110|w3110|NN #|#|# 3|3|CD
E.|e.|FW coli|coli|FW K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 110|110|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 170|170|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 230|230|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 30|30|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 350|350|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, 50|50|CD min|min|NN after|after|IN depletion|depletion|NN of|of|IN extracellular|extracellular|JJ acetate|acetate|NN
E.|E.|NNP coli|coli|NN K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN ,|,|, acetate|acetate|NN concentration|concentration|NN ≤|≤|CD 0.35|0.35|CD gL-1|gl-1|NN
E.|e.|FW coli|coli|FW K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, glucose|glucose|NN limitation|limitation|NN -LRB-|-lrb-|-LRB- glucose|glucose|NN concentration|concentration|NN <|<|JJR 0.05|0.05|CD gL-1|gl-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, unlimited|unlimited|JJ growth|growth|NN -LRB-|-lrb-|-LRB- batch|batch|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW K12|k12|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB- ,|,|, fed-batch/linear|fed-batch/linear|JJ feed|feed|NN ,|,|, unlimited|unlimited|JJ growth|growth|NN -LRB-|-lrb-|-LRB- batch|batch|NN -RRB-|-rrb-|-RRB-
E.coli|e.coli|NN K12|k12|NN was|be|VBD cultured|culture|VBN in|in|IN LB|lb|NN and|and|CC grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN
E.|e.|FW coli|coli|FW K-12|k-12|NN was|be|VBD incubated|incubate|VBN in|in|IN 5|5|CD ml|ml|NN LB|lb|NN liquid|liquid|NN for|for|IN 16|16|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN constant|constant|JJ shaking|shake|VBG ,|,|, and|and|CC then|then|RB 100|100|CD µl|µl|NN of|of|IN each|each|DT myxotoxin|myxotoxin|NN dissolved|dissolve|VBN in|in|IN acetonitrile|acetonitrile|NN was|be|VBD added|add|VBN to|to|TO each|each|DT culture|culture|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.2|0.2|CD ,|,|, and|and|CC 2|2|CD ppm|ppm|NN .|.|. Additional|additional|JJ incubation|incubation|NN was|be|VBD performed|perform|VBN for|for|IN 2|2|CD h.|h.|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 0|0|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 120|120|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 30|30|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 60|60|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 90|90|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 0|0|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 120|120|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 30|30|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 60|60|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN K12|k12|NN with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 90|90|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD WT|WT|NNP _|_|NNP M9|M9|NNP _|_|SYM rep1|rep1|CD
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD WT|WT|NNP _|_|NNP M9|M9|NNP _|_|SYM rep2|rep2|CD
E.|E.|NNP coli|coli|NN K12|k12|NN ybjN|ybjn|NN mutant|mutant|JJ cells|cell|NNS ,|,|, M9|m9|NN ,|,|, 8|8|CD h|h|NN
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD ybjN|ybjn|NN _|_|CD MUTANT|mutant|JJ _|_|NN M9|m9|NN _|_|CD rep1|rep1|NN
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD ybjN|ybjn|NN _|_|CD MUTANT|mutant|JJ _|_|NN M9|m9|NN _|_|CD rep2|rep2|NN
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD ybjN|ybjn|NN _|_|CD MUTANT|mutant|JJ _|_|NN M9|m9|NN _|_|CD rep3|rep3|NN
E.|E.|NNP coli|coli|NN K12|k12|NN ybjN|ybjn|NN over-expression|over-expression|NN cells|cell|NNS ,|,|, M9|m9|NN ,|,|, 8|8|CD h|h|NN
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD ybjN|ybjn|NN _|_|NN OVER-EXPRESSION|over-expression|NN _|_|CD M9|m9|NN _|_|CD rep1|rep1|NN
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD ybjN|ybjn|NN _|_|NN OVER-EXPRESSION|over-expression|NN _|_|CD M9|m9|NN _|_|CD rep2|rep2|NN
E.|E.|NNP coli|coli|NN K12|k12|NN _|_|CD ybjN|ybjn|NN _|_|NN OVER-EXPRESSION|over-expression|NN _|_|CD M9|m9|NN _|_|CD rep3|rep3|NN
Ecoli|Ecoli|NNP _|_|NNP Kanamycin|Kanamycin|NNP treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Kanamycin|kanamycin|NN treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Kanamycin|kanamycin|NN treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Kanamycin|kanamycin|NN treatment|treatment|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Kanamycin|kanamycin|NN treatment|treatment|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Kanamycin|kanamycin|NN treatment|treatment|NN T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample3|sample3|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample3|sample3|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW arcA|arca|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecoli|JJ ko-arcA|ko-arca|NN grown|grow|VBN in|in|IN MOPS|MOPS|NNP
Ecoli|Ecoli|NNP ko-arcA|ko-arcA|NNP grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN fur|fur|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecoli|JJ ko-fur|ko-fur|JJ grown|grow|VBN in|in|IN MOPS|MOPS|NNP
Ecoli|Ecoli|NNP ko-fur|ko-fur|JJ grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP ko-furgrown|ko-furgrown|NN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample3|sample3|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample3|sample3|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ihfA|ihfa|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecoli|JJ ko-ihfA|ko-ihfa|NN grown|grow|VBN in|in|IN MOPS|MOPS|NNP
Ecoli|Ecoli|NNP ko-ihfA|ko-ihfA|NNP grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample3|sample3|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample3|sample3|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW phoB|phob|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecoli|JJ ko-phoB|ko-phob|NN grown|grow|VBN in|in|IN MOPS|MOPS|NNP
Ecoli|Ecoli|NNP ko-phoB|ko-phob|NN grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ubiE|ubie|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep1|techrep1|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ubiE|ubie|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|Ecoli|NNP _|_|SYM ko|ko|FW _|_|FW ubiE|ubie|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP ko|ko|NN _|_|NN ubiE|ubie|NN _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecoli|JJ ko-ubiE|ko-ubie|NN grown|grow|VBN in|in|IN MOPS|MOPS|NNP
Ecoli|Ecoli|NNP ko-ubiE|ko-ubiE|NNP grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP _|_|NNP Late|Late|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T1|t1|NN
Ecoli|Ecoli|NNP _|_|NNP Late|Late|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T2|t2|NN
Ecoli|Ecoli|NNP _|_|NNP Late|Late|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T3|t3|NN
Ecoli|Ecoli|NNP _|_|NNP Late|Late|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T4|t4|NN
Ecoli|Ecoli|NNP _|_|NNP Late|Late|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T5|T5|NNP
Ecoli|Ecoli|NNP _|_|NNP Late|Late|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T6|T6|NNP
Ecoli|Ecoli|NNP _|_|NNP Late|Late|NNP Recovery|Recovery|NNP in|in|IN LB|LB|NNP T7|T7|NNP
Ecoli|Ecoli|NNP _|_|NNP LB|LB|NNP growth|growth|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T10|t10|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T11|t11|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T7|t7|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T8|t8|NN
Ecoli|ecolus|NNS _|_|VBP LB|lb|NN growth|growth|NN T9|t9|NN
E.coli|e.coli|NNS _|_|VBP LB|lb|NN _|_|CD rep2|rep2|NN
E.coli|e.coli|NNS _|_|VBP LB|lb|NN _|_|CD rep3|rep3|NN
E.coli|e.coli|NNS _|_|VBP log|log|NN _|_|NN dynamic|dynamic|JJ _|_|NN 1|1|CD
E.coli|e.coli|NNS _|_|VBP log|log|NN _|_|NN dynamic|dynamic|JJ _|_|NN 2|2|CD
E.coli|e.coli|NNS _|_|VBP log|log|NN _|_|NN dynamic|dynamic|JJ _|_|NN 3|3|CD
E.coli|e.coli|NNS _|_|VBP log|log|NN _|_|SYM rif|rif|FW _|_|FW 1|1|CD
E.coli|e.coli|NNS _|_|VBP log|log|NN _|_|CD rif|rif|NN _|_|NN 2|2|CD
E.coli|e.coli|NNS _|_|VBP log|log|NN _|_|SYM rif|rif|FW _|_|FW 3|3|CD
E.|E.|NNP Coli|Coli|NNP Lrp|Lrp|NNP ChIP|chip|NN DNA|dna|NN Leucine|leucine|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Lrp|Lrp|NNP ChIP|ChIP|NNP DNA|DNA|NNP Leucine|leucine|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Lrp|Lrp|NNP ChIP|chip|NN DNA|dna|NN Leucine|leucine|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Lrp|Lrp|NNP ChIP|ChIP|NNP DNA|DNA|NNP NH4Cl|nh4cl|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Lrp|Lrp|NNP ChIP|ChIP|NNP DNA|DNA|NNP NH4Cl|nh4cl|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Lrp|Lrp|NNP ChIP|ChIP|NNP DNA|DNA|NNP NH4Cl|nh4cl|NN 3|3|CD
E.|e.|FW coli|coli|FW MC4100|mc4100|NN strain|strain|NN was|be|VBD cultured|culture|VBN at|at|IN 37|37|CD °C|°c|NN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.4|0.4|CD -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN media|media|NNS
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN NaCl|nacl|NN 0.20|0.20|CD M|m|NN
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.20|0.20|CD M|m|NN
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN NaCl|nacl|NN 0.20|0.20|CD M|m|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.20|0.20|CD M|m|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.20|0.20|CD M|m|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.45|0.45|CD M|m|NN
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.45|0.45|CD M|m|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.45|0.45|CD M|m|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.45|0.45|CD M|m|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.55|0.55|CD M|m|NN
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.55|0.55|CD M|m|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.55|0.55|CD M|m|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, osmotic|osmotic|JJ pressure|pressure|NN ,|,|, NaCl|nacl|NN 0.55|0.55|CD M|m|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, regular|regular|JJ
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, regular|regular|JJ ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, regular|regular|JJ ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, regular|regular|JJ ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 100|100|CD ng/ml|ng/ml|NN
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 100|100|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 100|100|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 100|100|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 150|150|CD ng/ml|ng/ml|NN
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 150|150|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 150|150|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|shx|NN 150|150|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|SHX|NNP 50|50|CD ng/ml|ng/ml|NN
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|SHX|NNP 50|50|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|SHX|NNP 50|50|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, starvation|starvation|NN ,|,|, SHX|SHX|NNP 50|50|CD ng/ml|ng/ml|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 40.0|40.0|CD deg|deg|NN C|c|NN
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 40.0|40.0|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 40.0|40.0|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 40.0|40.0|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.5|41.5|CD deg|deg|NN C|c|NN
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.5|41.5|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.5|41.5|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.5|41.5|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.8|41.8|CD deg|deg|NN C|c|NN
E.|e.|FW coli|coli|FW MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.8|41.8|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.8|41.8|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN MDS42|mds42|NN ,|,|, temperature|temperature|NN change|change|NN ,|,|, 41.8|41.8|CD deg|deg|NN C|c|NN ,|,|, rep|rep|NN 3|3|CD
E.coli|e.coli|NNS MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 0|0|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 120|120|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 30|30|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 60|60|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 90|90|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 0|0|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 120|120|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 30|30|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 60|60|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN MG1063|mg1063|NN -LRB-|-lrb-|-LRB- recA56|reca56|NN =|=|JJ recA|reca|NN -|-|: -RRB-|-rrb-|-RRB- with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 90|90|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 10|10|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 10|10|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 10|10|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 10|10|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC thymine|thymine|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 10|10|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN LB|LB|NNP media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 10|10|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 120|120|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 120|120|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 120|120|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 120|120|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC thymine|thymine|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 120|120|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN LB|LB|NNP media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 120|120|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 30|30|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 30|30|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 30|30|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 30|30|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC thymine|thymine|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 30|30|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN LB|LB|NNP media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 30|30|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 60|60|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 60|60|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 60|60|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 60|60|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC thymine|thymine|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 60|60|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN LB|LB|NNP media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 60|60|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 90|90|CD min|min|NN after|after|IN TMP|tmp|NN +|+|CC adenine|adenine|NN +|+|CC glycine|glycine|NN +|+|CC methionine|methionine|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN 90|90|CD min|min|NN after|after|IN TMP|tmp|NN treatment|treatment|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ,|,|, BCM|BCM|NNP treated-Replicate1|treated-replicate1|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN ,|,|, BCM|BCM|NNP treated-Replicate2|treated-replicate2|NN
E.|E.|NNP coli|coli|NN MG1655-C8-1|mg1655-c8-1|NN
E.|e.|FW coli|coli|FW MG1655-C8-3|mg1655-c8-3|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN Cold|Cold|NNP Shock|shock|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN Cold|Cold|NNP Shock|shock|NN was|be|VBD grown|grow|VBN at|at|IN 15|15|CD °C|°c|NN for|for|IN 4|4|CD hour|hour|NN then|then|RB grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN LB|LB|NNP media|media|NNS .|.|.
E.|E.|NNP coli|coli|NN MG1655-control-1|mg1655-control-1|NN
E.|e.|FW coli|coli|FW MG1655-control-2|mg1655-control-2|NN
E.|e.|FW coli|coli|FW MG1655-control-3|mg1655-control-3|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN genomic|genomic|JJ DNA|dna|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN Heat|heat|NN Shock|shock|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN Heat|heat|NN Shock|shock|NN was|be|VBD grown|grow|VBN at|at|IN 50|50|CD °C|°c|NN for|for|IN 4|4|CD hour|hour|NN then|then|RB grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN LB|LB|NNP media|media|NNS .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN Low|low|JJ pH|ph|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN Low|low|JJ pH|ph|NN was|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 1|1|CD hour|hour|NN in|in|IN LB|LB|NNP media|media|NNS with|with|IN pH4|ph4|NN .5|.5|CD then|then|RB grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN LB|LB|NNP media|media|NNS .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN ,|,|, M9|m9|NN media|media|NNS with|with|IN 4|4|CD g/L|g/l|NN glucose|glucose|NN ,|,|, aerobic|aerobic|JJ ,|,|, log|log|NN phase|phase|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN ,|,|, M9|m9|NN media|media|NNS with|with|IN 4|4|CD g/L|g/l|NN glucose|glucose|NN ,|,|, anaerobic|anaerobic|JJ ,|,|, log|log|NN phase|phase|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN mid-log|mid-log|JJ phase|phase|NN in|in|IN LB|LB|NNP media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN mid-log|mid-log|JJ phase|phase|NN in|in|IN M9|m9|NN media|media|NNS
E.|e.|FW coli|coli|FW MG1655|mg1655|NN minimal|minimal|JJ C|c|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN minimal|minimal|JJ C&N|c&n|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN minimal|minimal|JJ C&N|C&N|NNP Source|Source|NNP was|be|VBD grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO quater|quater|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN minimal|minimal|JJ C|c|NN and|and|CC N|n|NN source|source|NN MOPS|mop|NNS media|media|NNS -LRB-|-lrb-|-LRB- C-N|c-n|NN -|-|: MOPS|mop|NNS -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN minimal|minimal|JJ C|c|NN Source|source|NN was|be|VBD grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN minimal|minimal|JJ C|c|NN source|source|NN MOPS|mop|NNS media|media|NNS -LRB-|-lrb-|-LRB- C|c|NN -|-|: MOPS|mop|NNS -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN minimal|minimal|JJ N|n|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN minimal|minimal|JJ N|n|NN Source|source|NN was|be|VBD grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN minimal|minimal|JJ N|n|NN source|source|NN MOPS|mop|NNS media|media|NNS -LRB-|-lrb-|-LRB- N|n|NN -|-|: MOPS|mop|NNS -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN MG1655-MOPS|mg1655-mops|NN +2|+2|CD %|%|NN Dextrose|dextrose|NN
E.|e.|FW coli|coli|FW MG1655-MOPS|mg1655-mops|NN +2|+2|CD %|%|NN Dextrose|dextrose|NN +10|+10|CD mM|mm|NN C8|c8|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN Osmotic|osmotic|JJ stress|stress|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN Osmotic|osmotic|JJ Stress|stress|NN was|be|VBD grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN 45|45|CD ml|ml|NN MOPS|mop|NNS media|media|NNS with|with|IN 6|6|CD ml|ml|NN 4M|4m|NN Sodium|sodium|NN Chloride|chloride|NN .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN Oxidative|oxidative|JJ stress|stress|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN Oxidative|oxidative|JJ Stress|stress|NN was|be|VBD grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN 49|49|CD ml|ml|NN MOPS|mop|NNS media|media|NNS with|with|IN 400μl|400μl|NN 7|7|CD %|%|NN Hydrogen|hydrogen|NN peroxide|peroxide|NN .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN parC|parc|NN :|:|: :|:|: flag|flag|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN parE|pare|NN :|:|: :|:|: flag|flag|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN /|/|: pCA24N|pca24n|NN ,|,|, -|-|: gfp|gfp|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN PhoB|phob|NN knock-out|knock-out|JJ strain|strain|NN grows|grow|VBZ under|under|IN phosphate|phosphate|NN starvation|starvation|NN condition|condition|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN /|/|: pORF1|porf1|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ∆|∆|CD Rac|rac|NN G324D|g324d|NN ,|,|, treated-Replicate1-mutant|treated-replicate1-mutant|JJ
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ∆|∆|CD Rac|rac|NN G324D|g324d|NN ,|,|, treated-Replicate2-mutant|treated-replicate2-mutant|JJ
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ∆|∆|CD Rac|rac|NN N340S|n340s|NN ,|,|, treated-Replicate1-mutant|treated-replicate1-mutant|JJ
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ∆|∆|CD Rac|rac|NN N340S|n340s|NN ,|,|, treated-Replicate2-mutant|treated-replicate2-mutant|JJ
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ∆|∆|CD Rac|rac|NN WT|WT|NNP ,|,|, control-Replicate1-Wildtype|control-replicate1-wildtype|JJ
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ∆|∆|CD Rac|rac|NN WT|WT|NNP ,|,|, control-Replicate2-Wildtype|control-replicate2-wildtype|JJ
E.|e.|FW coli|coli|FW MG1655|mg1655|NN RNA|rna|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN Standard|standard|JJ
E.|e.|FW coli|coli|FW MG1655|mg1655|NN Standard|Standard|NNP was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- O.D.|o.d.|NN 600nm|600nm|CD 0.6|0.6|CD ~|~|NN 0.8|0.8|CD -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN in|in|IN LB|LB|NNP media|media|NNS .|.|.
E.|E.|NNP coli|coli|NN MG1655star|mg1655star|NN ,|,|, A600|a600|NN =|=|JJ 0.2|0.2|CD on|on|IN mucus|mucus|NN
E.|E.|NNP coli|coli|NN MG1655star|mg1655star|NN ,|,|, A600|a600|NN =|=|JJ 0.4|0.4|CD on|on|IN glucose|glucose|NN
E.|e.|FW coli|coli|FW MG1655star|mg1655star|NN ,|,|, A600|a600|NN =|=|JJ 0.4|0.4|CD on|on|IN mannose|mannose|NN
E.|e.|FW coli|coli|FW MG1655star|mg1655star|NN ,|,|, A600|a600|NN =|=|JJ 0.5|0.5|CD on|on|IN mucus|mucus|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN strain|strain|NN was|be|VBD cultured|culture|VBN in|in|IN M9|m9|NN complete|complete|JJ medium|medium|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN constant|constant|JJ agitation|agitation|NN and|and|CC harvested|harvest|VBN at|at|IN mid-exponential|mid-exponential|JJ phase|phase|NN .|.|. -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN ~|~|NN 0.6|0.6|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW MG1655|mg1655|NN strain|strain|NN was|be|VBD cultured|culture|VBN in|in|IN M9|m9|NN complete|complete|JJ medium|medium|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN constant|constant|JJ agitation|agitation|NN and|and|CC harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN .|.|. -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN ~|~|NN 1.5|1.5|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW MG1655|mg1655|NN strain|strain|NN was|be|VBD cultured|culture|VBN in|in|IN M9|m9|NN complete|complete|JJ medium|medium|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN constant|constant|JJ agitation|agitation|NN .|.|. For|for|IN heat-shock|heat-shock|NN ,|,|, culture|culture|NN was|be|VBD mix|mix|NN with|with|IN pre-warmed|pre-warmed|JJ medium|medium|NN -LRB-|-lrb-|-LRB- 50|50|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN at|at|IN 45|45|CD °C|°c|NN for|for|IN 10|10|CD min|min|NN .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN strain|strain|NN was|be|VBD cultured|culture|VBN in|in|IN W2|w2|NN minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- for|for|IN nitrogen-limiting|nitrogen-limiting|JJ condition|condition|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN with|with|IN constant|constant|JJ agitation|agitation|NN and|and|CC harvested|harvest|VBN at|at|IN mid-exponential|mid-exponential|JJ phase|phase|NN .|.|. -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN ~|~|NN 0.6|0.6|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Powell|Powell|NNP ,|,|, B.|B.|NNP S.|S.|NNP et|et|FW al.|al.|FW .|.|. J|j|NN of|of|IN Biol|Biol|NNP .|.|. Chem|Chem|NNP .270|.270|CD -LRB-|-lrb-|-LRB- 9|9|CD -RRB-|-rrb-|-RRB- :|:|: 4822|4822|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW MG1655|mg1655|NN /|/|: Svi3-3|svi3-3|NN comp|comp|NN .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN thyA|thya|NN -|-|: cells|cell|NNS grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN and|and|CC 20|20|CD ug/ml|ug/ml|JJ thymine|thymine|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN UV|uv|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN UV|uv|NN was|be|VBD exposed|expose|VBN to|to|TO UV|uv|NN light|light|NN for|for|IN 15|15|CD minutes|minute|NNS then|then|RB grown|grow|VBN untill|untill|JJ reach|reach|NN to|to|TO half|half|NN of|of|IN O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN Standard|Standard|NNP sample|sample|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN LB|LB|NNP media|media|NNS .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN ,|,|, Vector|Vector|NNP control-Replicate1|control-replicate1|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN ,|,|, Vector|Vector|NNP control-Replicate2|control-replicate2|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN was|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP +|+|CC 2|2|CD %|%|NN Dextrose|dextrose|NN minimal|minimal|JJ media|media|NNS +|+|CC -|-|: 10|10|CD mM|mm|NN octanoic|octanoic|JJ acid|acid|NN -LRB-|-lrb-|-LRB- pH|ph|NN =|=|JJ 7.0|7.0|CD -RRB-|-rrb-|-RRB- from|from|IN OD550|od550|NN 0.05|0.05|CD to|to|TO ~|~|CD 0.8|0.8|CD and|and|CC harvested|harvest|VBN at|at|IN Midlog|Midlog|NNP .|.|.
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN wildtype|wildtype|JJ strain|strain|NN grows|grow|VBZ under|under|IN phosphate|phosphate|NN starvation|starvation|NN condition|condition|NN
E.|E.|NNP coli|coli|NN MG1655|mg1655|NN ,|,|, WT|WT|NNP Rho|rho|NN treated-Replicate1|treated-replicate1|NN
E.|e.|FW coli|coli|FW MG1655|mg1655|NN ,|,|, WT|WT|NNP Rho|rho|NN treated-Replicate2|treated-replicate2|NN
E.|e.|FW coli|coli|FW MG1693|mg1693|NN
E.coli|e.coli|NNS _|_|VBP Na10|na10|NN _|_|CD rep1|rep1|NN
E.coli|e.coli|NNS _|_|VBP Na10|na10|NN _|_|CD rep2|rep2|NN
E.coli|e.coli|NNS _|_|VBP Na10|na10|NN _|_|CD rep3|rep3|NN
E.coli|e.coli|NNS _|_|VBP Na20|na20|NN _|_|CD rep1|rep1|NN
E.coli|e.coli|NNS _|_|VBP Na20|na20|NN _|_|CD rep2|rep2|NN
E.coli|e.coli|NNS _|_|VBP Na20|na20|NN _|_|CD rep3|rep3|NN
E.coli|e.coli|NNS _|_|VBP Na45|na45|NN _|_|CD rep1|rep1|NN
E.coli|e.coli|NNS _|_|VBP Na45|na45|NN _|_|CD rep2|rep2|NN
E.coli|e.coli|NNS _|_|VBP Na45|na45|NN _|_|CD rep3|rep3|NN
E.|e.|FW coli|coli|FW NaCl|nacl|NN hyperosmotic|hyperosmotic|JJ treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 1|1|LS -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW NaCl|nacl|NN hyperosmotic|hyperosmotic|JJ treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 2|2|LS -RRB-|-rrb-|-RRB-
ecoli|ecolus|NNS NC|NC|NNP _|_|SYM 000913.2|000913.2|CD
E|e|NN _|_|CD coli|coli|NN _|_|NN negativ|negativ|NN _|_|NN control|control|NN _|_|CD left|leave|VBD _|_|RB chamber|chamber|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN negativ|negativ|NN _|_|NN control|control|NN _|_|CD left|leave|VBD _|_|RB chamber|chamber|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN negativ|negativ|NN _|_|NN control|control|NN _|_|CD left|leave|VBD _|_|RB chamber|chamber|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN negativ|negativ|NN _|_|NN control|control|NN _|_|RB right|right|JJ _|_|NN chamber|chamber|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN negativ|negativ|NN _|_|NN control|control|NN _|_|RB right|right|JJ _|_|NN chamber|chamber|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN negativ|negativ|NN _|_|NN control|control|NN _|_|RB right|right|JJ _|_|NN chamber|chamber|NN _|_|CD rep3|rep3|NN
E.coli|e.coli|NNS _|_|VBP nitrogen|nitrogen|NN _|_|NN dynamic|dynamic|JJ _|_|NN 1|1|CD
E.coli|e.coli|NNS _|_|VBP nitrogen|nitrogen|NN _|_|NN dynamic|dynamic|JJ _|_|NN 2|2|CD
Ecoli|Ecoli|NNP _|_|NNP Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Novobiocin|novobiocin|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- 200|200|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB-
Ecoli|ecolus|NNS _|_|VBP Novobiocin|novobiocin|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- 20|20|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB-
Ecoli|ecolus|NNS _|_|VBP Novobiocin|novobiocin|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB-
Ecoli|ecolus|NNS _|_|VBP Novobiocin|novobiocin|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- 5|5|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB-
Ecoli|ecolus|NNS _|_|VBP NOX|nox|SYM -|-|: _|_|NN balanced|balanced|JJ groNOX-h|gronox-h|NN at|at|IN OD|OD|NNP 0.19|0.19|CD
Ecoli|Ecoli|NNP _|_|NNP NOX|NOX|NNP -|-|: _|_|NN balanced|balanced|JJ groNOX-h|gronox-h|NN at|at|IN OD|od|NN 0.3|0.3|CD
Ecoli|Ecoli|NNP _|_|NNP NOX|NOX|NNP -|-|: _|_|NN balanced|balanced|JJ groNOX-h|gronox-h|NN at|at|IN OD|OD|NNP 0.41|0.41|CD
Ecoli|Ecoli|NNP _|_|NNP NOX|NOX|NNP -|-|: _|_|NN balanced|balanced|JJ groNOX-h|gronox-h|NN at|at|IN OD|OD|NNP 0.49|0.49|CD
Ecoli|Ecoli|NNP _|_|NNP NOX|NOX|NNP -|-|: _|_|NN balanced|balanced|JJ groNOX-h|gronox-h|NN at|at|IN OD|od|NN 0.6|0.6|CD
Ecoli|ecolus|NNS _|_|VBP NOX|nox|NN +|+|CC _|_|NN balanced|balanced|JJ growth|growth|NN at|at|IN OD|OD|NNP 0.13|0.13|CD
Ecoli|Ecoli|NNP _|_|SYM NOX|nox|NN +|+|CC _|_|NN balanced|balanced|JJ growth|growth|NN at|at|IN OD|OD|NNP 0.21|0.21|CD
Ecoli|Ecoli|NNP _|_|SYM NOX|nox|NN +|+|CC _|_|NN balanced|balanced|JJ growth|growth|NN at|at|IN OD|OD|NNP 0.28|0.28|CD
Ecoli|Ecoli|NNP _|_|SYM NOX|nox|NN +|+|CC _|_|NN balanced|balanced|JJ growth|growth|NN at|at|IN OD|OD|NNP 0.34|0.34|CD
Ecoli|Ecoli|NNP _|_|SYM NOX|nox|NN +|+|CC _|_|NN balanced|balanced|JJ growth|growth|NN at|at|IN OD|od|NN 0.4|0.4|CD
Ecoli|Ecoli|NNP _|_|SYM NP-TiO2|np-tio2|NN _|_|CD 5h|5h|JJ _|_|NN rep1|rep1|NN
Ecoli|ecolus|NNS _|_|VBP NP-TiO2|np-tio2|NN _|_|CD 5h|5h|JJ _|_|NN rep2|rep2|NN
Ecoli|ecolus|NNS _|_|VBP NP-TiO2|np-tio2|NN _|_|CD 5h|5h|JJ _|_|NN rep3|rep3|NN
Ecoli|ecolus|NNS _|_|VBP NP-TiO2|np-tio2|NN _|_|CD 5h|5h|JJ _|_|NN rep4|rep4|NN
E.coli|e.coli|NNS ,|,|, NP-TiO2|np-tio2|NN exposed|expose|VBN culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN 100mg/L|100mg/l|NN NP-TiO2|np-tio2|NN ,|,|, replicate|replicate|VB 1|1|CD
E.coli|e.coli|NNS ,|,|, NP-TiO2|np-tio2|NN exposed|expose|VBN culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN 100mg/L|100mg/l|NN NP-TiO2|np-tio2|NN ,|,|, replicate|replicate|VB 2|2|CD
E.coli|e.coli|NNS ,|,|, NP-TiO2|np-tio2|NN exposed|expose|VBN culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN 100mg/L|100mg/l|NN NP-TiO2|np-tio2|NN ,|,|, replicate|replicate|VB 3|3|CD
E.coli|e.coli|NNS ,|,|, NP-TiO2|np-tio2|NN exposed|expose|VBN culture|culture|NN ,|,|, 5h|5h|NN in|in|IN 10|10|CD mM|mm|NN NaCl|nacl|NN 100mg/L|100mg/l|NN NP-TiO2|np-tio2|NN ,|,|, replicate|replicate|VB 4|4|CD
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|NN _|_|NN 0|0|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|NN _|_|NN 0|0|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 15|15|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 15|15|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 30|30|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 30|30|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 5|5|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|VBP _|_|SYM 5|5|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|NN _|_|NN 60|60|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodiumbenzoate|sodiumbenzoate|NN _|_|NN 60|60|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|NN 0|0|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|NN 0|0|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 15|15|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 15|15|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 30|30|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 30|30|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 5|5|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 5|5|CD min|min|NN _|_|CD rep2|rep2|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 60|60|CD min|min|NN _|_|CD rep1|rep1|NN
E.coliO157|e.colio157|NN _|_|CD 0|0|CD %|%|NN sodiumbenzoate|sodiumbenzoate|NN _|_|CD 60|60|CD min|min|NN _|_|CD rep2|rep2|NN
E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN 86-24|86-24|CD in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN at|at|IN OD|od|NN 4.0|4.0|CD
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN 86-24|86-24|CD was|be|VBD inoculated|inoculate|VBN in|in|IN 25|25|CD ml|ml|NN of|of|IN LB|lb|NN in|in|IN 250|250|CD ml|ml|NN shake|shake|NN flasks|flask|NNS with|with|IN overnight|overnight|JJ cultures|culture|NNS that|that|WDT were|be|VBD diluted|dilute|VBN 1:100|1:100|CD .|.|. Cells|cell|NNS were|be|VBD shaken|shake|VBN at|at|IN 250|250|CD rpm|rpm|NN and|and|CC 37|37|CD °C|°c|NN for|for|IN an|a|DT absorbance|absorbance|NN of|of|IN 4.0|4.0|CD at|at|IN 600|600|CD nm|nm|NN .|.|. Cells|cell|NNS were|be|VBD immediately|immediately|RB chilled|chill|VBN with|with|IN dry|dry|JJ ice|ice|NN and|and|CC 95|95|CD %|%|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- to|to|TO prevent|prevent|VB RNA|rna|NN degradation|degradation|NN -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD sec|sec|NN before|before|IN centrifugation|centrifugation|NN at|at|IN 13,000|13,000|CD g|g|NN for|for|IN 2|2|CD min|min|NN ;|;|: cell|cell|NN pellets|pellet|NNS were|be|VBD frozen|frozen|JJ immediately|immediately|RB with|with|IN dry|dry|JJ ice|ice|NN and|and|CC stored|store|VBD -80|-80|CD °C|°c|NN .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN
E.coli|e.coli|NN O157|o157|NN :|:|: H7|h7|NN EDL|edl|NN 933|933|CD genomic|genomic|JJ DNA|dna|NN
E.coli|e.coli|NN O157|o157|NN :|:|: H7|h7|NN EDL|edl|NN 933|933|CD genomic|genomic|JJ DNA|dna|NN hybridization|hybridization|NN to|to|TO LLNL|llnl|NN virulence|virulence|NN mechanism|mechanism|NN array|array|NN v2A|v2a|NN
E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN at|at|IN 7|7|CD hrs|hr|NNS incubation|incubation|NN
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN at|at|IN 7|7|CD hrs|hr|NNS incubation|incubation|NN with|with|IN phloretin|phloretin|NN
E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN at|at|IN OD|od|NN 4.0|4.0|CD
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN for|for|IN 7|7|CD hrs|hr|NNS incubation|incubation|NN
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN for|for|IN 7|7|CD hrs|hr|NNS incubation|incubation|NN with|with|IN DMSO|dmso|NN
E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN for|for|IN 7|7|CD hrs|hr|NNS incubation|incubation|NN with|with|IN honey|honey|NN
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN for|for|IN 7|7|CD hrs|hr|NNS incubation|incubation|NN with|with|IN indole-3-acetaldehyde|indole-3-acetaldehyde|JJ
E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN was|be|VBD inoculated|inoculate|VBN in|in|IN 100|100|CD ml|ml|NN of|of|IN LB|lb|NN in|in|IN 250|250|CD ml|ml|NN shake|shake|NN flasks|flask|NNS with|with|IN overnight|overnight|JJ cultures|culture|NNS that|that|WDT were|be|VBD diluted|dilute|VBN 1:100|1:100|CD .|.|. Cells|cell|NNS were|be|VBD shaken|shake|VBN with|with|IN 4|4|CD g|g|NN of|of|IN glass|glass|NN wool|wool|NN at|at|IN 250|250|CD rpm|rpm|NN and|and|CC 37|37|CD °C|°c|NN for|for|IN 7|7|CD hrs|hr|NNS .|.|. Cells|cell|NNS were|be|VBD immediately|immediately|RB chilled|chill|VBN with|with|IN dry|dry|JJ ice|ice|NN and|and|CC 95|95|CD %|%|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- to|to|TO prevent|prevent|VB RNA|rna|NN degradation|degradation|NN -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD sec|sec|NN before|before|IN centrifugation|centrifugation|NN in|in|IN 50|50|CD ml|ml|NN centrifuge|centrifuge|NN tubes|tube|NNS at|at|IN 13,000|13,000|CD g|g|NN for|for|IN 2|2|CD min|min|NN ;|;|: cell|cell|NN pellets|pellet|NNS were|be|VBD frozen|frozen|JJ immediately|immediately|RB with|with|IN dry|dry|JJ ice|ice|NN and|and|CC stored|store|VBD -80|-80|CD °C|°c|NN .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- with|with|IN Qiagen|Qiagen|NNP RNase-free|RNase-free|NNP DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 79254|79254|CD -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN was|be|VBD inoculated|inoculate|VBN in|in|IN 250|250|CD ml|ml|NN of|of|IN LB|lb|NN in|in|IN 1000|1000|CD ml|ml|NN shake|shake|NN flasks|flask|NNS with|with|IN overnight|overnight|JJ cultures|culture|NNS that|that|WDT were|be|VBD diluted|dilute|VBN 1:100|1:100|CD .|.|. Cells|cell|NNS were|be|VBD shaken|shake|VBN with|with|IN 10|10|CD g|g|NN of|of|IN glass|glass|NN wool|wool|NN at|at|IN 100|100|CD rpm|rpm|NN and|and|CC 37|37|CD °C|°c|NN for|for|IN 7|7|CD hrs|hr|NNS .|.|. Cells|cell|NNS were|be|VBD immediately|immediately|RB chilled|chill|VBN with|with|IN dry|dry|JJ ice|ice|NN and|and|CC 95|95|CD %|%|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- to|to|TO prevent|prevent|VB RNA|rna|NN degradation|degradation|NN -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD sec|sec|NN before|before|IN centrifugation|centrifugation|NN in|in|IN 50|50|CD ml|ml|NN centrifuge|centrifuge|NN tubes|tube|NNS at|at|IN 13,000|13,000|CD g|g|NN for|for|IN 2|2|CD min|min|NN ;|;|: cell|cell|NN pellets|pellet|NNS were|be|VBD frozen|frozen|JJ immediately|immediately|RB with|with|IN dry|dry|JJ ice|ice|NN and|and|CC stored|store|VBD -80|-80|CD °C|°c|NN .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- with|with|IN Qiagen|Qiagen|NNP RNase-free|RNase-free|NNP DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 79254|79254|CD -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN was|be|VBD inoculated|inoculate|VBN in|in|IN 25|25|CD ml|ml|NN of|of|IN LB|lb|NN in|in|IN 250|250|CD ml|ml|NN shake|shake|NN flasks|flask|NNS with|with|IN overnight|overnight|JJ cultures|culture|NNS that|that|WDT were|be|VBD diluted|dilute|VBN 1:100|1:100|CD .|.|. Cells|cell|NNS were|be|VBD shaken|shake|VBN at|at|IN 100|100|CD rpm|rpm|NN and|and|CC 37|37|CD °C|°c|NN for|for|IN 7|7|CD hrs|hr|NNS .|.|. Cells|cell|NNS were|be|VBD immediately|immediately|RB chilled|chill|VBN with|with|IN dry|dry|JJ ice|ice|NN and|and|CC 95|95|CD %|%|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- to|to|TO prevent|prevent|VB RNA|rna|NN degradation|degradation|NN -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD sec|sec|NN before|before|IN centrifugation|centrifugation|NN in|in|IN 50|50|CD ml|ml|NN centrifuge|centrifuge|NN tubes|tube|NNS at|at|IN 13,000|13,000|CD g|g|NN for|for|IN 2|2|CD min|min|NN ;|;|: cell|cell|NN pellets|pellet|NNS were|be|VBD frozen|frozen|JJ immediately|immediately|RB with|with|IN dry|dry|JJ ice|ice|NN and|and|CC stored|store|VBD -80|-80|CD °C|°c|NN .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- with|with|IN Qiagen|Qiagen|NNP RNase-free|RNase-free|NNP DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 79254|79254|CD -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN was|be|VBD inoculated|inoculate|VBN in|in|IN 25|25|CD ml|ml|NN of|of|IN LB|lb|NN in|in|IN 250|250|CD ml|ml|NN shake|shake|NN flasks|flask|NNS with|with|IN overnight|overnight|JJ cultures|culture|NNS that|that|WDT were|be|VBD diluted|dilute|VBN 1:100|1:100|CD .|.|. Cells|cell|NNS were|be|VBD shaken|shake|VBN at|at|IN 250|250|CD rpm|rpm|NN and|and|CC 37|37|CD °C|°c|NN for|for|IN an|a|DT absorbance|absorbance|NN of|of|IN 4.0|4.0|CD at|at|IN 600|600|CD nm|nm|NN .|.|. Cells|cell|NNS were|be|VBD immediately|immediately|RB chilled|chill|VBN with|with|IN dry|dry|JJ ice|ice|NN and|and|CC 95|95|CD %|%|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- to|to|TO prevent|prevent|VB RNA|rna|NN degradation|degradation|NN -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD sec|sec|NN before|before|IN centrifugation|centrifugation|NN at|at|IN 13,000|13,000|CD g|g|NN for|for|IN 2|2|CD min|min|NN ;|;|: cell|cell|NN pellets|pellet|NNS were|be|VBD frozen|frozen|JJ immediately|immediately|RB with|with|IN dry|dry|JJ ice|ice|NN and|and|CC stored|store|VBD -80|-80|CD °C|°c|NN .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
E.coli|e.coli|NNS O157|o157|NN :|:|: H7|h7|NN in|in|IN LB|lb|NN at|at|IN mid-log|mid-log|JJ phase|phase|NN
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN biological|biological|JJ rep|rep|NN 1|1|CD slide|slide|NN 1|1|CD
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN biological|biological|JJ rep|rep|NN 1|1|CD slide|slide|NN 2|2|CD
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN biological|biological|JJ rep|rep|NN 2|2|CD slide|slide|NN 3|3|CD
E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN biological|biological|JJ rep|rep|NN 2|2|CD slide|slide|NN 4|4|CD
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN biological|biological|JJ rep|rep|NN 3|3|CD slide|slide|NN 5|5|CD
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN interacted|interact|VBD with|with|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN biological|biological|JJ rep|rep|NN 3|3|CD slide|slide|NN 6|6|CD
E.|E.|NNP coli|coli|NN O157|o157|NN :|:|: H7|h7|NN was|be|VBD grown|grow|VBN in|in|IN 15mL|15ml|NN falcon|falcon|NN tubes|tube|NNS containing|contain|VBG 8mL|8ml|NN of|of|IN filtered|filter|VBN rat|rat|NN 's|'s|POS caecal|caecal|JJ content|content|NN .|.|. Growth|growth|NN were|be|VBD performed|perform|VBN in|in|IN static|static|JJ condition|condition|NN at|at|IN 37|37|CD °C|°c|NN for|for|IN 6|6|CD hours|hour|NNS .|.|.
E.|E.|NNP coli|coli|NN O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- untreated|untreated|JJ -LRB-|-lrb-|-LRB- reference|reference|NN sample|sample|NN -RRB-|-rrb-|-RRB- _|_|SYM rep|rep|NN #|#|# 1|1|CD
E.|E.|NNP coli|coli|NN O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- untreated|untreated|JJ -LRB-|-lrb-|-LRB- reference|reference|NN sample|sample|NN -RRB-|-rrb-|-RRB- _|_|SYM rep|rep|NN #|#|# 2|2|CD
E.|E.|NNP coli|coli|NN O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- untreated|untreated|JJ -LRB-|-lrb-|-LRB- reference|reference|NN sample|sample|NN -RRB-|-rrb-|-RRB- _|_|SYM rep|rep|NN #|#|# 3|3|CD
E.|E.|NNP coli|coli|NN -LRB-|-lrb-|-LRB- OD660|od660|NN nm|nm|NN =|=|JJ 0.3|0.3|CD -RRB-|-rrb-|-RRB- was|be|VBD incubated|incubate|VBN with|with|IN control|control|NN protein|protein|NN or|or|CC antibacterial|antibacterial|JJ preparations|preparation|NNS in|in|IN 5|5|CD mM|mm|NN TRIS|tris|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.6|7.6|CD -RRB-|-rrb-|-RRB- with|with|IN 150|150|CD mM|mm|NN NaCl|nacl|NN ,|,|, 10|10|CD µM|µm|NN ZnSO4|znso4|NN ,|,|, and|and|CC 2|2|CD %|%|NN LB|lb|NN ,|,|, at|at|IN 37oC|37oc|NN aerobically|aerobically|RB with|with|IN shaking|shake|VBG .|.|.
E.coli|e.coli|NNS _|_|VBP ∆|∆|SYM ompR|ompr|NN pH|ph|NN 5.6|5.6|CD A|a|DT
E.coli|e.coli|NNS _|_|VBP ∆|∆|SYM ompR|ompr|NN pH|ph|NN 5.6|5.6|CD B|b|NN
E.coli|e.coli|NNS _|_|VBP ∆|∆|SYM ompR|ompr|NN pH|ph|NN 5.6|5.6|CD C|c|NN
E.coli|e.coli|NNS _|_|VBP ∆|∆|SYM ompR|ompr|NN pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN A|a|NN
E.coli|e.coli|NNS _|_|VBP ∆|∆|SYM ompR|ompr|NN pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN B|b|NN
E.|e.|FW coli|coli|FW _|_|SYM PGRP|pgrp|SYM _|_|SYM 30|30|CD min|min|NN
E.|E.|NNP coli|coli|NN phage|phage|NN 3538|3538|CD #|#|# 1|1|CD
E.|E.|NNP coli|coli|NN phage|phage|NN 3538|3538|CD #|#|# 2|2|CD
E.coli|e.coli|JJ _|_|NN polyphenols|polyphenol|NNS _|_|VBP repA|repa|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP polyphenols|polyphenol|NNS _|_|SYM repA|repA|NNP _|_|SYM t2|t2|FW
E.coli|e.coli|FW _|_|SYM polyphenols|polyphenol|NNS _|_|VBP repA|repa|NN _|_|CD t3|t3|NN
E.coli|e.coli|NNS _|_|VBP polyphenols|polyphenol|NNS _|_|VBP repB|repb|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP polyphenols|polyphenol|NNS _|_|VBP repB|repb|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP polyphenols|polyphenol|NNS _|_|VBP repB|repb|NN _|_|CD t3|t3|NN
E.coli|e.coli|NNS _|_|VBP polyphenols|polyphenol|NNS _|_|VBP repC|repc|NN _|_|CD t1|t1|NN
E.coli|e.coli|NNS _|_|VBP polyphenols|polyphenol|NNS _|_|VBP repC|repc|NN _|_|CD t2|t2|NN
E.coli|e.coli|NNS _|_|VBP polyphenols|polyphenol|NNS _|_|VBP repC|repc|NN _|_|CD t3|t3|NN
E.|e.|FW coli|coli|FW Progesterone|progesterone|NN Treatment|treatment|NN
Ecoli|ecolus|NNS _|_|VBP pUC|puc|NN expression|expression|NN OD|od|NN 0.2|0.2|CD
Ecoli|Ecoli|NNP _|_|NNP pUC|puc|NN expression|expression|NN OD|od|NN 0.5|0.5|CD
Ecoli|Ecoli|NNP _|_|NNP pUC|puc|NN expression|expression|NN OD|od|NN 0.9|0.9|CD
E.|E.|NNP Coli|Coli|NNP PurR|purr|NN ChIP|chip|NN DNA|dna|NN Adenine|adenine|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP PurR|purr|NN ChIP|chip|NN DNA|dna|NN Adenine|adenine|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP PurR|purr|NN ChIP|chip|NN DNA|dna|NN glucose|glucose|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP PurR|purr|NN ChIP|chip|NN DNA|dna|NN glucose|glucose|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP PurR|purr|NN Input|input|NN DNA|dna|NN Adenine|adenine|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP PurR|purr|NN Input|input|NN DNA|dna|NN Adenine|adenine|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP PurR|PurR|NNP Input|Input|NNP DNA|DNA|NNP glucose|glucose|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP PurR|PurR|NNP Input|Input|NNP DNA|DNA|NNP glucose|glucose|NN 2|2|CD
E.|E.|NNP coli|coli|NN recoded|recode|VBD ompF|ompf|NN
E.|E.|NNP coli|coli|NN recoded|recode|VBD ompF|ompf|NN -LRB-|-lrb-|-LRB- recoded|recode|VBN ompF|ompf|NN gene|gene|NN -RRB-|-rrb-|-RRB-
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN T7|t7|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN T5|t5|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN T6|t6|NN
Ecoli|ecolus|NNS _|_|VBP Recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN T7|t7|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN response|response|NN _|_|NN control|control|NN _|_|CD 1mM|1mm|NN _|_|CD H2O2|h2o2|NN _|_|NN added|add|VBD _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN response|response|NN _|_|NN control|control|NN _|_|CD 1mM|1mm|NN _|_|CD H2O2|h2o2|NN _|_|NN added|add|VBD _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN response|response|NN _|_|NN control|control|NN _|_|CD 1mM|1mm|NN _|_|CD H2O2|h2o2|NN _|_|NN added|add|VBD _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN response|response|NN _|_|NN control|control|NN _|_|CD water|water|NN _|_|NN added|add|VBD _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN response|response|NN _|_|NN control|control|NN _|_|CD water|water|NN _|_|NN added|add|VBD _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN response|response|NN _|_|NN control|control|NN _|_|CD water|water|NN _|_|NN added|add|VBD _|_|CD rep3|rep3|NN
E.coli|e.coli|NNS RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN heat-shocked|heat-shocked|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
E.coli|e.coli|NNS RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN mid-exponential|mid-exponential|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
E.coli|e.coli|NNS RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN mid-exponential|mid-exponential|JJ condition|condition|NN with|with|IN rifampicin|rifampicin|NN treatment|treatment|NN
E.coli|e.coli|NNS RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN nitrogen-limiting|nitrogen-limiting|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
E.coli|e.coli|NNS RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN stationary|stationary|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
E.|E.|NNP coli|coli|NN RNA|rna|NN polymerase|polymerase|NN core|core|NN enzyme|enzyme|NN was|be|VBD purchased|purchase|VBN from|from|IN Epicentre|Epicentre|NNP -LRB-|-lrb-|-LRB- Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. Histidine-tagged|histidine-tagged|JJ σ|σ|NN factors|factor|NNS were|be|VBD produced|produce|VBN and|and|CC purified|purify|VBN as|as|IN described|describe|VBN -LRB-|-lrb-|-LRB- Lacour|Lacour|NNP et|et|FW al.|al.|FW ,|,|, 2003|2003|CD ;|;|: Checroun|Checroun|NNP et|et|FW al.|al.|FW ,|,|, 2004|2004|CD -RRB-|-rrb-|-RRB- ;|;|: proteins|protein|NNS appeared|appear|VBD pure|pure|JJ from|from|IN contaminants|contaminant|NNS as|as|IN determined|determine|VBN by|by|IN denaturing|denature|VBG protein|protein|NN gel|gel|NN electrophoresis|electrophoresis|NN -LRB-|-lrb-|-LRB- data|datum|NNS not|not|RB shown|show|VBN -RRB-|-rrb-|-RRB- .|.|. For|for|IN reconstitution|reconstitution|NN of|of|IN RNA|rna|NN polymerase|polymerase|NN holoenzymes|holoenzyme|NNS ,|,|, the|the|DT core|core|NN enzyme|enzyme|NN was|be|VBD incubated|incubate|VBN for|for|IN 10|10|CD minutes|minute|NNS at|at|IN 37|37|CD °C|°c|NN with|with|IN either|either|CC σS|σs|NN or|or|CC σ70|σ70|NN at|at|IN a|a|DT 1:10|1:10|CD ratio|ratio|NN .|.|. For|for|IN calculation|calculation|NN of|of|IN RNA|rna|NN polymerase|polymerase|NN concentrations|concentration|NNS in|in|IN transcription|transcription|NN assays|assay|NNS ,|,|, it|it|PRP was|be|VBD assumed|assume|VBN that|that|IN ,|,|, after|after|IN reconstitution|reconstitution|NN ,|,|, core|core|NN enzyme|enzyme|NN would|would|MD be|be|VB 100|100|CD %|%|NN active|active|JJ and|and|CC fully|fully|RB saturated|saturate|VBN by|by|IN either|either|CC σ|σ|NN factor|factor|NN .|.|. 2|2|CD ug|ug|NN of|of|IN genomic|genomic|JJ DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN digested|digest|VBN with|with|IN EcoRI|ecori|NN were|be|VBD used|use|VBN in|in|IN transcription|transcription|NN assays|assay|NNS for|for|IN ROMA|roma|NN experiments|experiment|NNS .|.|. RNA|rna|NN polymerase|polymerase|NN holoenzyme|holoenzyme|NN concentrations|concentration|NNS were|be|VBD 100|100|CD nM|nm|NN in|in|IN 50|50|CD ul|ul|NN reaction|reaction|NN mixture|mixture|NN .|.|. Ten|ten|CD independent|independent|JJ run-off|run-off|JJ transcription|transcription|NN assays|assay|NNS were|be|VBD performed|perform|VBN ,|,|, and|and|CC transcripts|transcript|NNS were|be|VBD pooled|pool|VBN together|together|RB -LRB-|-lrb-|-LRB- ca.|ca.|FW 1|1|CD ug|ug|NN total|total|JJ RNA|rna|NN -RRB-|-rrb-|-RRB- .|.|.
E.|E.|NNP coli|coli|NN Rosetta|rosetta|NN cells|cell|NNS transformed|transform|VBN with|with|IN pET-28a|pet-28a|NN or|or|CC pET-28a-BnTR1|pet-28a-bntr1|NN -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN =|=|JJ 0.6|0.6|CD -RRB-|-rrb-|-RRB- were|be|VBD induced|induce|VBN with|with|IN 0.1|0.1|CD mM|mm|NN IPTG|iptg|NN at|at|IN 37|37|CD °C|°c|NN for|for|IN 1|1|CD hour|hour|NN .|.|.
E.coli|e.coli|NNS _|_|VBP RviaT1|rviat1|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP RviaT1|rviat1|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT1|rviat1|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP RviaT2|rviat2|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP RviaT2|rviat2|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT2|rviat2|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP RviaT3|rviat3|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP RviaT3|rviat3|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT3|rviat3|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP RviaT4|rviat4|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP RviaT4|rviat4|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT4|rviat4|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP RviaT5|rviat5|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT5|rviat5|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP RviaT6|rviat6|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT6|rviat6|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP RviaT7|rviat7|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT7|rviat7|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP RviaT8|rviat8|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP RviaT8|rviat8|NN _|_|CD SR3|sr3|NN
E.|E.|NNP coli|coli|NN samples|sample|NNS for|for|IN RNA|rna|NN extraction|extraction|NN were|be|VBD taken|take|VBN during|during|IN fermentation|fermentation|NN .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN the|the|DT cultivation|cultivation|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN ,|,|, 10,000|10,000|CD g|g|NN ,|,|, 1|1|CD min|min|NN -RRB-|-rrb-|-RRB- ,|,|, separated|separate|VBN from|from|IN the|the|DT supernatant|supernatant|NN ,|,|, and|and|CC rapidly|rapidly|RB frozen|freeze|VBN in|in|IN dry|dry|JJ ice|ice|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD stored|store|VBN at|at|IN -70|-70|CD °C|°c|NN until|until|IN analysis|analysis|NN
E.coli|e.coli|NN SE15|se15|NN is|be|VBZ cultured|culture|VBN in|in|IN LB|lb|NN broth|broth|NN and|and|CC LuxS|luxs|NN E.coli|e.coli|NN SE15|se15|NN is|be|VBZ cultured|culture|VBN in|in|IN LB|lb|NN broth|broth|NN with|with|IN kanamycine|kanamycine|NN at|at|IN 37|37|CD ℃|℃|NN and|and|CC in|in|IN 150rpm|150rpm|NN shaking|shake|VBG incubator|incubator|NN
E.coli|e.coli|NN SE15|se15|NN is|be|VBZ isolated|isolate|VBN from|from|IN indwelling|indwell|VBG catheter|catheter|NN of|of|IN patient|patient|NN and|and|CC deleted|delete|VBN LuxS|luxs|NN gene|gene|NN -LRB-|-lrb-|-LRB- related|related|JJ to|to|TO quorum|quorum|NN sensing|sense|VBG -RRB-|-rrb-|-RRB-
E.coli|e.coli|NN SE15|se15|NN isolated|isolate|VBN from|from|IN indwelling|indwell|VBG catheter|catheter|NN of|of|IN patient|patient|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|FW _|_|FW powerline|powerline|FW _|_|SYM interm|interm|FW _|_|FW 15h|15h|FW _|_|SYM rep1|rep1|CD
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|FW _|_|FW powerline|powerline|FW _|_|SYM interm|interm|FW _|_|FW 15h|15h|FW _|_|SYM rep2|rep2|CD
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|FW _|_|FW powerline|powerline|FW _|_|SYM interm|interm|FW _|_|FW 15h|15h|FW _|_|SYM rep3|rep3|CD
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 8|8|CD min|min|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 8|8|CD min|min|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 8|8|CD min|min|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 15h|15h|CD _|_|CD rep1|rep1|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 15h|15h|CD _|_|CD rep2|rep2|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 15h|15h|CD _|_|CD rep3|rep3|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|NN 8|8|CD min|min|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|NN 8|8|CD min|min|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|NN 8|8|CD min|min|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 15h|15h|JJ _|_|NN rep1|rep1|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 15h|15h|JJ _|_|NN rep2|rep2|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 15h|15h|JJ _|_|NN rep3|rep3|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 2.5|2.5|CD h|h|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 2.5|2.5|CD h|h|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|FW coli|coli|FW _|_|SYM sham|sham|VBP _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 2.5|2.5|CD h|h|NN _|_|SYM rep3|rep3|CD
Ecoli|Ecoli|NNP _|_|NNP Sodium|sodium|NN Azide|azide|NN treatment|treatment|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Sodium|sodium|NN Azide|azide|NN treatment|treatment|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Sodium|sodium|NN Azide|azide|NN treatment|treatment|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Sodium|sodium|NN Azide|azide|NN treatment|treatment|NN T4|t4|NN
E.|e.|FW coli|coli|FW ST131|st131|NN UR40|ur40|NN was|be|VBD treated|treat|VBN with|with|IN ciprofloxacin|ciprofloxacin|NN -LRB-|-lrb-|-LRB- 2µg/mL|2µg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC samples|sample|NNS were|be|VBD taken|take|VBN at|at|IN time|time|NN points|point|NNS 0|0|CD min|min|NN ,|,|, 30|30|CD min|min|NN and|and|CC 90|90|CD min|min|NN .|.|.
E.coli|e.coli|NNS _|_|VBP stat|stat|NN _|_|CD dynamic|dynamic|JJ _|_|NN 1|1|CD
E.coli|e.coli|NNS _|_|VBP stat|stat|NN _|_|CD dynamic|dynamic|JJ _|_|NN 2|2|CD
E.|E.|NNP coli|coli|NN stationary|stationary|JJ 1|1|CD
E.|e.|FW coli|coli|FW stationary|stationary|JJ 2|2|CD
Ecoli|ecolus|NNS _|_|VBP Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN T1|t1|NN
Ecoli|ecolus|NNS _|_|VBP Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN T2|t2|NN
Ecoli|ecolus|NNS _|_|VBP Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN T3|t3|NN
Ecoli|ecolus|NNS _|_|VBP Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN T4|t4|NN
Ecoli|ecolus|NNS _|_|VBP Stationary|stationary|JJ phase|phase|NN in|in|IN LB|LB|NNP T5|T5|NNP
Ecoli|Ecoli|NNP _|_|NNP Stationary|Stationary|NNP phase|phase|NN in|in|IN LB|LB|NNP T6|T6|NNP
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoB|rpob|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN DelS|dels|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN DelS|dels|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN DelS|dels|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoD|rpod|NN DelS|dels|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN 3|3|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 1|1|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 2|2|CD
E.|E.|NNP Coli|Coli|NNP Stationary|Stationary|NNP RpoS|rpos|NN ChIP|chip|NN DNA|dna|NN Mock|mock|NN 3|3|CD
E.|e.|FW coli|coli|FW strain|strain|NN B178|b178|NN -LRB-|-lrb-|-LRB- Georgopoulos|Georgopoulos|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- 1973|1973|CD -RRB-|-rrb-|-RRB- J|J|NNP Mol|Mol|NNP Biol|Biol|NNP 76|76|CD :|:|: 45-60|45-60|CD -RRB-|-rrb-|-RRB- in|in|IN which|which|WDT the|the|DT endogenous|endogenous|JJ groES|groes|NN and|and|CC groEL|groel|NN genes|gene|NNS have|have|VBP been|be|VBN deleted|delete|VBN and|and|CC that|that|DT is|be|VBZ maintained|maintain|VBN alive|alive|JJ by|by|IN the|the|DT pOFX-tac1-derived|pofx-tac1-derived|JJ plasmid|plasmid|NN carrying|carry|VBG an|a|DT IPTG-inducible|iptg-inducible|JJ operon|operon|NN with|with|IN cDNA|cdna|NN encoding|encode|VBG human|human|JJ Hsp10|hsp10|NN and|and|CC the|the|DT mature|mature|JJ part|part|NN of|of|IN human|human|JJ wild|wild|JJ type|type|NN Hsp60|hsp60|NN -LRB-|-lrb-|-LRB- Hansen|Hansen|NNP et|et|FW al.|al.|FW ,|,|, 2002|2002|CD -RRB-|-rrb-|-RRB- .|.|. These|these|DT cells|cell|NNS were|be|VBD subsequently|subsequently|RB transformed|transform|VBN by|by|IN electroporation|electroporation|NN with|with|IN a|a|DT second|second|JJ plasmid|plasmid|NN ,|,|, derivative|derivative|NN of|of|IN pBAD/hisA|pbad/hisa|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, that|that|WDT contained|contain|VBD an|a|DT operon|operon|NN with|with|IN Hsp10|hsp10|NN and|and|CC the|the|DT Val98Ile|val98ile|NN mutant|mutant|JJ variant|variant|NN of|of|IN Hsp60|hsp60|NN under|under|IN control|control|NN of|of|IN the|the|DT arabinose-inducible|arabinose-inducible|JJ BAD|bad|NN promoter|promoter|NN .|.|. The|the|DT pBAD/hisA-derived|pbad/hisa-derived|JJ plasmid|plasmid|NN carries|carry|VBZ a|a|DT pBR322|pbr322|NN origin|origin|NN of|of|IN replication|replication|NN and|and|CC an|a|DT ampicillin|ampicillin|NN resistance|resistance|NN gene|gene|NN and|and|CC can|can|MD be|be|VB stably|stably|RB maintained|maintain|VBN in|in|IN the|the|DT same|same|JJ cell|cell|NN with|with|IN the|the|DT p15A-origin/kanamycin|p15a-origin/kanamycin|NN resistance|resistance|NN gene|gene|NN containing|contain|VBG pOFX-tac|pofx-tac|NN derivative|derivative|NN .|.|.
E.|E.|NNP coli|coli|NN strain|strain|NN B178|b178|NN -LRB-|-lrb-|-LRB- Georgopoulos|Georgopoulos|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- 1973|1973|CD -RRB-|-rrb-|-RRB- J|J|NNP Mol|Mol|NNP Biol|Biol|NNP 76|76|CD :|:|: 45-60|45-60|CD -RRB-|-rrb-|-RRB- in|in|IN which|which|WDT the|the|DT endogenous|endogenous|JJ groES|groes|NN and|and|CC groEL|groel|NN genes|gene|NNS have|have|VBP been|be|VBN deleted|delete|VBN and|and|CC that|that|DT is|be|VBZ maintained|maintain|VBN alive|alive|JJ by|by|IN the|the|DT pOFX-tac1-derived|pofx-tac1-derived|JJ plasmid|plasmid|NN carrying|carry|VBG an|a|DT IPTG-inducible|iptg-inducible|JJ operon|operon|NN with|with|IN cDNA|cdna|NN encoding|encode|VBG human|human|JJ Hsp10|hsp10|NN and|and|CC the|the|DT mature|mature|JJ part|part|NN of|of|IN human|human|JJ wild|wild|JJ type|type|NN Hsp60|hsp60|NN -LRB-|-lrb-|-LRB- Hansen|Hansen|NNP et|et|FW al.|al.|FW ,|,|, 2002|2002|CD -RRB-|-rrb-|-RRB- .|.|. These|these|DT cells|cell|NNS were|be|VBD subsequently|subsequently|RB transformed|transform|VBN by|by|IN electroporation|electroporation|NN with|with|IN a|a|DT second|second|JJ plasmid|plasmid|NN ,|,|, derivative|derivative|NN of|of|IN pBAD/hisA|pbad/hisa|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, that|that|WDT contained|contain|VBD an|a|DT operon|operon|NN with|with|IN Hsp10|hsp10|NN and|and|CC wild|wild|JJ type|type|NN Hsp60|hsp60|NN under|under|IN control|control|NN of|of|IN the|the|DT arabinose-inducible|arabinose-inducible|JJ BAD|bad|NN promoter|promoter|NN .|.|. The|the|DT pBAD/hisA-derived|pbad/hisa-derived|JJ plasmids|plasmid|NNS carry|carry|VBP a|a|DT pBR322|pbr322|NN origin|origin|NN of|of|IN replication|replication|NN and|and|CC an|a|DT ampicillin|ampicillin|NN resistance|resistance|NN gene|gene|NN and|and|CC can|can|MD be|be|VB stably|stably|RB maintained|maintain|VBN in|in|IN the|the|DT same|same|JJ cell|cell|NN with|with|IN the|the|DT p15A-origin/kanamycin|p15a-origin/kanamycin|NN resistance|resistance|NN gene|gene|NN containing|contain|VBG pOFX-tac|pofx-tac|NN derivative|derivative|NN .|.|.
E.|E.|NNP coli|coli|NN strain|strain|NN B-a|b-a|JJ
E.|e.|FW coli|coli|FW strain|strain|NN B-b|b-b|JJ
E.|e.|FW coli|coli|FW strain|strain|NN B|b|NN DNA|dna|NN
E.|e.|FW coli|coli|FW strain|strain|NN DH5α|dh5α|NN harboring|harbor|VBG pAR060302|par060302|NN was|be|VBD grown|grow|VBN in|in|IN 10|10|CD mL|ml|NN DifcoTM|difcotm|NN Luria-Bertani|luria-bertani|NN -LRB-|-lrb-|-LRB- LB|lb|NN -RRB-|-rrb-|-RRB- broth|broth|NN aliquots|aliquot|NNS at|at|IN 37º|37º|CD C|c|NN with|with|IN shaking|shake|VBG until|until|IN an|a|DT OD600|od600|NN of|of|IN 0.5|0.5|CD .|.|.
E.coli|e.coli|NNS strain|strain|NN ,|,|, DY330|dy330|NN ,|,|, was|be|VBD grown|grow|VBN at|at|IN 30C|30C|NNP in|in|IN M9|M9|NNP media|media|NNS supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN ,|,|, vitamins|vitamin|NNS and|and|CC amino|amino|NN acids|acid|NNS .|.|.
E.|E.|NNP coli|coli|NN strain|strain|NN FHI12|fhi12|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI24|fhi24|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI25|fhi25|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI27|fhi27|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI36|fhi36|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI4|fhi4|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI43|fhi43|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI48|fhi48|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI6|fhi6|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI63|fhi63|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI66|fhi66|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI7|fhi7|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI79|fhi79|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI8|fhi8|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI83|fhi83|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI9|fhi9|NN
E.|e.|FW coli|coli|FW strain|strain|NN FHI95|fhi95|NN
E.|E.|NNP coli|coli|NN ,|,|, strain|strain|NN Frag1|frag1|NN
E.|e.|FW coli|coli|FW strain|strain|NN isolated|isolate|VBN from|from|IN CF|cf|NN patient|patient|NN stool|stool|VBP
E.|e.|FW coli|coli|FW strain|strain|NN isolated|isolate|VBN from|from|IN healthy|healthy|JJ child|child|NN stool|stool|NN
E.|E.|NNP coli|coli|NN strain|strain|NN K12|k12|NN
E.|e.|FW coli|coli|FW strain|strain|NN K12-a|k12-a|NN
E.|e.|FW coli|coli|FW strain|strain|NN K12-b|k12-b|NN
E.|e.|FW coli|coli|FW strain|strain|NN K12-c|k12-c|NN
E.|e.|FW coli|coli|FW strain|strain|NN K12-d|k12-d|JJ
E.|e.|FW coli|coli|FW strain|strain|NN K12|k12|NN DNA|dna|NN
E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 100|100|CD μg/ml|μg/ml|NN NA|na|NN
E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 10|10|CD μg/ml|μg/ml|NN NA|na|NN
E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS without|without|IN treatment|treatment|NN .|.|.
E.|E.|NNP coli|coli|NN strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEF|mazef|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 100|100|CD μg/ml|μg/ml|NN NA|na|NN
E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEF|mazef|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 10|10|CD μg/ml|μg/ml|NN NA|na|NN
E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEF|mazef|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS without|without|IN treatment|treatment|NN
E.|E.|NNP coli|coli|NN strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEFlexA3|mazeflexa3|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 100|100|CD μg/ml|μg/ml|NN NA|na|NN
E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEFlexA3|mazeflexa3|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 10|10|CD μg/ml|μg/ml|NN NA|na|NN
E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEFlexA3|mazeflexa3|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS without|without|IN treatment|treatment|NN
E.coli|e.coli|NN strain|strain|NN MG1655|mg1655|NN
E.|e.|FW coli|coli|FW strain|strain|NN NM580|nm580|NN -LRB-|-lrb-|-LRB- genotype|genotype|NN MG1655|mg1655|NN ermBL-ermB|ermbl-ermb|NN '|'|'' :|:|: :|:|: LacZ|lacz|NN -RRB-|-rrb-|-RRB- cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN broth|broth|NN -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN -RRB-|-rrb-|-RRB- until|until|IN OD600|od600|NN of|of|IN ~|~|NN 0.3|0.3|CD .|.|.
E.Coli|e.coli|NNS ,|,|, strain|strain|NN P4XB2|p4xb2|NN mutant|mutant|NN ,|,|, grown|grow|VBN in|in|IN presence|presence|NN of|of|IN arginine|arginine|NN -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB-
E.Coli|e.coli|NNS ,|,|, strain|strain|NN P4X|p4x|NN ,|,|, grown|grow|VBN in|in|IN presence|presence|NN of|of|IN arginine|arginine|NN -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB-
E.Coli|e.coli|NNS ,|,|, strain|strain|NN P4X|p4x|NN ,|,|, grown|grow|VBN on|on|IN minimal|minimal|JJ medium|medium|NN ,|,|, reference|reference|NN sample|sample|NN
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG ArgR-8myc|argr-8myc|NN were|be|VBD grown|grow|VBN in|in|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ W2|w2|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 1g/L|1g/l|NN arginine|arginine|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG ArgR-8myc|argr-8myc|NN were|be|VBD grown|grow|VBN in|in|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ W2|w2|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 2g/L|2g/l|NN glutamine|glutamine|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG Lrp-8myc|lrp-8myc|JJ were|be|VBD grown|grow|VBN in|in|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 10|10|CD mM|mm|NN leucine|leucine|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG Lrp-8myc|lrp-8myc|JJ were|be|VBD grown|grow|VBN in|in|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN without|without|IN 10|10|CD mM|mm|NN leucine|leucine|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG PurR-8myc|purr-8myc|NN were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- then|then|RB inoculated|inoculate|VBN into|into|IN 100mL|100ml|NN of|of|IN fresh|fresh|JJ M9|m9|NN minimal|minimal|JJ medium|medium|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG PurR-8myc|purr-8myc|NN were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- then|then|RB inoculated|inoculate|VBN into|into|IN 100mL|100ml|NN of|of|IN fresh|fresh|JJ M9|m9|NN minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN 100ug/L|100ug/l|NN adenine|adenine|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG TrpR-8myc|trpr-8myc|NN were|be|VBD grown|grow|VBN in|in|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 20|20|CD mg/L|mg/l|NN tryptophan|tryptophan|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG TrpR-8myc|trpr-8myc|NN were|be|VBD grown|grow|VBN in|in|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN without|without|IN 20|20|CD mg/L|mg/l|NN tryptophan|tryptophan|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS harboring|harbor|VBG σ70|σ70|NN mutant|mutant|JJ B8|b8|NN and|and|CC WT|wt|NN were|be|VBD cultured|culture|VBN overnight|overnight|JJ and|and|CC inoculated|inoculate|VBN -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN -RRB-|-rrb-|-RRB- into|into|IN fresh|fresh|JJ medium|medium|NN .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS HT874|ht874|NN ,|,|, HT873|ht873|NN ,|,|, HT875|ht875|NN ,|,|, HT873|ht873|NN treated|treat|VBN with|with|IN or|or|CC no|no|DT polyamines|polyamine|NNS by|by|IN Trizol|trizol|NN protocol|protocol|NN .|.|.
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav104|Olav104|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav157|Olav157|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav164|Olav164|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav17|Olav17|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav172|Olav172|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav173|Olav173|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav174|Olav174|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav176|Olav176|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav178|Olav178|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav179|Olav179|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav39|Olav39|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav40|Olav40|NNP
E.|E.|NNP coli|coli|NN strain|strain|NN St.|St.|NNP Olav63|Olav63|NNP
E.|E.|NNP coli|coli|NN strains|strain|NNS was|be|VBD grown|grow|VBN in|in|IN MgM|MgM|NNP media|media|NNS at|at|IN pH|ph|NN 5.6|5.6|CD ,|,|, 7.2|7.2|CD and|and|CC 7.2|7.2|CD with|with|IN 15|15|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sucrose|sucrose|NN to|to|TO O.D|O.D|NNP ~|~|NNP 0.6|0.6|CD .|.|.
E.|E.|NNP coli|coli|NN strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- and|and|CC additional|additional|JJ iron|iron|NN to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN
E.|E.|NNP coli|coli|NN strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN
E.|E.|NNP coli|coli|NN strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN and|and|CC treated|treat|VBN with|with|IN heatshock|heatshock|NN for|for|IN 10|10|CD min|min|NN
E.|E.|NNP coli|coli|NN strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN with|with|IN heatshock|heatshock|NN for|for|IN 10|10|CD min|min|NN
E.|E.|NNP coli|coli|NN strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- to|to|TO stationary|stationary|JJ phase|phase|NN
E.|E.|NNP coli|coli|NN strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN minimal|minimal|JJ W2|w2|NN medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- and|and|CC glutamine|glutamine|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN
E.|E.|NNP coli|coli|NN ,|,|, stressed|stress|VBN by|by|IN NaCl|nacl|NN ,|,|, in|in|IN presence|presence|NN of|of|IN glycine|glycine|NN betaine|betaine|NN
e.|e.|FW coli|coli|FW subset|subset|NN :|:|: enterohemorrhagic|enterohemorrhagic|JJ E.coli|e.coli|JJ
E.|e.|FW coli|coli|FW sucrose|sucrose|NN hyperosmotic|hyperosmotic|JJ treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 1|1|LS -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW sucrose|sucrose|NN hyperosmotic|hyperosmotic|JJ treatment|treatment|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP 2|2|LS -RRB-|-rrb-|-RRB-
E.coli|e.coli|NNS _|_|VBP T1viaR|t1viar|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP T1viaR|t1viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T1viaR|t1viar|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP T2viaR|t2viar|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP T2viaR|t2viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T2viaR|t2viar|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP T3viaR|t3viar|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP T3viaR|t3viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T3viaR|t3viar|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP T4viaR|t4viar|NN _|_|CD SR1|sr1|NN
E.coli|e.coli|NNS _|_|VBP T4viaR|t4viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T4viaR|t4viar|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP T5viaR|t5viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T5viaR|t5viar|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP T6viaR|t6viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T6viaR|t6viar|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP T7viaR|t7viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T7viaR|t7viar|NN _|_|CD SR3|sr3|NN
E.coli|e.coli|NNS _|_|VBP T8viaR|t8viar|NN _|_|CD SR2|sr2|NN
E.coli|e.coli|NNS _|_|VBP T8viaR|t8viar|NN _|_|CD SR3|sr3|NN
E.|E.|NNP coli|coli|NN -|-|: TAP|tap|NN
E.|e.|FW coli|coli|FW +|+|CC TAP|tap|FW
Ecoli|ecoli|FW _|_|FW Temperature|temperature|NN upshift|upshift|NN in|in|IN gyrBT|gyrBT|NNP mutant|mutant|JJ T1|t1|NN
Ecoli|Ecoli|NNP _|_|NNP Temperature|Temperature|NNP upshift|upshift|NN in|in|IN gyrBT|gyrBT|NNP mutant|mutant|JJ T2|t2|NN
Ecoli|Ecoli|NNP _|_|NNP Temperature|Temperature|NNP upshift|upshift|NN in|in|IN gyrBT|gyrBT|NNP mutant|mutant|JJ T3|t3|NN
Ecoli|Ecoli|NNP _|_|NNP Temperature|Temperature|NNP upshift|upshift|NN in|in|IN gyrBT|gyrBT|NNP mutant|mutant|JJ T4|t4|NN
E.|e.|FW coli|coli|FW TolC|tolc|NN cells|cell|NNS were|be|VBD grown|grow|VBN o/n|o/n|RB in|in|IN LB|lb|NN medium|medium|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC 200|200|CD rpm|rpm|NN .|.|.
E|e|NN _|_|CD coli|coli|NN _|_|NN transcriptome|transcriptome|NN _|_|NN 1|1|CD
E|e|NN _|_|CD coli|coli|NN _|_|NN transcriptome|transcriptome|NN _|_|NN 2|2|CD
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 15h|15h|CD _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 15h|15h|CD _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 15h|15h|CD _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 8|8|CD min|min|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 8|8|CD min|min|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM powerline|powerline|FW _|_|FW interm|interm|FW _|_|SYM 8|8|CD min|min|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 15h|15h|CD _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 15h|15h|CD _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 15h|15h|CD _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|SYM 2.5|2.5|CD h|h|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|NN 8|8|CD min|min|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|NN 8|8|CD min|min|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN cont|cont|NN _|_|NN 8|8|CD min|min|NN _|_|CD rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 15h|15h|JJ _|_|NN rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 15h|15h|JJ _|_|NN rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 15h|15h|JJ _|_|NN rep3|rep3|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 2.5|2.5|CD h|h|NN _|_|CD rep1|rep1|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 2.5|2.5|CD h|h|NN _|_|CD rep2|rep2|NN
E|e|NN _|_|CD coli|coli|NN _|_|NN treated|treat|VBN _|_|SYM sinusoidal|sinusoidal|JJ _|_|NN interm|interm|NN _|_|CD 2.5|2.5|CD h|h|NN _|_|CD rep3|rep3|NN
E.|e.|FW coli|coli|FW treated|treat|VBN with|with|IN bicontinious|bicontinious|JJ microemulsion|microemulsion|NN
E.|E.|NNP coli|coli|NNS treated|treat|VBN with|with|IN o/w|o/w|NN microemulsion|microemulsion|NN
E.|E.|NNP coli|coli|NNS treated|treat|VBN with|with|IN w/o|w/o|NN microemulsion|microemulsion|NN
E.|E.|NNP Coli|Coli|NNP TrpR|trpr|NN ChIP|chip|NN DNA|dna|NN glucose|glucose|NN
E.|E.|NNP Coli|Coli|NNP TrpR|trpr|NN ChIP|chip|NN DNA|dna|NN Tryptophan|tryptophan|NN
E.|e.|FW coli|coli|FW Type|type|NN _|_|CD II|ii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD II|ii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD II|ii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW Type|type|NN _|_|CD II|ii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD II|ii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD II|ii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW Type|type|NN _|_|CD III|iii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD III|iii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD III|iii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 37ºC|37ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|e.|FW coli|coli|FW Type|type|NN _|_|CD III|iii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 1|1|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD III|iii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 2|2|CD
E.|E.|NNP coli|coli|NN Type|type|NN _|_|CD III|iii|CD genotype|genotype|NN strain|strain|NN ,|,|, under|under|IN 45ºC|45ºc|NN ,|,|, rep|rep|NN 3|3|CD
E.|E.|NNP coli|coli|NN ,|,|, unlimited|unlimited|JJ growth|growth|NN -LRB-|-lrb-|-LRB- batch|batch|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW ,|,|, unlimited|unlimited|JJ growth|growth|NN -LRB-|-lrb-|-LRB- batch|batch|NN -RRB-|-rrb-|-RRB-
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 0|0|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 30|30|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 60|60|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN ccdB|ccdb|NN upregulation|upregulation|NN 90|90|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 0|0|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 30|30|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 60|60|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W1863|w1863|NN wt|wt|JJ lambda|lambda|NN -|-|: with|with|IN lacZ|lacz|NN upregulation|upregulation|NN 90|90|CD minutes|minute|NNS after|after|IN induction|induction|NN
E.coli|e.coli|NN W3110|w3110|NN ,|,|, 15|15|CD minutes|minute|NNS after|after|IN oxygen|oxygen|NN downshift|downshift|NN ,|,|, sample|sample|NN S2|s2|NN
E.coli|e.coli|NN W3110|w3110|NN ,|,|, 15|15|CD minutes|minute|NNS before|before|IN oxygen|oxygen|NN downshift|downshift|NN ,|,|, sample|sample|NN S1|s1|NN
ecoli|ecolus|NNS _|_|VBP W3110|w3110|NN _|_|SYM 2x|2x|FW _|_|FW v2|v2|FW
ecoli|ecolus|NNS _|_|VBP W3110|w3110|NN _|_|SYM 3x|3x|FW _|_|FW v2|v2|FW
E.coli|e.coli|NN W3110|w3110|NN ,|,|, 45|45|CD minutes|minute|NNS after|after|IN oxygen|oxygen|NN downshift|downshift|NN ,|,|, sample|sample|NN S3|s3|NN
ecoli|ecolus|NNS _|_|VBP W3110|w3110|NN _|_|SYM 4x|4x|FW _|_|FW v2|v2|FW
E.coli|e.coli|NN W3110|w3110|NN ,|,|, 75|75|CD minutes|minute|NNS after|after|IN oxygen|oxygen|NN downshift|downshift|NN ,|,|, sample|sample|NN S4|s4|NN
E.|e.|FW coli|coli|FW W3110|w3110|NN -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110|w3110|NN expressing|express|VBG PCK|pck|NN
E.|e.|FW coli|coli|FW W3110|w3110|NN expressing|express|VBG ppc|ppc|NN
E.|e.|FW coli|coli|FW W3110|w3110|NN expressing|express|VBG ppc|ppc|NN at|at|IN LB-GlC|lb-glc|JJ medium|medium|NN ,|,|, D|d|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN
E.coli|e.coli|NN W3110|w3110|NN ,|,|, fermentation|fermentation|NN sample|sample|NN taken|take|VBN 15|15|CD minutes|minute|NNS after|after|IN oxygen|oxygen|NN downshift|downshift|NN
E.coli|e.coli|NN W3110|w3110|NN ,|,|, fermentation|fermentation|NN sample|sample|NN taken|take|VBN 15|15|CD minutes|minute|NNS before|before|IN oxygen|oxygen|NN downshift|downshift|NN
E.coli|e.coli|NN W3110|w3110|NN ,|,|, fermentation|fermentation|NN sample|sample|NN taken|take|VBN 45|45|CD minutes|minute|NNS after|after|IN oxygen|oxygen|NN downshift|downshift|NN
E.coli|e.coli|NN W3110|w3110|NN ,|,|, fermentation|fermentation|NN sample|sample|NN taken|take|VBN 75|75|CD minutes|minute|NNS after|after|IN oxygen|oxygen|NN downshift|downshift|NN
E.|E.|NNP coli|coli|NN W3110|w3110|NN grown|grow|VBN at|at|IN glucose-minimal|glucose-minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN induction|induction|NN -RRB-|-rrb-|-RRB- in|in|IN early|early|JJ log|log|NN phase|phase|NN -LRB-|-lrb-|-LRB- u|u|NN =|=|JJ 0.25|0.25|CD h-1|h-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110|w3110|NN grown|grow|VBN at|at|IN LB-glucose|lb-glucose|JJ medium|medium|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN induction|induction|NN -RRB-|-rrb-|-RRB- in|in|IN chemostat|chemostat|NN -LRB-|-lrb-|-LRB- D|d|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110|w3110|NN -LRB-|-lrb-|-LRB- KCTC|kctc|NN 2223|2223|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110|w3110|NN -LRB-|-lrb-|-LRB- KCTC|kctc|NN 2223|2223|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110|w3110|NN -LRB-|-lrb-|-LRB- KCTC|kctc|NN 2223|2223|CD -RRB-|-rrb-|-RRB- at|at|IN LB-GlC|lb-glc|JJ medium|medium|NN ,|,|, D|d|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN
E.|E.|NNP coli|coli|NN W3110/pck|w3110/pck|NN grown|grow|VBN at|at|IN LB-glucose|lb-glucose|JJ medium|medium|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN induction|induction|NN -RRB-|-rrb-|-RRB- in|in|IN chemostat|chemostat|NN -LRB-|-lrb-|-LRB- D|d|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110/PCK|w3110/pck|NN with|with|IN glucose-minimal|glucose-minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN induced|induce|VBN -RRB-|-rrb-|-RRB- at|at|IN early|early|JJ log|log|NN phase|phase|NN -LRB-|-lrb-|-LRB- u|u|NN =|=|JJ 0.25|0.25|CD -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110/ppc|w3110/ppc|NN grown|grow|VBN at|at|IN glucose-minimal|glucose-minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN induction|induction|NN -RRB-|-rrb-|-RRB- in|in|IN early|early|JJ log|log|NN phase|phase|NN -LRB-|-lrb-|-LRB- u|u|NN =|=|JJ 0.25|0.25|CD h-1|h-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110/ppc|w3110/ppc|NN grown|grow|VBN at|at|IN LB-glucose|lb-glucose|JJ medium|medium|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN induction|induction|NN -RRB-|-rrb-|-RRB- in|in|IN chemostat|chemostat|NN -LRB-|-lrb-|-LRB- D|d|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN -RRB-|-rrb-|-RRB-
E.|e.|FW coli|coli|FW W3110|w3110|NN with|with|IN glucose-minimal|glucose-minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN induced|induce|VBN -RRB-|-rrb-|-RRB- at|at|IN early|early|JJ log|log|NN phase|phase|NN -LRB-|-lrb-|-LRB- u|u|NN =|=|JJ 0.25|0.25|CD -RRB-|-rrb-|-RRB-
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 7|7|CD in|in|IN the|the|DT presence|presence|NN of|of|IN 5.4|5.4|CD µM|µm|NN -LRB-|-lrb-|-LRB- 1|1|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- total|total|JJ cadmium|cadmium|NN ,|,|, added|add|VBD as|as|IN CdCl2|cdcl2|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 15|15|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 7|7|CD .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 15|15|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 7|7|CD .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO four|four|CD 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 5|5|CD in|in|IN the|the|DT presence|presence|NN of|of|IN 5.4|5.4|CD µM|µm|NN -LRB-|-lrb-|-LRB- 1|1|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- total|total|JJ cadmium|cadmium|NN ,|,|, added|add|VBD as|as|IN CdCl2|cdcl2|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 15|15|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO four|four|CD 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 5|5|CD in|in|IN the|the|DT presence|presence|NN of|of|IN 5.4|5.4|CD µM|µm|NN -LRB-|-lrb-|-LRB- 1|1|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- total|total|JJ cadmium|cadmium|NN ,|,|, added|add|VBD as|as|IN CdCl2|cdcl2|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO four|four|CD 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 5|5|CD in|in|IN the|the|DT presence|presence|NN of|of|IN 5.4|5.4|CD µM|µm|NN -LRB-|-lrb-|-LRB- 1|1|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- total|total|JJ cadmium|cadmium|NN ,|,|, added|add|VBD as|as|IN CdCl2|cdcl2|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO four|four|CD 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 5|5|CD .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 15|15|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO four|four|CD 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 5|5|CD .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO four|four|CD 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 7|7|CD in|in|IN the|the|DT presence|presence|NN of|of|IN 5.4|5.4|CD µM|µm|NN -LRB-|-lrb-|-LRB- 1|1|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- total|total|JJ cadmium|cadmium|NN ,|,|, added|add|VBD as|as|IN CdCl2|cdcl2|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN in|in|IN M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.4|0.4|CD %|%|NN glucose|glucose|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN until|until|IN the|the|DT contents|contents|NNS of|of|IN the|the|DT flask|flask|NN reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN 0.3|0.3|CD -LRB-|-lrb-|-LRB- mid-log|mid-log|JJ phase|phase|NN of|of|IN growth|growth|NN -RRB-|-rrb-|-RRB- .|.|. Each|each|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN 25|25|CD mL|ml|NN aliquots|aliquot|NNS ,|,|, transferred|transfer|VBN to|to|TO four|four|CD 50|50|CD mL|ml|NN conical|conical|JJ tubes|tube|NNS ,|,|, and|and|CC centrifuged|centrifuge|VBD at|at|IN 2540|2540|CD x|x|CC g|g|NN for|for|IN 12|12|CD minutes|minute|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN ,|,|, and|and|CC the|the|DT cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 25|25|CD mL|ml|NN of|of|IN M9|m9|NN medium|medium|NN at|at|IN pH|ph|NN 7|7|CD in|in|IN the|the|DT presence|presence|NN of|of|IN 5.4|5.4|CD µM|µm|NN -LRB-|-lrb-|-LRB- 1|1|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB- total|total|JJ cadmium|cadmium|NN ,|,|, added|add|VBD as|as|IN CdCl2|cdcl2|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 25|25|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS with|with|IN manual|manual|JJ rotations|rotation|NNS of|of|IN the|the|DT flasks|flask|NNS once|once|RB per|per|IN minute|minute|NN to|to|TO resuspend|resuspend|VB the|the|DT cells|cell|NNS .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN in|in|IN glucose|glucose|NN minimal|minimal|JJ medium|medium|NN in|in|IN the|the|DT presence|presence|NN of|of|IN the|the|DT osmoprotectant|osmoprotectant|JJ glycine|glycine|NN beatine|beatine|NN with|with|IN a|a|DT range|range|NN of|of|IN salt|salt|NN concentrations|concentration|NNS at|at|IN 2|2|CD ,|,|, 3.5|3.5|CD -LRB-|-lrb-|-LRB- 2|2|CD repeats|repeat|NNS -RRB-|-rrb-|-RRB- ,|,|, 4.5|4.5|CD ,|,|, 5|5|CD and|and|CC 5.5|5.5|CD %|%|NN NaCl|nacl|NN .|.|. E.|e.|FW coli|coli|FW were|be|VBD inoculated|inoculate|VBN at|at|IN 104|104|CD cfu/ml|cfu/ml|NN and|and|CC cultures|culture|NNS incubated|incubate|VBN to|to|TO reach|reach|VB 107|107|CD cfu/ml|cfu/ml|NN ,|,|, an|a|DT ODs|od|NNS of|of|IN about|about|RB 0.03|0.03|CD -LRB-|-lrb-|-LRB- cultures|culture|NNS entered|enter|VBD stationary|stationary|JJ phase|phase|NN at|at|IN 108|108|CD cfu/ml|cfu/ml|NN -RRB-|-rrb-|-RRB- before|before|IN harvesting|harvest|VBG .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN in|in|IN the|the|DT presence|presence|NN of|of|IN dimethyl|dimethyl|JJ sulfoxide|sulfoxide|NN -LRB-|-lrb-|-LRB- DMSO|dmso|NN -RRB-|-rrb-|-RRB- -|-|: dissolved|dissolve|VBN cholic|cholic|JJ acid|acid|NN at|at|IN 1|1|CD mM|mm|NN final|final|JJ culture|culture|NN concentration|concentration|NN .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN in|in|IN the|the|DT presence|presence|NN of|of|IN dimethyl|dimethyl|JJ sulfoxide|sulfoxide|NN -LRB-|-lrb-|-LRB- DMSO|dmso|NN -RRB-|-rrb-|-RRB- -|-|: dissolved|dissolve|VBN estradiol|estradiol|NN at|at|IN 1|1|CD mM|mm|NN final|final|JJ culture|culture|NN concentration|concentration|NN .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN in|in|IN the|the|DT presence|presence|NN of|of|IN dimethyl|dimethyl|JJ sulfoxide|sulfoxide|NN -LRB-|-lrb-|-LRB- DMSO|dmso|NN -RRB-|-rrb-|-RRB- -|-|: dissolved|dissolve|VBN hydrocortisone|hydrocortisone|NN at|at|IN 1|1|CD mM|mm|NN final|final|JJ culture|culture|NN concentration|concentration|NN .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN in|in|IN the|the|DT presence|presence|NN of|of|IN dimethyl|dimethyl|JJ sulfoxide|sulfoxide|NN -LRB-|-lrb-|-LRB- DMSO|dmso|NN -RRB-|-rrb-|-RRB- -|-|: dissolved|dissolve|VBN progesterone|progesterone|NN at|at|IN 1|1|CD mM|mm|NN final|final|JJ culture|culture|NN concentration|concentration|NN .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- Miller|Miller|NNP -RRB-|-rrb-|-RRB- broth|broth|JJ medium|medium|NN at|at|IN 37C|37c|NN in|in|IN the|the|DT presence|presence|NN of|of|IN dimethyl|dimethyl|JJ sulfoxide|sulfoxide|NN -LRB-|-lrb-|-LRB- DMSO|dmso|NN -RRB-|-rrb-|-RRB- -|-|: only|only|RB steroid|steroid|NN carrier|carrier|NN .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- O.D.|o.d.|NN 600nm|600nm|CD 0.3-0.4|0.3-0.4|CD -RRB-|-rrb-|-RRB- in|in|IN Lennox|Lennox|NNP LB|LB|NNP broth|broth|NN -LRB-|-lrb-|-LRB- Becton|Becton|NNP Dickinson|Dickinson|NNP ,|,|, Franklin|Franklin|NNP Lakes|Lakes|NNP ,|,|, NJ|NJ|NNP -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN .|.|.
E.|E.|NNP coli|coli|NN was|be|VBD treated|treat|VBN at|at|IN 37C|37c|NN aerobically|aerobically|RB with|with|IN shaking|shake|VBG with|with|IN BSA|bsa|NN -LRB-|-lrb-|-LRB- control|control|NN ,|,|, 100|100|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- ,|,|, PGRP|pgrp|NN -LRB-|-lrb-|-LRB- human|human|JJ recombinant|recombinant|JJ PGLYRP4|pglyrp4|NN ,|,|, 100|100|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- ,|,|, or|or|CC gentamicin|gentamicin|NN -LRB-|-lrb-|-LRB- 5|5|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD min|min|NN ,|,|, or|or|CC with|with|IN CCCP|cccp|NN -LRB-|-lrb-|-LRB- carbonyl|carbonyl|NN cyanide|cyanide|NN 3-chlorophenylhydrazone|3-chlorophenylhydrazone|NN ,|,|, 800|800|CD µM|µm|NN -RRB-|-rrb-|-RRB- for|for|IN 15|15|CD min|min|NN .|.|. Each|each|DT experiment|experiment|NN was|be|VBD repeated|repeat|VBN 3|3|CD times|time|NNS .|.|.
E.|E.|NNP coli|coli|NNS were|be|VBD grown|grow|VBN in|in|IN defined|define|VBN rich|rich|JJ media|media|NNS at|at|IN 30C|30C|NNP .|.|.
E.|E.|NNP coli|coli|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN or|or|CC minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN casaminoacids|casaminoacid|NNS -LRB-|-lrb-|-LRB- 0,1|0,1|CD %|%|NN -RRB-|-rrb-|-RRB- and|and|CC succinate|succinate|NN -LRB-|-lrb-|-LRB- 0,1|0,1|CD %|%|NN -RRB-|-rrb-|-RRB- until|until|IN OD|od|NN 0,2-0,4|0,2-0,4|CD
E.|E.|NNP coli|coli|NNS were|be|VBD incubated|incubate|VBN in|in|IN S-Basal|s-basal|JJ complete|complete|JJ medium|medium|NN alone|alone|RB or|or|CC in|in|IN the|the|DT presence|presence|NN of|of|IN C.|C.|NNP elegans|elegan|NNS ,|,|, Giardia|Giardia|NNP conditioned|condition|VBD meida|meida|NN ,|,|, and|and|CC both|both|DT C.|c.|FW elegans|elegan|NNS and|and|CC Giardia|Giardia|NNP conditioned|condition|VBN media|media|NNS .|.|.
E.|E.|NNP coli|coli|NNS were|be|VBD sampled|sample|VBN at|at|IN times|time|NNS =|=|JJ 0|0|CD ,|,|, 1|1|CD hour|hour|NN ,|,|, and|and|CC 2|2|CD hours|hour|NNS following|follow|VBG release|release|NN from|from|IN stationary|stationary|JJ phase|phase|NN .|.|.
Ecoli|Ecoli|NNP _|_|SYM wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample1|sample1|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample1|sample1|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample4|sample4|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD butanol|butanol|NN _|_|SYM Sample4|sample4|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample2|sample2|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|NN Sample4|sample4|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample5|sample5|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 1|1|CD %|%|NN _|_|CD isobutanol|isobutanol|NN _|_|SYM Sample5|sample5|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|SYM Sample1|sample1|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|NN Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|SYM Sample3|sample3|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|SYM Sample4|sample4|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN 3|3|CD %|%|NN _|_|CD ethanol|ethanol|NN _|_|SYM Sample4|sample4|FW _|_|FW TechRep2|techrep2|NN
E.|e.|FW coli|coli|FW wild-type|wild-type|JJ ,|,|, A600|a600|NN =|=|JJ 0.2|0.2|CD on|on|IN mucus|mucus|NN
E.|E.|NNP coli|coli|NN wild-type|wild-type|JJ ,|,|, A600|a600|NN =|=|JJ 0.4|0.4|CD on|on|IN glucose|glucose|NN
E.|e.|FW coli|coli|FW wild-type|wild-type|JJ ,|,|, A600|a600|NN =|=|JJ 0.4|0.4|CD on|on|IN mannose|mannose|NN
E.|e.|FW coli|coli|FW wild-type|wild-type|JJ ,|,|, A600|a600|NN =|=|JJ 0.5|0.5|CD on|on|IN mucus|mucus|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD acetate|acetate|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD acetate|acetate|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN and|and|CC its|its|PRP$ mutants|mutant|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN with|with|IN 10mM|10mm|NN glucose|glucose|NN or|or|CC 30mM|30mm|NN acetate|acetate|NN as|as|IN sole|sole|JJ carbon|carbon|NN source|source|NN .|.|. Samples|sample|NNS for|for|IN RNA|rna|NN extraction|extraction|NN were|be|VBD taken|take|VBN in|in|IN middle|middle|JJ exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ≈|≈|CD 0.5|0.5|CD -RRB-|-rrb-|-RRB- and|and|CC in|in|IN stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ≈|≈|CD 1.5|1.5|CD -RRB-|-rrb-|-RRB-
Ecoli|Ecoli|NNP _|_|SYM wildtype|wildtype|JJ _|_|NN calibration|calibration|NN _|_|CD Sample1|sample1|NN _|_|CD TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN calibration|calibration|NN _|_|CD Sample1|sample1|NN _|_|CD TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN calibration|calibration|NN _|_|SYM Sample2|sample2|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP wildtype|wildtype|JJ _|_|NN calibration|calibration|NN _|_|CD Sample2|sample2|NN _|_|CD TechRep2|techrep2|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD glucose|glucose|NN _|_|NN exponential|exponential|JJ phase|phase|NN _|_|NN repl2|repl2|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|NN repl1|repl1|NN
E.|E.|NNP coli|coli|NN Wild|Wild|NNP type|type|NN _|_|CD glucose|glucose|NN _|_|NN stationary|stationary|JJ phase|phase|NN _|_|SYM repl2|repl2|CD
Ecoli|ecoli|JJ wildtype|wildtype|JJ grown|grow|VBN in|in|IN MOPS|MOPS|NNP
Ecoli|Ecoli|NNP wildtype|wildtype|JJ grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN butanol|butanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP wildtype|wildtype|JJ grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP wildtype|wildtype|JJ grown|grow|VBN in|in|IN MOPS|MOPS|NNP ,|,|, 10|10|CD minutes|minute|NNS after|after|IN 3|3|CD %|%|NN ethanol|ethanol|NN treatment|treatment|NN
Ecoli|Ecoli|NNP _|_|NNP wild-type|wild-type|JJ _|_|NN rep1|rep1|NN _|_|NN anaerobic|anaerobic|JJ
Ecoli|ecolus|NNS _|_|VBP wild-type|wild-type|JJ _|_|NN rep2|rep2|NN _|_|CD anaerobic|anaerobic|JJ
E.|E.|NNP coli|coli|NN without|without|IN microemulsion|microemulsion|NN treatment|treatment|NN
Ecoli|Ecoli|NNP _|_|NNP WT|WT|NNP _|_|NNP 100uM|100uM|NNP _|_|SYM KCN|KCN|NNP _|_|SYM Sample1|sample1|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP WT|wt|JJ _|_|NN 100uM|100um|NN _|_|CD KCN|KCN|NNP _|_|SYM Sample1|sample1|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP WT|wt|JJ _|_|NN 100uM|100um|NN _|_|CD KCN|KCN|NNP _|_|SYM Sample2|sample2|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP WT|wt|JJ _|_|NN 100uM|100um|NN _|_|CD KCN|KCN|NNP _|_|SYM Sample2|sample2|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP WT|wt|JJ _|_|NN 100uM|100um|NN _|_|CD KCN|KCN|NNP _|_|SYM Sample3|sample3|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP WT|wt|JJ _|_|NN 100uM|100um|NN _|_|CD KCN|KCN|NNP _|_|SYM Sample3|sample3|FW _|_|FW TechRep2|techrep2|NN
Ecoli|ecolus|NNS _|_|VBP WT|wt|JJ _|_|NN 100uM|100um|NN _|_|CD KCN|KCN|NNP _|_|SYM Sample4|sample4|FW _|_|FW TechRep1|techrep1|NN
Ecoli|ecolus|NNS _|_|VBP WT|wt|JJ _|_|NN 100uM|100um|NN _|_|CD KCN|KCN|NNP _|_|SYM Sample4|sample4|FW _|_|FW TechRep2|techrep2|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN acetate|acetate|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN exponential|exponential|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep1|rep1|NN
E.|e.|FW coli|coli|FW wt|wt|JJ grown|grow|VBN in|in|IN glucose|glucose|NN batch|batch|NN minimal|minimal|JJ media|media|NNS ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN at|at|IN stationary|stationary|JJ phase|phase|NN ,|,|, biological|biological|JJ rep2|rep2|NN
E.coli|e.coli|NNS _|_|VBP WT|wt|JJ pH|ph|NN 5.6|5.6|CD A|a|DT
E.coli|e.coli|NN _|_|CD WT|WT|NNP pH|ph|NN 5.6|5.6|CD B|b|NN
E.coli|e.coli|NNS _|_|VBP WT|wt|JJ pH|ph|NN 5.6|5.6|CD C|c|NN
E.coli|e.coli|NNS _|_|VBP WT|wt|JJ pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN A|a|NN
E.coli|e.coli|NNS _|_|VBP WT|wt|JJ pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN B|b|NN
E.coli|e.coli|NNS _|_|VBP WT|wt|JJ pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN C|c|NN
Ecoli|Ecoli|NNP _|_|NNP WT|WT|NNP _|_|NNP RNAseq|RNAseq|NNP
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|NN 0|0|CD min|min|NN _|_|NN A|a|NN
Eco|eco|NN _|_|CD TolC|tolc|NN _|_|NN 0|0|CD min|min|NN _|_|NN B|b|NN
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 15|15|CD min|min|NN _|_|CD Carolacton|Carolacton|NNP _|_|NNP A|A|NNP
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 15|15|CD min|min|NN _|_|CD Carolacton|Carolacton|NNP _|_|NN B|b|NN
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 15|15|CD min|min|NN _|_|NN control|control|NN _|_|CD A|a|DT
Eco|eco|NN _|_|CD TolC|tolc|NN _|_|CD 15|15|CD min|min|NN _|_|NN control|control|NN _|_|CD B|b|NN
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 30|30|CD min|min|NN _|_|CD Carolacton|Carolacton|NNP _|_|NNP A|A|NNP
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 30|30|CD min|min|NN _|_|CD Carolacton|Carolacton|NNP _|_|NN B|b|NN
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 30|30|CD min|min|NN _|_|NN control|control|NN _|_|CD A|a|DT
Eco|eco|NN _|_|CD TolC|tolc|NN _|_|CD 30|30|CD min|min|NN _|_|NN control|control|NN _|_|CD B|b|NN
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 5|5|CD min|min|NN _|_|CD Carolacton|Carolacton|NNP _|_|NNP A|A|NNP
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 5|5|CD min|min|NN _|_|CD Carolacton|Carolacton|NNP _|_|NN B|b|NN
Eco|Eco|NNP _|_|SYM TolC|tolc|NN _|_|CD 5|5|CD min|min|NN _|_|NN control|control|NN _|_|CD A|a|DT
Eco|eco|NN _|_|CD TolC|tolc|NN _|_|CD 5|5|CD min|min|NN _|_|NN control|control|NN _|_|NN B|b|NN
Ec-pR|ec-pr|NN VS|vs|NN Ec-1558|ec-1558|NN rep1|rep1|NN
Ec-pR|ec-pr|NN VS|vs|NN Ec-1558|ec-1558|NN rep2|rep2|NN
Ec-pR|ec-pr|NN VS|vs|NN Ec-1558|ec-1558|NN rep3|rep3|NN
EC|EC|NNP _|_|VBD Trim1|trim1|NN _|_|NN DNA|dna|NN
EC|ec|NN _|_|CD Trim1|trim1|NN _|_|NN RNA|rna|NN
EC|ec|NN _|_|CD Trim2|trim2|NN _|_|NN DNA|dna|NN
EC|ec|NN _|_|CD Trim2|trim2|NN _|_|NN RNA|rna|NN
EDC1|edc1|NN _|_|CD AP|ap|NN
EDC1|edc1|NN _|_|CD Total|total|JJ
EDL932|edl932|NN exposure|exposure|NN to|to|TO CL|cl|NN MC|MC|NNP fraction|fraction|NN
EDL932|edl932|NN unexposed|unexposed|JJ
EDL933|edl933|NN 24|24|CD h|h|NN post|post|NN infection|infection|NN in|in|IN THP-1|thp-1|NN humans|human|NNS cells|cell|NNS
EDL933|edl933|NN 8h|8h|NN post-infection|post-infection|NN in|in|IN THP-1|thp-1|NN human|human|JJ cells|cell|NNS
EDL933|edl933|NN 8h|8h|NN post|post|NN THP-1|thp-1|NN infection|infection|NN
EDL|edl|NN 933|933|CD at|at|IN 37oC|37oc|NN at|at|IN OD|od|NN 1.0|1.0|CD
EDL933|edl933|NN cDNA|cdna|NN 24|24|CD h|h|NN post-infcetion|post-infcetion|NN of|of|IN THP-1|thp-1|NN human|human|JJ cells|cell|NNS
EDL933|edl933|NN cDNA|cdna|NN obtained|obtain|VBN 24|24|CD h|h|NN post|post|NN -|-|: infection|infection|NN of|of|IN THP-1|thp-1|NN human|human|JJ cells|cell|NNS
EDL933|edl933|NN cDNA|cdna|NN obtained|obtain|VBN 24h|24h|JJ post-infection|post-infection|NN of|of|IN THP-1|thp-1|NN human|human|JJ cells|cell|NNS
EDL933|edl933|NN from|from|IN overnight|overnight|JJ culture|culture|NN in|in|IN LB|lb|NN broth|broth|NN
EDL933|edl933|NN genomic|genomic|JJ DNA|dna|NN
EDL933|edl933|NN genomic|genomic|JJ DNA|dna|NN
EDL933|edl933|NN genommic|genommic|JJ DNA|dna|NN
EDL933|edl933|NN infection|infection|NN of|of|IN THP-1|thp-1|NN cells|cell|NNS ,|,|, recovered|recover|VBD 2|2|CD h|h|NN post-infection|post-infection|JJ
EDL933|edl933|NN infection|infection|NN of|of|IN THP-1|thp-1|NN cells|cell|NNS ,|,|, recovered|recover|VBD 2h|2h|JJ post-infection|post-infection|JJ
EDL933|edl933|NN in|in|IN humans|human|NNS macrophages|macrophage|NNS 8h|8h|VBP post-infection|post-infection|JJ
EDL933|edl933|NN in|in|IN RPMI|rpmi|NN medium|medium|NN
EDL933|edl933|NN in|in|IN THP-1|thp-1|NN cells|cell|NNS 8h|8h|VBP post-infection|post-infection|JJ
EDL933|edl933|NN _|_|CD LB|lb|NN _|_|NN I|I|PRP
EDL933|edl933|NN _|_|CD LB|lb|NN _|_|NN II|ii|CD
EDL|edl|NN 933|933|CD with|with|IN 0.1|0.1|CD mg/ml|mg/ml|NN IAN|IAN|NNP at|at|IN 37oC|37oC|NNP at|at|IN OD|OD|NNP 1.0|1.0|CD
EDL|edl|NN 933|933|CD with|with|IN 0.1|0.1|CD mg/ml|mg/ml|NN IAN|ian|NN at|at|IN 37oC|37oc|NN at|at|IN OD|od|NN 1.0|1.0|CD
EDL|edl|NN -LRB-|-lrb-|-LRB- O157|o157|NN :|:|: H7|h7|NN -RRB-|-rrb-|-RRB-
Efflux|efflux|NN Mutant|mutant|JJ Parent|Parent|NNP Strain|Strain|NNP
EGS084|egs084|NN
EGS084|egs084|NN _|_|NN control|control|NN _|_|CD rep|rep|NN _|_|NN 1|1|CD
EGS084|egs084|NN _|_|NN control|control|NN _|_|CD rep|rep|NN _|_|NN 2|2|CD
EGS084|egs084|NN _|_|NN control|control|NN _|_|CD rep|rep|NN _|_|NN 3|3|CD
EGS084|egs084|NN _|_|NN control|control|NN _|_|CD rep|rep|NN _|_|NN 4|4|CD
EGS084|egs084|NN _|_|NN control|control|NN _|_|CD rep|rep|NN _|_|SYM 5|5|CD
EGS084|egs084|NN _|_|NN control|control|NN _|_|CD rep|rep|NN _|_|NN 6|6|CD
EGS212|egs212|NN
EGS212|egs212|NN _|_|CD MlfabH|mlfabh|NN _|_|CD rep|rep|NN _|_|NN 1|1|CD
EGS212|egs212|NN _|_|CD MlfabH|mlfabh|NN _|_|CD rep|rep|NN _|_|NN 2|2|CD
EGS212|egs212|NN _|_|CD MlfabH|mlfabh|NN _|_|CD rep|rep|NN _|_|NN 3|3|CD
EGS212|egs212|NN _|_|CD MlfabH|mlfabh|NN _|_|CD rep|rep|NN _|_|NN 4|4|CD
EGS212|egs212|NN _|_|CD MlfabH|mlfabh|NN _|_|NN rep|rep|NN _|_|CD 5|5|CD
EHEC|ehec|NN
EHEC|ehec|NN either|either|CC grown|grow|VBN on|on|IN plain|plain|JJ LB|lb|NN plates|plate|NNS or|or|CC LB|lb|NN plates|plate|NNS containing|contain|VBG Symbioflor|symbioflor|NN within|within|IN the|the|DT agar|agar|NN
EHEC|ehec|NN in|in|IN LB|LB|NNP Experiment|Experiment|NNP 1|1|CD -LSB-|-lsb-|-LRB- RIBO-Seq|ribo-seq|NN -RSB-|-rsb-|-RRB-
EHEC|ehec|NN in|in|IN LB|LB|NNP Experiment|Experiment|NNP 1|1|CD -LSB-|-lsb-|-LRB- RNA-Seq|rna-seq|NN -RSB-|-rsb-|-RRB-
EHEC|ehec|NN in|in|IN LB|LB|NNP Experiment|Experiment|NNP 2|2|CD -LSB-|-lsb-|-LRB- RIBO-Seq|ribo-seq|NN -RSB-|-rsb-|-RRB-
EHEC|ehec|NN in|in|IN LB|LB|NNP Experiment|Experiment|NNP 2|2|CD -LSB-|-lsb-|-LRB- RNA-Seq|rna-seq|NN -RSB-|-rsb-|-RRB-
EHEC|ehec|NN LB|lb|NN 7|7|CD h|h|NN 7HI|7HI|NNP biofilm|biofilm|NN cells|cell|NNS
EHEC|ehec|NN LB|lb|NN 7|7|CD h|h|NN biofilm|biofilm|NN cells|cell|NNS
EHEC|ehec|NN LB|lb|NN 7|7|CD h|h|NN isatin|isatin|NN biofilm|biofilm|NN cells|cell|NNS
EHEC|ehec|NN LB|lb|NN 7|7|CD h|h|NN suspension|suspension|NN cells|cell|NNS
EHEC|ehec|NN plus|plus|CC Symbioflor|symbioflor|JJ
ehec|ehec|NN strain|strain|NN :|:|: 86-24|86-24|CD
EHEC|ehec|NN strain|strain|NN 86-24|86-24|CD
EJW3|ejw3|NN ,|,|, BW25113|bw25113|NN rpoC|rpoc|NN K370|k370|NN _|_|CD A396dup|a396dup|NN
EJW3|ejw3|NN in|in|IN M9|m9|NN Replicate|replicate|VB 1|1|CD
EJW3|ejw3|NN in|in|IN M9|m9|NN Replicate|replicate|VB 2|2|CD
EJW3|ejw3|NN in|in|IN M9|m9|NN supplemented|supplement|VBN with|with|IN 0.6|0.6|CD M|m|NN NaCl|nacl|NN Replicate|replicate|VB 1|1|CD
EJW3|ejw3|NN in|in|IN M9|m9|NN supplemented|supplement|VBN with|with|IN 0.6|0.6|CD M|m|NN NaCl|nacl|NN Replicate|replicate|VB 2|2|CD
Elements|element|NNS with|with|IN poor|poor|JJ spot|spot|NN morphology|morphology|NN or|or|CC exhibiting|exhibit|VBG uneven|uneven|JJ hybridization|hybridization|NN caused|cause|VBN by|by|IN dust|dust|NN particles|particle|NNS or|or|CC scratches|scratch|NNS ,|,|, were|be|VBD flagged|flag|VBN manually|manually|RB and|and|CC excluded|exclude|VBN from|from|IN further|further|JJ analyses|analysis|NNS .|.|. After|after|IN local|local|JJ background|background|NN subtraction|subtraction|NN and|and|CC global|global|JJ normalization|normalization|NN relative|relative|JJ to|to|TO the|the|DT genomic|genomic|JJ DNA|dna|NN reference|reference|NN ,|,|, duplicate|duplicate|VB measurements|measurement|NNS on|on|IN the|the|DT same|same|JJ array|array|NN were|be|VBD averaged|average|VBN ,|,|, yielding|yield|VBG a|a|DT single|single|JJ vector|vector|NN for|for|IN each|each|DT time-point|time-point|NN across|across|IN a|a|DT perturbation|perturbation|NN .|.|. The|the|DT data|datum|NNS from|from|IN all|all|DT hybridizations|hybridization|NNS were|be|VBD combined|combine|VBN into|into|IN a|a|DT matrix|matrix|NN and|and|CC scaled|scale|VBD relative|relative|JJ to|to|TO each|each|DT other|other|JJ using|use|VBG quantile-normalization|quantile-normalization|NN as|as|IN implemented|implement|VBN in|in|IN the|the|DT Matlab|Matlab|NNP Bioinformatics|Bioinformatics|NNPS toolbox|toolbox|NN .|.|. Biological|biological|JJ duplicates|duplicate|NNS from|from|IN all|all|DT experiments|experiment|NNS were|be|VBD averaged|average|VBN ,|,|, leading|lead|VBG to|to|TO a|a|DT single|single|JJ set|set|NN of|of|IN time-series|time-series|NNS data|datum|NNS for|for|IN each|each|DT perturbation|perturbation|NN .|.|. Seven|seven|CD time-points|time-point|NNS were|be|VBD assayed|assay|VBN for|for|IN each|each|DT perturbation|perturbation|NN ,|,|, corresponding|correspond|VBG to|to|TO 0|0|CD ,|,|, 4|4|CD ,|,|, 8|8|CD ,|,|, 12|12|CD ,|,|, 20|20|CD ,|,|, 28|28|CD ,|,|, and|and|CC 44|44|CD minutes|minute|NNS post|post|JJ transition|transition|NN .|.|.
EM1456|em1456|NN wild-type|wild-type|JJ pNM12|pnm12|NN #|#|# 1|1|CD +|+|CC arabinose|arabinose|NN
Emplty|Emplty|NNP Vector|Vector|NNP ,|,|, 37|37|CD °C|°c|NN ,|,|, replicate|replicate|VB 1|1|CD
Emplty|Emplty|NNP Vector|Vector|NNP ,|,|, 37|37|CD °C|°c|NN ,|,|, replicate|replicate|VB 2|2|CD
Emplty|Emplty|NNP Vector|Vector|NNP ,|,|, 37|37|CD °C|°c|NN ,|,|, replicate|replicate|VB 3|3|CD
Emplty|Emplty|NNP Vector|Vector|NNP ,|,|, 42|42|CD °C|°c|NN ,|,|, replicate|replicate|VB 1|1|CD
Emplty|Emplty|NNP Vector|Vector|NNP ,|,|, 42|42|CD °C|°c|NN ,|,|, replicate|replicate|VB 2|2|CD
Emplty|Emplty|NNP Vector|Vector|NNP ,|,|, 42|42|CD °C|°c|NN ,|,|, replicate|replicate|VB 3|3|CD
emptyvec|emptyvec|NN _|_|NN mRNA|mrna|NN _|_|SYM 5m|5m|FW _|_|FW rep1|rep1|NN
emptyvec|emptyvec|NN _|_|NN mRNA|mrna|NN _|_|SYM 5m|5m|FW _|_|FW rep2|rep2|NN
EmptyVector|EmptyVector|NNP _|_|SYM 37|37|CD _|_|CD rep1|rep1|NN
EmptyVector|EmptyVector|NNP _|_|SYM 37|37|CD _|_|CD rep2|rep2|NN
EmptyVector|EmptyVector|NNP _|_|SYM 37|37|CD _|_|CD rep3|rep3|NN
EmptyVector|EmptyVector|NNP _|_|SYM 42|42|CD _|_|CD rep1|rep1|NN
EmptyVector|EmptyVector|NNP _|_|SYM 42|42|CD _|_|CD rep2|rep2|NN
EmptyVector|EmptyVector|NNP _|_|SYM 42|42|CD _|_|CD rep3|rep3|NN
emptyvec|emptyvec|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 30m|30m|FW _|_|FW rep1|rep1|NN
emptyvec|emptyvec|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 30m|30m|FW _|_|FW rep2|rep2|NN
emptyvec|emptyvec|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 5m|5m|FW _|_|FW rep1|rep1|NN
emptyvec|emptyvec|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 5m|5m|FW _|_|FW rep2|rep2|NN
emrR|emrr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
emrR|emrr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
emrR|emrr|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- fis|fi|VBZ early-exponential|early-exponential|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- fis|fi|VBZ mid-exponential|mid-exponential|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- H-NS|h-ns|NN early-exponential|early-exponential|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- H-NS|h-ns|NN mid-exponential|mid-exponential|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- H-NS|h-ns|NN stationary|stationary|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- H-NS|h-ns|NN transition-to-stationary|transition-to-stationary|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- rpo|rpo|NN delfis|delfi|VBZ mid-exponential|mid-exponential|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- rpo|rpo|NN delhns|delhn|VBZ mid-exponential|mid-exponential|JJ
-LSB-|-lsb-|-LRB- E-MTAB-332|e-mtab-332|NN -RSB-|-rsb-|-RRB- rpo|rpo|NN wt|wt|JJ mid-exponential|mid-exponential|JJ
Eno|eno|NN -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40mM|40mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40mM|40mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40mM|40mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1.5|1.5|CD '|'|'' post|post|JJ rif|rif|NN
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40mM|40mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3.0|3.0|CD '|'|'' post|post|JJ rif|rif|NN
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40mM|40mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
Eno|Eno|NNP -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40mM|40mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6.0|6.0|CD '|'|'' post|post|JJ rif|rif|NN
∆|∆|CD entC|entc|NN parent|parent|NN Sample|sample|NN 12|12|CD
∆|∆|CD entC|entc|NN parent|parent|NN Sample|Sample|NNP 31|31|CD
∆|∆|CD entC|entc|NN parent|parent|NN Sample|sample|NN 50|50|CD
entC|entc|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|Sample|NNP 13|13|CD
entC|entc|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 32|32|CD
entC|entc|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 51|51|CD
entC|entc|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 14|14|CD
entC|entc|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 33|33|CD
entC|entc|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 52|52|CD
entC|entc|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|Sample|NNP 15|15|CD
entC|entc|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 34|34|CD
entC|entc|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 53|53|CD
Enteroheamorragic|enteroheamorragic|JJ E.|e.|FW coli|coli|FW
enterohemorrhagic|enterohemorrhagic|JJ E.|e.|FW coli|coli|FW _|_|SYM 172mM|172mm|NN short|short|JJ chain|chain|NN fatty|fatty|JJ acid|acid|NN mix|mix|NN
enterohemorrhagic|enterohemorrhagic|JJ E.|e.|FW coli|coli|FW _|_|SYM 30mM|30mM|NNP short|short|JJ chain|chain|NN fatty|fatty|JJ acid|acid|NN mix|mix|NN
Enterohemorrhagic|enterohemorrhagic|JJ Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN strain|strain|NN EDL933|edl933|NN
Enteropathogenic|enteropathogenic|JJ E.|e.|FW coli|coli|FW
entF|entf|NN KO|ko|NN rep1|rep1|NN
entF|entf|NN KO|ko|NN rep2|rep2|NN
entF|entf|NN KO|ko|NN rep3|rep3|NN
envz3600|envz3600|NN
envz600|envz600|NN
envz900|envz900|NN
envzM1200|envzm1200|NN
envzM2400|envzm2400|NN
envzM3600|envzm3600|NN
envzM600|envzm600|NN
envzM900|envzm900|NN
Epicentre|Epicentre|NNP MasterPure|MasterPure|NNP RNA|rna|NN isolation|isolation|NN Kit|kit|NN ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP
era|era|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
era|era|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r2|r2|NN
era|era|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
era|era|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
ercc|ercc|NN spike-in|spike-in|NN :|:|: No|no|DT
ercc|ercc|NN spike-in|spike-in|NN :|:|: Prior|prior|RB to|to|TO extraction|extraction|NN
error-prone|error-prone|JJ in|in|FW vitro|vitro|FW -LRB-|-lrb-|-LRB- Mn2|mn2|NN +|+|CC -RRB-|-rrb-|-RRB-
error-prone|error-prone|JJ in|in|FW vitro|vitro|FW MnCl2|mncl2|NN
error-proof|error-proof|JJ in|in|FW vitro|vitro|FW 1|1|CD -LRB-|-lrb-|-LRB- GreAB/Mg2|greab/mg2|NN +|+|CC -RRB-|-rrb-|-RRB-
error-proof|error-proof|JJ in|in|FW vitro|vitro|FW 2|2|CD -LRB-|-lrb-|-LRB- GreAB/Mn2|greab/mn2|NN +|+|CC -RRB-|-rrb-|-RRB-
error-proof|error-proof|JJ in|in|FW vitro|vitro|FW MgCl2|mgcl2|NN +|+|CC GreAB|greab|NN
error-proof|error-proof|JJ in|in|FW vitro|vitro|FW MnCl2|mncl2|NN +|+|CC GreAB|greab|NN
Erythromycin|erythromycin|NN _|_|NN replicate|replicate|VBP _|_|SYM 1|1|CD
Erythromycin|erythromycin|NN _|_|NN replicate|replicate|VBP _|_|NN 2|2|CD
Erythromycin|Erythromycin|NNP _|_|NNP replicate|replicate|VB _|_|SYM 3|3|CD
ESBL019|esbl019|NN Coliform|coliform|NN
ESBL019|esbl019|NN Filamented|filamented|JJ
ESBL019|esbl019|NN Reverted|revert|VBD
ESBL019|esbl019|NN Transition|transition|NN
Escherchia|escherchia|FW coli|coli|FW HB101|hb101|NN
Escherchia|escherchia|FW coli|coli|FW HB101|hb101|NN exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS and|and|CC Giardia|Giardia|NNP for|for|IN 24|24|CD hours|hour|NNS
Escherchia|Escherchia|NNP coli|coli|NN HB101|hb101|NN exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS for|for|IN 24|24|CD hours|hour|NNS
Escherchia|Escherchia|NNP coli|coli|NN HB101|hb101|NN exposed|expose|VBN to|to|TO Giardia|Giardia|NNP for|for|IN 24|24|CD hours|hour|NNS
Escherichia|escherichia|FW coli|coli|FW
Escherichia|escherichia|FW coli|coli|FW 042|042|CD
Escherichia|escherichia|FW coli|coli|FW ,|,|, 0|0|CD µM|µm|NN AgNO3|agno3|NN
Escherichia|escherichia|FW coli|coli|FW ,|,|, 0|0|CD µM|µm|NN AgNO3|agno3|NN
Escherichia|escherichia|FW coli|coli|FW 0|0|CD min|min|NN vs|vs|CC 10|10|CD min|min|NN Rep1|rep1|NN
Escherichia|escherichia|FW coli|coli|FW 10|10|CD min|min|NN vs|vs|CC 0|0|CD min|min|NN Rep2|rep2|JJ
Escherichia|escherichia|FW coli|coli|FW 30|30|CD min|min|NN vs|vs|CC 60|60|CD min|min|NN Rep1|rep1|NN
Escherichia|escherichia|FW coli|coli|FW ,|,|, 5|5|CD µM|µm|NN AgNO3|agno3|NN
Escherichia|escherichia|FW coli|coli|FW 60|60|CD min|min|NN vs|vs|CC 30|30|CD min|min|NN Rep2|rep2|JJ
Escherichia|escherichia|FW coli|coli|FW ,|,|, 6.5|6.5|CD µM|µm|NN AgNO3|agno3|NN
Escherichia|escherichia|FW coli|coli|FW ,|,|, 8.5|8.5|CD µM|µm|NN AgNO3|agno3|NN
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD grown|grow|VBN in|in|IN DMEM|DMEM|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD grown|grow|VBN in|in|IN DMEM|dmem|NN with|with|IN AI3|ai3|NN
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD grown|grow|VBN in|in|IN DMEM|dmem|NN with|with|IN Epinephrine|epinephrine|NN
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD grown|grow|VBN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD kdpE|kdpe|NN deletion|deletion|NN mutant|mutant|JJ
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD kdpE|kdpe|NN deletion|deletion|NN mutant|mutant|JJ grown|grow|VBN in|in|IN DMEM|DMEM|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseB|qseb|NN deletion|deletion|NN mutant|mutant|JJ
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseB|qseb|NN deletion|deletion|NN mutant|mutant|JJ grown|grow|VBN in|in|IN DMEM|DMEM|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN deletion|deletion|NN mutant|mutant|JJ grown|grow|VBN in|in|IN DMEM|DMEM|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN deletion|deletion|NN mutant|mutant|JJ grown|grow|VBN in|in|IN DMEM|dmem|NN with|with|IN AI3|ai3|NN
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN deletion|deletion|NN mutant|mutant|JJ grown|grow|VBN in|in|IN DMEM|dmem|NN with|with|IN Epinephrine|epinephrine|NN
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN mutant|mutant|JJ grown|grow|VBN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN mutant|mutant|NN in|in|IN DMEM|DMEM|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN mutant|mutant|NN in|in|IN DMEM|dmem|NN with|with|IN AI3|ai3|NN
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN mutant|mutant|NN in|in|IN DMEM|dmem|NN with|with|IN epinephrine|epinephrine|NN
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseC|qsec|NN mutant|mutant|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseF|qsef|NN deletion|deletion|NN mutant|mutant|JJ
Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD qseF|qsef|NN deletion|deletion|NN mutant|mutant|JJ grown|grow|VBN in|in|IN DMEM|DMEM|NNP media|media|NNS
Escherichia|escherichia|FW coli|coli|FW AB1157|ab1157|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 1a|1a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 1b|1b|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 2a|2a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 2b|2b|JJ
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 3a|3a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 3b|3b|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 4a|4a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO aerobically|aerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 4b|4b|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 1a|1a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 1b|1b|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 2a|2a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 2b|2b|JJ
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 3a|3a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 3b|3b|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 4a|4a|NN
Escherichia|escherichia|FW coli|coli|FW after|after|IN addition|addition|NN of|of|IN CO-RMs|co-rm|NNS to|to|TO anaerobically|anaerobically|RB growing|grow|VBG cells|cell|NNS -|-|: Sample|sample|NN 4b|4b|NN
Escherichia|escherichia|FW coli|coli|FW APEC|apec|NN O2|o2|CD
Escherichia|escherichia|FW coli|coli|FW ATCC|atcc|NN 25922|25922|CD
Escherichia|escherichia|FW coli|coli|FW ATCC|atcc|NN 8739|8739|CD
Escherichia|escherichia|FW coli|coli|FW B|b|NN
Escherichia|escherichia|FW coli|coli|FW _|_|SYM Biofilm|Biofilm|NNP _|_|SYM bioreplicate1|bioreplicate1|CD _|_|NN techreplicate|techreplicate|NN _|_|NN 1|1|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM Biofilm|Biofilm|NNP _|_|SYM bioreplicate1|bioreplicate1|CD _|_|NN techreplicate|techreplicate|NN _|_|NN 2|2|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM Biofilm|Biofilm|NNP _|_|SYM bioreplicate2|bioreplicate2|CD _|_|NN techreplicate|techreplicate|NN _|_|NN 1|1|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM Biofilm|Biofilm|NNP _|_|SYM bioreplicate2|bioreplicate2|CD _|_|NN techreplicate|techreplicate|NN _|_|NN 2|2|CD
Escherichia|escherichia|FW coli|coli|FW BL21|bl21|NN
Escherichia|escherichia|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.46|0.46|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW BL21/pOri1|bl21/pori1|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.39|0.39|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.20|0.20|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW BL21/pOri2|bl21/pori2|NN -LRB-|-lrb-|-LRB- mu|mu|NN =|=|JJ 0.29|0.29|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW B|b|NN strain|strain|NN REL606|rel606|NN was|be|VBD revived|revive|VBN from|from|IN a|a|DT freezer|freezer|NN stock|stock|NN via|via|IN overnight|overnight|JJ growth|growth|NN in|in|IN 10|10|CD ml|ml|NN Davis|Davis|NNP Minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN limiting|limit|VBG glucose|glucose|NN at|at|IN 0.5|0.5|CD g/l|g/l|NN -LRB-|-lrb-|-LRB- DM500|dm500|CD -RRB-|-rrb-|-RRB- in|in|IN a|a|DT 50|50|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flask|flask|NN .|.|. This|this|DT culture|culture|NN was|be|VBD diluted|dilute|VBN 100-fold|100-fold|RB into|into|IN 50|50|CD ml|ml|NN fresh|fresh|JJ DM500|dm500|CD in|in|IN a|a|DT 250|250|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flask|flask|NN and|and|CC incubated|incubate|VBN for|for|IN 24|24|CD hours|hour|NNS .|.|. To|to|TO initiate|initiate|VB the|the|DT experiment|experiment|NN ,|,|, these|these|DT preconditioned|preconditioned|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN 100-fold|100-fold|RB into|into|IN 50|50|CD ml|ml|NN fresh|fresh|JJ DM500|dm500|CD in|in|IN multiple|multiple|JJ 250|250|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN the|the|DT specified|specify|VBN times|time|NNS until|until|IN harvesting|harvesting|NN cells|cell|NNS for|for|IN total|total|JJ RNA|rna|NN isolation|isolation|NN .|.|. All|all|DT growth|growth|NN steps|step|NNS were|be|VBD conducted|conduct|VBN with|with|IN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC orbital|orbital|JJ shaking|shake|VBG at|at|IN 120|120|CD r.p.m.|r.p.m.|NN over|over|IN a|a|DT one-inch|one-inch|JJ diameter|diameter|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW B|b|NN str|str|NN .|.|. REL606|rel606|NN
Escherichia|escherichia|FW coli|coli|FW BW13711|bw13711|NN grown|grow|VBN anaerobically|anaerobically|RB in|in|IN continuous|continuous|JJ culture|culture|NN in|in|IN MOPS|MOPS|NNP medium|medium|NN plus|plus|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN with|with|IN 1|1|CD %|%|NN Acacia|Acacia|NNP mearnsii|mearnsii|NN condensed|condensed|JJ tannins|tannin|NNS .|.|.
Escherichia|escherichia|FW coli|coli|FW BW13711|bw13711|NN grown|grow|VBN anaerobically|anaerobically|RB in|in|IN continuous|continuous|JJ culture|culture|NN in|in|IN MOPS|MOPS|NNP medium|medium|NN plus|plus|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN without|without|IN Acacia|Acacia|NNP mearnsii|mearnsii|NN condensed|condensed|JJ tannins|tannin|NNS .|.|.
Escherichia|escherichia|FW coli|coli|FW BW13711|bw13711|NN grown|grow|VBN anaerobically|anaerobically|RB in|in|IN continuous|continuous|JJ culture|culture|NN in|in|IN MOPS|MOPS|NNP medium|medium|NN plus|plus|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN without|without|IN Acacia|Acacia|NNP mearnsii|mearnsii|NN condensed|condensed|JJ tannins|tannin|NNS .|.|.
Escherichia|escherichia|FW coli|coli|FW BW25113|bw25113|NN
Escherichia|escherichia|FW coli|coli|FW BW25113|bw25113|NN and|and|CC fur|fur|NN mutant|mutant|JJ strains|strain|NNS were|be|VBD cultivated|cultivate|VBN at|at|IN 37Co|37co|NN in|in|IN 25|25|CD ml|ml|NN of|of|IN LB|lb|NN medium|medium|NN using|use|VBG Erlenmeyer|Erlenmeyer|NNP flasks|flask|NNS .|.|. 1|1|CD ml|ml|NN of|of|IN OVN|ovn|NN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 20|20|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN and|and|CC cells|cell|NNS were|be|VBD incubated|incubate|VBN in|in|IN the|the|DT presence|presence|NN or|or|CC absence|absence|NN of|of|IN ciprofloxacin|ciprofloxacin|NN -LRB-|-lrb-|-LRB- 100|100|CD ng/ml|ng/ml|NN -RRB-|-rrb-|-RRB- .|.|.
Escherichia|escherichia|FW coli|coli|FW BW38028|bw38028|NN
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN ,|,|, 10|10|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN ,|,|, 20|20|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN ,|,|, 2|2|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN ,|,|, 30|30|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN ,|,|, 5|5|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 2|2|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 2|2|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 30|30|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 30|30|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 5|5|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, 5|5|CD min|min|NN after|after|IN Norfloxacin|Norfloxacin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, LB|lb|NN
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN -LRB-|-lrb-|-LRB- gyrArparCr|gyrarparcr|NN -RRB-|-rrb-|-RRB- ,|,|, LB|lb|NN ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN ,|,|, LB|lb|NN
Escherichia|escherichia|FW coli|coli|FW C600|c600|NN ,|,|, LB|lb|NN ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW cell|cell|NN lysate|lysate|NN
Escherichia|escherichia|FW coli|coli|FW cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD RPM|rpm|NNS
Escherichia|escherichia|FW coli|coli|FW CFT073|cft073|NN
Escherichia|escherichia|FW coli|coli|FW Colony|Colony|NNP Biofilm|Biofilm|NNP Interior|Interior|NNP
Escherichia|escherichia|FW coli|coli|FW Colony|Colony|NNP Biofilm|Biofilm|NNP Perimeter|Perimeter|NNP
Escherichia|escherichia|FW coli|coli|FW continous|continous|JJ culture|culture|NN without|without|IN tannins|tannin|NNS
Escherichia|escherichia|FW coli|coli|FW continuous|continuous|JJ culture|culture|NN with|with|IN 1|1|CD %|%|NN tannins|tannin|NNS
Escherichia|escherichia|FW coli|coli|FW _|_|FW control|control|NN condition|condition|NN
Escherichia|escherichia|FW coli|coli|FW control|control|NN vs|vs|CC H2O2|h2o2|NN Rep1|rep1|JJ
Escherichia|escherichia|FW coli|coli|FW control|control|NN vs|vs|CC H2O2|h2o2|NN Rep2|rep2|JJ
Escherichia|escherichia|FW coli|coli|FW CSH50|csh50|NN
Escherichia|escherichia|FW coli|coli|FW CSH50|csh50|NN Δfis|Δfis|NNP
Escherichia|escherichia|FW coli|coli|FW CSH50|csh50|NN Δhns|δhns|NNS
Escherichia|escherichia|FW coli|coli|FW DH1|dh1|NN ∆|∆|CD fadE|fade|NN control|control|NN and|and|CC test|test|NN strains|strain|NNS were|be|VBD seeded|seed|VBN with|with|IN OD600nm|od600nm|NN 0.03|0.03|CD overnight|overnight|JJ cultures|culture|NNS into|into|IN 15|15|CD ml|ml|NN tryptic|tryptic|JJ soy|soy|NN broth|broth|NN media|media|NNS and|and|CC grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN 200rpm|200rpm|JJ agitation|agitation|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW DH5|dh5|NN -LSB-|-lsb-|-LRB- alpha|alpha|NN -RSB-|-rsb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW DH5alpha|dh5alpha|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, OD|od|NN 0.2|0.2|CD in|in|IN LB|lb|NN +|+|CC Amp|amp|NN ,|,|, pUC|puc|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW DH5alpha|dh5alpha|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, OD|od|NN 0.2|0.2|CD in|in|IN LB|LB|NNP ,|,|, no|no|DT pUC|puc|NN
Escherichia|escherichia|FW coli|coli|FW DH5alpha|dh5alpha|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, OD|od|NN 0.5|0.5|CD in|in|IN LB|lb|NN +|+|CC Amp|amp|NN ,|,|, pUC|puc|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW DH5alpha|dh5alpha|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, OD|od|NN 0.5|0.5|CD in|in|IN LB|LB|NNP ,|,|, no|no|DT pUC|puc|NN
Escherichia|escherichia|FW coli|coli|FW DH5alpha|dh5alpha|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, OD|od|NN 0.9|0.9|CD in|in|IN LB|lb|NN +|+|CC Amp|amp|NN ,|,|, pUC|puc|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW DH5alpha|dh5alpha|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, OD|od|NN 0.9|0.9|CD in|in|IN LB|LB|NNP ,|,|, no|no|DT pUC|puc|NN
Escherichia|escherichia|FW coli|coli|FW EDL|edl|NN 933|933|CD cells|cell|NNS grown|grow|VBN in|in|IN the|the|DT hydroponic|hydroponic|JJ system|system|NN without|without|IN interacting|interact|VBG with|with|IN the|the|DT lettuce|lettuce|NN rhizosphere|rhizosphere|NN for|for|IN 3|3|CD days|day|NNS
Escherichia|escherichia|FW coli|coli|FW EDL|edl|NN 933|933|CD cells|cell|NNS interacted|interact|VBD with|with|IN the|the|DT lettuce|lettuce|NN rhizosphere|rhizosphere|NN for|for|IN 3|3|CD days|day|NNS
Escherichia|escherichia|FW coli|coli|FW EDL|edl|NN 933|933|CD were|be|VBD grown|grow|VBN in|in|IN 10|10|CD ml|ml|NN of|of|IN LB|lb|NN medium|medium|NN until|until|IN stationary|stationary|JJ phase|phase|NN ,|,|, collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 8,000|8,000|CD ×|×|CD g|g|NN for|for|IN 10|10|CD min|min|NN ,|,|, and|and|CC washed|wash|VBN twice|twice|RB with|with|IN sterilized|sterilize|VBN ,|,|, plant|plant|NN growth|growth|NN medium|medium|NN -LRB-|-lrb-|-LRB- Caspersen|Caspersen|NNP et|et|FW al.|al.|FW 1999|1999|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT resultant|resultant|JJ cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ in|in|IN 10|10|CD ml|ml|NN of|of|IN the|the|DT same|same|JJ plant|plant|NN growth|growth|NN medium|medium|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN approximately|approximately|RB 10E9|10e9|CD cells/ml|cells/ml|NNS .|.|. Germinated|germinate|VBN lettuce|lettuce|NN seedlings|seedling|NNS were|be|VBD each|each|DT aseptically|aseptically|RB transferred|transfer|VBN into|into|IN holes|hole|NNS in|in|IN the|the|DT growth|growth|NN boxes|box|NNS filled|fill|VBN with|with|IN 300|300|CD ml|ml|NN of|of|IN plant|plant|NN growth|growth|NN medium|medium|NN ,|,|, and|and|CC 3|3|CD ml|ml|NN washed|wash|VBN bacterial|bacterial|JJ suspension|suspension|NN was|be|VBD added|add|VBN to|to|TO provide|provide|VB approximately|approximately|RB 10E7|10e7|CD cells/ml|cells/ml|NNS of|of|IN growth|growth|NN medium|medium|NN .|.|. Seedling|seedle|VBG boxes|box|NNS were|be|VBD germinated|germinate|VBN for|for|IN a|a|DT week|week|NN and|and|CC transferred|transfer|VBN to|to|TO a|a|DT plant|plant|NN growth|growth|NN chamber|chamber|NN ,|,|, and|and|CC the|the|DT aeration|aeration|NN pump|pump|NN -LRB-|-lrb-|-LRB- Luft|luft|NN Pump|pump|NN ;|;|: Oceanic|Oceanic|NNP systems|system|NNS Inc.|Inc.|NNP .|.|. Dallas|Dallas|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- was|be|VBD immediately|immediately|RB started|start|VBN .|.|. Each|each|DT pump|pump|NN supplied|supply|VBD aeration|aeration|NN of|of|IN three|three|CD growth|growth|NN boxes|box|NNS ,|,|, at|at|IN a|a|DT rate|rate|NN of|of|IN 1.3|1.3|CD L|l|NN /|/|: min|min|NN .|.|. The|the|DT seedling|seedling|NN boxes|box|NNS were|be|VBD incubated|incubate|VBN under|under|IN 80|80|CD %|%|NN RH|rh|NN at|at|IN 25|25|CD °C|°c|NN with|with|IN a|a|DT photoperiod|photoperiod|NN of|of|IN 16|16|CD h|h|NN for|for|IN 3|3|CD days|day|NNS
Escherichia|escherichia|FW coli|coli|FW ,|,|, expressing|express|VBG NsrR|nsrr|NN with|with|IN a|a|DT C-terminal|c-terminal|JJ Flag-tag|flag-tag|NN ,|,|, was|be|VBD grown|grow|VBN anaerobically|anaerobically|RB in|in|IN L|l|NN broth|broth|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW ,|,|, expressing|express|VBG NsrR|nsrr|NN with|with|IN a|a|DT C-terminal|c-terminal|JJ Flag-tag|flag-tag|NN ,|,|, was|be|VBD grown|grow|VBN anaerobically|anaerobically|RB in|in|IN L|l|NN broth|broth|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW ,|,|, expressing|express|VBG NsrR|nsrr|NN with|with|IN a|a|DT C-terminal|c-terminal|JJ Flag-tag|flag-tag|NN ,|,|, was|be|VBD grown|grow|VBN anaerobically|anaerobically|RB in|in|IN L|l|NN broth|broth|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW ,|,|, expressing|express|VBG NsrR|nsrr|NN with|with|IN a|a|DT C-terminal|c-terminal|JJ Flag-tag|flag-tag|NN ,|,|, was|be|VBD grown|grow|VBN anaerobically|anaerobically|RB in|in|IN L|l|NN broth|broth|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN and|and|CC nitrate|nitrate|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW ,|,|, expressing|express|VBG NsrR|nsrr|NN with|with|IN a|a|DT C-terminal|c-terminal|JJ Flag-tag|flag-tag|NN ,|,|, was|be|VBD grown|grow|VBN anaerobically|anaerobically|RB in|in|IN L|l|NN broth|broth|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN and|and|CC nitrate|nitrate|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW GLBRCE1|glbrce1|NN
Escherichia|escherichia|FW coli|coli|FW GLBRCE1|glbrce1|NN _|_|CD pBBR|pbbr|NN
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN
Escherichia|escherichia|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN was|be|VBD cultivated|cultivate|VBN using|use|VBG M9|m9|NN minimal|minimal|JJ medium|medium|NN containing|contain|VBG 4.5|4.5|CD g/L|g/l|NN α|α|SYM -|-|: -LRB-|-lrb-|-LRB- D|d|NN -RRB-|-rrb-|-RRB- -|-|: glucose|glucose|NN ,|,|, pH|ph|NN =|=|JJ 7|7|CD ,|,|, temperature|temperature|NN 37|37|CD ºC|ºc|NN ,|,|, aerobic|aerobic|JJ conditions|condition|NNS
Escherichia|escherichia|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN with|with|IN 10|10|CD g/L|g/l|NN glucose|glucose|NN .|.|. The|the|DT bacteria|bacterium|NNS were|be|VBD cultivated|cultivate|VBN in|in|IN a|a|DT chemostat|chemostat|NN at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.3|0.3|CD h-1|h-1|NN .|.|. After|after|IN reaching|reach|VBG steady|steady|JJ state|state|NN ,|,|, dilution|dilution|NN rate|rate|NN was|be|VBD increased|increase|VBN with|with|IN constant|constant|JJ rate|rate|NN -LRB-|-lrb-|-LRB- 0.01|0.01|CD h-2|h-2|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT samples|sample|NNS were|be|VBD acquired|acquire|VBN when|when|WRB specific|specific|JJ growth|growth|NN rate|rate|NN reached|reach|VBD 0.47|0.47|CD h-1|h-1|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN with|with|IN 10|10|CD g/L|g/l|NN glucose|glucose|NN .|.|. The|the|DT bacteria|bacterium|NNS were|be|VBD cultivated|cultivate|VBN in|in|IN a|a|DT chemostat|chemostat|NN at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.3|0.3|CD h-1|h-1|NN and|and|CC the|the|DT samples|sample|NNS were|be|VBD acquired|acquire|VBN after|after|IN culture|culture|NN reached|reach|VBD steady|steady|JJ state|state|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW K12|k12|NN strain|strain|NN BW25113|bw25113|NN -LRB-|-lrb-|-LRB- Datsenko|Datsenko|NNP &|&|CC Wanner|Wanner|NNP 2000|2000|CD .|.|. PNAS|PNAS|NNP 97|97|CD :|:|: 6640|6640|CD -RRB-|-rrb-|-RRB- was|be|VBD cultivated|cultivate|VBN in|in|IN 100|100|CD mL|ml|NN of|of|IN LB|lb|NN broth|broth|NN -LRB-|-lrb-|-LRB- Miller|Miller|NNP 1972|1972|CD .|.|. In|in|IN :|:|: Experiments|experiment|NNS in|in|IN molecular|molecular|JJ genetics|genetics|NNS .|.|. Cold|Cold|NNP Spring|Spring|NNP Harbor|Harbor|NNP Laboratory|Laboratory|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- in|in|IN a|a|DT 250|250|CD mL|ml|NN Erlenmeyer|erlenmeyer|NN flask|flask|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- to|to|TO an|a|DT O.D.|O.D.|NNP 600nm|600nm|NNP of|of|IN 0.6|0.6|CD .|.|. S.|S.|NNP coelicolor|coelicolor|NN A3|a3|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- strain|strain|NN M145|m145|NN -LRB-|-lrb-|-LRB- Kieser|Kieser|NNP et|et|FW al.|al.|FW 2000|2000|CD .|.|. Practical|Practical|NNP Streptomyces|Streptomyces|NNP Genetics|Genetics|NNP .|.|. The|the|DT John|John|NNP Innes|Innes|NNP Foundation|Foundation|NNP ,|,|, Norwich|Norwich|NNP .|.|. -RRB-|-rrb-|-RRB- was|be|VBD incubated|incubate|VBN in|in|IN YEME|yeme|NN broth|broth|NN -LRB-|-lrb-|-LRB- Kieser|Kieser|NNP et|et|FW al.|al.|FW 2000|2000|CD -RRB-|-rrb-|-RRB- at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG until|until|IN the|the|DT mycelia|mycelia|NN became|become|VBD pigmented|pigmented|JJ .|.|.
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN strain|strain|NN MG1655|mg1655|NN was|be|VBD cultivated|cultivate|VBN aerobically|aerobically|RB -LRB-|-lrb-|-LRB- ~|~|SYM 0.5|0.5|CD l/min|l/min|JJ air|air|NN supply|supply|NN -RRB-|-rrb-|-RRB- in|in|IN a|a|DT defined|define|VBN mineral|mineral|NN medium|medium|NN containing|contain|VBG 1|1|CD g/l|g/l|NN glucose|glucose|NN in|in|IN continous|continous|JJ cultures|culture|NNS growing|grow|VBG in|in|IN a|a|DT chemostat|chemostat|NN -LRB-|-lrb-|-LRB- dilution|dilution|NN rate|rate|NN =|=|JJ 0.4|0.4|CD h-1|h-1|NN ,|,|, working|work|VBG volume|volume|NN =|=|JJ 100|100|CD ml|ml|NN -RRB-|-rrb-|-RRB- .|.|.
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN treated|treat|VBN with|with|IN menadione|menadione|NN _|_|CD rep|rep|NN #|#|# 1|1|CD
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN treated|treat|VBN with|with|IN menadione|menadione|NN _|_|CD rep|rep|NN #|#|# 2|2|CD
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN treated|treat|VBN with|with|IN menadione|menadione|NN _|_|CD rep|rep|NN #|#|# 3|3|CD
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN tynA|tyna|NN -|-|: 1h|1h|NN after|after|IN induction|induction|NN of|of|IN tynA|tyna|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN tynA|tyna|NN -|-|: 4h|4h|NN after|after|IN the|the|DT induction|induction|NN of|of|IN tynA|tyna|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN tynA|tyna|NN -|-|: at|at|IN time|time|NN of|of|IN induction|induction|NN of|of|IN tynA|tyna|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW K12|k12|NN wild-type|wild-type|JJ
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN wt|wt|JJ 1h|1h|NN after|after|IN the|the|DT induction|induction|NN of|of|IN tynA|tyna|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN wt|wt|JJ 4h|4h|NN after|after|IN the|the|DT induction|induction|NN of|of|IN tynA|tyna|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN wt|wt|JJ at|at|IN time|time|NN of|of|IN induction|induction|NN of|of|IN tynA|tyna|NN expression|expression|NN
Escherichia|escherichia|FW coli|coli|FW LE234|le234|NN acrD|acrd|NN -|-|: ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW LE234|le234|NN acrD|acrd|NN -|-|: ,|,|, 5|5|CD min|min|NN after|after|IN Novobiocin|Novobiocin|NNP -LRB-|-lrb-|-LRB- 200|200|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW LE234|le234|NN acrD|acrd|NN -|-|: ,|,|, 5|5|CD min|min|NN after|after|IN Novobiocin|Novobiocin|NNP -LRB-|-lrb-|-LRB- 20|20|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW LE234|le234|NN acrD|acrd|NN -|-|: ,|,|, 5|5|CD min|min|NN after|after|IN Novobiocin|Novobiocin|NNP -LRB-|-lrb-|-LRB- 50|50|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW LE234|le234|NN acrD|acrd|NN -|-|: ,|,|, 5|5|CD min|min|NN after|after|IN Novobiocin|Novobiocin|NNP -LRB-|-lrb-|-LRB- 5|5|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN LB|LB|NNP
Escherichia|escherichia|FW coli|coli|FW LE234|le234|NN acrD|acrd|NN -|-|: ,|,|, LB|LB|NNP ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN ,|,|, Davis|Davis|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 0|0|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 1.0|1.0|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 105|105|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 10|10|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 10|10|CD min|min|NN after|after|IN Gamma|gamma|NN treatment|treatment|NN in|in|IN Davis|Davis|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 10|10|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN 10|10|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 133|133|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 1440|1440|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 15|15|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 1.0|1.0|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 163|163|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 191|191|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 20|20|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 20|20|CD min|min|NN after|after|IN Gamma|gamma|NN treatment|treatment|NN in|in|IN Davis|Davis|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 20|20|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 218|218|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 261|261|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN 2|2|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 30|30|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 1.0|1.0|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 313|313|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 40|40|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 40|40|CD min|min|NN after|after|IN Gamma|gamma|NN treatment|treatment|NN in|in|IN Davis|Davis|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 40|40|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 443|443|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 45|45|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 1.0|1.0|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN 4|4|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 50|50|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 50|50|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 5|5|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 5|5|CD min|min|NN after|after|IN Gamma|gamma|NN treatment|treatment|NN in|in|IN Davis|Davis|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 5|5|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 5|5|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 5|5|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN after|after|IN Gamma|gamma|NN treatment|treatment|NN in|in|IN Davis|Davis|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 10|10|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN after|after|IN Indol-acrylate|indol-acrylate|JJ -LRB-|-lrb-|-LRB- 15|15|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 60|60|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 1.0|1.0|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN 6|6|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN after|after|IN Ampicillin|Ampicillin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN after|after|IN Kanamycin|Kanamycin|NNP -LRB-|-lrb-|-LRB- 100|100|CD ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- addition|addition|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 75|75|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 1.0|1.0|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 78|78|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +0.2|+0.2|CD %|%|NN glc|glc|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN 8|8|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 90|90|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 90|90|CD min|min|NN recovery|recovery|NN in|in|IN 10mM|10mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 90|90|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN +|+|CC 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 90|90|CD min|min|NN recovery|recovery|NN in|in|IN 10|10|CD mM|mm|NN Na-P|na-p|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 90|90|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, 90|90|CD min|min|NN recovery|recovery|NN in|in|IN LB|lb|NN +|+|CC glucose|glucose|NN at|at|IN OD|od|NN 1.0|1.0|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN Aerobic|aerobic|JJ growth|growth|NN OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN Aerobic|aerobic|JJ growth|growth|NN on|on|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|, OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN Aerobic|aerobic|JJ growth|growth|NN on|on|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, OD|od|NN 0.4|0.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN after|after|IN 30|30|CD min|min|NN incubation|incubation|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN after|after|IN 30|30|CD min|min|NN incubation|incubation|NN following|follow|VBG colicin|colicin|NN M|m|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN after|after|IN 60|60|CD min|min|NN incubation|incubation|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN after|after|IN 60|60|CD min|min|NN incubation|incubation|NN following|follow|VBG colicin|colicin|NN M|m|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN before|before|IN paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Bonner-Vogel|Bonner-Vogel|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Bonner-Vogel|Bonner-Vogel|NNP ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Bonner-Vogel|Bonner-Vogel|NNP OD|OD|NNP ~|~|NNP 0.5|0.5|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN cells|cell|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN cells|cell|NNS grown|grow|VBN in|in|IN the|the|DT hydroponic|hydroponic|JJ system|system|NN without|without|IN interacting|interact|VBG with|with|IN the|the|DT lettuce|lettuce|NN rhizosphere|rhizosphere|NN for|for|IN 3|3|CD days|day|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN cells|cell|NNS interacted|interact|VBD with|with|IN the|the|DT lettuce|lettuce|NN rhizosphere|rhizosphere|NN for|for|IN 3|3|CD days|day|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Davis|Davis|NNP ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN fis|fis|NN :|:|: :|:|: kan|kan|NN grown|grow|VBN 150|150|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN fis|fis|NN :|:|: :|:|: kan|kan|NN grown|grow|VBN 240|240|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN fis|fis|NN :|:|: :|:|: kan|kan|NN grown|grow|VBN 360|360|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN fis|fis|NN :|:|: :|:|: kan|kan|NN grown|grow|VBN 90|90|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN genomic|genomic|JJ DNA|dna|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN dFNR|dfnr|NN -LRB-|-lrb-|-LRB- PK4854|pk4854|NN -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN WT|WT|NNP
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN WT|wt|NN and|and|CC ∆|∆|NN fnr|fnr|NN were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- O.D.|o.d.|NN 600nm|600nm|CD 0.3|0.3|CD -RRB-|-rrb-|-RRB- anerobically|anerobically|RB -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN N2|n2|NN ,|,|, 5|5|CD %|%|NN CO2|co2|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN in|in|IN MOPS|MOPS|NNP +0.2|+0.2|CD %|%|NN glucose|glucose|NN media|media|NNS -LRB-|-lrb-|-LRB- Ref|ref|NN -RRB-|-rrb-|-RRB- .|.|.
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, M9|m9|NN +|+|CC glucose|glucose|NN ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.03|0.03|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.05|0.05|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.08|0.08|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.15|0.15|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.15|0.15|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.21|0.21|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.2|0.2|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.30|0.30|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.34|0.34|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.35|0.35|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.43|0.43|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.43|0.43|CD LB|lb|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.63|0.63|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.6|0.6|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.73|0.73|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.7|0.7|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.85|0.85|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 0.9|0.9|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 1.02|1.02|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 1.07|1.07|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 1.27|1.27|CD anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 1.29|1.29|CD anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, OD|od|NN 1.2|1.2|CD ,|,|, anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN +|+|CC -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.06|0.06|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN +|+|CC -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.13|0.13|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN -|-|: -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.19|0.19|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN -|-|: -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.1|0.1|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN +|+|CC -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.21|0.21|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN +|+|CC -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.28|0.28|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN +|+|CC -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.34|0.34|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655/pTrc99a|mg1655/ptrc99a|NN -LRB-|-lrb-|-LRB- NOX|nox|NN +|+|CC -RRB-|-rrb-|-RRB- ,|,|, Balanced|balanced|JJ growth|growth|NN OD|od|NN 0.4|0.4|CD in|in|IN M9|m9|NN +|+|CC salts|salt|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Sample|sample|NN washed|wash|VBN in|in|IN 0.1|0.1|CD M|m|NN CaCl2|cacl2|NN +|+|CC 15|15|CD %|%|NN glycerol|glycerol|NN vs|vs|CC before|before|IN washing|wash|VBG OD|od|NN 0.43|0.43|CD in|in|IN LB|LB|NNP ,|,|, 10|10|CD min|min|NN timepoint|timepoint|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Sample|sample|NN washed|wash|VBN in|in|IN 0.1|0.1|CD M|m|NN CaCl2|cacl2|NN +|+|CC 15|15|CD %|%|NN glycerol|glycerol|NN vs|vs|CC before|before|IN washing|wash|VBG OD|od|NN 0.43|0.43|CD in|in|IN LB|LB|NNP ,|,|, 20|20|CD min|min|NN timepoint|timepoint|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Sample|sample|NN washed|wash|VBN in|in|IN 0.1|0.1|CD M|m|NN CaCl2|cacl2|NN +|+|CC 15|15|CD %|%|NN glycerol|glycerol|NN vs|vs|CC before|before|IN washing|wash|VBG OD|od|NN 0.43|0.43|CD in|in|IN LB|LB|NNP ,|,|, 2|2|CD min|min|NN timepoint|timepoint|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Sample|sample|NN washed|wash|VBN in|in|IN 0.1|0.1|CD M|m|NN CaCl2|cacl2|NN +|+|CC 15|15|CD %|%|NN glycerol|glycerol|NN vs|vs|CC before|before|IN washing|wash|VBG OD|od|NN 0.43|0.43|CD in|in|IN LB|LB|NNP ,|,|, 40|40|CD min|min|NN timepoint|timepoint|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Sample|sample|NN washed|wash|VBN in|in|IN 0.1|0.1|CD M|m|NN CaCl2|cacl2|NN +|+|CC 15|15|CD %|%|NN glycerol|glycerol|NN vs|vs|CC before|before|IN washing|wash|VBG OD|od|NN 0.43|0.43|CD in|in|IN LB|LB|NNP ,|,|, 5|5|CD min|min|NN timepoint|timepoint|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Sample|sample|NN washed|wash|VBN in|in|IN 0.1|0.1|CD M|m|NN CaCl2|cacl2|NN +|+|CC 15|15|CD %|%|NN glycerol|glycerol|NN vs|vs|CC before|before|IN washing|wash|VBG OD|od|NN 0.43|0.43|CD in|in|IN LB|LB|NNP ,|,|, 60|60|CD min|min|NN timepoint|timepoint|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, stationary|stationary|JJ phase|phase|NN anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, stationary|stationary|JJ phase|phase|NN anaerobic|anaerobic|JJ growth|growth|NN in|in|IN M9|m9|NN +|+|CC glucose|glucose|NN +|+|CC fumarate|fumarate|NN ,|,|,
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN OD|od|NN 2.4|2.4|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN OD|od|NN 2.8|2.8|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN OD|od|NN 3.1|3.1|CD
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN OD|od|NN 3.1|3.1|CD for|for|IN 20|20|CD min|min|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, Stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN OD|od|NN 3.1|3.1|CD for|for|IN 40|40|CD min|min|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN ,|,|, stationary|stationary|JJ phase|phase|NN in|in|IN LB|lb|NN ,|,|, OD|od|NN 3.1|3.1|CD for|for|IN 60|60|CD min|min|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN were|be|VBD grown|grow|VBN in|in|IN 10|10|CD ml|ml|NN of|of|IN LB|lb|NN medium|medium|NN until|until|IN stationary|stationary|JJ phase|phase|NN ,|,|, collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 8,000|8,000|CD ×|×|CD g|g|NN for|for|IN 10|10|CD min|min|NN ,|,|, and|and|CC washed|wash|VBN twice|twice|RB with|with|IN sterilized|sterilize|VBN ,|,|, plant|plant|NN growth|growth|NN medium|medium|NN -LRB-|-lrb-|-LRB- Caspersen|Caspersen|NNP et|et|FW al.|al.|FW 1999|1999|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT resultant|resultant|JJ cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ in|in|IN 10|10|CD ml|ml|NN of|of|IN the|the|DT same|same|JJ plant|plant|NN growth|growth|NN medium|medium|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN approximately|approximately|RB 10E9|10e9|CD cells/ml|cells/ml|NNS .|.|. Germinated|germinate|VBN lettuce|lettuce|NN seedlings|seedling|NNS were|be|VBD each|each|DT aseptically|aseptically|RB transferred|transfer|VBN into|into|IN holes|hole|NNS in|in|IN the|the|DT growth|growth|NN boxes|box|NNS filled|fill|VBN with|with|IN 300|300|CD ml|ml|NN of|of|IN plant|plant|NN growth|growth|NN medium|medium|NN ,|,|, and|and|CC 3|3|CD ml|ml|NN washed|wash|VBN bacterial|bacterial|JJ suspension|suspension|NN was|be|VBD added|add|VBN to|to|TO provide|provide|VB approximately|approximately|RB 10E7|10e7|CD cells/ml|cells/ml|NNS of|of|IN growth|growth|NN medium|medium|NN .|.|. Seedling|seedle|VBG boxes|box|NNS were|be|VBD germinated|germinate|VBN for|for|IN a|a|DT week|week|NN and|and|CC transferred|transfer|VBN to|to|TO a|a|DT plant|plant|NN growth|growth|NN chamber|chamber|NN ,|,|, and|and|CC the|the|DT aeration|aeration|NN pump|pump|NN -LRB-|-lrb-|-LRB- Luft|luft|NN Pump|pump|NN ;|;|: Oceanic|Oceanic|NNP systems|system|NNS Inc.|Inc.|NNP .|.|. Dallas|Dallas|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- was|be|VBD immediately|immediately|RB started|start|VBN .|.|. Each|each|DT pump|pump|NN supplied|supply|VBD aeration|aeration|NN of|of|IN three|three|CD growth|growth|NN boxes|box|NNS ,|,|, at|at|IN a|a|DT rate|rate|NN of|of|IN 1.3|1.3|CD L|l|NN /|/|: min|min|NN .|.|. The|the|DT seedling|seedling|NN boxes|box|NNS were|be|VBD incubated|incubate|VBN under|under|IN 80|80|CD %|%|NN RH|rh|NN at|at|IN 25|25|CD °C|°c|NN with|with|IN a|a|DT photoperiod|photoperiod|NN of|of|IN 16|16|CD h|h|NN for|for|IN 3|3|CD days|day|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN with|with|IN a|a|DT precise|precise|JJ deletion|deletion|NN in|in|IN soxR|soxr|NN and|and|CC 10|10|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN with|with|IN a|a|DT precise|precise|JJ deletion|deletion|NN in|in|IN soxR|soxr|NN and|and|CC 2|2|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN with|with|IN a|a|DT precise|precise|JJ deletion|deletion|NN in|in|IN soxR|soxr|NN and|and|CC 4|4|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN with|with|IN a|a|DT precise|precise|JJ deletion|deletion|NN in|in|IN soxR|soxr|NN and|and|CC 6|6|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN with|with|IN a|a|DT precise|precise|JJ deletion|deletion|NN in|in|IN soxR|soxr|NN and|and|CC 8|8|CD minutes|minute|NNS paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN with|with|IN a|a|DT precise|precise|JJ deletion|deletion|NN in|in|IN soxR|soxr|NN before|before|IN paraquat|paraquat|NN treatment|treatment|NN
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN wt|wt|JJ grown|grown|JJ 150|150|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN wt|wt|JJ grown|grown|JJ 240|240|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN wt|wt|JJ grown|grown|JJ 360|360|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN wt|wt|JJ grown|grown|JJ 90|90|CD minutes|minute|NNS
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP _|_|CD bioreplicate1|bioreplicate1|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 1|1|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP _|_|CD bioreplicate1|bioreplicate1|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 2|2|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP _|_|CD bioreplicate1|bioreplicate1|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 3|3|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP _|_|CD bioreplicate2|bioreplicate2|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 1|1|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesBiofilm|MixedSpeciesBiofilm|NNP _|_|CD bioreplicate2|bioreplicate2|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 2|2|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP _|_|CD bioreplicate1|bioreplicate1|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 1|1|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP _|_|CD bioreplicate1|bioreplicate1|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 2|2|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP _|_|CD bioreplicate2|bioreplicate2|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 1|1|CD
Escherichia|escherichia|FW coli|coli|FW _|_|SYM MixedSpeciesPlanktonic|MixedSpeciesPlanktonic|NNP _|_|CD bioreplicate2|bioreplicate2|NN _|_|NN techreplicate|techreplicate|NN _|_|NN 2|2|CD
Escherichia|escherichia|FW coli|coli|FW _|_|FW nickel|nickel|NN condition|condition|NN
Escherichia|escherichia|FW coli|coli|FW O08|o08|NN
Escherichia|escherichia|FW coli|coli|FW O104|o104|NN :|:|: H4|h4|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN cultivated|cultivate|VBN for|for|IN 6|6|CD hours|hour|NNS in|in|IN the|the|DT caecal|caecal|JJ content|content|NN of|of|IN rats|rat|NNS
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 1|1|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 2|2|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 3|3|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 4|4|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 5|5|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 6|6|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 7|7|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 8|8|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Inside|inside|IN Acanthamoeba|acanthamoeba|NN vs.|vs.|CC Control|control|NN Slide|slide|NN 9|9|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN Outside|outside|JJ Control|control|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN str|str|NN .|.|. EDL933|edl933|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN str|str|NN .|.|. Sakai|Sakai|NNP
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- treated|treat|VBN with|with|IN menadione|menadione|NN _|_|CD rep|rep|NN #|#|# 1|1|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- treated|treat|VBN with|with|IN menadione|menadione|NN _|_|CD rep|rep|NN #|#|# 2|2|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- treated|treat|VBN with|with|IN menadione|menadione|NN _|_|CD rep|rep|NN #|#|# 3|3|CD
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN MEM-HEPES|mem-hepes|NN +|+|CC 20uM|20um|NN ME0052|me0052|NN -LRB-|-lrb-|-LRB- in|in|IN DMSO|dmso|NN -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN MEM-HEPES|mem-hepes|NN +|+|CC 20uM|20um|NN ME0053|me0053|NN -LRB-|-lrb-|-LRB- in|in|IN DMSO|dmso|NN -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN MEM-HEPES|mem-hepes|NN +|+|CC 20uM|20um|NN ME0054|me0054|NN -LRB-|-lrb-|-LRB- in|in|IN DMSO|dmso|NN -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN MEM-HEPES|mem-hepes|NN +|+|CC 20uM|20um|NN ME0055|me0055|NN -LRB-|-lrb-|-LRB- in|in|IN DMSO|dmso|NN -RRB-|-rrb-|-RRB-
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN MEM-HEPES|mem-hepes|NN +|+|CC DMSO|dmso|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN was|be|VBD grown|grow|VBN at|at|IN 37|37|CD degrees|degree|NNS C|c|NN to|to|TO OD|od|NN 0.7|0.7|CD in|in|IN MEM-HEPES|mem-hepes|NN supplemented|supplement|VBN with|with|IN 0.1|0.1|CD %|%|NN Glucose|glucose|NN and|and|CC 250nM|250nm|NN Fe|Fe|NNP -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB- 2|2|CD .|.|.
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN was|be|VBD grown|grow|VBN at|at|IN 37|37|CD degrees|degree|NNS C|c|NN to|to|TO OD|od|NN 0.7|0.7|CD in|in|IN MEM-HEPES|mem-hepes|NN supplemented|supplement|VBN with|with|IN 0.1|0.1|CD %|%|NN Glucose|glucose|NN and|and|CC 250nM|250nm|NN Fe|Fe|NNP -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB- 2|2|CD and|and|CC and|and|CC equivalent|equivalent|JJ volume|volume|NN of|of|IN DMSO|dmso|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN was|be|VBD grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN 20uM|20um|NN ME0052|me0052|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN was|be|VBD grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN 20uM|20um|NN ME0053|me0053|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN was|be|VBD grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN 20uM|20um|NN ME0054|me0054|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN was|be|VBD grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN 20uM|20um|NN ME0055|me0055|NN
Escherichia|escherichia|FW coli|coli|FW O157|o157|NN TUV93-0|tuv93-0|NN was|be|VBD grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN DMSO|dmso|NN
Escherichia|escherichia|FW coli|coli|FW O25b|o25b|NN :|:|: H4-ST131|h4-st131|NN
Escherichia|escherichia|FW coli|coli|FW ptsN|ptsn|NN mutant|mutant|JJ strain|strain|NN
Escherichia|escherichia|FW coli|coli|FW SCI-07|sci-07|NN
Escherichia|escherichia|FW coli|coli|FW SE15|se15|NN
Escherichia|escherichia|FW coli|coli|FW strains|strain|NNS E.coli|e.coli|JJ C|c|NN -LRB-|-lrb-|-LRB- DSMZ|dsmz|NN 4860|4860|CD -RRB-|-rrb-|-RRB- ,|,|, E.|e.|FW coli|coli|FW Crooks|crook|NNS -LRB-|-lrb-|-LRB- DSMZ|dsmz|NN 1576|1576|CD -RRB-|-rrb-|-RRB- ,|,|, E.|e.|FW coli|coli|FW DH5α|dh5α|NN -LRB-|-lrb-|-LRB- DSMZ|dsmz|NN 6897|6897|CD -RRB-|-rrb-|-RRB- E.|e.|FW coli|coli|FW W|w|NN -LRB-|-lrb-|-LRB- DSMZ|dsmz|NN 1116|1116|CD -RRB-|-rrb-|-RRB- ,|,|, E.|e.|FW coli|coli|FW W3110|w3110|NN -LRB-|-lrb-|-LRB- DSMZ|dsmz|NN 5911|5911|CD -RRB-|-rrb-|-RRB- were|be|VBD obtained|obtain|VBN from|from|IN DSMZ-German|DSMZ-German|NNP Collection|Collection|NNP of|of|IN Microorganism|Microorganism|NNP and|and|CC Cell|cell|NN Cultures|culture|NNS ;|;|: E.|e.|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- was|be|VBD purchased|purchase|VBN as|as|IN competent|competent|JJ cells|cell|NNS from|from|IN Agilent|Agilent|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS Inc.|Inc.|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- ,|,|, E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- ATCC|atcc|NN 700926|700926|CD -RRB-|-rrb-|-RRB- .|.|. All|all|DT strains|strain|NNS were|be|VBD cultured|culture|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- containing|contain|VBG Na2HPO4|na2hpo4|NN x|x|NN 7H2O|7h2o|NN -LRB-|-lrb-|-LRB- 6.8|6.8|CD g|g|NN -RRB-|-rrb-|-RRB- ,|,|, KH2PO4|kh2po4|NN -LRB-|-lrb-|-LRB- 3|3|CD g|g|NN -RRB-|-rrb-|-RRB- ,|,|, NaCl|nacl|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD g|g|NN -RRB-|-rrb-|-RRB- ,|,|, NH4Cl|nh4cl|NN -LRB-|-lrb-|-LRB- 1|1|CD g|g|NN -RRB-|-rrb-|-RRB- ,|,|, MgSO4|mgso4|NN -LRB-|-lrb-|-LRB- 2|2|CD mmol|mmol|NN -RRB-|-rrb-|-RRB- ,|,|, CaCl2|cacl2|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD mmol|mmol|NN -RRB-|-rrb-|-RRB- ,|,|, trace|trace|NN elements|element|NNS ,|,|, Wolf|Wolf|NNP 's|'s|POS vitamin|vitamin|NN solution|solution|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- and|and|CC glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g|g|NN L-1|l-1|NN -RRB-|-rrb-|-RRB- .|.|. Anoxic|anoxic|JJ M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN glucose|glucose|NN was|be|VBD obtained|obtain|VBN by|by|IN flushing|flush|VBG solution|solution|NN with|with|IN oxygen|oxygen|NN free|free|JJ nitrogen|nitrogen|NN -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN -RRB-|-rrb-|-RRB- .|.|. Overnight|overnight|JJ cultures|culture|NNS from|from|IN single|single|JJ colonies|colony|NNS of|of|IN each|each|DT of|of|IN seven|seven|CD E.|e.|FW coli|coli|FW strains|strain|NNS were|be|VBD diluted|dilute|VBN to|to|TO a|a|DT starting|start|VBG optical|optical|JJ density|density|NN -LRB-|-lrb-|-LRB- OD600|od600|NN -RRB-|-rrb-|-RRB- of|of|IN 0.01|0.01|CD .|.|. Cultures|culture|NNS were|be|VBD grown|grow|VBN in|in|IN 250|250|CD ml|ml|NN flasks|flask|NNS or|or|CC 300|300|CD ml|ml|NN oxygen-free|oxygen-free|JJ sealed|sealed|JJ bottles|bottle|NNS containing|contain|VBG 50|50|CD ml|ml|NN glucose-M9|glucose-m9|NN minimal|minimal|JJ media|media|NNS in|in|IN a|a|DT shaking|shake|VBG incubator|incubator|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC 250|250|CD rpm|rpm|NN .|.|.
Escherichia|escherichia|FW coli|coli|FW _|_|FW stress|stress|NN experiment|experiment|NN
Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN
Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655star|mg1655star|JJ
Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. W3110|w3110|CD
Escherichia|escherichia|FW coli|coli|FW treated|treat|VBN with|with|IN 0.5|0.5|CD MIC|mic|NN of|of|IN cyadox|cyadox|NN
Escherichia|escherichia|FW coli|coli|FW treated|treat|VBN with|with|IN 1|1|CD %|%|NN DMSO|dmso|NN
Escherichia|escherichia|FW coli|coli|FW treated|treat|VBN with|with|IN MBC|mbc|NN of|of|IN cyadox|cyadox|NN
Escherichia|escherichia|FW coli|coli|FW treated|treat|VBN with|with|IN MBC|mbc|NN of|of|IN olaquindox|olaquindox|NN
Escherichia|escherichia|FW coli|coli|FW treated|treat|VBN with|with|IN MIC|mic|NN of|of|IN olaquindox|olaquindox|NN
Escherichia|escherichia|FW coli|coli|FW W3110|w3110|NN ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN ,|,|, Bonner-Vogel|Bonner-Vogel|NNP +|+|CC 50|50|CD ug/ml|ug/ml|NN Tryptophan|tryptophan|NN
Escherichia|escherichia|FW coli|coli|FW W3110|w3110|NN ,|,|, 0|0|CD min|min|NN before|before|IN treatment|treatment|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP +|+|CC 50|50|CD ug/ml|ug/ml|NN Tryptophan|tryptophan|NN
Escherichia|escherichia|FW coli|coli|FW W3110|w3110|NN ,5|,5|CD min|min|NN 0.01|0.01|CD M|m|NN Sodium|sodium|NN Azide|azide|NN treatment|treatment|NN vs|vs|CC 0|0|CD min|min|NN before|before|IN treatment|treatment|NN in|in|IN Bonner-Vogel|Bonner-Vogel|NNP +|+|CC 50|50|CD ug/ml|ug/ml|NN Tryptophan|tryptophan|NN
Escherichia|escherichia|FW coli|coli|FW W3110gyrb234|w3110gyrb234|NN ,|,|, LB|lb|NN
Escherichia|escherichia|FW coli|coli|FW W3110gyrb234|w3110gyrb234|NN ,|,|, LB|lb|NN ,|,|, 10|10|CD min|min|NN after|after|IN upshift|upshift|NN to|to|TO 42|42|CD C|c|NN
Escherichia|escherichia|FW coli|coli|FW W3110gyrb234|w3110gyrb234|NN ,|,|, LB|lb|NN ,|,|, 20|20|CD min|min|NN after|after|IN upshift|upshift|NN to|to|TO 42|42|CD C|c|NN
Escherichia|escherichia|FW coli|coli|FW W3110gyrb234|w3110gyrb234|NN ,|,|, LB|lb|NN ,|,|, 2|2|CD min|min|NN after|after|IN upshift|upshift|NN to|to|TO 42|42|CD C|c|NN
Escherichia|escherichia|FW coli|coli|FW W3110gyrb234|w3110gyrb234|NN ,|,|, LB|lb|NN ,|,|, 5|5|CD min|min|NN after|after|IN upshift|upshift|NN to|to|TO 42|42|CD C|c|NN
Escherichia|escherichia|FW coli|coli|FW was|be|VBD grown|grow|VBN aerobically|aerobically|RB in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- broth|broth|NN and|and|CC LB|lb|NN +|+|CC glycerol|glycerol|NN at|at|IN 30|30|CD °C|°c|NN in|in|IN an|a|DT incubator|incubator|NN shaker|shaker|NN at|at|IN 150|150|CD r.p.m.|r.p.m.|NN
Escherichia|escherichia|FW coli|coli|FW was|be|VBD grown|grow|VBN aerobically|aerobically|RB in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- broth|broth|NN at|at|IN 30|30|CD °C|°c|NN in|in|IN an|a|DT incubator|incubator|NN shaker|shaker|NN at|at|IN 150|150|CD r.p.m.|r.p.m.|NN
Escherichia|escherichia|FW coli|coli|FW wild|wild|JJ type|type|NN strain|strain|NN
Escherichia|escherichia|FW coli|coli|FW wild|wild|JJ type|type|NN vs|vs|CC luxS|luxs|NN mutants|mutant|NNS with|with|IN 10|10|CD %|%|NN H2O2|h2o2|NN Rep1|rep1|JJ
Escherichia|escherichia|FW coli|coli|FW wild|wild|JJ type|type|NN vs|vs|CC luxS|luxs|NN mutants|mutant|NNS with|with|IN 10|10|CD %|%|NN H2O2|h2o2|NN Rep2|rep2|JJ
Escherichia|escherichia|FW coli|coli|FW wild|wild|JJ type|type|NN vs|vs|CC luxS|luxs|NN mutants|mutant|NNS with|with|IN 30|30|CD %|%|NN H2O2|h2o2|NN Rep1|rep1|JJ
Escherichia|escherichia|FW coli|coli|FW wild|wild|JJ type|type|NN vs|vs|CC luxS|luxs|NN mutants|mutant|NNS with|with|IN 30|30|CD %|%|NN H2O2|h2o2|NN Rep2|rep2|JJ
Escherichia|escherichia|FW coli|coli|FW wild|wild|JJ type|type|NN vs|vs|CC luxS|luxs|NN mutants|mutant|NNS without|without|IN H2O2|h2o2|NN Rep1|rep1|JJ
Escherichia|escherichia|FW coli|coli|FW wild|wild|JJ type|type|NN vs|vs|CC luxS|luxs|NN mutants|mutant|NNS without|without|IN H2O2|h2o2|NN Rep2|rep2|JJ
Escherichia|escherichia|FW coli|coli|FW with|with|IN 1|1|CD %|%|NN tannins|tannin|NNS
Escherichia|escherichia|FW ProQ|ProQ|NNP coIP|coIP|NNP
Escherichia|escherichia|FW ProQ|ProQ|NNP Lysate|Lysate|NNP
Escherichia|escherichia|FW WT|WT|NNP coIP|coIP|NNP
Escherichia|escherichia|FW WT|WT|NNP Lysate|Lysate|NNP
Estradiol|Estradiol|NNP Treatment|treatment|NN
EtBr|etbr|NN replicate|replicate|VBP 1|1|CD
EtBr|etbr|NN replicate|replicate|VBP 2|2|CD
EtBr|etbr|NN replicate|replicate|VBP 3|3|CD
ethanol|ethanol|NN treatment|treatment|NN :|:|: 40|40|CD g|g|NN EtOH/L|etoh/l|NN ,|,|, 10|10|CD min|min|NN
ethanol|ethanol|NN treatment|treatment|NN :|:|: 40|40|CD g|g|NN EtOH/L|etoh/l|NN ,|,|, 70|70|CD min|min|NN
ethanol|ethanol|NN treatment|treatment|NN :|:|: no|no|DT ethanol|ethanol|NN exposure|exposure|NN
Ethanol|ethanol|NN was|be|VBD added|add|VBN to|to|TO 40|40|CD g/L|g/l|NN once|once|RB A600|a600|NN of|of|IN cultures|culture|NNS reached|reach|VBD 0.3|0.3|CD .|.|. Samples|sample|NNS were|be|VBD taken|take|VBN prior|prior|RB to|to|TO ethanol|ethanol|NN addition|addition|NN -LRB-|-lrb-|-LRB- T0|t0|NN -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD min|min|NN after|after|IN addition|addition|NN -LRB-|-lrb-|-LRB- T1|t1|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC 70|70|CD min|min|NN after|after|IN addition|addition|NN -LRB-|-lrb-|-LRB- T2|t2|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN rapidly|rapidly|RB onto|onto|IN 0.2|0.2|CD µm|µm|NN filters|filter|NNS by|by|IN vacuum|vacuum|NN then|then|RB flash-frozen|flash-frozen|JJ in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN to|to|TO arrest|arrest|VB ribosomes|ribosome|NNS .|.|. Ribosome|ribosome|NN footprinting|footprinting|NN samples|sample|NNS were|be|VBD subjected|subject|VBN to|to|TO micrococcal|micrococcal|JJ nuclease|nuclease|NN digestion|digestion|NN followed|follow|VBN by|by|IN monosome|monosome|JJ isolation|isolation|NN by|by|IN sucrose|sucrose|NN gradient|gradient|NN centrifugation|centrifugation|NN .|.|.
EtOH|etoh|NN replicate|replicate|VB 1|1|CD
EtOH|etoh|NN replicate|replicate|VB 2|2|CD
EtOH|etoh|NN replicate|replicate|VBP 3|3|CD
-LSB-|-lsb-|-LRB- Eubacterium|eubacterium|NN -RSB-|-rsb-|-RRB- rectale|rectale|JJ ATCC|atcc|NN 33656|33656|CD
Eureka|eureka|FW
EvgSc|evgsc|NN _|_|NN 1|1|CD
EvgSc|evgsc|NN _|_|NN 2|2|CD
EvgSc|evgsc|NN mutant|mutant|JJ rep|rep|NN 1|1|CD
EvgSc|evgsc|NN mutant|mutant|JJ rep|rep|NN 2|2|CD
EvgSc|evgsc|NN _|_|CD ompR|ompr|NN _|_|NN 1|1|CD
EvgSc|evgsc|NN _|_|CD ompR|ompr|NN _|_|NN 2|2|CD
EvgSc|evgsc|NN ompR|ompr|NN double|double|JJ mutant|mutant|JJ rep|rep|NN 1|1|CD
EvgSc|evgsc|NN ompR|ompr|NN double|double|JJ mutant|mutant|JJ rep|rep|NN 2|2|CD
evolved|evolve|VBD 1|1|CD min|min|NN rep6|rep6|NN
evolved|evolve|VBD 1|1|CD min|min|NN rep8|rep8|NN
evolved|evolve|VBD 5|5|CD min|min|NN rep6|rep6|NN
evolved|evolve|VBD 5|5|CD min|min|NN rep8|rep8|NN
evolved|evolve|VBD 9|9|CD min|min|NN rep6|rep6|NN
evolved|evolve|VBD 9|9|CD min|min|NN rep7|rep7|NN
Evolved|evolve|VBD I|I|PRP -|-|: cells|cell|NNS at|at|IN amino|amino|NN acid|acid|NN starvation|starvation|NN in|in|IN monoculture|monoculture|NN
Evolved|evolve|VBD I|I|PRP -|-|: cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN
Evolved|evolve|VBD I|I|PRP -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN
Evolved|evolve|VBD I|I|PRP -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN ,|,|, a|a|DT biological|biological|JJ replicate|replicate|VBP
Evolved|evolve|VBD L|l|NN -|-|: cells|cell|NNS at|at|IN amino|amino|NN acid|acid|NN starvation|starvation|NN in|in|IN monoculture|monoculture|NN
Evolved|evolve|VBD L|l|NN -|-|: cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN
Evolved|evolve|VBD L|l|NN -|-|: cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN ,|,|, a|a|DT technical|technical|JJ replicate|replicate|VBP
Evolved|evolve|VBD L|l|NN -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN
Evolved|evolve|VBD L|l|NN -|-|: cells|cell|NNS in|in|IN coculture|coculture|NN ,|,|, a|a|DT biological|biological|JJ replicate|replicate|VBP
Evolved|evolve|VBD strain|strain|NN A|a|NN ,|,|, time|time|NN point|point|NN 1|1|CD
Evolved|evolve|VBN strain|strain|NN A|a|NN ,|,|, time|time|NN point|point|NN 2|2|CD
Evolved|evolve|VBN strain|strain|NN A|a|NN ,|,|, time|time|NN point|point|NN 3|3|CD
Evolved|evolve|VBN strain|strain|NN A|a|NN ,|,|, time|time|NN point|point|NN 4|4|CD
Evolved|evolve|VBN strain|strain|NN A|a|NN ,|,|, time|time|NN point|point|NN 5|5|CD
Evolved|evolve|VBN strain|strain|NN B|b|NN ,|,|, time|time|NN point|point|NN 1|1|CD
Evolved|evolve|VBN strain|strain|NN B|b|NN ,|,|, time|time|NN point|point|NN 2|2|CD
Evolved|evolve|VBN strain|strain|NN B|b|NN ,|,|, time|time|NN point|point|NN 3|3|CD
Evolved|evolve|VBN strain|strain|NN B|b|NN ,|,|, time|time|NN point|point|NN 4|4|CD
Evolved|evolve|VBN strain|strain|NN B|b|NN ,|,|, time|time|NN point|point|NN 5|5|CD
Evolved|evolve|VBN strain|strain|NN C|c|NN ,|,|, time|time|NN point|point|NN 1|1|CD
Evolved|evolve|VBN strain|strain|NN C|c|NN ,|,|, time|time|NN point|point|NN 2|2|CD
Evolved|evolve|VBN strain|strain|NN C|c|NN ,|,|, time|time|NN point|point|NN 3|3|CD
Evolved|evolve|VBN strain|strain|NN C|c|NN ,|,|, time|time|NN point|point|NN 4|4|CD
Evolved|evolve|VBN strain|strain|NN C|c|NN ,|,|, time|time|NN point|point|NN 5|5|CD
Evolved|evolve|VBN strain|strain|NN D|d|NN ,|,|, time|time|NN point|point|NN 1|1|CD
Evolved|evolve|VBN strain|strain|NN D|d|NN ,|,|, time|time|NN point|point|NN 2|2|CD
Evolved|evolve|VBN strain|strain|NN D|d|NN ,|,|, time|time|NN point|point|NN 3|3|CD
Evolved|evolve|VBN strain|strain|NN D|d|NN ,|,|, time|time|NN point|point|NN 4|4|CD
Evolved|evolve|VBN strain|strain|NN D|d|NN ,|,|, time|time|NN point|point|NN 5|5|CD
Evolved|evolve|VBN strain|strain|NN E|e|NN ,|,|, time|time|NN point|point|NN 1|1|CD
Evolved|evolve|VBN strain|strain|NN E|e|NN ,|,|, time|time|NN point|point|NN 2|2|CD
Evolved|evolve|VBN strain|strain|NN E|e|NN ,|,|, time|time|NN point|point|NN 3|3|CD
Evolved|evolve|VBN strain|strain|NN E|e|NN ,|,|, time|time|NN point|point|NN 4|4|CD
Evolved|evolve|VBN strain|strain|NN E|e|NN ,|,|, time|time|NN point|point|NN 5|5|CD
Evolved|evolve|VBN strain|strain|NN F|f|NN ,|,|, time|time|NN point|point|NN 1|1|CD
Evolved|evolve|VBN strain|strain|NN F|f|NN ,|,|, time|time|NN point|point|NN 2|2|CD
Evolved|evolve|VBN strain|strain|NN F|f|NN ,|,|, time|time|NN point|point|NN 3|3|CD
Evolved|evolve|VBN strain|strain|NN F|f|NN ,|,|, time|time|NN point|point|NN 4|4|CD
Evolved|evolve|VBN strain|strain|NN F|f|NN ,|,|, time|time|NN point|point|NN 5|5|CD
evolved|evolve|VBD _|_|CD temperature|temperature|NN _|_|CD Up|up|IN _|_|CD 0|0|CD min|min|NN
evolved|evolve|VBD _|_|CD temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 16|16|CD min|min|NN
evolved|evolve|VBD _|_|CD temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 44|44|CD min|min|NN
evolved|evolve|VBD temperature|temperature|NN up|up|IN shift|shift|NN 0|0|CD min|min|NN
evolved|evolve|VBD temperature|temperature|NN up|up|IN shift|shift|NN 16|16|CD min|min|NN
evolved|evolve|VBD temperature|temperature|NN up|up|IN shift|shift|NN 44|44|CD min|min|NN
Exact|exact|JJ details|detail|NNS for|for|IN the|the|DT full|full|JJ computational|computational|JJ pipeline|pipeline|NN are|be|VBP available|available|JJ at|at|IN https://github.com/wilkelab/AG3C_starvation_tc_RNAseq|https://github.com/wilkelab/ag3c_starvation_tc_rnaseq|NN .|.|.
exopolyphosphatase|exopolyphosphatase|NN -LRB-|-lrb-|-LRB- PPX|ppx|NN -RRB-|-rrb-|-RRB- mutant|mutant|JJ
Exp|exp|NN 1|1|CD _|_|NN control|control|NN
Exp|Exp|NNP 1|1|CD _|_|CD IP|IP|NNP sample|sample|NN
Exp|exp|NN 2|2|CD _|_|NN control|control|NN
Exp|exp|NN 2|2|CD _|_|CD IP|IP|NNP sample|sample|NN
experiment|experiment|NN #|#|# 115|115|CD
experiment|experiment|NN #|#|# 116|116|CD
experiment|experiment|NN #|#|# 203|203|CD
experiment|experiment|NN #|#|# 204|204|CD
experiment|experiment|NN #|#|# 205|205|CD
experiment|experiment|NN #|#|# 206|206|CD
experiment|experiment|NN #|#|# 303|303|CD
experiment|experiment|NN #|#|# 305|305|CD
experiment|experiment|NN #|#|# 306|306|CD
Experimental|experimental|JJ ,|,|, biological|biological|JJ rep1|rep1|NN G1|g1|NN
Experimental|experimental|JJ ,|,|, biological|biological|JJ rep1|rep1|NN G2|g2|NN
Experimental|experimental|JJ ,|,|, biological|biological|JJ rep1|rep1|NN G3|g3|NN
Experimental|experimental|JJ ,|,|, biological|biological|JJ rep2|rep2|NN G4|g4|NN
Experimental|experimental|JJ ,|,|, biological|biological|JJ rep2|rep2|NN G5|g5|NN
Experimental|experimental|JJ ,|,|, biological|biological|JJ rep2|rep2|NN G6|g6|NN
Experiments|experiment|NNS were|be|VBD performed|perform|VBN at|at|IN 37|37|CD °C|°c|NN and|and|CC followed|follow|VBD three|three|CD steps|step|NNS :|:|: seed|seed|NN culture|culture|NN ,|,|, pre-culture|pre-culture|JJ and|and|CC experimental|experimental|JJ culture|culture|NN .|.|. In|in|IN the|the|DT seed|seed|NN culture|culture|NN the|the|DT cells|cell|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN Luria|Luria|NNP Broth|Broth|NNP ,|,|, then|then|RB diluted|dilute|VBN 1:100|1:100|CD in|in|IN either|either|CC M9|m9|NN minimal|minimal|JJ media|media|NNS with|with|IN glycerol|glycerol|NN or|or|CC glucose|glucose|NN for|for|IN the|the|DT pre-cultures|pre-culture|NNS .|.|. Finally|finally|RB ,|,|, the|the|DT experimental|experimental|JJ cultures|culture|NNS were|be|VBD started|start|VBN from|from|IN the|the|DT overnight|overnight|JJ grown|grown|JJ pre-cultures|pre-culture|NNS containing|contain|VBG the|the|DT same|same|JJ carbon|carbon|NN source|source|NN at|at|IN a|a|DT normalized|normalize|VBN optical|optical|JJ density|density|NN at|at|IN 600|600|CD nm|nm|NN -LRB-|-lrb-|-LRB- OD600|od600|NN -RRB-|-rrb-|-RRB- of|of|IN 0.05|0.05|CD .|.|. Cultures|culture|NNS were|be|VBD harvested|harvest|VBN at|at|IN mid-exponential|mid-exponential|JJ phase|phase|NN ,|,|, cells|cell|NNS were|be|VBD immediately|immediately|RB spun|spin|VBN down|down|RP and|and|CC cell|cell|NN pellets|pellet|NNS stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN until|until|IN processed|process|VBN .|.|.
Exponential|exponential|JJ cells|cell|NNS -LRB-|-lrb-|-LRB- DO600|do600|NN =|=|JJ 0,4|0,4|CD -RRB-|-rrb-|-RRB-
exponential|exponential|JJ culture|culture|NN
Exponential|Exponential|NNP cultures|culture|NNS of|of|IN transformants|transformant|NNS were|be|VBD inoculated|inoculate|VBN from|from|IN fresh|fresh|JJ overnight|overnight|JJ cultures|culture|NNS in|in|IN LB|lb|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 25|25|CD µg/ml|µg/ml|NN of|of|IN kanamycin|kanamycin|NN to|to|TO an|a|DT optical|optical|JJ density|density|NN at|at|IN 600|600|CD nm|nm|NN -LRB-|-lrb-|-LRB- OD|od|NN -RRB-|-rrb-|-RRB- of|of|IN 0.1|0.1|CD and|and|CC grown|grow|VBN for|for|IN 30|30|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN to|to|TO an|a|DT OD|od|NN of|of|IN 0.15|0.15|CD .|.|. Then|then|RB ,|,|, IPTG|iptg|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD mM|mm|NN for|for|IN induction|induction|NN of|of|IN expression|expression|NN .|.|. After|after|IN 60|60|CD min|min|NN of|of|IN additional|additional|JJ growth|growth|NN cells|cell|NNS were|be|VBD harvested|harvest|VBN for|for|IN RNA|rna|NN isolation|isolation|NN .|.|.
exponentially|exponentially|RB growing|grow|VBG cells|cell|NNS
exponential|exponential|JJ phase|phase|NN
Exponential|Exponential|NNP phase|phase|NN culture|culture|NN of|of|IN EDL933|edl933|NN rpoS|rpos|NN mutants|mutant|NNS in|in|IN LB|lb|NN at|at|IN OD600|od600|NN of|of|IN 0.3|0.3|CD
Exponential|exponential|JJ phase|phase|NN culture|culture|NN of|of|IN EDL933|edl933|NN wild|wild|JJ type|type|NN in|in|IN LB|lb|NN at|at|IN OD600|od600|NN of|of|IN 0.3|0.3|CD
expose|expose|VBP Bacillus|bacillus|NN VOC|voc|NN 12h|12h|VBP
Expose|expose|VB Bacillus|bacillus|NN VOC-12h|voc-12h|JJ rep1|rep1|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-12h|voc-12h|JJ rep2|rep2|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-12h|voc-12h|JJ rep3|rep3|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-12h|voc-12h|JJ rep4|rep4|NN
expose|expose|VBP Bacillus|bacillus|NN VOC24h|voc24h|JJ
Expose|expose|VB Bacillus|bacillus|NN VOC-24h|voc-24h|JJ rep1|rep1|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-24h|voc-24h|JJ rep2|rep2|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-24h|voc-24h|JJ rep3|rep3|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-24h|voc-24h|JJ rep4|rep4|NN
expose|expose|VBP Bacillus|bacillus|NN VOC|voc|NN 6h|6h|VBP
Expose|expose|VB Bacillus|bacillus|NN VOC-6h|voc-6h|JJ rep1|rep1|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-6h|voc-6h|JJ rep2|rep2|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-6h|voc-6h|JJ rep3|rep3|NN
Expose|expose|VB Bacillus|bacillus|NN VOC-6h|voc-6h|JJ rep4|rep4|NN
Expression|expression|NN data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN the|the|DT Microarray|Microarray|NNP Analysis|analysis|NN Suite|suite|NN ,|,|, version|version|NN 5.0|5.0|CD -LRB-|-lrb-|-LRB- Affymetrix|Affymetrix|NNP -RRB-|-rrb-|-RRB- .|.|. Global|global|JJ scaling|scaling|NN was|be|VBD performed|perform|VBN to|to|TO compare|compare|VB genes|gene|NNS between|between|IN chips|chip|NNS .|.|. Each|each|DT chip|chip|NN was|be|VBD normalized|normalize|VBN to|to|TO a|a|DT target|target|NN intensity|intensity|NN value|value|NN of|of|IN 2,500|2,500|CD .|.|. Expression|expression|NN analysis|analysis|NN files|file|NNS created|create|VBN by|by|IN Microarray|Microarray|NNP Suite|Suite|NNP ,|,|, version|version|NN 5.0|5.0|CD ,|,|, were|be|VBD exported|export|VBN to|to|TO Microsoft|Microsoft|NNP Excel|Excel|NNP for|for|IN data|datum|NNS formatting|formatting|NN .|.|.
Expression|expression|NN data|datum|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT Affymetrix|Affymetrix|NNP microarray|microarray|NN suite|suite|NN 5|5|CD -LRB-|-lrb-|-LRB- MAS5|mas5|NN -RRB-|-rrb-|-RRB- algorithm|algorithm|NN implemented|implement|VBD in|in|IN Affymetrix|Affymetrix|NNP expression|expression|NN console|console|NN software|software|NN .|.|. To|to|TO reduce|reduce|VB noise|noise|NN for|for|IN the|the|DT significance|significance|NN analysis|analysis|NN ,|,|, probe|probe|NN sets|set|NNS that|that|WDT did|do|VBD not|not|RB show|show|VB detection|detection|NN call|call|NN rate|rate|NN at|at|IN least|least|JJS 50|50|CD %|%|NN of|of|IN the|the|DT samples|sample|NNS in|in|IN the|the|DT comparison|comparison|NN were|be|VBD filtered|filter|VBN out|out|RP .|.|. Highly|highly|RB expressed|express|VBN genes|gene|NNS that|that|WDT showed|show|VBD a|a|DT 2-fold|2-fold|JJ change|change|NN in|in|IN expression|expression|NN were|be|VBD selected|select|VBN .|.|.
Expression|expression|NN of|of|IN introduced|introduce|VBN enzymes|enzyme|NNS for|for|IN 3-HP|3-hp|NN productionm|productionm|NN was|be|VBD induced|induce|VBN by|by|IN 0.05|0.05|CD mM|mm|NN IPTG|iptg|NN and|and|CC 50|50|CD µM|µm|NN vitamin|vitamin|NN B12|b12|NN when|when|WRB the|the|DT cell|cell|NN reached|reach|VBN at|at|IN the|the|DT early-exponential|early-exponential|JJ growth|growth|NN phase|phase|NN .|.|. T|t|NN
Expression|expression|NN values|value|NNS were|be|VBD calculated|calculate|VBN by|by|IN the|the|DT software|software|NN package|package|NN Feature|Feature|NNP Extraction|Extraction|NNP 10.5.1.1|10.5.1.1|CD using|use|VBG protocol|protocol|NN GE1|ge1|NN _|_|NN 105|105|CD _|_|SYM Dec08|dec08|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ;|;|: Waldbronn|Waldbronn|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB-
Exp-rpoS-rep1|exp-rpos-rep1|NN
Exp-rpoS-Rep1|exp-rpos-rep1|NN
Exp-rpoS-rep2|exp-rpos-rep2|NN
Exp-rpoS-Rep2|exp-rpos-rep2|NN
Exp-rpoS-rep3|exp-rpos-rep3|NN
Exp-rpoS-Rep3|exp-rpos-rep3|NN
Exp-WT-rep1|exp-wt-rep1|NN
Exp-WT-Rep1|exp-wt-rep1|NN
Exp-WT-rep2|exp-wt-rep2|NN
Exp-WT-Rep2|exp-wt-rep2|NN
Exp-WT-rep3|exp-wt-rep3|NN
Exp-WT-Rep3|exp-wt-rep3|NN
extracted|extract|VBN molecule|molecule|NN :|:|: plasmid|plasmid|NN DNA|dna|NN
Extraction|extraction|NN followed|follow|VBN by|by|IN DNase|dnase|NN treatment|treatment|NN with|with|IN TURBO|TURBO|NNP DNA-free|dna-free|JJ kit|kit|NN from|from|IN Ambion|Ambion|NNP .|.|. rRNA|rrna|NN depleted|deplete|VBN using|use|VBG an|a|DT Illumina|Illumina|NNP Ribo-zero|ribo-zero|NN rRNA|rrna|NN removal|removal|NN kit|kit|NN .|.|. Followed|follow|VBN by|by|IN RNA-seq|rna-seq|JJ library|library|NN prep|prep|NN using|use|VBG an|a|DT Illumina|Illumina|NNP TruSeq|TruSeq|NNP Stranded|Stranded|NNP mRNA|mrna|NN Library|Library|NNP Prep|Prep|NNP Kit|kit|NN .|.|.
Extraction|extraction|NN :|:|: Rneasy|Rneasy|NNP
Extraction|Extraction|NNP :|:|: TRI|TRI|NNP Reagent|Reagent|NNP
Extraction|extraction|NN was|be|VBD performed|perform|VBN as|as|IN described|describe|VBN in|in|IN detail|detail|NN previously|previously|RB -LRB-|-lrb-|-LRB- Li|Li|NNP et|et|FW al.|al.|FW ,|,|, 2012|2012|CD ;|;|: Oh|oh|UH et|et|FW al.|al.|FW ,|,|, 2011|2011|CD -RRB-|-rrb-|-RRB- .|.|. 200|200|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD rapidly|rapidly|RB filtered|filter|VBN at|at|IN 37C|37c|NN by|by|IN passing|pass|VBG through|through|IN a|a|DT nitrocellulose|nitrocellulose|NN filter|filter|NN .|.|. Cell|cell|NN pellets|pellet|NNS was|be|VBD were|be|VBD rapidly|rapidly|RB collected|collect|VBN using|use|VBG a|a|DT pre-warmed|pre-warmed|JJ metal|metal|NN table|table|NN crumber|crumber|NN ,|,|, flash|flash|NN frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN ,|,|, and|and|CC combined|combine|VBN with|with|IN frozen|frozen|JJ droplets|droplet|NNS of|of|IN lysis|lysis|NN buffer|buffer|NN .|.|. Cells|cell|NNS and|and|CC lysis|lysis|NN buffer|buffer|NN were|be|VBD pulverized|pulverize|VBN in|in|IN 10|10|CD ml|ml|NN canisters|canister|NNS -LRB-|-lrb-|-LRB- Retsch|retsch|NN -RRB-|-rrb-|-RRB- pre-chilled|pre-chilled|JJ in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN using|use|VBG Qiagen|Qiagen|NNP TissueLyser|TissueLyser|NNP II|II|NNP .|.|. Pulverized|pulverize|VBN lysate|lysate|NN was|be|VBD thawed|thaw|VBN on|on|IN ice|ice|NN and|and|CC clarified|clarify|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 4C|4c|NN .|.|.
Extraction|extraction|NN was|be|VBD performed|perform|VBN as|as|IN described|describe|VBN in|in|IN detail|detail|NN previously|previously|RB -LRB-|-lrb-|-LRB- Li|Li|NNP et|et|FW al.|al.|FW ,|,|, 2012|2012|CD ;|;|: Oh|oh|UH et|et|FW al.|al.|FW ,|,|, 2011|2011|CD ;|;|: Rouskin|Rouskin|NNP et|et|FW al.|al.|FW ,|,|, 2014|2014|CD -RRB-|-rrb-|-RRB- .|.|. For|for|IN ribosome|ribosome|NN profiling|profiling|NN ,|,|, 200|200|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD rapidly|rapidly|RB filtered|filter|VBN by|by|IN passing|pass|VBG through|through|IN a|a|DT nitrocellulose|nitrocellulose|NN filter|filter|NN .|.|. Cell|cell|NN pellets|pellet|NNS was|be|VBD were|be|VBD rapidly|rapidly|RB collected|collect|VBN using|use|VBG a|a|DT pre-warmed|pre-warmed|JJ metal|metal|NN table|table|NN crumber|crumber|NN ,|,|, flash|flash|NN frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN ,|,|, and|and|CC combined|combine|VBN with|with|IN frozen|frozen|JJ droplets|droplet|NNS of|of|IN lysis|lysis|NN buffer|buffer|NN .|.|. Cells|cell|NNS and|and|CC lysis|lysis|NN buffer|buffer|NN were|be|VBD pulverized|pulverize|VBN in|in|IN 10|10|CD ml|ml|NN canisters|canister|NNS -LRB-|-lrb-|-LRB- Retsch|retsch|NN -RRB-|-rrb-|-RRB- pre-chilled|pre-chilled|JJ in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN using|use|VBG Qiagen|Qiagen|NNP TissueLyser|TissueLyser|NNP II|II|NNP .|.|. Pulverized|pulverize|VBN lysate|lysate|NN was|be|VBD thawed|thaw|VBN on|on|IN ice|ice|NN and|and|CC clarified|clarify|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Lysate|lysate|NN containing|contain|VBG 0.5|0.5|CD mg|mg|NN of|of|IN RNA|rna|NN was|be|VBD digested|digest|VBN for|for|IN 1|1|CD h|h|NN with|with|IN 750|750|CD U|u|NN of|of|IN micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- at|at|IN 25|25|CD °C|°c|NN .|.|. The|the|DT ribosome-protected|ribosome-protected|JJ RNA|rna|NN fragments|fragment|NNS were|be|VBD isolated|isolate|VBN using|use|VBG a|a|DT sucrose|sucrose|NN gradient|gradient|NN followed|follow|VBN by|by|IN hot|hot|JJ acid|acid|NN phenol|phenol|NN extraction|extraction|NN .|.|.
Extraction|extraction|NN was|be|VBD performed|perform|VBN as|as|IN described|describe|VBN previously|previously|RB -LRB-|-lrb-|-LRB- Li|Li|NNP et|et|FW al.|al.|FW ,|,|, 2012|2012|CD ;|;|: Oh|oh|UH et|et|FW al.|al.|FW ,|,|, 2011|2011|CD -RRB-|-rrb-|-RRB- .|.|. For|for|IN ribosome|ribosome|NN profiling|profiling|NN ,|,|, 200|200|CD mL|ml|NN of|of|IN cell|cell|NN culture|culture|NN were|be|VBD filtered|filter|VBN rapidly|rapidly|RB and|and|CC the|the|DT resulting|result|VBG cell|cell|NN pellet|pellet|NN was|be|VBD flash-frozen|flash-frozen|JJ in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC combined|combine|VBN with|with|IN 650|650|CD µL|µl|NN of|of|IN frozen|frozen|JJ lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN MgCl2|mgcl2|NN ,|,|, 100mM|100mm|NN NH4Cl|nh4cl|NN ,|,|, 20mM|20mm|NN Tris-HCl|tris-hcl|NN pH|ph|NN 8.0|8.0|CD ,|,|, 0.1|0.1|CD %|%|NN Nonidet|nonidet|JJ P40|p40|NN ,|,|, 0.4|0.4|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 100|100|CD U/mL|u/ml|NN DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- ,|,|, 1mM|1mm|NN chloramphenicol|chloramphenicol|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD pulverized|pulverize|VBN in|in|IN 10mL|10ml|NN canisters|canister|NNS pre-chilled|pre-chill|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|. Lysate|lysate|NN containing|contain|VBG 0.5|0.5|CD mg|mg|NN of|of|IN RNA|rna|NN was|be|VBD digested|digest|VBN for|for|IN 1|1|CD h|h|NN with|with|IN 750|750|CD U|u|NN of|of|IN micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- at|at|IN 25|25|CD °C|°c|NN .|.|. The|the|DT ribosome-protected|ribosome-protected|JJ RNA|rna|NN fragments|fragment|NNS were|be|VBD isolated|isolate|VBN using|use|VBG a|a|DT sucrose|sucrose|NN gradient|gradient|NN followed|follow|VBN by|by|IN hot|hot|JJ acid|acid|NN phenol|phenol|NN extraction|extraction|NN .|.|. For|for|IN mRNA-seq|mrna-seq|NN and|and|CC DMS-seq|dms-seq|NN ,|,|, cells|cell|NNS were|be|VBD pelleted|pellete|VBN by|by|IN centrifuging|centrifuge|VBG for|for|IN 2|2|CD min|min|NN at|at|IN 8000rpm|8000rpm|CD .|.|. Total|total|JJ RNA|rna|NN was|be|VBD then|then|RB hot|hot|JJ acid|acid|NN phenol|phenol|NN extracted|extract|VBN .|.|. Ribosomal|ribosomal|JJ RNA|rna|NN and|and|CC small|small|JJ RNA|rna|NN were|be|VBD removed|remove|VBN with|with|IN MICROBExpress|microbexpress|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- or|or|CC Ribozero|ribozero|NN -LRB-|-lrb-|-LRB- Epicenter|epicenter|NN -RRB-|-rrb-|-RRB- and|and|CC MEGAclear|megaclear|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB .|.|.
EYG1|eyg1|NN in|in|IN M9|m9|NN Replicate|replicate|VB 1|1|CD
EYG1|eyg1|NN in|in|IN M9|m9|NN Replicate|replicate|VB 2|2|CD
EYG1|eyg1|NN ,|,|, MG1655|mg1655|NN rpoC|rpoc|NN K370|k370|NN _|_|CD A396dup|a396dup|NN
EYG|eyg|NN in|in|IN M9|m9|NN supplemented|supplement|VBN with|with|IN 0.6|0.6|CD M|m|NN NaCl|nacl|NN Replicate|replicate|VB 1|1|CD
EYG|eyg|NN in|in|IN M9|m9|NN supplemented|supplement|VBN with|with|IN 0.6|0.6|CD M|m|NN NaCl|nacl|NN Replicate|replicate|VB 2|2|CD
fadr|fadr|NN KO|ko|NN LB|lb|NN rep1|rep1|NN
fadr|fadr|NN KO|ko|NN LB|lb|NN rep2|rep2|NN
fadr|fadr|NN KO|ko|NN M9|m9|NN rep1|rep1|NN
fadr|fadr|NN KO|ko|NN M9|m9|NN rep2|rep2|NN
Faecal|faecal|JJ samples|sample|NNS were|be|VBD collected|collect|VBN by|by|IN the|the|DT Department|Department|NNP of|of|IN Microbiology|Microbiology|NNP and|and|CC Alimentary|Alimentary|NNP Pharmabiotic|Pharmabiotic|NNP Centre|Centre|NNP -LRB-|-lrb-|-LRB- Cork|Cork|NNP ,|,|, Ireland|Ireland|NNP -RRB-|-rrb-|-RRB- from|from|IN three|three|CD elderly|elderly|JJ patients|patient|NNS -LRB-|-lrb-|-LRB- 176|176|CD ,|,|, 204|204|CD and|and|CC 205|205|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT mock|mock|JJ community|community|NN was|be|VBD performed|perform|VBN after|after|IN culture|culture|NN of|of|IN each|each|DT individual|individual|JJ bacterial|bacterial|JJ strain|strain|NN in|in|IN their|they|PRP$ reference|reference|NN medium|medium|NN at|at|IN their|they|PRP$ optimal|optimal|JJ temperature|temperature|NN for|for|IN several|several|JJ days|day|NNS .|.|.
FastQ|fastq|NN files|file|NNS were|be|VBD examined|examine|VBN using|use|VBG the|the|DT FastQC|fastqc|NN tool|tool|NN .|.|. All|all|PDT the|the|DT relevant|relevant|JJ SPET-seq|spet-seq|NN data|datum|NNS -LRB-|-lrb-|-LRB- nascent|nascent|JJ RNA|rna|NN -RRB-|-rrb-|-RRB- analysis|analysis|NN and|and|CC normalization|normalization|NN steps|step|NNS were|be|VBD performed|perform|VBN using|use|VBG a|a|DT custom|custom|NN wrapper|wrapper|NN built|build|VBN on|on|IN top|top|NN of|of|IN the|the|DT RNA|rna|NN Framework13|framework13|NN .|.|. Briefly|briefly|RB ,|,|, reads|read|VBZ were|be|VBD clipped|clip|VBN from|from|IN 3|3|CD '|'|'' adapter|adapter|NN sequences|sequence|NNS using|use|VBG Cutadapt|cutadapt|JJ v1|v1|NN .10|.10|CD ,|,|, discarding|discard|VBG reads|read|VBZ shorter|shorter|JJR than|than|IN 15|15|CD nucleotides|nucleotide|NNS .|.|. Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN :|:|: U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN as|as|IN the|the|DT reference|reference|NN genome|genome|NN to|to|TO extract|extract|NN transcripts|transcript|NNS '|'|POS sequences|sequence|NNS .|.|. Forward|forward|RB and|and|CC reverse|reverse|RB reads|read|VBZ were|be|VBD independently|independently|RB mapped|map|VBN to|to|TO the|the|DT reference|reference|NN transcriptome|transcriptome|NN using|use|VBG Bowtie|Bowtie|NNP v1|v1|NN .1.2|.1.2|CD ,|,|, by|by|IN allowing|allow|VBG up|up|RP to|to|TO 7|7|CD mapping|mapping|NN positions|position|NNS to|to|TO enable|enable|VB mapping|map|VBG to|to|TO the|the|DT 7|7|CD E.|e.|FW coli|coli|FW rRNA|rrna|NN genes|gene|NNS -LRB-|-lrb-|-LRB- parameters|parameter|NNS :|:|: -|-|: n|n|NN 2|2|CD -|-|: m|m|NN 7|7|CD -|-|: a|a|DT --|--|: best|best|JJS --|--|: strata|strata|NN -5|-5|CD 5|5|CD -LSB-|-lsb-|-LRB- --|--|: norc|norc|NN for|for|IN forward|forward|RB reads|read|VBZ ,|,|, --|--|: nofw|nofw|NN for|for|IN reverse|reverse|JJ reads|read|VBZ -RSB-|-rsb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. Forward|forward|RB and|and|CC reverse|reverse|VB mapped|map|VBN reads|read|VBZ were|be|VBD then|then|RB re-paired|re-paired|JJ .|.|. Using|use|VBG reverse|reverse|JJ read|read|NN mapping|mapping|NN positions|position|NNS -LRB-|-lrb-|-LRB- corresponding|correspond|VBG to|to|TO RNA|rna|NN Polymerase|polymerase|NN positions|position|NNS along|along|IN gene|gene|NN -RRB-|-rrb-|-RRB- ,|,|, forward|forward|RB reads|read|VBZ were|be|VBD split|split|VBN into|into|IN separate|separate|JJ SAM|SAM|NNP files|file|NNS for|for|IN each|each|DT transcription|transcription|NN intermediate|intermediate|NN .|.|. When|when|WRB analysis|analysis|NN was|be|VBD performed|perform|VBN in|in|IN deciles|decile|NNS of|of|IN transcription|transcription|NN ,|,|, genes|gene|NNS were|be|VBD split|split|VBN into|into|IN 10|10|CD equally|equally|RB sized|size|VBN deciles|decile|NNS ,|,|, and|and|CC reads|read|VBZ belonging|belong|VBG to|to|TO transcription|transcription|NN intermediates|intermediate|NNS falling|fall|VBG in|in|IN the|the|DT same|same|JJ decile|decile|NN were|be|VBD pooled|pool|VBN .|.|. SAM|SAM|NNP files|file|NNS were|be|VBD then|then|RB passed|pass|VBN to|to|TO the|the|DT rf-count|rf-count|JJ tool|tool|NN of|of|IN the|the|DT RNA|rna|NN Framework|framework|NN to|to|TO generate|generate|VB RT-stop|rt-stop|JJ counts|count|NNS -LRB-|-lrb-|-LRB- RC|rc|NN -RRB-|-rrb-|-RRB- files|file|NNS .|.|. Resulting|result|VBG RC|rc|NN files|file|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT rf-norm|rf-norm|NN tool|tool|NN of|of|IN the|the|DT RNA|rna|NN Framework|framework|NN in|in|IN 50|50|CD nt|nt|NNS sliding|slide|VBG windows|window|NNS ,|,|, with|with|IN a|a|DT 25|25|CD nt|nt|NNS offset|offset|VBP -LRB-|-lrb-|-LRB- parameters|parameter|NNS :|:|: -|-|: sm|sm|NN 2|2|CD -|-|: nm|nm|NN 2|2|CD -|-|: ec|ec|NN 0|0|CD -|-|: mc|mc|NN 0|0|CD -|-|: n|n|NN 50|50|CD -|-|: nw|nw|NN 50|50|CD -|-|: wo|will|MD 25|25|CD -RRB-|-rrb-|-RRB- .|.|. Mapping|mapping|NN of|of|IN DMS-seq|dms-seq|JJ data|datum|NNS -LRB-|-lrb-|-LRB- mature|mature|JJ RNA|rna|NN -RRB-|-rrb-|-RRB- was|be|VBD performed|perform|VBN by|by|IN using|use|VBG the|the|DT rf-count|rf-count|JJ tool|tool|NN -LRB-|-lrb-|-LRB- parameters|parameter|NNS :|:|: -|-|: cl|cl|NN 15|15|CD -|-|: bm|bm|NN 7|7|CD -|-|: ba|ba|SYM -|-|: b5|b5|NN 5|5|CD -RRB-|-rrb-|-RRB- .|.|. Resulting|result|VBG RC|rc|NN files|file|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT rf-norm|rf-norm|NN tool|tool|NN -LRB-|-lrb-|-LRB- parameters|parameter|NNS :|:|: -|-|: sm|sm|NN 2|2|CD -|-|: nm|nm|NN 2|2|CD -|-|: ec|ec|NN 50|50|CD -|-|: mc|mc|NN 50|50|CD -|-|: n|n|NN 50|50|CD -|-|: nw|nw|NN 50|50|CD -|-|: wo|will|MD 25|25|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT rf-norm|rf-norm|JJ tool|tool|NN generates|generate|VBZ a|a|DT XML|xml|NN file|file|NN for|for|IN each|each|DT transcript|transcript|NN -LRB-|-lrb-|-LRB- or|or|CC for|for|IN each|each|DT transcription|transcription|NN intermediate/decile|intermediate/decile|NN in|in|IN the|the|DT case|case|NN of|of|IN SPET-seq|spet-seq|JJ data|datum|NNS -RRB-|-rrb-|-RRB- .|.|. XML|xml|NN files|file|NNS for|for|IN mature|mature|JJ RNA|rna|NN were|be|VBD passed|pass|VBN to|to|TO the|the|DT rf-fold|rf-fold|JJ tool|tool|NN of|of|IN the|the|DT RNA|rna|NN Framework|framework|NN -LRB-|-lrb-|-LRB- using|use|VBG ViennaRNA|viennarna|NN Package|package|NN 2.2|2.2|CD with|with|IN soft|soft|JJ constraints14|constraints14|NN -RRB-|-rrb-|-RRB- to|to|TO infer|infer|VB mature|mature|JJ RNA|rna|NN structures|structure|NNS -LRB-|-lrb-|-LRB- parameters|parameter|NNS :|:|: -|-|: md|md|NN 600|600|CD -|-|: nlp|nlp|NN -RRB-|-rrb-|-RRB- .|.|.
FastQ|fastq|NN files|file|NNS were|be|VBD examined|examine|VBN using|use|VBG the|the|DT FastQC|fastqc|NN tool|tool|NN .|.|. All|all|PDT the|the|DT relevant|relevant|JJ SPET-seq|spet-seq|NN data|datum|NNS -LRB-|-lrb-|-LRB- nascent|nascent|JJ RNA|rna|NN -RRB-|-rrb-|-RRB- analysis|analysis|NN and|and|CC normalization|normalization|NN steps|step|NNS were|be|VBD performed|perform|VBN using|use|VBG a|a|DT custom|custom|NN wrapper|wrapper|NN built|build|VBN on|on|IN top|top|NN of|of|IN the|the|DT RNA|rna|NN Framework13|framework13|NN .|.|. Briefly|briefly|RB ,|,|, reads|read|VBZ were|be|VBD clipped|clip|VBN from|from|IN 3|3|CD '|'|'' adapter|adapter|NN sequences|sequence|NNS using|use|VBG Cutadapt|cutadapt|JJ v1|v1|NN .10|.10|CD ,|,|, discarding|discard|VBG reads|read|VBZ shorter|shorter|JJR than|than|IN 15|15|CD nucleotides|nucleotide|NNS .|.|. Forward|forward|RB and|and|CC reverse|reverse|RB reads|read|VBZ were|be|VBD independently|independently|RB mapped|map|VBN to|to|TO the|the|DT RNase|rnase|NN P|p|NN -LRB-|-lrb-|-LRB- rnpB|rnpb|NN -RRB-|-rrb-|-RRB- gene|gene|NN using|use|VBG Bowtie|Bowtie|NNP v1|v1|NN .1.2|.1.2|CD ,|,|, by|by|IN allowing|allow|VBG up|up|RP to|to|TO 7|7|CD mapping|mapping|NN positions|position|NNS to|to|TO enable|enable|VB mapping|map|VBG to|to|TO the|the|DT 7|7|CD E.|e.|FW coli|coli|FW rRNA|rrna|NN genes|gene|NNS -LRB-|-lrb-|-LRB- parameters|parameter|NNS :|:|: -|-|: n|n|NN 2|2|CD -|-|: m|m|NN 7|7|CD -|-|: a|a|DT --|--|: best|best|JJS --|--|: strata|strata|NN -5|-5|CD 5|5|CD -LSB-|-lsb-|-LRB- --|--|: norc|norc|NN for|for|IN forward|forward|RB reads|read|VBZ ,|,|, --|--|: nofw|nofw|NN for|for|IN reverse|reverse|JJ reads|read|VBZ -RSB-|-rsb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. Forward|forward|RB and|and|CC reverse|reverse|VB mapped|map|VBN reads|read|VBZ were|be|VBD then|then|RB re-paired|re-paired|JJ .|.|. Using|use|VBG reverse|reverse|JJ read|read|NN mapping|mapping|NN positions|position|NNS -LRB-|-lrb-|-LRB- corresponding|correspond|VBG to|to|TO RNA|rna|NN Polymerase|polymerase|NN positions|position|NNS along|along|IN gene|gene|NN -RRB-|-rrb-|-RRB- ,|,|, forward|forward|RB reads|read|VBZ were|be|VBD split|split|VBN into|into|IN separate|separate|JJ SAM|SAM|NNP files|file|NNS for|for|IN each|each|DT transcription|transcription|NN intermediate|intermediate|NN .|.|. SAM|SAM|NNP files|file|NNS were|be|VBD then|then|RB passed|pass|VBN to|to|TO the|the|DT rf-count|rf-count|JJ tool|tool|NN of|of|IN the|the|DT RNA|rna|NN Framework|framework|NN to|to|TO generate|generate|VB RT-stop|rt-stop|JJ counts|count|NNS -LRB-|-lrb-|-LRB- RC|rc|NN -RRB-|-rrb-|-RRB- files|file|NNS ,|,|, that|that|WDT were|be|VBD then|then|RB normalized|normalize|VBN using|use|VBG the|the|DT rf-norm|rf-norm|NN tool|tool|NN .|.|.
FastQ|fastq|NN files|file|NNS were|be|VBD examined|examine|VBN using|use|VBG the|the|DT FastQC|fastqc|NN tool|tool|NN .|.|. Reads|read|NNS were|be|VBD clipped|clip|VBN from|from|IN 3|3|CD '|'|'' adapter|adapter|NN sequences|sequence|NNS using|use|VBG Cutadapt|cutadapt|JJ v1|v1|NN .10|.10|CD ,|,|, discarding|discard|VBG reads|read|VBZ shorter|shorter|JJR than|than|IN 15|15|CD nucleotides|nucleotide|NNS .|.|. Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN :|:|: U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN as|as|IN the|the|DT reference|reference|NN genome|genome|NN .|.|. Reads|read|NNS were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN using|use|VBG Bowtie|Bowtie|NNP v1|v1|NN .1.2|.1.2|CD ,|,|, by|by|IN allowing|allow|VBG up|up|RP to|to|TO 7|7|CD mapping|mapping|NN positions|position|NNS to|to|TO enable|enable|VB mapping|map|VBG to|to|TO the|the|DT 7|7|CD E.|e.|FW coli|coli|FW rRNA|rrna|NN genes|gene|NNS -LRB-|-lrb-|-LRB- parameters|parameter|NNS :|:|: -|-|: n|n|NN 2|2|CD -|-|: m|m|NN 7|7|CD -|-|: a|a|DT --|--|: best|best|JJS --|--|: strata|strata|NN -5|-5|CD 5|5|CD -RRB-|-rrb-|-RRB- .|.|.
FASTQ|fastq|NN formatted|format|VBD sequence|sequence|NN files|file|NNS from|from|IN strand-specific|strand-specific|JJ Illumina|Illumina|NNP RNA-Seq|rna-seq|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT GLBRCE1|glbrce1|NN reference|reference|NN genome|genome|NN NC|nc|NN _|_|CD 000913|000913|CD using|use|VBG Bowtie|Bowtie|NNP version|version|NN 0.12.7|0.12.7|CD -LRB-|-lrb-|-LRB- Langmead|Langmead|NNP et|et|FW al.|al.|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- with|with|IN '|'|'' --|--|: nofw|nofw|NN '|'|'' strand-specific|strand-specific|JJ parameter|parameter|NN and|and|CC maximal|maximal|JJ distance|distance|NN between|between|IN the|the|DT paired|paired|JJ reads|read|VBZ of|of|IN 1000|1000|CD bp|bp|NN .|.|. NOTE|note|VB :|:|: Genome|Genome|NNP NC|NC|NNP _|_|SYM 000913|000913|CD -LRB-|-lrb-|-LRB- ASM584v2|asm584v2|NN -RRB-|-rrb-|-RRB- represents|represent|VBZ the|the|DT parental|parental|JJ strain|strain|NN .|.|. The|the|DT strain|strain|NN used|use|VBN in|in|IN our|we|PRP$ study|study|NN was|be|VBD modified|modify|VBN from|from|IN the|the|DT parental|parental|JJ strain|strain|NN by|by|IN replacing|replace|VBG gene|gene|NN pflB|pflb|NN with|with|IN an|a|DT insertion|insertion|NN that|that|WDT contained|contain|VBD 3|3|CD different|different|JJ genes|gene|NNS .|.|.
Fastq|fastq|JJ quality|quality|NN trimming|trim|VBG using|use|VBG FastX|fastx|NN and|and|CC a|a|DT cut-off|cut-off|JJ value|value|NN of|of|IN 20|20|CD
FastQ|fastq|NN quality|quality|NN trimming|trim|VBG using|use|VBG FastX|fastx|NN -LRB-|-lrb-|-LRB- version|version|NN 0.0.13|0.0.13|CD -RRB-|-rrb-|-RRB- and|and|CC a|a|DT cut-off|cut-off|JJ value|value|NN of|of|IN 20|20|CD
Fastq|fastq|NN to|to|TO fasta|fasta|NN conversion|conversion|NN using|use|VBG FastX|fastx|NN
Fastq|fastq|NN to|to|TO fasta|fasta|NN conversion|conversion|NN using|use|VBG FastX|fastx|NN FastX|fastx|NN -LRB-|-lrb-|-LRB- version|version|NN 0.0.13|0.0.13|CD -RRB-|-rrb-|-RRB-
Feature|Feature|NNP fluorescence|fluorescence|NN intensities|intensity|NNS -LSB-|-lsb-|-LRB- F532|f532|NN media-B532|media-b532|NN and|and|CC F635media-B635|f635media-b635|NN -RSB-|-rsb-|-RRB- were|be|VBD extracted|extract|VBN using|use|VBG GenePix|GenePix|NNP Pro|pro|FW 6.0|6.0|CD .|.|. Local|local|JJ hybridization|hybridization|NN and|and|CC intensity-dependent|intensity-dependent|JJ artifacts|artifact|NNS were|be|VBD removed|remove|VBN with|with|IN Lowess|lowess|NN normalization|normalization|NN using|use|VBG Standardization|standardization|NN and|and|CC Normalization|normalization|NN of|of|IN Microarray|Microarray|NNP Data|Data|NNP -LRB-|-lrb-|-LRB- SNOMAD|SNOMAD|NNP ,|,|, http://pevsnerlab.kennedykrieger.org/snomadinput.html|http://pevsnerlab.kennedykrieger.org/snomadinput.html|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT three|three|CD replicate|replicate|VBP spots|spot|NNS for|for|IN each|each|DT gene|gene|NN were|be|VBD averaged|average|VBN and|and|CC variance|variance|NN was|be|VBD calculated|calculate|VBN .|.|.
Feature|Feature|NNP intensity|intensity|NN was|be|VBD extracted|extract|VBN by|by|IN GeneChip|GeneChip|NNP Operating|Operating|NNP System|System|NNP as|as|IN CEL|CEL|NNP files|file|NNS .|.|. The|the|DT probe-level|probe-level|JJ analysis|analysis|NN of|of|IN the|the|DT CEL|CEL|NNP files|file|NNS was|be|VBD done|do|VBN by|by|IN the|the|DT PLIER|plier|NN algorithm|algorithm|NN in|in|IN the|the|DT Affymetrix|Affymetrix|NNP Expression|expression|NN Console|console|NN .|.|. No|no|DT further|further|JJ adjustments|adjustment|NNS were|be|VBD made|make|VBN to|to|TO the|the|DT data|datum|NNS in|in|IN the|the|DT table|table|NN .|.|.
Feature|Feature|NNP pixel|pixel|NN median|median|NN minus|minus|CC background|background|NN pixel|pixel|NN mean|mean|NN ;|;|:
Fecal|fecal|JJ samples|sample|NNS obtained|obtain|VBN from|from|IN mice|mouse|NNS were|be|VBD immediately|immediately|RB frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN until|until|IN processing|processing|NN .|.|. All|all|DT of|of|IN the|the|DT samples|sample|NNS were|be|VBD suspended|suspend|VBN in|in|IN a|a|DT solution|solution|NN containing|contain|VBG 500|500|CD ul|ul|NN of|of|IN acid-washed|acid-washed|JJ glass|glass|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Sigma-Aldrich|Sigma-Aldrich|NNP -RRB-|-rrb-|-RRB- ,|,|, 500|500|CD ul|ul|NN of|of|IN extraction|extraction|NN buffer|buffer|NN A|a|NN -LRB-|-lrb-|-LRB- 200|200|CD mM|mm|NN Tris|tris|NN -LSB-|-lsb-|-LRB- pH|ph|NN 8|8|CD -RSB-|-rsb-|-RRB- ,|,|, 200|200|CD mM|mm|NN NaCl|nacl|NN ,|,|, 20|20|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, 200|200|CD ul|ul|NN of|of|IN 20|20|CD %|%|NN SDS|sds|NN ,|,|, and|and|CC 500|500|CD ul|ul|NN of|of|IN a|a|DT mixture|mixture|NN of|of|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN -LRB-|-lrb-|-LRB- 25:24:1|25:24:1|CD ,|,|, pH|ph|NN 8.0|8.0|CD ;|;|: Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- and|and|CC lysed|lyse|VBN by|by|IN using|use|VBG a|a|DT bead|bead|NN beater|beater|NN -LRB-|-lrb-|-LRB- BioSpec|BioSpec|NNP Products|Products|NNPS -RRB-|-rrb-|-RRB- .|.|. Cellular|cellular|JJ debris|debris|NN was|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 8,000|8,000|CD g|g|NN ;|;|: 3|3|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT nucleic|nucleic|JJ acids|acid|NNS were|be|VBD precipitated|precipitate|VBN with|with|IN isopropanol|isopropanol|NN and|and|CC sodium|sodium|NN acetate|acetate|NN and|and|CC resuspended|resuspend|VBN in|in|IN 100|100|CD ul|ul|NN TE|TE|NNP .|.|. The|the|DT resuspension|resuspension|NN was|be|VBD further|further|JJ purified|purify|VBN with|with|IN a|a|DT Qiagen|Qiagen|NNP PCR|pcr|NN column|column|NN and|and|CC eluted|elute|VBN into|into|IN 30|30|CD ul|ul|NN of|of|IN EB|EB|NNP buffer|buffer|NN .|.|.
Fecal|fecal|JJ samples|sample|NNS obtained|obtain|VBN from|from|IN mice|mouse|NNS were|be|VBD immediately|immediately|RB frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN until|until|IN processing|processing|NN .|.|. All|all|DT of|of|IN the|the|DT samples|sample|NNS were|be|VBD treated|treat|VBN with|with|IN RNAProtect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC suspended|suspend|VBN in|in|IN a|a|DT solution|solution|NN containing|contain|VBG 500|500|CD μl|μl|NN of|of|IN acid-washed|acid-washed|JJ glass|glass|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Sigma-Aldrich|Sigma-Aldrich|NNP -RRB-|-rrb-|-RRB- ,|,|, 500|500|CD μl|μl|NN of|of|IN extraction|extraction|NN buffer|buffer|NN A|a|NN -LRB-|-lrb-|-LRB- 200|200|CD mM|mm|NN NaCl|nacl|NN ,|,|, 20|20|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- ,|,|, 210|210|CD μl|μl|NN of|of|IN 20|20|CD %|%|NN SDS|sds|NN ,|,|, and|and|CC 500|500|CD μl|μl|NN of|of|IN a|a|DT mixture|mixture|NN of|of|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN -LRB-|-lrb-|-LRB- 125:24:1|125:24:1|CD ,|,|, pH|ph|NN 4.5|4.5|CD ;|;|: Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- and|and|CC lysed|lyse|VBN by|by|IN using|use|VBG a|a|DT bead|bead|NN beater|beater|NN -LRB-|-lrb-|-LRB- BioSpec|BioSpec|NNP Products|Products|NNPS -RRB-|-rrb-|-RRB- .|.|. Cellular|cellular|JJ debris|debris|NN was|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 8,000|8,000|CD ×|×|CD g|g|NN ;|;|: 3|3|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT nucleic|nucleic|JJ acids|acid|NNS were|be|VBD precipitated|precipitate|VBN with|with|IN isopropanol|isopropanol|NN and|and|CC sodium|sodium|NN acetate|acetate|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.5|5.5|CD -RRB-|-rrb-|-RRB- .|.|.
Fecal|fecal|JJ samples|sample|NNS obtained|obtain|VBN from|from|IN mice|mouse|NNS were|be|VBD span|span|NN frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD ¬|¬|CD ∞|∞|NN C|c|NN and|and|CC maintained|maintain|VBD at|at|IN this|this|DT temperature|temperature|NN prior|prior|RB to|to|TO processing|processing|NN .|.|.
Fed|Fed|NNP batch|batch|NN high|high|JJ cell|cell|NN density|density|NN cultivation|cultivation|NN
fepA|fepa|NN KO|ko|NN LB|lb|NN rep1|rep1|NN
fepA|fepa|NN KO|ko|NN LB|lb|NN rep2|rep2|NN
fepA|fepa|NN KO|ko|NN M9|m9|NN rep1|rep1|NN
fepA|fepa|NN KO|ko|NN M9|m9|NN rep2|rep2|NN
Fermentations|fermentation|NNS were|be|VBD carried|carry|VBN out|out|RP in|in|IN 3|3|CD L|l|NN bioreactors|bioreactor|NNS -LRB-|-lrb-|-LRB- Applikon|Applikon|NNP Biotechnology|Biotechnology|NNP -RRB-|-rrb-|-RRB- containing|contain|VBG 2.45|2.45|CD L|l|NN of|of|IN ACSH|acsh|NN or|or|CC SynH|synh|NN media|media|NNS ,|,|, and|and|CC cultures|culture|NNS were|be|VBD diluted|dilute|VBN into|into|IN ACSH|acsh|NN or|or|CC SynH|synh|NN with|with|IN initial|initial|JJ OD|od|NN at|at|IN 0.2|0.2|CD ,|,|, grown|grow|VBN anaerobically|anaerobically|RB overnight|overnight|RB ,|,|, and|and|CC then|then|RB inoculated|inoculate|VBN into|into|IN bioreactors|bioreactor|NNS to|to|TO a|a|DT starting|start|VBG OD600|od600|NN of|of|IN 0.2|0.2|CD
Fermentations|fermentation|NNS were|be|VBD carried|carry|VBN out|out|RP in|in|IN 3L|3l|NN bioreactors|bioreactor|NNS -LRB-|-lrb-|-LRB- Applikon|Applikon|NNP Biotechnology|Biotechnology|NNP -RRB-|-rrb-|-RRB- containing|contain|VBG 2.45|2.45|CD L|l|NN of|of|IN ACSH|ACSH|NNP ,|,|, SynH|synh|NN ,|,|, SynH|synh|NN +|+|CC LT|lt|NN ,|,|, or|or|CC SynH|synh|NN +|+|CC Acid/Amide|Acid/Amide|NNP LTs|LTs|NNP ,|,|, and|and|CC cultures|culture|NNS were|be|VBD diluted|dilute|VBN into|into|IN ACSH|acsh|NN or|or|CC SynH|synh|NN with|with|IN initial|initial|JJ OD|od|NN at|at|IN 0.2|0.2|CD ,|,|, grown|grow|VBN anaerobically|anaerobically|RB overnight|overnight|RB ,|,|, and|and|CC then|then|RB inoculated|inoculate|VBN into|into|IN bioreactors|bioreactor|NNS to|to|TO a|a|DT starting|start|VBG OD600|od600|NN of|of|IN 0.2|0.2|CD
fermentation|fermentation|NN time|time|NN :|:|: 20h|20h|JJ
fermentation|fermentation|NN time|time|NN :|:|: 30h|30h|CD
fermentation|fermentation|NN time|time|NN :|:|: 40h|40h|JJ
Fifteen|fifteen|CD mL|ml|NN fermentation|fermentation|NN broth|broth|NN was|be|VBD used|use|VBN for|for|IN each|each|DT RNA|rna|NN extraction|extraction|NN .|.|. Harvested|harvest|VBN cells|cell|NNS were|be|VBD rapidly|rapidly|RB cooled|cool|VBN in|in|IN a|a|DT -80|-80|CD °C|°c|NN ethanol|ethanol|NN bath|bath|NN ,|,|, then|then|RB centrifuged|centrifuge|VBD at|at|IN 5000|5000|CD g|g|NN for|for|IN seven|seven|CD minutes|minute|NNS at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD discarded|discard|VBN .|.|. The|the|DT cell|cell|NN pellet|pellet|NN was|be|VBD frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|. Thawed|thaw|VBN -LRB-|-lrb-|-LRB- on|on|IN ice|ice|NN -RRB-|-rrb-|-RRB- cell|cell|NN pellets|pellet|NNS were|be|VBD suspended|suspend|VBN in|in|IN 150|150|CD mL|ml|NN of|of|IN TE|TE|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 7.6|7.6|CD ,|,|, 0.1|0.1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- containing|contain|VBG 0.75|0.75|CD mg/mL|mg/ml|NN lysozyme|lysozyme|NN ,|,|, and|and|CC incubated|incubate|VBN for|for|IN 15|15|CD minutes|minute|NNS at|at|IN room|room|NN temperature|temperature|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG RNAqueousTM-Midi|RNAqueousTM-Midi|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT concentration|concentration|NN of|of|IN purified|purify|VBN total|total|JJ RNA|rna|NN was|be|VBD determined|determine|VBN spectrophotometrically|spectrophotometrically|RB by|by|IN measuring|measure|VBG absorbance|absorbance|NN at|at|IN 260|260|CD nm|nm|NN .|.|. The|the|DT quality|quality|NN and|and|CC integrity|integrity|NN of|of|IN the|the|DT isolated|isolate|VBN RNA|rna|NN was|be|VBD confirmed|confirm|VBN by|by|IN agarose|agarose|NN gels|gel|NNS -LRB-|-lrb-|-LRB- clear|clear|JJ 23S|23s|NN and|and|CC 16S|16s|NN rRNA|rrna|NN bands|band|NNS -RRB-|-rrb-|-RRB- .|.|.
Files|Files|NNPS were|be|VBD coverted|covert|VBN to|to|TO .|.|. bam|bam|NN format|format|NN using|use|VBG samtools|samtool|NNS
Filter|Filter|NNP for|for|IN map|map|NN quality|quality|NN >|>|JJR =|=|JJ 20|20|CD using|use|VBG Samtools|Samtools|NNP 0.1.18|0.1.18|CD
Filtering|Filtering|NNP ,|,|, Mapping|mapping|NN quality|quality|NN =|=|JJ 30|30|CD ,|,|, no|no|DT ambiguous|ambiguous|JJ reads|read|VBZ
Filter|Filter|NNP out|out|IN rRNA|rrna|NN reads|read|VBZ ,|,|, multi-mapped|multi-mapped|JJ reads|read|VBZ ,|,|, >|>|JJR 3|3|CD mismatches|mismatch|NNS ,|,|, and|and|CC gapped|gap|VBD mappings|mapping|NNS using|use|VBG custom|custom|NN Python|Python|NNP script|script|NN -LRB-|-lrb-|-LRB- FilterBAM2BAM|filterbam2bam|NN from|from|IN http://uwgenomics.org/downloads/RNA-Seq-1.1.tar.gz|http://uwgenomics.org/downloads/rna-seq-1.1.tar.gz|NN -RRB-|-rrb-|-RRB-
First|First|NNP and|and|CC second|second|JJ strand|strand|NN cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD carried|carry|VBN out|out|RP using|use|VBG the|the|DT Ovation|Ovation|NNP ®|®|NNP Prokaryotic|Prokaryotic|NNP RNA-Seq|RNA-Seq|NNP System|System|NNP -LRB-|-lrb-|-LRB- NuGEN|NuGEN|NNP Technologies|Technologies|NNPS Inc.|Inc.|NNP ,|,|, San|San|NNP Carlos|Carlos|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC NuGEN|nugen|NN 's|'s|POS Encore|encore|NN NGS|ngs|NN Library|Library|NNP System|System|NNP was|be|VBD applied|apply|VBN to|to|TO construct|construct|VB the|the|DT cDNA|cdna|NN library|library|NN for|for|IN the|the|DT IlluminaHiSeq|IlluminaHiSeq|NNP platform|platform|NN .|.|.
First|First|NNP biological|biological|JJ repeat|repeat|NN 37|37|CD °C|°c|NN
First|First|NNP biological|biological|JJ repeat|repeat|NN 50|50|CD °C|°c|NN
First|First|NNP ,|,|, ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD depleted|deplete|VBN from|from|IN 1|1|CD μg|μg|NN of|of|IN total|total|JJ RNA|rna|NN using|use|VBG the|the|DT Ribo-ZeroTM|Ribo-ZeroTM|NNP Magnetic|magnetic|JJ Kit|kit|NN -LRB-|-lrb-|-LRB- Bacteria|bacterium|NNS -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. Next|next|RB ,|,|, mRNA|mrna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN using|use|VBG the|the|DT TruSeq|truseq|NN mRNA|mrna|NN Library|Library|NNP Prep|Prep|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, San|San|NNP Diego|Diego|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. mRNA|mrna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS .|.|.
first|first|JJ strand|strand|NN cDNA|cdna|NN was|be|VBD performed|perform|VBN by|by|IN the|the|DT use|use|NN of|of|IN SuperScriptII|superscriptii|NN and|and|CC the|the|DT second|second|JJ strand|strand|NN cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD done|do|VBN before|before|IN end-pair|end-pair|JJ and|and|CC dA-tailing|da-tailing|JJ
Fis|fis|NN --|--|: 120|120|CD min|min|NN
fis|fis|NN 150|150|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
fis|fi|VBZ 150|150|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
fis|fi|VBZ 150|150|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
Fis|fi|VBZ --|--|: 180|180|CD min|min|NN
fis|fis|NN 240|240|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
fis|fi|VBZ 240|240|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
fis|fi|VBZ 240|240|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
fis|fi|VBZ 360|360|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
fis|fi|VBZ 360|360|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
fis|fi|VBZ 360|360|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
Fis|fi|VBZ --|--|: 420|420|CD min|min|NN
Fis|Fis|NNP --|--|: 60|60|CD min|min|NN
fis|fi|VBZ 90|90|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
fis|fi|VBZ 90|90|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
fis|fi|VBZ 90|90|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
Fis|fis|NN ,|,|, EE|ee|NN
fis.ee.chipseq|fis.ee.chipseq|JJ
fis.ee.input|fis.ee.input|JJ
fis|fi|VBZ Escherichia|escherichia|FW coli|coli|FW
Fis|fis|NN ,|,|, ME|me|NN
fis.me.chipseq|fis.me.chipseq|JJ
fis.me.input|fis.me.input|JJ
fismutant.crp.ee.chipseq|fismutant.crp.ee.chipseq|NN
fismutant.crp.ee.input|fismutant.crp.ee.input|JJ
fismutant.crp.me.chipseq|fismutant.crp.me.chipseq|NN
fismutant.crp.me.input|fismutant.crp.me.input|JJ
fis.rep1.ee|fis.rep1.ee|NN
fis.rep1.me|fis.rep1.me|JJ
fis.rep2.ee|fis.rep2.ee|NN
fis.rep2.me|fis.rep2.me|JJ
fis|fi|VBZ ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
fis|fi|VBZ ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
fis|fi|VBZ ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
fis|fis|FW upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
fklB|fklb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
fklB|fklb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
fklB|fklb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
fklB|fklb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
Flask|flask|NN state|state|NN 1|1|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Flask|flask|NN state|state|NN 2|2|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Flask|flask|NN state|state|NN 3|3|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Flask|flask|NN state|state|NN 4|4|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Flask|flask|NN state|state|NN 5|5|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
Flask|flask|NN state|state|NN 6|6|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
Flask|flask|NN state|state|NN 7|7|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
Flask|flask|NN state|state|NN 8|8|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
flhD-glucose|flhd-glucose|JJ
flhD-mannose|flhd-mannose|NN
flhD-mucus-P1|flhd-mucus-p1|NN
flhD-mucus-P2|flhd-mucus-p2|NN
fliY|fliy|NN KO|ko|NN rep1|rep1|NN
fliY|fliy|NN KO|ko|NN rep2|rep2|NN
fliY|fliy|NN KO|ko|NN rep3|rep3|NN
florfenicol|florfenicol|NN treatment|treatment|NN
Florfenicol|florfenicol|NN _|_|NN treatment|treatment|NN _|_|NN plasmidmappedreads|plasmidmappedread|NNS _|_|VBP statistical|statistical|JJ _|_|NN output.txt|output.txt|NN :|:|: NC|NC|NNP _|_|NNP 012692.1|012692.1|CD
Flor|Flor|NNP _|_|JJ treatment|treatment|NN _|_|NN genomemappedreads|genomemappedread|NNS _|_|VBP statistical|statistical|JJ _|_|NN output.txt|output.txt|NN :|:|: NC|NC|NNP _|_|NNP 000913.2|000913.2|CD
Fluorescence|fluorescence|NN intensities|intensity|NNS of|of|IN oligonucleotide|oligonucleotide|NN spots|spot|NNS were|be|VBD extracted|extract|VBN from|from|IN the|the|DT scanned|scan|VBN images|image|NNS using|use|VBG the|the|DT Feature|Feature|NNP Extraction|extraction|NN software|software|NN -LRB-|-lrb-|-LRB- V11|v11|NN .0|.0|CD ,|,|, Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|. Then|then|RB data|datum|NNS were|be|VBD processed|process|VBN with|with|IN dedicated|dedicated|JJ scripts|script|NNS based|base|VBN on|on|IN C++|C++|NNP and|and|CC Delphi|Delphi|NNP languages|language|NNS .|.|. For|for|IN each|each|DT probe|probe|NN ,|,|, median|median|JJ intensity|intensity|NN value|value|NN of|of|IN the|the|DT 3|3|CD replicates|replicate|VBZ was|be|VBD conserved|conserve|VBN and|and|CC used|use|VBN as|as|IN the|the|DT probe|probe|NN signal|signal|NN value|value|NN .|.|. The|the|DT SNR|snr|NN -LRB-|-lrb-|-LRB- Signal-to-Noise|Signal-to-Noise|NNP Ratio|Ratio|NNP -RRB-|-rrb-|-RRB- ,|,|, similar|similar|JJ to|to|TO the|the|DT detection|detection|NN threshold|threshold|NN response|response|NN -LRB-|-lrb-|-LRB- positive|positive|JJ hybridization|hybridization|NN -RRB-|-rrb-|-RRB- and|and|CC corresponding|correspond|VBG to|to|TO the|the|DT probe|probe|NN signal|signal|NN value|value|NN divided|divide|VBN by|by|IN the|the|DT local|local|JJ background|background|NN intensity|intensity|NN value|value|NN ,|,|, was|be|VBD calculated|calculate|VBN for|for|IN each|each|DT probe|probe|NN .|.|. The|the|DT SNR|SNR|NNP thresholds|threshold|NNS were|be|VBD set|set|VBN to|to|TO 3|3|CD for|for|IN 25-mer|25-mer|JJ probes|probe|NNS and|and|CC 6|6|CD for|for|IN 54-mer|54-mer|JJ probes|probe|NNS .|.|. Such|such|JJ SNR|snr|NN threshold|threshold|NN values|value|NNS ensured|ensure|VBD a|a|DT very|very|RB specific|specific|JJ response|response|NN of|of|IN the|the|DT FibroChip|FibroChip|NNP ,|,|, except|except|IN for|for|IN genes|gene|NNS belonging|belong|VBG to|to|TO very|very|RB close|close|JJ strains|strain|NNS from|from|IN the|the|DT same|same|JJ species|species|NNS .|.|. Results|result|NNS for|for|IN 25|25|CD -|-|: and|and|CC 54-mer|54-mer|JJ probes|probe|NNS were|be|VBD treated|treat|VBN independently|independently|RB and|and|CC for|for|IN each|each|DT probe|probe|NN type|type|NN ,|,|, a|a|DT gene|gene|NN was|be|VBD considered|consider|VBN as|as|IN detected|detect|VBN when|when|WRB 65|65|CD %|%|NN of|of|IN probes|probe|NNS were|be|VBD positive|positive|JJ .|.|. The|the|DT SNR|snr|NN value|value|NN of|of|IN a|a|DT detected|detect|VBN gene|gene|NN was|be|VBD then|then|RB calculated|calculate|VBN by|by|IN the|the|DT mean|mean|NN of|of|IN the|the|DT SNR|snr|NN of|of|IN all|all|DT 25|25|CD -|-|: or|or|CC 54-mer|54-mer|JJ probes|probe|NNS targeting|target|VBG this|this|DT gene|gene|NN ,|,|, meeting|meeting|NN or|or|CC not|not|RB the|the|DT defined|define|VBN SNR|snr|NN threshold|threshold|NN .|.|.
fluorescent|fluorescent|JJ labeling|labeling|NN and|and|CC hybridization|hybridization|NN and|and|CC scanning|scanning|NN of|of|IN the|the|DT microarray|microarray|NN images|image|NNS -LRB-|-lrb-|-LRB- Balazsi|balazsus|NNS et|et|FW al.|al.|FW .|.|.
fnr|fnr|SYM -|-|: aerobic|aerobic|JJ
fnr|fnr|SYM -|-|: aerobic|aerobic|JJ AN|a|DT rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: aerobic|aerobic|JJ AN|a|DT rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: aerobic|aerobic|JJ AN|a|DT rep|rep|NN 3|3|CD
fnr|fnr|SYM -|-|: aerobic|aerobic|JJ rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: aerobic|aerobic|JJ rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: aerobic|aerobic|JJ rep|rep|NN 3|3|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|JJ
FNR|fnr|SYM -|-|: Anaerobic|anaerobic|JJ -|-|: A|a|NN
FNR|fnr|SYM -|-|: Anaerobic|anaerobic|JJ -|-|: Affinity|affinity|NN Purified|purify|VBN -|-|: A|a|NN
FNR|fnr|SYM -|-|: Anaerobic|anaerobic|JJ -|-|: Affinity|affinity|NN Purified|purify|VBN -|-|: B|b|NN
fnr|fnr|SYM -|-|: anaerobic|anaerobic|JJ AN|a|DT rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|JJ AN|a|DT rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|JJ AN|a|DT rep|rep|NN 3|3|CD
FNR|fnr|SYM -|-|: Anaerobic|anaerobic|JJ -|-|: B|b|NN
FNR|fnr|SYM -|-|: Anaerobic|anaerobic|JJ -|-|: C|c|NN
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN AN|a|DT rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN AN|a|DT rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN AN|a|DT rep|rep|NN 3|3|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN rep|rep|NN 3|3|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN AN|a|DT rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN AN|a|DT rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN AN|a|DT rep|rep|NN 3|3|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN rep|rep|NN 3|3|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|JJ rep|rep|NN 1|1|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|JJ rep|rep|NN 2|2|CD
fnr|fnr|SYM -|-|: anaerobic|anaerobic|JJ rep|rep|NN 3|3|CD
FNR|fnr|SYM -|-|: _|_|SYM Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|CD A|a|DT _|_|NN Tag|tag|NN _|_|CD Count.txt|count.txt|NN :|:|: U00096|u00096|NN .2|.2|NN
FNR|fnr|SYM -|-|: _|_|SYM Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|CD A|a|DT _|_|NN WIG.wig|wig.wig|NN :|:|: U00096|u00096|NN .2|.2|NN
FNR|fnr|SYM -|-|: _|_|SYM Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|NN B|b|NN _|_|CD Tag|tag|NN _|_|CD Count.txt|count.txt|NN :|:|: U00096|u00096|NN .2|.2|NN
FNR|fnr|SYM -|-|: _|_|SYM Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|NN B|b|NN _|_|CD WIG.wig|wig.wig|NN :|:|: U00096|u00096|NN .2|.2|NN
∆|∆|CD fnr|fnr|SYM -|-|: Anaeroibc|Anaeroibc|NNP
FNR|FNR|NNP ChIP|chip|NN DNA|dna|NN from|from|IN ∆|∆|CD hns|hn|NNS /|/|: ∆|∆|SYM stpA|stpA|NNP E.|e.|FW coli|coli|FW MG1655|mg1655|NN
∆|∆|CD fnr|fnr|NN ChIP|chip|NN DNA|dna|NN from|from|IN PK4854|pk4854|NN
FNR|fnr|NN ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherchia|Escherchia|NNP coli|coli|NN MG1655|mg1655|NN K-12|k-12|NN
FNR|fnr|SYM -|-|: ∆|∆|SYM hns|hn|VBZ ∆|∆|SYM stpA|stpa|NN A|a|NN
FNR|fnr|SYM -|-|: ∆|∆|SYM hns|hn|VBZ ∆|∆|SYM stpA|stpa|NN B|b|NN
FNR|fnr|NN INPUT|input|NN from|from|IN PK8263|pk8263|NN with|with|IN 16|16|CD µM|µm|NN INPUTTG|inputtg|NN
FNR|fnr|NN INPUT|input|NN from|from|IN PK8263|pk8263|NN with|with|IN 4|4|CD µM|µm|NN INPUTTG|inputtg|NN
FNR|fnr|NN INPUT|input|NN from|from|IN PK8263|pk8263|NN with|with|IN 8|8|CD µM|µm|NN INPUTTG|inputtg|NN
FNR|fnr|NN INPUT|input|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
FNR|fnr|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Anaerobic|Anaerobic|NNP A|A|NNP
FNR|FNR|NNP _|_|SYM IP|IP|NNP _|_|SYM ChIP-seq|ChIP-seq|NNP _|_|SYM Anaerobic|anaerobic|JJ _|_|NN A|a|DT _|_|NN WIG.wig|wig.wig|NN :|:|: U00096|u00096|NN .2|.2|NN
FNR|fnr|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Anaerobic|anaerobic|JJ B|b|NN
FNR|fnr|NN _|_|CD IP|IP|NNP _|_|SYM ChIP-seq|ChIP-seq|NNP _|_|SYM Anaerobic|anaerobic|JJ _|_|NN B|b|NN _|_|CD WIG.wig|wig.wig|NN :|:|: U00096|u00096|NN .2|.2|NN
FNR|fnr|NN IP|IP|NNP from|from|IN PK8263|pk8263|NN with|with|IN 16|16|CD µM|µm|NN IPTG|iptg|NN
FNR|fnr|NN IP|IP|NNP from|from|IN PK8263|pk8263|NN with|with|IN 4|4|CD µM|µm|NN IPTG|iptg|NN
FNR|fnr|NN IP|IP|NNP from|from|IN PK8263|pk8263|NN with|with|IN 8|8|CD µM|µm|NN IPTG|iptg|NN
FNR|fnr|NN IP|IP|NNP from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
folA|fola|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
folA|fola|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
folA|fola|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
folA|fola|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
Following|follow|VBG \|\|SYM
Following|follow|VBG background|background|NN subtraction|subtraction|NN ,|,|, spot|spot|NN signal|signal|NN intensities|intensity|NNS were|be|VBD calculated|calculate|VBN as|as|IN percentages|percentage|NNS of|of|IN total|total|JJ signal|signal|NN intensities|intensity|NNS of|of|IN Cy-3|cy-3|NN or|or|CC Cy-5|cy-5|NN signals|signal|NNS on|on|IN each|each|DT microarray|microarray|NN ,|,|, as|as|IN a|a|DT means|means|NN of|of|IN normalization|normalization|NN .|.|. Spots|spot|NNS with|with|IN low|low|JJ intensities|intensity|NNS were|be|VBD excluded|exclude|VBN .|.|.
Following|follow|VBG incubation|incubation|NN ,|,|, roots|root|NNS had|have|VBD been|be|VBN gently|gently|RB rinsed|rinse|VBN to|to|TO remove|remove|VB loosely|loosely|RB attached|attach|VBN bacteria|bacterium|NNS and|and|CC roots|root|NNS were|be|VBD cut|cut|VBN directly|directly|RB into|into|IN 100|100|CD ml|ml|NN ice|ice|NN cold|cold|JJ stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN H2O-saturated|h2o-saturated|JJ phenol|phenol|NN ,|,|, pH|ph|NN 4.3|4.3|CD ,|,|, in|in|IN 95|95|CD %|%|NN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- .|.|. Root|root|NN extracts|extract|NNS were|be|VBD filtered|filter|VBN using|use|VBG 0.5|0.5|CD µm|µm|NN filters|filter|NNS to|to|TO separate|separate|JJ bacteria|bacterium|NNS cells|cell|NNS from|from|IN plant|plant|NN cells|cell|NNS in|in|IN order|order|NN to|to|TO prevent|prevent|VB interference|interference|NN of|of|IN the|the|DT cDNA|cdna|NN labeling|labeling|NN .|.|. Qiagen|Qiagen|NNP RNA|rna|NN protect|protect|VB solution|solution|NN was|be|VBD used|use|VBN to|to|TO stabilize|stabilize|VB RNA|rna|NN during|during|IN extraction|extraction|NN .|.|. Bacteria|bacterium|NNS had|have|VBD been|be|VBN collected|collect|VBN by|by|IN shaking|shake|VBG and|and|CC washing|wash|VBG and|and|CC stored|store|VBN in|in|IN -80|-80|CD °C|°c|NN until|until|IN using|use|VBG for|for|IN RNA|rna|NN isolation|isolation|NN .|.|.
For|for|IN 3C-seq|3c-seq|NN :|:|: ≈|≈|SYM 1-2|1-2|CD x|x|CC 109|109|CD crosslinked|crosslink|VBN cells|cell|NNS -LRB-|-lrb-|-LRB- 7|7|CD %|%|NN formaldehyde|formaldehyde|NN ,|,|, unless|unless|IN otherwise|otherwise|RB stated|state|VBN -RRB-|-rrb-|-RRB- are|be|VBP suspended|suspend|VBN in|in|IN 600|600|CD μl|μl|NN Tris|Tris|NNP 10|10|CD mM|mm|NN EDTA|edta|NN 0.5|0.5|CD mM|mm|NN -LRB-|-lrb-|-LRB- TE|te|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- pH|ph|NN 8|8|CD -RRB-|-rrb-|-RRB- with|with|IN 4|4|CD μl|μl|NN of|of|IN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- 35|35|CD U/μl|u/μl|NN ;|;|: Tebu|Tebu|NNP Bio|Bio|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC incubated|incubate|VBN at|at|IN RT|rt|NN for|for|IN 20|20|CD minutes|minute|NNS .|.|. SDS|sds|NN is|be|VBZ added|add|VBN to|to|TO the|the|DT mix|mix|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN 0.5|0.5|CD %|%|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT cells|cell|NNS are|be|VBP incubated|incubate|VBN for|for|IN 10|10|CD minutes|minute|NNS at|at|IN RT.|RT.|NNP 50μl|50μl|CD of|of|IN lysed|lysed|JJ cells|cell|NNS are|be|VBP then|then|RB transferred|transfer|VBN in|in|IN 8|8|CD tubes|tube|NNS containing|contain|VBG 450μL|450μl|NN of|of|IN digestion|digestion|NN mix|mix|NN -LRB-|-lrb-|-LRB- 1X|1x|NN NEB|neb|NN 1|1|CD buffer|buffer|NN ,|,|, 1|1|CD %|%|NN triton|triton|NN X-100|x-100|NN ,|,|, and|and|CC 100U|100u|NN HpaII|hpaii|NN enzyme|enzyme|NN -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN is|be|VBZ digested|digest|VBN for|for|IN 3|3|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN ,|,|, split|split|NN in|in|IN 4|4|CD aliquots|aliquot|NNS ,|,|, and|and|CC diluted|dilute|VBN in|in|IN 8|8|CD ml|ml|NN ligation|ligation|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 1X|1x|NN ligation|ligation|NN buffer|buffer|NN NEB|neb|NN without|without|IN ATP|atp|NN ,|,|, 1|1|CD mM|mm|NN ATP|atp|NN ,|,|, 0.1|0.1|CD mg/ml|mg/ml|JJ BSA|bsa|NN ,|,|, 125|125|CD Units|unit|NNS of|of|IN T4|t4|NN DNA|dna|NN ligase|ligase|NN 5|5|CD U/μl|u/μl|NN -RRB-|-rrb-|-RRB- .|.|. Ligation|ligation|NN is|be|VBZ then|then|RB performed|perform|VBN at|at|IN 16|16|CD °C|°c|NN for|for|IN 4|4|CD hours|hour|NNS ,|,|, followed|follow|VBN by|by|IN incubation|incubation|NN overnight|overnight|JJ -LRB-|-lrb-|-LRB- ON|on|IN -RRB-|-rrb-|-RRB- at|at|IN 65|65|CD °C|°c|NN in|in|IN presence|presence|NN of|of|IN 250|250|CD μg/ml|μg/ml|JJ proteinase|proteinase|NN K|k|NN and|and|CC 5|5|CD mM|mm|NN EDTA|edta|NN .|.|. Precipitation|precipitation|NN of|of|IN DNA|dna|NN is|be|VBZ performed|perform|VBN using|use|VBG an|a|DT equal|equal|JJ volume|volume|NN of|of|IN 3|3|CD M|m|NN Na-Acetate|na-acetate|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- and|and|CC two|two|CD volumes|volume|NNS of|of|IN iso-propanol|iso-propanol|NN .|.|. After|after|IN one|one|CD hour|hour|NN at|at|IN -80|-80|CD °C|°c|NN ,|,|, DNA|dna|NN is|be|VBZ pelleted|pelleted|JJ ,|,|, suspended|suspend|VBN in|in|IN 500μl|500μl|JJ 1X|1x|NN TE|te|NN buffer|buffer|NN ,|,|, and|and|CC incubated|incubate|VBN for|for|IN 30|30|CD minutes|minute|NNS at|at|IN 37|37|CD °C|°c|NN in|in|IN presence|presence|NN of|of|IN RNAse|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 0.03|0.03|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN is|be|VBZ then|then|RB transferred|transfer|VBN into|into|IN 2|2|CD ml|ml|NN centrifuge|centrifuge|NN tubes|tube|NNS ,|,|, extracted|extract|VBN twice|twice|RB with|with|IN 500|500|CD μl|μl|NN phenol-chloroform|phenol-chloroform|NN pH|ph|NN 8.0|8.0|CD ,|,|, precipitated|precipitated|JJ ,|,|, washed|wash|VBN with|with|IN 1|1|CD ml|ml|NN cold|cold|JJ ethanol|ethanol|NN 70|70|CD %|%|NN and|and|CC diluted|dilute|VBN in|in|IN 30|30|CD μl|μl|NN 1X|1x|NN TE|te|NN buffer|buffer|NN .|.|. All|all|DT tubes|tube|NNS are|be|VBP pooled|pool|VBN and|and|CC the|the|DT resulting|result|VBG 3C|3c|NN library|library|NN is|be|VBZ quantified|quantify|VBN on|on|IN gel|gel|NN using|use|VBG Quantity|Quantity|NNP One|one|CD software|software|NN -LRB-|-lrb-|-LRB- BioRad|biorad|NN -RRB-|-rrb-|-RRB- .|.|.
For|for|IN alignment|alignment|NN of|of|IN the|the|DT reads|read|VBZ contained|contain|VBN within|within|IN the|the|DT fastq|fastq|NN files|file|VBZ to|to|TO the|the|DT E.|e.|FW coli|coli|FW MG1655|mg1655|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- RefSeq|refseq|NN NC|nc|NN _|_|CD U00096|u00096|NN .3|.3|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT short|short|JJ read|read|NN alignment|alignment|NN tool|tool|NN Bowtie2|bowtie2|NN was|be|VBD utilized|utilize|VBN under|under|IN default|default|NN settings|setting|NNS .|.|. Bowtie|Bowtie|NNP parameters|parameter|NNS were|be|VBD set|set|VBN to|to|TO include|include|VB only|only|RB perfect|perfect|JJ matches|match|NNS and|and|CC map|map|NN once|once|RB reads|read|VBZ that|that|IN map|map|NN to|to|TO more|more|JJR than|than|IN one|one|CD genome|genome|NN location|location|NN ,|,|, i.e.|i.e.|FW ,|,|, uniquely|uniquely|RB mapped|map|VBN reads|read|VBZ are|be|VBP retained|retain|VBN .|.|. The|the|DT output|output|NN Bowtie2|bowtie2|NN was|be|VBD a|a|DT SAM|SAM|NNP files|file|NNS for|for|IN each|each|DT sample|sample|NN .|.|.
For|for|IN alignment|alignment|NN of|of|IN the|the|DT SAET|SAET|NNP reads|read|VBZ to|to|TO the|the|DT E.|e.|FW coli|coli|FW MG1655|mg1655|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- RefSeq|refseq|NN NC|nc|NN _|_|SYM 000913|000913|CD -RRB-|-rrb-|-RRB- ,|,|, the|the|DT short|short|JJ read|read|NN alignment|alignment|NN tool|tool|NN Bowtie|Bowtie|NNP ver|ver|NN .|.|. 1.8|1.8|CD -LRB-|-lrb-|-LRB- Langmead|Langmead|NNP ,|,|, et|et|FW al.|al.|FW ,|,|, PMID|pmid|NN 19261174|19261174|CD -RRB-|-rrb-|-RRB- was|be|VBD utilized|utilize|VBN in|in|IN three|three|CD consecutive|consecutive|JJ passes|pass|NNS for|for|IN each|each|DT sample|sample|NN dataset|dataset|NN .|.|. For|for|IN the|the|DT first|first|JJ pass|pass|NN ,|,|, we|we|PRP use|use|VBP paired|paired|JJ end|end|NN color|color|NN space|space|NN mapping|mapping|NN with|with|IN a|a|DT distance|distance|NN cutoff|cutoff|NN of|of|IN 350|350|CD bases|basis|NNS between|between|IN read|read|NN mates|mate|NNS .|.|. Bowtie|Bowtie|NNP parameters|parameter|NNS were|be|VBD set|set|VBN to|to|TO include|include|VB only|only|RB perfect|perfect|JJ matches|match|NNS and|and|CC suppress|suppress|VBP reads|read|VBZ that|that|IN map|map|NN to|to|TO more|more|JJR than|than|IN one|one|CD genome|genome|NN location|location|NN ,|,|, i.e.|i.e.|FW ,|,|, uniquely|uniquely|RB mapped|map|VBN reads|read|VBZ are|be|VBP retained|retain|VBN .|.|. In|in|IN practice|practice|NN we|we|PRP found|find|VBD the|the|DT efficiency|efficiency|NN of|of|IN paired|paired|JJ end|end|NN mapping|mapping|NN was|be|VBD between|between|IN 3|3|CD and|and|CC 10|10|CD %|%|NN .|.|. To|to|TO improve|improve|VB the|the|DT overall|overall|JJ alignment|alignment|NN we|we|PRP mapped|map|VBD the|the|DT orphan|orphan|JJ 5|5|CD '|'|'' and|and|CC 3|3|CD '|'|'' end|end|NN reads|read|VBZ in|in|IN two|two|CD additional|additional|JJ passes|pass|NNS with|with|IN Bowtie|Bowtie|NNP .|.|. The|the|DT output|output|NN of|of|IN the|the|DT three|three|CD passes|pass|VBZ through|through|IN Bowtie|Bowtie|NNP was|be|VBD three|three|CD SAM|SAM|NNP files|file|NNS for|for|IN each|each|DT sample|sample|NN .|.|. Overall|overall|RB ,|,|, we|we|PRP achieved|achieve|VBD 40-60|40-60|CD %|%|NN mapping|mapping|NN efficiency|efficiency|NN with|with|IN this|this|DT three-pass|three-pass|JJ strategy|strategy|NN .|.|.
For|for|IN all|all|PDT the|the|DT samples|sample|NNS ;|;|: when|when|WRB 1/3|1/3|CD of|of|IN the|the|DT maximum|maximum|NN OD600|od600|NN was|be|VBD reached|reach|VBN ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 7,500|7,500|CD rcf|rcf|NN for|for|IN 5|5|CD min|min|NN -RRB-|-rrb-|-RRB- and|and|CC frozen|freeze|VBN .|.|. DNA|dna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT Wizard|Wizard|NNP Genomic|genomic|JJ DNA|dna|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Promega|promega|NN -RRB-|-rrb-|-RRB- .|.|.
For|for|IN all|all|PDT the|the|DT samples|sample|NNS ;|;|: when|when|WRB 1/3|1/3|CD of|of|IN the|the|DT maximum|maximum|NN OD600|od600|NN was|be|VBD reached|reach|VBN ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 7,500|7,500|CD rcf|rcf|NN for|for|IN 5|5|CD min|min|NN -RRB-|-rrb-|-RRB- and|and|CC frozen|freeze|VBN .|.|. For|for|IN RNA|rna|NN isolation|isolation|NN ,|,|, cells|cell|NNS were|be|VBD lysed|lyse|VBN by|by|IN bead|bead|NN beating|beating|NN and|and|CC RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG phenol-chloroform|phenol-chloroform|JJ extractions|extraction|NNS and|and|CC ethanol|ethanol|NN precipitations|precipitation|NNS .|.|. DNA|dna|NN was|be|VBD removed|remove|VBN from|from|IN the|the|DT sample|sample|NN with|with|IN RNase-free|rnase-free|JJ DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Fermentas|fermentas|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN for|for|IN 45|45|CD min|min|NN .|.|. Ribolock|ribolock|NN -LRB-|-lrb-|-LRB- Fermentas|fermentas|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO avoid|avoid|VB RNA|rna|NN degradation|degradation|NN .|.|.
For|for|IN analysis|analysis|NN of|of|IN ChIP-seq|ChIP-seq|NNP data|datum|NNS ,|,|, Hiseq|Hiseq|NNP 2500|2500|CD Illumina|Illumina|NNP short|short|JJ reads|read|VBZ -LRB-|-lrb-|-LRB- 50|50|CD bp|bp|NN -RRB-|-rrb-|-RRB- were|be|VBD mapped|map|VBN back|back|RB to|to|TO the|the|DT Caulobacter|Caulobacter|NNP NA1000|na1000|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NCBI|ncbi|NN Reference|Reference|NNP Sequence|sequence|NN :|:|: NC-011916.1|nc-011916.1|NN -RRB-|-rrb-|-RRB- using|use|VBG Bowtie|Bowtie|NNP 1|1|CD -LRB-|-lrb-|-LRB- Langmead|Langmead|NNP et|et|FW al.|al.|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT following|follow|VBG command|command|NN :|:|: bowtie|bowtie|NN -|-|: m|m|NN 1|1|CD -|-|: n|n|NN 1|1|CD --|--|: best|best|JJS --|--|: strata|strata|SYM -|-|: p|p|NN 4|4|CD --|--|: chunkmbs|chunkmb|NNS 512|512|CD NA1000-bowtie|na1000-bowtie|NN --|--|: sam|sam|NN *|*|NN .|.|. fastq|fastq|NN >|>|JJR output.sam|output.sam|NN .|.|. Subsequently|subsequently|RB ,|,|, the|the|DT sequencing|sequencing|NN coverage|coverage|NN at|at|IN each|each|DT nucleotide|nucleotide|NN position|position|NN was|be|VBD computed|compute|VBN using|use|VBG BEDTools|bedtool|NNS -LRB-|-lrb-|-LRB- Quinlan|Quinlan|NNP and|and|CC Hall|Hall|NNP ,|,|, 2010|2010|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT following|follow|VBG command|command|NN :|:|: bedtools|bedtool|NNS genomecov|genomecov|NN -|-|: d|d|SYM -|-|: ibam|ibam|NN output.sorted.bam|output.sorted.bam|NN -|-|: g|g|NN NA1000.fna|na1000.fna|NN >|>|JJR coverage_output.txt|coverage_output.txt|NN .|.|. For|for|IN analysis|analysis|NN of|of|IN E.|e.|FW coli|coli|FW ChIP-seq|ChIP-seq|NNP data|datum|NNS ,|,|, reference|reference|NN genomes|genome|NNS were|be|VBD first|first|JJ reconstructed|reconstruct|VBN in|in|IN silico|silico|NN by|by|IN inserting|insert|VBG the|the|DT nucleotide|nucleotide|NN sequence|sequence|NN of|of|IN parS|pars|NN and|and|CC apramycin|apramycin|NN antibiotic|antibiotic|JJ resistance|resistance|NN cassette|cassette|NN to|to|TO the|the|DT ybbD|ybbd|NN locus|locus|NN of|of|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN genome|genome|NN .|.|. Afterwards|afterwards|RB ,|,|, Hiseq|Hiseq|NNP 2500|2500|CD Illumina|Illumina|NNP short|short|JJ reads|read|VBZ were|be|VBD mapped|map|VBN back|back|RB to|to|TO these|these|DT reconstructed|reconstruct|VBN reference|reference|NN genomes|genome|NNS using|use|VBG Bowtie|Bowtie|NNP 1|1|CD .|.|. Sequence|sequence|NN coverage|coverage|NN at|at|IN each|each|DT nucleotide|nucleotide|NN position|position|NN was|be|VBD also|also|RB computed|compute|VBN using|use|VBG BEDTools|bedtool|NNS .|.|. Finally|finally|RB ,|,|, ChIP-seq|chip-seq|JJ profiles|profile|NNS were|be|VBD plotted|plot|VBN with|with|IN the|the|DT x-axis|x-axis|JJ representing|represent|VBG genomic|genomic|JJ positions|position|NNS and|and|CC the|the|DT y-axis|y-axis|NN is|be|VBZ the|the|DT number|number|NN of|of|IN reads|read|VBZ per|per|IN base|base|NN pair|pair|NN per|per|IN million|million|CD mapped|map|VBD reads|read|VBZ -LRB-|-lrb-|-LRB- RPBPM|rpbpm|NN -RRB-|-rrb-|-RRB- using|use|VBG custom|custom|NN R|r|NN scripts|script|NNS .|.|.
For|for|IN analysis|analysis|NN of|of|IN IDAP-seq|idap-seq|JJ data|datum|NNS ,|,|, Hiseq|Hiseq|NNP 2500|2500|CD Illumina|Illumina|NNP short|short|JJ reads|read|VBZ -LRB-|-lrb-|-LRB- 50|50|CD bp|bp|NN -RRB-|-rrb-|-RRB- were|be|VBD mapped|map|VBN back|back|RB to|to|TO the|the|DT Caulobacter|Caulobacter|NNP NA1000|na1000|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NCBI|ncbi|NN Reference|Reference|NNP Sequence|sequence|NN :|:|: NC-011916.1|nc-011916.1|NN -RRB-|-rrb-|-RRB- using|use|VBG Bowtie|Bowtie|NNP 1|1|CD -LRB-|-lrb-|-LRB- Langmead|Langmead|NNP et|et|FW al.|al.|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT following|follow|VBG command|command|NN :|:|: bowtie|bowtie|NN -|-|: m|m|NN 1|1|CD -|-|: n|n|NN 1|1|CD --|--|: best|best|JJS --|--|: strata|strata|SYM -|-|: p|p|NN 4|4|CD --|--|: chunkmbs|chunkmb|NNS 512|512|CD NA1000-bowtie|na1000-bowtie|NN --|--|: sam|sam|NN *|*|NN .|.|. fastq|fastq|NN >|>|JJR output.sam|output.sam|NN .|.|. Subsequently|subsequently|RB ,|,|, sequencing|sequencing|NN reads|read|VBZ were|be|VBD sorted|sort|VBN to|to|TO either|either|CC being|be|VBG mapped|map|VBN to|to|TO the|the|DT upper|upper|JJ DNA|dna|NN strand|strand|NN or|or|CC to|to|TO the|the|DT lower|lower|JJR strand|strand|NN of|of|IN the|the|DT reference|reference|NN genome|genome|NN ,|,|, as|as|IN suggested|suggest|VBN in|in|IN the|the|DT original|original|JJ IDAP-seq|idap-seq|JJ publication|publication|NN -LRB-|-lrb-|-LRB- Belitsky|Belitsky|NNP and|and|CC Sonenshein|Sonenshein|NNP ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT number|number|NN of|of|IN 5|5|CD '|'|'' end|end|NN of|of|IN reads|read|VBZ that|that|DT were|be|VBD mapped|map|VBN to|to|TO the|the|DT upper|upper|JJ strand|strand|NN was|be|VBD counted|count|VBN for|for|IN each|each|DT nucleotide|nucleotide|NN position|position|NN along|along|IN the|the|DT Caulobacter|Caulobacter|NNP genome|genome|NN using|use|VBG BEDTools|bedtool|NNS -LRB-|-lrb-|-LRB- Quinlan|Quinlan|NNP &|&|CC Hall|Hall|NNP ,|,|, 2010|2010|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT following|follow|VBG command|command|NN :|:|: bedtools|bedtool|NNS genomecov|genomecov|NN -|-|: d|d|NN -5|-5|CD -|-|: strand|strand|NN +|+|CC -|-|: ibam|ibam|NN output.sorted.bam|output.sorted.bam|NN -|-|: g|g|NN NA1000.fna|na1000.fna|NN >|>|JJR upper_strand_output.txt|upper_strand_output.txt|NN .|.|. To|to|TO count|count|VB the|the|DT number|number|NN of|of|IN 5|5|CD '|'|'' end|end|NN of|of|IN reads|read|VBZ that|that|DT were|be|VBD mapped|map|VBN to|to|TO the|the|DT lower|lower|JJR strand|strand|NN ,|,|, the|the|DT following|follow|VBG command|command|NN was|be|VBD used|use|VBN instead|instead|RB :|:|: bedtools|bedtool|NNS genomecov|genomecov|NN -|-|: d|d|NN -5|-5|CD -|-|: strand|strand|NN -|-|: -|-|: ibam|ibam|NN output.sorted.bam|output.sorted.bam|NN -|-|: g|g|NN NA1000.fna|na1000.fna|NN >|>|JJR lower_strand_output.txt|lower_strand_output.txt|NN .|.|. The|the|DT IDAP-seq|idap-seq|JJ profile|profile|NN was|be|VBD then|then|RB plotted|plot|VBN using|use|VBG R|r|NN .|.|. The|the|DT sequence|sequence|NN in|in|IN between|between|IN the|the|DT summit|summit|NN of|of|IN upper|upper|JJ strand|strand|NN profile|profile|NN and|and|CC that|that|IN of|of|IN the|the|DT lower|lower|JJR strand|strand|NN profile|profile|NN defines|define|VBZ the|the|DT minimal|minimal|JJ parS|pars|NN sequence|sequence|NN required|require|VBN for|for|IN binding|bind|VBG to|to|TO ParB|parb|NN .|.|.
For|for|IN ChIP-seq|chip-seq|JJ experiments|experiment|NNS E.|e.|FW coli|coli|FW culture|culture|NN were|be|VBD fixed|fix|VBN with|with|IN formaldehyde|formaldehyde|NN -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB- ;|;|: for|for|IN NorfliP|norflip|NN experiments|experiment|NNS TopoIV|topoiv|NN was|be|VBD crosslinked|crosslink|VBN with|with|IN Norfloxacin|norfloxacin|NN -LRB-|-lrb-|-LRB- 2µM|2µm|NN -RRB-|-rrb-|-RRB-
For|for|IN chromatin|chromatin|NN immunoprecipitation|immunoprecipitation|NN ,|,|, cells|cell|NNS were|be|VBD fixed|fix|VBN with|with|IN formaldehyde|formaldehyde|NN and|and|CC glycine|glycine|NN and|and|CC sheared|shear|VBD via|via|IN sonication|sonication|NN .|.|. Sheared|shear|VBN DNA|dna|NN from|from|IN lysate|lysate|NN was|be|VBD immunoprecipitated|immunoprecipitate|VBN -LRB-|-lrb-|-LRB- IP|IP|NNP -RRB-|-rrb-|-RRB- out|out|IN using|use|VBG an|a|DT anti-FLAG|anti-flag|JJ mAb|mab|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN was|be|VBD washed|wash|VBN with|with|IN IPP150|ipp150|NN buffer|buffer|NN and|and|CC purified|purify|VBN via|via|IN ProteinaseK|ProteinaseK|NNP digestion|digestion|NN and|and|CC Qiaquick|qiaquick|NN PCR|pcr|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -|-|: Cat|cat|NN .|.|. No.|no.|NN 28106|28106|CD -RRB-|-rrb-|-RRB- .|.|.
For|for|IN control|control|NN and|and|CC test|test|NN RNAs|rna|NNS ,|,|, the|the|DT synthesis|synthesis|NN of|of|IN target|target|NN cRNA|crna|NN probes|probe|NNS and|and|CC hybridization|hybridization|NN were|be|VBD performed|perform|VBN using|use|VBG Agilent|Agilent|NNP 's|'s|POS Low|low|JJ Input|Input|NNP Quick|Quick|NNP Amp|Amp|NNP WT|WT|NNP Labeling|label|VBG Kit|kit|NN ,|,|, one|one|CD color|color|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technology|Technology|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Briefly|briefly|RB ,|,|, each|each|DT 0.2|0.2|CD ug|ug|NN total|total|JJ RNA|rna|NN was|be|VBD mixed|mix|VBN with|with|IN WT|wt|JJ primer|primer|NN mix|mix|NN and|and|CC incubated|incubate|VBN at|at|IN 65ºC|65ºc|NN for|for|IN 10|10|CD min|min|NN .|.|. cDNA|cdna|NN master|master|NN mix|mix|NN -LRB-|-lrb-|-LRB- 5X|5x|NN First|first|JJ strand|strand|NN buffer|buffer|NN ,|,|, 0.1|0.1|CD M|m|NN DTT|dtt|NN ,|,|, 10mM|10mm|NN dNTP|dntp|NN mix|mix|NN ,|,|, RNase-Out|rnase-out|NN ,|,|, and|and|CC MMLV-RT|mmlv-rt|NN -RRB-|-rrb-|-RRB- was|be|VBD prepared|prepare|VBN and|and|CC added|add|VBN to|to|TO the|the|DT reaction|reaction|NN mixer|mixer|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN at|at|IN 40ºC|40ºc|NN for|for|IN 2|2|CD hours|hour|NNS and|and|CC then|then|RB the|the|DT RT|rt|NN and|and|CC dsDNA|dsdna|NN synthesis|synthesis|NN was|be|VBD terminated|terminate|VBN by|by|IN incubating|incubate|VBG at|at|IN 70ºC|70ºC|NNP for|for|IN 15|15|CD min|min|NN .|.|.
For|for|IN cross-linking|cross-linking|NN ,|,|, 30|30|CD mL|ml|NN of|of|IN cells|cell|NNS were|be|VBD mixed|mix|VBN with|with|IN 300|300|CD uL|ul|NN 1M|1m|NN sodium|sodium|NN phosphates|phosphate|NNS -LRB-|-lrb-|-LRB- pH|ph|NN 7.6|7.6|CD -RRB-|-rrb-|-RRB- and|and|CC 810|810|CD uL|ul|NN 37|37|CD %|%|NN formaldehyde|formaldehyde|NN .|.|. Cross-linking|cross-linking|NN was|be|VBD quenched|quench|VBN by|by|IN addition|addition|NN of|of|IN 2|2|CD mL|ml|NN 2M|2m|NN glycine|glycine|NN .|.|. Protein-DNA|protein-dna|JJ complexes|complex|NNS were|be|VBD isolated|isolate|VBN from|from|IN cells|cell|NNS grown|grow|VBN to|to|TO early|early|JJ -LRB-|-lrb-|-LRB- 2.4|2.4|CD x|x|CC 10|10|CD ^|^|NN 7|7|CD CFU/ml|cfu/ml|NN -RRB-|-rrb-|-RRB- or|or|CC late|late|JJ -LRB-|-lrb-|-LRB- 2.4|2.4|CD x|x|CC 10|10|CD ^|^|SYM 8|8|CD CFU/ml|cfu/ml|NN -RRB-|-rrb-|-RRB- exponential|exponential|JJ phase|phase|NN .|.|. Batch|batch|NN cultures|culture|NNS of|of|IN E.|e.|FW coli|coli|FW MDS42|mds42|NN were|be|VBD grown|grow|VBN to|to|TO early|early|JJ exponential|exponential|JJ phase|phase|NN .|.|. To|to|TO obtain|obtain|VB tiling-resolution|tiling-resolution|JJ RNA|rna|NN measures|measure|NNS across|across|IN the|the|DT E.|e.|FW coli|coli|FW genome|genome|NN ,|,|, wild-type|wild-type|JJ cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN biological|biological|JJ duplicate|duplicate|VBP in|in|IN LB|lb|NN to|to|TO early|early|JJ exponential|exponential|JJ phase|phase|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD moved|move|VBN to|to|TO ice|ice|NN ,|,|, and|and|CC the|the|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- P/N|p/n|NN 74104|74104|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO isolate|isolate|VB total|total|JJ cellular|cellular|JJ RNA|rna|NN .|.|.
For|for|IN DMS-MaPSeq|dms-mapseq|NN ,|,|, reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT 5|5|CD '|'|'' UTR|utr|NN of|of|IN cspA|cspa|NN using|use|VBG bowtie2|bowtie2|NN and|and|CC an|a|DT alignment|alignment|NN seed|seed|NN of|of|IN 12nt|12nt|JJ .|.|. Low|low|JJ sequence|sequence|NN quality|quality|NN bases|basis|NNS -LRB-|-lrb-|-LRB- Q|Q|NNP score|score|NN <|<|JJR 20|20|CD %|%|NN -RRB-|-rrb-|-RRB- and|and|CC missing|miss|VBG bases|basis|NNS due|due|JJ to|to|TO truncated|truncate|VBN reads|read|VBZ were|be|VBD set|set|VBN to|to|TO question|question|VB marks|mark|NNS .|.|. Reads|read|NNS that|that|WDT consisted|consist|VBD of|of|IN more|more|JJR than|than|IN 20|20|CD %|%|NN question|question|NN marks|mark|NNS were|be|VBD filtered|filter|VBN out|out|RP .|.|. Only|only|RB mutations|mutation|NNS that|that|WDT agreed|agree|VBD between|between|IN the|the|DT forward|forward|JJ and|and|CC the|the|DT reverse|reverse|JJ read|read|NN were|be|VBD considered|consider|VBN true|true|JJ mutations|mutation|NNS .|.|. Mutation|mutation|NN rate|rate|NN per|per|IN base|base|NN was|be|VBD calculated|calculate|VBN as|as|IN number|number|NN of|of|IN reads|read|VBZ with|with|IN a|a|DT mutation|mutation|NN at|at|IN the|the|DT base|base|NN divided|divide|VBN by|by|IN total|total|JJ number|number|NN of|of|IN reads|read|VBZ covering|cover|VBG the|the|DT base|base|NN .|.|.
For|for|IN each|each|DT biological|biological|JJ replicate|replicate|VB ,|,|, frozen|frozen|JJ aliquots|aliquot|NNS -LRB-|-lrb-|-LRB- 500μl|500μl|NN -RRB-|-rrb-|-RRB- of|of|IN E.|e.|FW coli|coli|FW K12|k12|NN stock|stock|NN cultures|culture|NNS were|be|VBD subcultured|subculture|VBN in|in|IN 10|10|CD ml|ml|NN of|of|IN Brain|brain|NN Heart|Heart|NNP Infusion|Infusion|NNP -LRB-|-lrb-|-LRB- BHI|BHI|NNP -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN overnight|overnight|JJ at|at|IN 37|37|CD °C|°c|NN .|.|. Cells|cell|NNS were|be|VBD then|then|RB sub-cultured|sub-cultured|JJ -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN v/v|v/v|NN -RRB-|-rrb-|-RRB- into|into|IN 50|50|CD ml|ml|NN BHI|BHI|NNP broth|broth|NN and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 24h|24h|NN under|under|IN constant|constant|JJ agitation|agitation|NN -LRB-|-lrb-|-LRB- 150|150|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT bacterial|bacterial|JJ suspensions|suspension|NNS were|be|VBD then|then|RB inoculated|inoculate|VBN -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN v/v|v/v|NN -RRB-|-rrb-|-RRB- in|in|IN 200|200|CD ml|ml|NN BHI|BHI|NNP broth|broth|NN and|and|CC grown|grow|VBN in|in|IN the|the|DT same|same|JJ conditions|condition|NNS to|to|TO stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN of|of|IN 0.9|0.9|CD -RRB-|-rrb-|-RRB- .|.|.
For|for|IN each|each|DT biological|biological|JJ RNA-Seq|rna-seq|NN replicate|replicate|VB E|e|NN coli|coli|NN K-12|k-12|NN MG1655|mg1655|NN was|be|VBD subcultured|subculture|VBN from|from|IN cyrostorage|cyrostorage|NN on|on|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- agar|agar|NN overnight|overnight|JJ at|at|IN 37|37|CD °C|°c|NN .|.|. A|a|DT half-dozen|half-dozen|JJ well-isolated|well-isolated|JJ colonies|colony|NNS were|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB a|a|DT 20|20|CD ml|ml|NN starter|starter|JJ culture|culture|NN in|in|IN Neidhardt|Neidhardt|NNP MOPS|MOPS|NNP Minimal|minimal|JJ Medium|medium|NN -LRB-|-lrb-|-LRB- NM3|nm3|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Neidhardt|Neidhardt|NNP et|et|FW al.|al.|FW ,|,|, 1974|1974|CD ,|,|, J|J|NNP Bacteriol|Bacteriol|NNP -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 0.2|0.2|CD %|%|NN final|final|JJ glucose|glucose|NN concentration|concentration|NN -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 20|20|CD mg/L|mg/l|NN uracil|uracil|NN and|and|CC 500|500|CD µg/L|µg/l|NN thiamine|thiamine|NN ,|,|, which|which|WDT was|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD rpm|rpm|NN overnight|overnight|JJ -LRB-|-lrb-|-LRB- ~|~|SYM 18|18|CD hr|hr|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT overnight|overnight|JJ starter|starter|JJ culture|culture|NN was|be|VBD diluted|dilute|VBN 1:30|1:30|CD to|to|TO initiate|initiate|VB the|the|DT experimental|experimental|JJ culture|culture|NN and|and|CC divided|divide|VBN into|into|IN three|three|CD 500|500|CD ml|ml|NN flasks|flask|NNS with|with|IN 100|100|CD ml|ml|NN NM3|nm3|NN in|in|IN each|each|DT ,|,|, which|which|WDT were|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD rpm|rpm|NN .|.|.
For|for|IN each|each|DT co-ordinate|co-ordinate|JJ coverage|coverage|NN was|be|VBD calculated|calculate|VBN as|as|IN the|the|DT number|number|NN of|of|IN reads|read|VBZ which|which|WDT was|be|VBD aligned|align|VBN againist|againist|IN the|the|DT position|position|NN .|.|. The|the|DT coverage|coverage|NN was|be|VBD normalized|normalize|VBN and|and|CC converted|convert|VBN into|into|IN a|a|DT z|z|SYM score|score|NN .|.|. Z|z|NN score|score|NN threshold|threshold|NN of|of|IN 12|12|CD was|be|VBD selected|select|VBN to|to|TO identify|identify|VB H-NS|h-ns|NN binding|binding|NN regions|region|NNS .|.|.
For|for|IN each|each|DT of|of|IN the|the|DT 4|4|CD libraries|library|NNS -LRB-|-lrb-|-LRB- 2|2|CD bacterial|bacterial|JJ samples|sample|NNS x|x|CC 2|2|CD treatments|treatment|NNS -RRB-|-rrb-|-RRB- ,|,|, we|we|PRP counted|count|VBD the|the|DT number|number|NN of|of|IN times|time|NNS each|each|DT nucleotide|nucleotide|NN position|position|NN was|be|VBD the|the|DT first|first|JJ in|in|IN a|a|DT sequence|sequence|NN read|read|VBN using|use|VBG a|a|DT simple|simple|JJ script|script|NN -LRB-|-lrb-|-LRB- unpubl|unpubl|NN .|.|. resource|resource|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT forward|forward|JJ and|and|CC reverse|reverse|JJ strands|strand|NNS were|be|VBD then|then|RB processed|process|VBN separately|separately|RB .|.|.
For|for|IN each|each|DT peak|peak|NN detected|detect|VBN with|with|IN MACE|MACE|NNP ,|,|, binding|bind|VBG intensity|intensity|NN was|be|VBD calculated|calculate|VBN by|by|IN averaging|average|VBG read|read|VBN counts|count|NNS from|from|IN two|two|CD biological|biological|JJ replicates|replicate|VBZ and|and|CC dividing|divide|VBG by|by|IN background|background|NN intensity|intensity|NN .|.|.
For|for|IN each|each|DT sample|sample|NN ,|,|, 500|500|CD mL|ml|NN liquid|liquid|JJ cultures|culture|NNS were|be|VBD grown|grow|VBN in|in|IN 2.8|2.8|CD L|l|NN flasks|flask|NNS with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 180|180|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN from|from|IN an|a|DT OD|od|NN -LRB-|-lrb-|-LRB- 600|600|CD nm|nm|NN -RRB-|-rrb-|-RRB- 0.05|0.05|CD to|to|TO OD|od|CD 0.45|0.45|CD ±|±|SYM 0.05|0.05|CD .|.|. Cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP EZ|EZ|NNP rich|rich|JJ defined|define|VBN medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- Teknova|teknova|NN -RRB-|-rrb-|-RRB- .|.|.
For|for|IN each|each|DT uniquely|uniquely|RB mapped|map|VBN fragment|fragment|NN -LRB-|-lrb-|-LRB- ribozero|ribozero|NN treated|treat|VBN samples|sample|NNS -RRB-|-rrb-|-RRB- or|or|CC all|all|DT mapped|map|VBN fragments|fragment|NNS -LRB-|-lrb-|-LRB- total|total|JJ RNA|rna|NN samples|sample|NNS -RRB-|-rrb-|-RRB- ,|,|, at|at|IN all|all|DT aligned|align|VBN positions|position|NNS a|a|DT count|count|NN was|be|VBD added|add|VBN .|.|.
foreground|foreground|NN and|and|CC background|background|NN ,|,|, and|and|CC the|the|DT median|median|JJ Cy3|cy3|NN -LRB-|-lrb-|-LRB- green|green|JJ -RRB-|-rrb-|-RRB- foreground|foreground|NN and|and|CC background|background|NN
foreground|foreground|NN -LRB-|-lrb-|-LRB- f|f|FW _|_|FW g|g|NN -RRB-|-rrb-|-RRB- and|and|CC background|background|NN -LRB-|-lrb-|-LRB- b|b|NN _|_|CD g|g|NN -RRB-|-rrb-|-RRB- intensity|intensity|NN .|.|. The|the|DT position|position|NN of|of|IN each|each|DT probe|probe|NN within|within|IN a|a|DT block|block|NN ,|,|,
For|for|IN further|further|JJ analyses|analysis|NNS the|the|DT processed|process|VBN signal|signal|NN intensities|intensity|NNS of|of|IN all|all|DT coding|code|VBG regions|region|NNS and|and|CC RNA|rna|NN genes|gene|NNS were|be|VBD extracted|extract|VBN and|and|CC used|use|VBN .|.|. Variance|variance|NN stabilization|stabilization|NN and|and|CC normalization|normalization|NN of|of|IN the|the|DT extracted|extract|VBN intensities|intensity|NNS were|be|VBD performed|perform|VBN with|with|IN the|the|DT vsn|vsn|NN packages|package|NNS of|of|IN the|the|DT R|r|NN software|software|NN environment|environment|NN -LRB-|-lrb-|-LRB- R|r|NN Development|development|NN Core|core|NN Team|Team|NNP ,|,|, 2007|2007|CD -RRB-|-rrb-|-RRB- and|and|CC back-transformed|back-transformed|JJ to|to|TO normal|normal|JJ intensity|intensity|NN scale|scale|NN .|.|. For|for|IN each|each|DT probeset|probeset|NN ,|,|, e.g.|e.g.|FW all|all|DT probes|probe|NNS representing|represent|VBG for|for|IN example|example|NN ,|,|, a|a|DT single|single|JJ coding|coding|NN gene|gene|NN ,|,|, outliers|outlier|NNS were|be|VBD removed|remove|VBN by|by|IN boxplot|boxplot|NN statistics|statistics|NNS and|and|CC the|the|DT outlier-removed|outlier-removed|JJ probe|probe|NN intensities|intensity|NNS were|be|VBD averaged|average|VBN in|in|IN a|a|DT robust|robust|JJ way|way|NN by|by|IN computing|compute|VBG the|the|DT Tukey|tukey|NN biweight|biweight|NN .|.|.
For|for|IN immunoprecipitation|immunoprecipitation|NN ,|,|, 800|800|CD μl|μl|NN of|of|IN collected|collect|VBN chromatin|chromatin|NN -LRB-|-lrb-|-LRB- ~|~|CD 1000|1000|CD μg|μg|NN of|of|IN protein|protein|NN -RRB-|-rrb-|-RRB- were|be|VBD incubated|incubate|VBN on|on|IN a|a|DT rotating|rotate|VBG wheel|wheel|NN over|over|IN night|night|NN at|at|IN 4|4|CD °C|°c|NN with|with|IN 10|10|CD μg|μg|NN of|of|IN either|either|CC rabbit|rabbit|NN anti-Dps|anti-dps|JJ antibodies|antibody|NNS -LRB-|-lrb-|-LRB- experimental|experimental|JJ sample|sample|NN -RRB-|-rrb-|-RRB- or|or|CC rabbit|rabbit|NN pre-immune|pre-immune|JJ IgG|igg|NN -LRB-|-lrb-|-LRB- negative|negative|JJ control|control|NN -RRB-|-rrb-|-RRB- .|.|. Next|next|JJ day|day|NN 30|30|CD μl|μl|NN of|of|IN Ultra|Ultra|NNP Link|Link|NNP Protein|protein|NN A/G|a/g|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO the|the|DT samples|sample|NNS ,|,|, and|and|CC incubation|incubation|NN was|be|VBD allowed|allow|VBN for|for|IN a|a|DT further|further|RBR 2|2|CD hours|hour|NNS at|at|IN 4|4|CD °C|°c|NN on|on|IN a|a|DT rotating|rotate|VBG wheel|wheel|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD washed|wash|VBN 3|3|CD times|time|NNS with|with|IN 1|1|CD ml|ml|NN of|of|IN the|the|DT low-salt|low-salt|JJ buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN HEPES|hepes|NN pH|ph|NN 7.5|7.5|CD ,|,|, 140|140|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 1xPIC|1xpic|NN -RRB-|-rrb-|-RRB- and|and|CC then|then|RB with|with|IN 1|1|CD ml|ml|NN of|of|IN the|the|DT high-salt|high-salt|JJ buffer|buffer|NN -LRB-|-lrb-|-LRB- 500|500|CD mM|mm|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- .|.|. Immunoprecipitated|immunoprecipitate|VBN DNA-protein|dna-protein|JJ complexes|complex|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT beads|bead|NNS by|by|IN 3|3|CD h|h|NN shaking|shake|VBG at|at|IN 65|65|CD °C|°c|NN and|and|CC 1000|1000|CD rpm|rpm|NN in|in|IN 110|110|CD μl|μl|NN of|of|IN freshly|freshly|RB prepared|prepared|JJ elution|elution|NN buffer|buffer|NN ,|,|, containing|contain|VBG 100|100|CD mM|mm|NN NaHCO3|nahco3|NN and|and|CC 1|1|CD %|%|NN SDS|sds|NN .|.|. After|after|IN centrifugation|centrifugation|NN at|at|IN 3000|3000|CD rpm|rpm|NN for|for|IN 5|5|CD minutes|minute|NNS ,|,|, 100|100|CD μl|μl|NN of|of|IN the|the|DT supernatant|supernatant|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT new|new|JJ tube|tube|NN ,|,|, and|and|CC the|the|DT DNA|dna|NN was|be|VBD purified|purify|VBN with|with|IN a|a|DT PCR|pcr|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT DNA|dna|NN concentration|concentration|NN was|be|VBD measured|measure|VBN on|on|IN Qubit|Qubit|NNP 2.0|2.0|CD using|use|VBG Qubit|Qubit|NNP dsDNA|dsDNA|NNP HS|hs|NN Assay|assay|NN kit|kit|NN .|.|. A|a|DT total|total|NN of|of|IN 8-10|8-10|CD identical|identical|JJ samples|sample|NNS were|be|VBD combined|combine|VBN and|and|CC concentrated|concentrate|VBN to|to|TO a|a|DT volume|volume|NN of|of|IN 30-50|30-50|CD μl|μl|NN containing|contain|VBG 5-10|5-10|CD ng|ng|NN of|of|IN the|the|DT DNA|dna|NN .|.|.
For|for|IN in|in|FW vivo|vivo|FW DMS|dms|FW modification|modification|NN ,|,|, 15|15|CD mL|ml|NN of|of|IN E.|e.|FW coli|coli|FW culture|culture|NN was|be|VBD incubated|incubate|VBN with|with|IN 750|750|CD µL|µl|NN DMS|dms|NN .|.|. Incubation|incubation|NN was|be|VBD performed|perform|VBN for|for|IN 2|2|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN or|or|CC for|for|IN 45|45|CD min|min|NN at|at|IN 10|10|CD °C|°c|NN .|.|. DMS|dms|NN was|be|VBD quenched|quench|VBN by|by|IN adding|add|VBG 30|30|CD mL|ml|NN 0|0|CD °C|°c|NN stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 30|30|CD %|%|NN β-mercaptoethanol|β-mercaptoethanol|NN ,|,|, 25|25|CD %|%|NN isoamyl|isoamyl|NN alcohol|alcohol|NN -RRB-|-rrb-|-RRB- ,|,|, after|after|IN which|which|WDT cells|cell|NNS were|be|VBD quickly|quickly|RB put|put|VBN on|on|IN ice|ice|NN ,|,|, collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 8000|8000|CD x|x|CC g|g|NN ,|,|, 4|4|CD °C|°c|NN for|for|IN 2|2|CD min|min|NN ,|,|, and|and|CC washed|wash|VBN with|with|IN 8|8|CD mL|ml|NN 30|30|CD %|%|NN BME|bme|NN solution|solution|NN .|.|. Cells|cell|NNS were|be|VBD then|then|RB resuspended|resuspend|VBN in|in|IN 450|450|CD µL|µl|NN total|total|JJ RNA|rna|NN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 50|50|CD mM|mm|NN sodium|sodium|NN acetate|acetate|NN pH|ph|NN 5.5|5.5|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN with|with|IN hot|hot|JJ acid|acid|NN phenol|phenol|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|.
For|for|IN in|in|FW vivo|vivo|FW DMS|dms|FW modification|modification|NN ,|,|, 15|15|CD mL|ml|NN of|of|IN exponentially|exponentially|RB growing|grow|VBG E.|e.|FW coli|coli|FW were|be|VBD incubated|incubate|VBN with|with|IN 750|750|CD µL|µl|NN DMS|dms|NN for|for|IN 2|2|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN .|.|. For|for|IN kasugamycin|kasugamycin|NN -LRB-|-lrb-|-LRB- ksg|ksg|NN -RRB-|-rrb-|-RRB- experiments|experiment|NNS ,|,|, ksg|ksg|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 10|10|CD mg/mL|mg/ml|NN to|to|TO ΔgcvB|δgcvb|NN cells|cell|NNS for|for|IN 2|2|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN prior|prior|RB to|to|TO DMS|DMS|NNP modification|modification|NN .|.|. DMS|dms|NN was|be|VBD quenched|quench|VBN by|by|IN adding|add|VBG 30|30|CD mL|ml|NN 0|0|CD °C|°c|NN stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 30|30|CD %|%|NN β-mercaptoethanol|β-mercaptoethanol|NN ,|,|, 25|25|CD %|%|NN isoamyl|isoamyl|NN alcohol|alcohol|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN in|in|FW vitro|vitro|FW DMS|dms|NN modifications|modification|NNS ,|,|, mRNA|mrna|NN was|be|VBD denatured|denature|VBN at|at|IN 95|95|CD °C|°c|NN for|for|IN 2|2|CD min|min|NN ,|,|, cooled|cool|VBN on|on|IN ice|ice|NN and|and|CC refolded|refold|VBN in|in|IN 90|90|CD µL|µl|NN RNA|rna|NN folding|folding|JJ buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8.0|8.0|CD ,|,|, 100|100|CD mM|mm|NN NaCl|nacl|NN ,|,|, 6|6|CD mM|mm|NN MgCl2|mgcl2|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD min|min|NN then|then|RB incubated|incubate|VBN in|in|IN either|either|CC .2|.2|NN %|%|NN DMS|dms|NN for|for|IN 1|1|CD min|min|NN -LRB-|-lrb-|-LRB- 95|95|CD °C|°c|NN -RRB-|-rrb-|-RRB- or|or|CC 4|4|CD %|%|NN DMS|dms|NN for|for|IN 5|5|CD min|min|NN -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|.
Formaldehyde|Formaldehyde|NNP was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD %|%|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 20|20|CD minutes|minute|NNS ,|,|, glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD M|m|NN and|and|CC incubated|incubate|VBN for|for|IN 5|5|CD minutes|minute|NNS .|.|.
For|for|IN metagene|metagene|NN analyses|analysis|NNS -LRB-|-lrb-|-LRB- gene-segment|gene-segment|NN analyses|analysis|NNS and|and|CC codon-type|codon-type|JJ analyses|analysis|NNS -RRB-|-rrb-|-RRB- ,|,|, pseudogenes|pseudogene|NNS and|and|CC genes|gene|NNS not|not|RB represented|represent|VBN in|in|IN one|one|CD or|or|CC more|more|JJR datasets|dataset|NNS were|be|VBD excluded|exclude|VBN ,|,|, leaving|leave|VBG 3048|3048|CD genes|gene|NNS in|in|IN the|the|DT \|\|CD
For|for|IN proteolysis|proteolysis|NN ,|,|, affinity|affinity|NN gel|gel|NN obtained|obtain|VBN after|after|IN the|the|DT last|last|JJ centrifugation|centrifugation|NN step|step|NN was|be|VBD diluted|dilute|VBN with|with|IN TES|tes|NN buffer|buffer|NN up|up|IN to|to|TO final|final|JJ volume|volume|NN 200|200|CD μl|μl|NN ,|,|, proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- Sigma-Aldrich|sigma-aldrich|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC samples|sample|NNS were|be|VBD incubated|incubate|VBN at|at|IN 55|55|CD °C|°c|NN for|for|IN at|at|IN least|least|JJS 3|3|CD hours|hour|NNS .|.|. After|after|IN this|this|DT step|step|NN samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN -LRB-|-lrb-|-LRB- 2|2|CD minutes|minute|NNS ,|,|, 2000xg|2000xg|NN at|at|IN room|room|NN temperature|temperature|NN -RRB-|-rrb-|-RRB- and|and|CC supernatants|supernatant|NNS were|be|VBD collected|collect|VBN for|for|IN DNA|dna|NN extraction|extraction|NN .|.|.
For|for|IN quantification|quantification|NN of|of|IN gene|gene|NN expression|expression|NN -LRB-|-lrb-|-LRB- read|read|NN counting|counting|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT alignments|alignment|NNS generated|generate|VBN with|with|IN the|the|DT Genomics|Genomics|NNP Workbench|Workbench|NNP were|be|VBD exported|export|VBN in|in|IN BAM|BAM|NNP format|format|NN .|.|. Read|Read|NNP counting|counting|NN was|be|VBD then|then|RB performed|perform|VBN with|with|IN the|the|DT FeatureCounts|FeatureCounts|NNP v.|v.|CC 1.5.0-p1|1.5.0-p1|CD program|program|NN using|use|VBG the|the|DT following|follow|VBG parameters|parameter|NNS ;|;|: Level|Level|NNP :|:|: meta-feature|meta-feature|JJ leve|leve|NN .|.|. Paired-end|paired-end|NN :|:|: no|no|DT .|.|. Strand|strand|VB specific|specific|JJ :|:|: yes|yes|UH .|.|. Multimapping|multimapp|VBG reads|read|VBZ :|:|: counted|count|VBN -LRB-|-lrb-|-LRB- as|as|IN fractions|fraction|NNS -RRB-|-rrb-|-RRB- .|.|. Multi-overlapping|multi-overlapping|JJ reads|read|VBZ :|:|: not|not|RB counted|count|VBN .|.|. Overlapping|overlapping|JJ bases|basis|NNS :|:|: 30|30|CD .|.|. Read|Read|NNP orientations|orientation|NNS :|:|: fr|fr|NN
For|for|IN REC-Seq|rec-seq|NN -LRB-|-lrb-|-LRB- restriction|restriction|NN enzyme|enzyme|NN cleavage|cleavage|NN --|--|: sequencing|sequencing|NN -RRB-|-rrb-|-RRB- 1|1|CD ug|ug|NN of|of|IN genomic|genomic|JJ DNA|dna|NN from|from|IN C.|c.|FW crescentus|crescentus|FW NA1000|na1000|NN and|and|CC S.|S.|NNP meliloti|melilotus|NNS Rm2011|rm2011|NN was|be|VBD cleaved|cleave|VBN with|with|IN HinfI|hinfi|NN ,|,|, a|a|DT blocked|block|VBN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' biotinylated|biotinylate|VBN -RRB-|-rrb-|-RRB- specific|specific|JJ adaptor|adaptor|NN was|be|VBD ligated|ligate|VBN to|to|TO the|the|DT ends|end|NNS and|and|CC the|the|DT ligated|ligate|VBN fragments|fragment|NNS were|be|VBD then|then|RB sheared|shear|VBN to|to|TO an|a|DT average|average|JJ size|size|NN of|of|IN 150-400|150-400|CD bp|bp|NN -LRB-|-lrb-|-LRB- Fasteris|fasteris|NN SA|SA|NNP ,|,|, Geneva|Geneva|NNP ,|,|, CH|ch|NN -RRB-|-rrb-|-RRB- .|.|. Illumina|Illumina|NNP adaptors|adaptor|NNS were|be|VBD then|then|RB ligated|ligate|VBN to|to|TO the|the|DT sheared|sheared|JJ ends|end|NNS followed|follow|VBN by|by|IN deep-sequencing|deep-sequencing|NN using|use|VBG a|a|DT Hi-Seq|hi-seq|JJ Illumina|Illumina|NNP sequencer|sequencer|NN ,|,|, and|and|CC the|the|DT -LRB-|-lrb-|-LRB- 50|50|CD bp|bp|NN single|single|JJ end|end|NN -RRB-|-rrb-|-RRB- reads|read|VBZ were|be|VBD quality|quality|NN controlled|control|VBN with|with|IN FastQC|fastqc|NN -LRB-|-lrb-|-LRB- http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|NN -RRB-|-rrb-|-RRB- .|.|.
For|for|IN ribozero|ribozero|NN treated|treat|VBN samples|sample|NNS ,|,|, counts|count|VBZ at|at|IN all|all|DT positions|position|NNS were|be|VBD log2|log2|NN transformed|transform|VBN and|and|CC a|a|DT cleavage|cleavage|NN ratio|ratio|NN was|be|VBD calculated|calculate|VBN -LRB-|-lrb-|-LRB- +|+|CC MazF|mazf|NN -|-|: empty|empty|JJ vector|vector|NN -RRB-|-rrb-|-RRB- for|for|IN assessing|assess|VBG MazF|mazf|NN cleavage|cleavage|NN in|in|IN transcripts|transcript|NNS .|.|.
For|for|IN RNA|rna|NN isolation|isolation|NN ,|,|, 0.5|0.5|CD mL|ml|NN of|of|IN the|the|DT cultures|culture|NNS were|be|VBD mixed|mix|VBN with|with|IN 1|1|CD mL|ml|NN RNA|rna|NN protect|protect|VBP -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Ontario|Ontario|NNP ,|,|, Canada|Canada|NNP -RRB-|-rrb-|-RRB- and|and|CC RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD quantified|quantify|VBN with|with|IN a|a|DT Nanodrop|Nanodrop|NNP Spectrophotometer|Spectrophotometer|NNP -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP scientific|scientific|JJ ,|,|, Wilmington|Wilmington|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC RNA|rna|NN quality|quality|NN was|be|VBD determined|determine|VBN with|with|IN a|a|DT Bioanalyzer|Bioanalyzer|NNP 2100|2100|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN samples|sample|NNS -LRB-|-lrb-|-LRB- approximately|approximately|RB 30|30|CD µg|µg|NN -RRB-|-rrb-|-RRB- were|be|VBD treated|treat|VBN with|with|IN 1U|1u|NN RNase|rnase|NN free|free|JJ DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Ontario|Ontario|NNP ,|,|, Canada|Canada|NNP -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD min|min|NN and|and|CC 1U|1u|NN RNase|rnase|NN inhibitor|inhibitor|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN prior|prior|RB to|to|TO storage|storage|NN at|at|IN 4|4|CD °C|°c|NN .|.|. RNA|rna|NN was|be|VBD reverse-transcribed|reverse-transcribed|JJ using|use|VBG the|the|DT Array|array|NN 900MPX|900mpx|NN Expression|expression|NN Array|array|NN Detection|detection|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Genisphere|Genisphere|NNP ,|,|, Hatfield|Hatfield|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT instructions|instruction|NNS of|of|IN the|the|DT manufacturer|manufacturer|NN .|.|. The|the|DT cDNA|cdna|NN was|be|VBD purified|purify|VBN using|use|VBG the|the|DT MinElute|MinElute|NNP PCR|pcr|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Quiagen|quiagen|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC the|the|DT purified|purify|VBN DNA|dna|NN was|be|VBD used|use|VBN for|for|IN microarray|microarray|NN and|and|CC qPCR|qpcr|NN experiments|experiment|NNS .|.|.
For|for|IN RNA-Seq|rna-seq|NN analysis|analysis|NN ,|,|, the|the|DT fastq|fastq|NN file|file|NN produced|produce|VBN from|from|IN the|the|DT machine|machine|NN was|be|VBD demultiplexed|demultiplex|VBN into|into|IN a|a|DT separate|separate|JJ file|file|NN for|for|IN each|each|DT sample|sample|NN .|.|.
For|for|IN RNA-seq|rna-seq|NN :|:|: total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNeasy|RNeasy|NNP Protect|protect|VB Bacteria|bacterium|NNS according|accord|VBG to|to|TO manufacturer|manufacturer|NN instructions|instruction|NNS -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP -|-|: #|#|# 74524|74524|CD -RRB-|-rrb-|-RRB-
For|for|IN the|the|DT first|first|JJ batch|batch|NN -LRB-|-lrb-|-LRB- from|from|IN WT|WT|NNP _|_|NNP LB|LB|NNP _|_|SYM 1|1|CD to|to|TO lacA|lacA|NNP _|_|NNP M9|M9|NNP _|_|SYM 2|2|LS -RRB-|-rrb-|-RRB- ,|,|, fresh|fresh|JJ colonies|colony|NNS of|of|IN E.|e.|FW coli|coli|FW cells|cell|NNS were|be|VBD taken|take|VBN and|and|CC inoculated|inoculate|VBN in|in|IN 1|1|CD ml|ml|NN LB|lb|NN and|and|CC grown|grow|VBN for|for|IN 8|8|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN .|.|. 20|20|CD µL|µl|NN of|of|IN grown|grown|JJ culture|culture|NN was|be|VBD taken|take|VBN and|and|CC transferred|transfer|VBN to|to|TO 3|3|CD ml|ml|NN LB/M9|lb/m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.3|0.3|CD %|%|NN glucose|glucose|NN and|and|CC grown|grow|VBN for|for|IN 12|12|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN .|.|. At|at|IN 12|12|CD h|h|NN ,|,|, cells|cell|NNS were|be|VBD harvested|harvest|VBN for|for|IN the|the|DT RNA-seq|rna-seq|NN .|.|. For|for|IN the|the|DT second|second|JJ batch|batch|NN -LRB-|-lrb-|-LRB- from|from|IN WT|WT|NNP _|_|SYM 1|1|CD to|to|TO aspC|aspC|NNP _|_|SYM 3|3|LS -RRB-|-rrb-|-RRB- ,|,|, a|a|DT 1:100|1:100|CD dilution|dilution|NN from|from|IN an|a|DT overnight|overnight|JJ culture|culture|NN in|in|IN M9|m9|NN 0.4|0.4|CD %|%|NN glucose|glucose|NN was|be|VBD done|do|VBN .|.|. When|when|WRB the|the|DT late|late|JJ stationary|stationary|JJ phase|phase|NN was|be|VBD reached|reach|VBN ,|,|, the|the|DT samples|sample|NNS were|be|VBD harvested|harvest|VBN .|.|.
For|for|IN the|the|DT Illumina|Illumina|NNP GAII|GAII|NNP platform|platform|NN ,|,|, the|the|DT directional|directional|JJ RNA-seq|rna-seq|NN libraries|library|NNS were|be|VBD constructed|construct|VBN by|by|IN following|follow|VBG an|a|DT Illumina|Illumina|NNP 's|'s|POS instruction|instruction|NN using|use|VBG their|they|PRP$ Small|small|JJ RNA|rna|NN Sample|sample|NN Prep|Prep|NNP Kit|kit|NN with|with|IN some|some|DT modifications|modification|NNS .|.|. For|for|IN the|the|DT HiSeq|HiSeq|NNP 2000|2000|CD platform|platform|NN ,|,|, the|the|DT directional|directional|JJ RNA-seq|rna-seq|NN libraries|library|NNS were|be|VBD constructed|construct|VBN using|use|VBG Illumina|Illumina|NNP 's|'s|POS TruSeq|TruSeq|NNP Small|Small|NNP RNA|rna|NN Sample|sample|NN Prep|Prep|NNP Kit|kit|NN .|.|.
For|for|IN the|the|DT whole-transcriptome|whole-transcriptome|JJ analysis|analysis|NN ,|,|, sequencing|sequencing|NN was|be|VBD verified|verify|VBN using|use|VBG FASTQC|fastqc|NN -LRB-|-lrb-|-LRB- version|version|NN 0.11.2|0.11.2|CD -RRB-|-rrb-|-RRB- to|to|TO confirm|confirm|VB base-call|base-call|JJ quality|quality|NN in|in|IN each|each|DT indexed|index|VBN file|file|NN .|.|.
For|for|IN total|total|JJ RNA|rna|NN extraction|extraction|NN ,|,|, cells|cell|NNS were|be|VBD pelleted|pellete|VBN in|in|IN 4|4|CD °C|°c|NN .|.|.
For|for|IN total|total|JJ RNA|rna|NN isolation|isolation|NN ,|,|, the|the|DT bacteria|bacterium|NNS were|be|VBD inoculated|inoculate|VBN in|in|IN 5|5|CD ml|ml|NN LB|lb|NN broth|broth|NN at|at|IN 37|37|CD ℃|℃|NN with|with|IN shaking|shake|VBG for|for|IN 16|16|CD h.|h.|NN 50|50|CD µl|µl|NN of|of|IN the|the|DT above|above|JJ culture|culture|NN was|be|VBD inoculated|inoculate|VBN in|in|IN 5|5|CD ml|ml|NN fresh|fresh|JJ LB|lb|NN broth|broth|NN and|and|CC the|the|DT culture|culture|NN was|be|VBD shaken|shake|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN about|about|IN 2.5|2.5|CD h|h|NN until|until|IN the|the|DT OD600|od600|NN reached|reach|VBD 0.6|0.6|CD .|.|. 500|500|CD µl|µl|NN of|of|IN the|the|DT culture|culture|NN were|be|VBD mixed|mix|VBN with|with|IN 1|1|CD ml|ml|NN RNA|rna|NN protect|protect|VBP bacterial|bacterial|JJ reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- to|to|TO stabilize|stabilize|VB RNA|rna|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
Forward|forward|RB -|-|: and|and|CC reverse-read|reverse-read|JJ mate-pairs|mate-pair|NNS were|be|VBD assembled|assemble|VBN and|and|CC aligned|align|VBN to|to|TO the|the|DT Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN genome|genome|NN using|use|VBG Bowtie2|bowtie2|NN -LRB-|-lrb-|-LRB- Langmead|langmead|NN and|and|CC Salzberg|Salzberg|NNP ,|,|, 2012|2012|CD ,|,|, Nat|Nat|NNP Methods|method|NNS -RRB-|-rrb-|-RRB- .|.|. SAMtools|samtool|NNS -LRB-|-lrb-|-LRB- Li|Li|NNP et|et|FW al.|al.|FW ,|,|, 2009|2009|CD ,|,|, Bioinformatics|bioinformatic|NNS -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO convert|convert|VB Bowtie2|bowtie2|NN output|output|NN -LRB-|-lrb-|-LRB- .|.|. bam|bam|NN file|file|NN -RRB-|-rrb-|-RRB- to|to|TO SAM|SAM|NNP format|format|NN .|.|.
Four|four|CD ml|ml|NN of|of|IN the|the|DT bacterial|bacterial|JJ suspension|suspension|NN in|in|IN RNALater|rnalater|NN II|ii|CD and|and|CC Medium|medium|NN E|e|NN growth|growth|NN medium|medium|NN were|be|VBD spun|spin|VBN down|down|RP at|at|IN 200g|200g|NN for|for|IN 5|5|CD min|min|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD discarded|discard|VBN and|and|CC the|the|DT pellet|pellet|NN were|be|VBD resuspended|resuspend|VBN in|in|IN 200ul|200ul|JJ PBS|PBS|NNP and|and|CC mixed|mix|VBN by|by|IN pipetting|pipetting|NN .|.|. 100ul|100ul|NN aliquots|aliquot|NNS were|be|VBD taken|take|VBN out|out|RP for|for|IN DNA|dna|NN and|and|CC RNA|rna|NN extraction|extraction|NN from|from|IN the|the|DT same|same|JJ sample|sample|NN .|.|. RNA|rna|NN extraction|extraction|NN was|be|VBD done|do|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- with|with|IN on-column|on-column|JJ DNase|dnase|NN digestion|digestion|NN .|.|. Final|final|JJ elution|elution|NN was|be|VBD made|make|VBN in|in|IN 30|30|CD μL|μl|NN dH2O|dh2o|NN .|.|. The|the|DT concentration|concentration|NN and|and|CC integrity|integrity|NN of|of|IN the|the|DT total|total|JJ RNA|rna|NN was|be|VBD estimated|estimate|VBN by|by|IN Quant-iT|quant-it|NN ™|™|CD RiboGreen|RiboGreen|NNP ®|®|CD RNA|rna|NN Assay|assay|NN Kit|kit|NN -LRB-|-lrb-|-LRB- ThermoFisher|ThermoFisher|NNP Scientific|Scientific|NNP ,|,|, Waltham|Waltham|NNP ,|,|, MA|MA|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Applied|Applied|NNP Biosystems|Biosystems|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB .|.|.
Four|four|CD morphologic|morphologic|JJ states|state|NNS of|of|IN ESBL019|esbl019|NN were|be|VBD used|use|VBN during|during|IN the|the|DT experiments|experiment|NNS .|.|. A|a|DT first|first|JJ ESBL019|esbl019|NN morphological|morphological|JJ state|state|NN was|be|VBD prepared|prepare|VBN by|by|IN resuspension|resuspension|NN of|of|IN ESBL019|esbl019|NN in|in|IN cell|cell|NN culture|culture|NN medium|medium|NN -LRB-|-lrb-|-LRB- CCM|ccm|NN -RRB-|-rrb-|-RRB- without|without|IN ceftibuten|ceftibuten|NN supplementation|supplementation|NN prior|prior|RB to|to|TO its|its|PRP$ inoculation|inoculation|NN of|of|IN primary|primary|JJ human|human|JJ bladder|bladder|NN epithelial|epithelial|JJ cells|cell|NNS -LRB-|-lrb-|-LRB- HBEP|hbep|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- designated|designate|VBN ;|;|: ESBL019|esbl019|NN Coliform|coliform|NN -RRB-|-rrb-|-RRB- .|.|. A|a|DT second|second|JJ ESBL019|esbl019|NN morphological|morphological|JJ state|state|NN was|be|VBD prepared|prepare|VBN by|by|IN resuspension|resuspension|NN in|in|IN CCM|CCM|NNP and|and|CC then|then|RB used|use|VBN to|to|TO inoculate|inoculate|VB HBEP|hbep|NN cells|cell|NNS with|with|IN ceftibuten|ceftibuten|NN supplementation|supplementation|NN -LRB-|-lrb-|-LRB- 480ng/mL|480ng/ml|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- designated|designate|VBN ;|;|: ESBL019|esbl019|NN Transition|transition|NN -RRB-|-rrb-|-RRB- .|.|. This|this|DT transition|transition|NN from|from|IN coliform|coliform|NN into|into|IN filamented|filamented|JJ occurs|occur|VBZ in|in|IN the|the|DT presence|presence|NN of|of|IN HBEP|hbep|NN cells|cell|NNS .|.|. A|a|DT third|third|JJ ESBL019|esbl019|NN morphological|morphological|JJ state|state|NN was|be|VBD prepared|prepare|VBN by|by|IN resuspension|resuspension|NN and|and|CC pre-incubation|pre-incubation|NN for|for|IN 3|3|CD hours|hour|NNS in|in|IN CCM|ccm|NN with|with|IN ceftibuten|ceftibuten|NN in|in|IN a|a|DT tube|tube|NN ,|,|, in|in|IN order|order|NN to|to|TO induce|induce|VB complete|complete|JJ filamentation|filamentation|NN of|of|IN all|all|DT bacteria|bacterium|NNS .|.|. The|the|DT third|third|JJ pre-filamented|pre-filamented|JJ ESBL019|esbl019|NN fraction|fraction|NN was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB HBEP|hbep|NN cells|cell|NNS in|in|IN the|the|DT presence|presence|NN of|of|IN ceftibuten|ceftibuten|NN to|to|TO keep|keep|VB the|the|DT bacteria|bacterium|NNS filamented|filament|VBN -LRB-|-lrb-|-LRB- designated|designate|VBN ;|;|: ESBL019|esbl019|NN Filamented|filamented|JJ -RRB-|-rrb-|-RRB- .|.|. The|the|DT CCM|CCM|NNP of|of|IN the|the|DT pre-filamented|pre-filamented|JJ ESBL019|esbl019|NN fraction|fraction|NN was|be|VBD replaced|replace|VBN with|with|IN CCM|ccm|NN without|without|IN ceftibuten|ceftibuten|NN and|and|CC the|the|DT filamented|filamented|JJ ESBL019|esbl019|NN were|be|VBD allowed|allow|VBN to|to|TO revert|revert|VB completely|completely|RB back|back|RB to|to|TO its|its|PRP$ coliform|coliform|NN during|during|IN 1|1|CD hour|hour|NN in|in|IN a|a|DT tube|tube|NN prior|prior|RB to|to|TO the|the|DT inoculation|inoculation|NN of|of|IN HBEP|hbep|NN cells|cell|NNS without|without|IN ceftibuten|ceftibuten|NN -LRB-|-lrb-|-LRB- designated|designate|VBN ;|;|: ESBL019|esbl019|NN Reverted|revert|VBD -RRB-|-rrb-|-RRB- .|.|. Prior|prior|RB to|to|TO inoculation|inoculation|NN the|the|DT bacterial|bacterial|JJ concentrations|concentration|NNS of|of|IN all|all|DT fractions|fraction|NNS were|be|VBD adjusted|adjust|VBN in|in|IN order|order|NN to|to|TO inoculate|inoculate|VB HBEP|hbep|NN cells|cell|NNS with|with|IN a|a|DT multiplicity|multiplicity|NN of|of|IN infection|infection|NN -LRB-|-lrb-|-LRB- MOI|moi|NN -RRB-|-rrb-|-RRB- of|of|IN 10|10|CD .|.|. All|all|DT inoculated|inoculate|VBN cells|cell|NNS were|be|VBD incubated|incubate|VBN for|for|IN 4|4|CD hours|hour|NNS in|in|IN 5|5|CD %|%|NN CO2|co2|NN at|at|IN 37oC|37oc|NN after|after|IN which|which|WDT supernatants|supernatant|NNS were|be|VBD collected|collect|VBN and|and|CC centrifuged|centrifuge|VBN 5|5|CD min|min|NN at|at|IN 5000|5000|CD x|x|CC g|g|NN to|to|TO collect|collect|VB the|the|DT bacteria|bacterium|NNS .|.|.
FPKM|fpkm|NNS were|be|VBD calculated|calculate|VBN using|use|VBG Cufflinks|Cufflinks|NNP v.|v.|CC 2.0.2|2.0.2|CD with|with|IN upper-quartile|upper-quartile|JJ normalization|normalization|NN and|and|CC fr-firststrand|fr-firststrand|NN for|for|IN library|library|NN type|type|NN
fraction|fraction|NN :|:|: input|input|NN DNA|dna|NN
fraction|fraction|NN :|:|: input|input|NN DNA|dna|NN ,|,|, SeqA|seqa|NN ChIP|chip|NN supernatant|supernatant|JJ
fraction|fraction|NN :|:|: input|input|NN DNA|dna|NN ,|,|, σ32|σ32|NN ChIP|chip|NN supernatant|supernatant|JJ
Fragmentation|fragmentation|NN and|and|CC reverse|reverse|JJ transcription|transcription|NN of|of|IN RNA|rna|NN with|with|IN random|random|JJ primers|primer|NNS was|be|VBD carried|carry|VBN out|out|RP using|use|VBG the|the|DT NEB|NEB|NNP First|First|NNP Strand|Strand|NNP Synthesis|synthesis|NN Module|module|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- .|.|. Second|second|JJ strand|strand|NN synthesis|synthesis|NN was|be|VBD done|do|VBN with|with|IN the|the|DT NEBNext|nebnext|NN Ultra|Ultra|NNP Directional|Directional|NNP RNA|rna|NN Second|second|JJ Strand|strand|NN Synthesis|synthesis|NN Module|module|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- ,|,|, then|then|RB purified|purify|VBN with|with|IN 1.7|1.7|CD x|x|CC AMPURE|AMPURE|NNP Bead|Bead|NNP XP|xp|NN -LRB-|-lrb-|-LRB- Beckman|Beckman|NNP Coulter|Coulter|NNP -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN end|end|NN repair|repair|NN was|be|VBD carried|carry|VBN out|out|RP with|with|IN the|the|DT NEBNext|nebnext|NN end|end|NN repair|repair|NN module|module|NN ,|,|, dA-tailing|da-tailing|NN used|use|VBD the|the|DT NEBNext|nebnext|NN dA-Tailing|da-tailing|NN Module|module|NN and|and|CC adapter|adapter|NN ligation|ligation|NN used|use|VBD the|the|DT NEBNext|NEBNext|NNP Quick|Quick|NNP Ligation|ligation|NN module|module|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- .|.|. PCR|pcr|NN amplification|amplification|NN was|be|VBD carried|carry|VBN out|out|RP for|for|IN 10|10|CD rounds|round|NNS of|of|IN synthesis|synthesis|NN using|use|VBG the|the|DT NEBNext|nebnext|NN High-Fidelity|high-fidelity|NN PCR|pcr|NN Master|master|NN Mix|mix|VB with|with|IN NEBNext|nebnext|NN USER|user|NN Enzyme|enzyme|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- ,|,|, samples|sample|NNS were|be|VBD purified|purify|VBN with|with|IN 1.0|1.0|CD x|x|CC AMPURE|AMPURE|NNP Bead|Bead|NNP XP|xp|NN -LRB-|-lrb-|-LRB- Beckman|Beckman|NNP Coulter|Coulter|NNP -RRB-|-rrb-|-RRB- .|.|. Library|Library|NNP quality|quality|NN was|be|VBD verified|verify|VBN on|on|IN a|a|DT Bio-Analyzer|Bio-Analyzer|NNP DNA|DNA|NNP chip|chip|NN -LRB-|-lrb-|-LRB- Agilent|agilent|NN -RRB-|-rrb-|-RRB- .|.|.
Fragments|fragment|NNS Per|per|IN Kilobase|kilobase|NN of|of|IN exon|exon|NN per|per|IN Megabase|megabase|NN of|of|IN library|library|NN size|size|NN -LRB-|-lrb-|-LRB- FPKM|fpkm|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN using|use|VBG cufflinks|cufflink|NNS v.|v.|CC 1.3.0|1.3.0|CD
FRIK2000|frik2000|NN Cy3|cy3|NN rep1|rep1|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy5|cy5|NN
FRIK2000|frik2000|CD Cy3|cy3|NN rep3|rep3|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy5|cy5|NN
FRIK2000|frik2000|CD Cy5|cy5|NN rep2|rep2|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy3|cy3|NN
FRIK2000|frik2000|CD Cy5|cy5|NN rep4|rep4|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy3|cy3|NN
FRIK966|frik966|NN Cy3|cy3|NN rep1|rep1|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy5|cy5|NN
FRIK966|frik966|NN Cy3|cy3|NN rep3|rep3|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy5|cy5|NN
FRIK966|frik966|NN Cy5|cy5|NN rep2|rep2|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy3|cy3|NN
FRIK966|frik966|NN Cy5|cy5|NN rep4|rep4|NN vs|vs|CC EDL933|edl933|NN pool|pool|NN Cy3|cy3|NN
From|from|IN the|the|DT cells|cell|NNS cultured|culture|VBN in|in|IN LB|LB|NNP media|media|NNS at|at|IN 37|37|CD ℃|℃|CD ,|,|, total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNAsnapTM|rnasnaptm|NN method|method|NN ,|,|, followed|follow|VBN by|by|IN the|the|DT ethanol|ethanol|NN precipitation|precipitation|NN .|.|. rRNA|rrna|NN was|be|VBD removed|remove|VBN using|use|VBG ribo-zeroTM|ribo-zerotm|JJ magnetic|magnetic|JJ kit|kit|NN for|for|IN bacteria|bacterium|NNS in|in|IN accordance|accordance|NN with|with|IN manufacturer|manufacturer|NN 's|'s|POS instruction|instruction|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|. rRNA|rrna|NN removal|removal|NN was|be|VBD confirmed|confirm|VBN using|use|VBG ExperionTM|experiontm|NN system|system|NN .|.|. Subsequently|subsequently|RB ,|,|, 4|4|CD µg|µg|NN of|of|IN the|the|DT purified|purify|VBN RNA|rna|NN was|be|VBD fragmented|fragmented|JJ to|to|TO sizes|size|NNS of|of|IN ~|~|NN 300|300|CD bp|bp|NN using|use|VBG RNA|rna|NN fragmentation|fragmentation|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Grand|Grand|NNP Island|Island|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- .|.|.
From|from|IN the|the|DT rRNA|rrna|NN depleted|deplete|VBN RNA|rna|NN samples|sample|NNS ,|,|, first-strand|first-strand|JJ cDNA|cdna|NN was|be|VBD synthesized|synthesize|VBN using|use|VBG a|a|DT N6|n6|NN randomized|randomize|VBD primer|primer|NN .|.|. After|after|IN fragmentation|fragmentation|NN ,|,|, the|the|DT Illumina|Illumina|NNP TruSeq|TruSeq|NNP sequencing|sequencing|NN adapters|adapter|NNS were|be|VBD ligated|ligate|VBN in|in|IN a|a|DT strand|strand|NN specific|specific|JJ manner|manner|NN to|to|TO the|the|DT 5|5|CD '|'|'' and|and|CC 3|3|CD '|'|'' ends|end|NNS of|of|IN the|the|DT cDNA|cdna|NN fragments|fragment|NNS .|.|. The|the|DT cDNA|cdna|NN was|be|VBD finally|finally|RB amplified|amplify|VBN with|with|IN PCR|pcr|NN -LRB-|-lrb-|-LRB- 15|15|CD PCR|pcr|NN cycles|cycle|NNS -RRB-|-rrb-|-RRB- using|use|VBG a|a|DT proof|proof|NN reading|reading|NN enzyme|enzyme|NN .|.|. For|for|IN Illumina|Illumina|NNP sequencing|sequencing|NN ,|,|, cDNA|cdna|NN libraries|library|NNS were|be|VBD pooled|pool|VBN in|in|IN a|a|DT 25:1|25:1|CD ratio|ratio|NN .|.|. The|the|DT library|library|NN pool|pool|NN was|be|VBD fractionated|fractionate|VBN in|in|IN the|the|DT size|size|NN range|range|NN of|of|IN 250-500|250-500|CD bp|bp|NN using|use|VBG a|a|DT differential|differential|JJ clean|clean|JJ -|-|: up|up|RP with|with|IN the|the|DT Agencourt|Agencourt|NNP AMPure|AMPure|NNP kit|kit|NN .|.|. The|the|DT cDNA|cdna|NN pool|pool|NN was|be|VBD sequenced|sequence|VBN on|on|IN an|a|DT Illumina|Illumina|NNP NextSeq|NextSeq|NNP 500|500|CD system|system|NN using|use|VBG 75|75|CD bp|bp|NN read|read|VBD length|length|NN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 12|12|CD hours|hour|NNS 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 12hours|12hours|CD 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 18|18|CD hours|hour|NNS 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 18hours|18hours|CD 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 3.5|3.5|CD hours|hour|NNS 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 4|4|CD hours|hour|NNS 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 4hours|4hours|CD 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ bacteria|bacterium|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN 18|18|CD mm|mm|NN test|test|NN tubes|tube|NNS containing|contain|VBG DMga|dmga|JJ medium|medium|NN ,|,|, 500µL|500µl|NN of|of|IN culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO 50mL|50ml|NN of|of|IN fresh|fresh|JJ DMga|dmga|NN in|in|IN 500mL|500ml|NN flasks|flask|NNS and|and|CC grown|grow|VBN for|for|IN 7hours|7hours|CD 37|37|CD °C|°c|NN ,|,|, 250rpm|250rpm|NN .|.|. Extraction|extraction|NN was|be|VBD performed|perform|VBN just|just|RB after|after|IN .|.|.
Frozen|frozen|JJ cell|cell|NN pellets|pellet|NNS were|be|VBD lyzed|lyze|VBN with|with|IN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP -RRB-|-rrb-|-RRB- and|and|CC proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- at|at|IN room|room|NN temperature|temperature|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN cell|cell|NN lysates|lysate|NNS using|use|VBG RNeasy|RNeasy|NNP Midi|Midi|NNP Kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- .|.|. All|all|DT RNA|rna|NN samples|sample|NNS were|be|VBD then|then|RB treated|treat|VBN with|with|IN DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Life|Life|NNP technologies|technology|NNS -RRB-|-rrb-|-RRB- before|before|IN a|a|DT phenol/chloroform|phenol/chloroform|NN purification|purification|NN and|and|CC an|a|DT overnight|overnight|JJ precipitation|precipitation|NN at|at|IN -20|-20|CD °C|°c|NN in|in|IN absolute|absolute|JJ ethanol|ethanol|NN containing|contain|VBG LiCl|licl|NN 8M|8m|NN .|.|. After|after|IN centrifugation|centrifugation|NN ,|,|, RNA|rna|NN pellets|pellet|NNS were|be|VBD air-dried|air-dried|JJ in|in|IN a|a|DT vacuum|vacuum|NN concentrator|concentrator|NN -LRB-|-lrb-|-LRB- vacufuge|vacufuge|NN plus|plus|CC ;|;|: Eppendorf|eppendorf|NN -RRB-|-rrb-|-RRB- .|.|.
Functional|functional|JJ annotation|annotation|NN was|be|VBD done|do|VBN using|use|VBG the|the|DT Database|database|NN for|for|IN Annotation|Annotation|NNP ,|,|, Visualization|visualization|NN and|and|CC Integrated|Integrated|NNP Discovery|Discovery|NNP -LRB-|-lrb-|-LRB- DAVID|DAVID|NNP -RRB-|-rrb-|-RRB- Bioinformatics|Bioinformatics|NNP Resources|Resources|NNP 6.7|6.7|CD ,|,|, NIAID|NIAID|NNP ,|,|, NIH|NIH|NNP -LRB-|-lrb-|-LRB- http://david.abcc.ncifcrf.gov|http://david.abcc.ncifcrf.gov|NN -RRB-|-rrb-|-RRB- .|.|.
∆|∆|SYM fur|fur|NN Aerobic|aerobic|JJ A|a|NN
∆|∆|CD fur|fur|NN Aerobic|aerobic|JJ B|b|NN
∆|∆|CD fur|fur|NN Anaerobic|anaerobic|JJ A|a|NN
∆|∆|CD fur|fur|NN Anaerobic|anaerobic|JJ B|b|NN
∆|∆|CD fur|fur|NN Anaerobic|anaerobic|JJ -LSB-|-lsb-|-LRB- IP|IP|NNP vs|vs|CC nput|nput|NN -RSB-|-rsb-|-RRB-
furanone-free|furanone-free|JJ control|control|NN
FUR|fur|NN _|_|CD CPR|CPR|NNP _|_|SYM 1|1|CD
FUR|fur|NN _|_|CD CPR|CPR|NNP _|_|NN 2|2|CD
Furfural-tolerant|furfural-tolerant|JJ IrrE|irre|NN mutant|mutant|JJ F1-37|f1-37|NN ,|,|, biological|biological|JJ rep1|rep1|NN
Furfural-tolerant|furfural-tolerant|JJ IrrE|irre|NN mutant|mutant|JJ F1-37|f1-37|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Furfural-tolerant|furfural-tolerant|JJ IrrE|irre|NN mutant|mutant|JJ F1-37|f1-37|NN ,|,|, biological|biological|JJ rep3|rep3|NN
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Aerobic|Aerobic|NNP A|A|NNP
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Aerobic|Aerobic|NNP B|B|NNP
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Aerobic|Aerobic|NNP C|C|NNP
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Anaerobic|Anaerobic|NNP A|A|NNP
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Anaerobic|anaerobic|JJ B|b|NN
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Anaerobic|Anaerobic|NNP C|C|NNP
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Anaerobic|Anaerobic|NNP ,|,|, Iron|Iron|NNP Deficient|Deficient|NNP A|A|NNP
Fur|Fur|NNP IP|IP|NNP ChIP-Seq|ChIP-Seq|NNP Anaerobic|Anaerobic|NNP ,|,|, Iron|Iron|NNP Deficient|deficient|JJ B|b|NN
Fur-minus|fur-minus|NN _|_|CD cDNA|cdna|NN _|_|CD Aerobic|aerobic|JJ
Fur-minus|fur-minus|NN _|_|CD cDNA|cdna|NN _|_|CD Anaerobic|anaerobic|JJ
Fur-minus|fur-minus|NN _|_|CD RyhB-minus|RyhB-minus|NNP _|_|NNP cDNA|cdna|NN _|_|CD Aerobic|aerobic|JJ
Fur-minus|fur-minus|NN _|_|CD RyhB-minus|RyhB-minus|NNP _|_|NNP cDNA|cdna|NN _|_|CD Anaerobic|anaerobic|JJ
fur|fur|NN mutant|mutant|JJ pBAD-ryhB|pbad-ryhb|NN #|#|# 1|1|CD +|+|CC arabinose|arabinose|NN
fur|fur|NN mutant|mutant|JJ pBAD-ryhB|pbad-ryhb|NN #|#|# 2|2|CD +|+|CC arabinose|arabinose|NN
fur|fur|NN mutant|mutant|JJ pNM12|pnm12|NN #|#|# 1|1|CD +|+|CC arabinose|arabinose|NN
fur|fur|NN mutant|mutant|JJ pNM12|pnm12|NN #|#|# 2|2|CD +|+|CC arabinose|arabinose|NN
FUR|fur|NN _|_|CD noCPR|nocpr|NN _|_|NN 1|1|CD
FUR|fur|NN _|_|CD noCPR|nocpr|NN _|_|NN 2|2|CD
∆|∆|CD fur|fur|NN ∆|∆|CD ryhB|ryhb|NN Aerobic|aerobic|JJ A|a|NN
∆|∆|CD fur|fur|NN ∆|∆|CD ryhB|ryhb|NN Aerobic|aerobic|JJ B|b|NN
∆|∆|CD fur|fur|NN ∆|∆|CD ryhB|ryhb|NN Anaerobic|anaerobic|JJ A|a|NN
∆|∆|CD fur|fur|NN ∆|∆|CD ryhB|ryhb|NN Anaerobic|anaerobic|JJ B|b|NN
further|further|JJ analysis|analysis|NN if|if|IN the|the|DT foreground|foreground|NN intensity|intensity|NN of|of|IN less|less|JJR than|than|IN 50|50|CD %|%|NN of|of|IN the|the|DT pixels|pixel|NNS within|within|IN the|the|DT spot|spot|NN
further|further|RB processing|process|VBG
Fur|Fur|NNP with|with|IN DPD|dpd|NN 1|1|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
Fur|Fur|NNP with|with|IN DPD|dpd|NN 2|2|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
Fur|Fur|NNP with|with|IN Fe|Fe|NNP 1|1|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
Fur|Fur|NNP with|with|IN Fe|Fe|NNP 2|2|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
G21|g21|NN MG1655GFP|mg1655gfp|NN _|_|CD pD864|pd864|NN _|_|NN 3|3|CD
G23|g23|NN MG1655GFP|mg1655gfp|NN _|_|CD pLys|ply|VBZ _|_|SYM M1|m1|NN _|_|NN 3|3|CD
G28|g28|NN MG1655GFP|mg1655gfp|NN _|_|CD pD864|pd864|NN _|_|NN 3|3|CD
G29|g29|NN DH10BGFP|dh10bgfp|NN _|_|CD None|none|NN _|_|NN 3|3|CD
G2|g2|NN ,|,|, osmotolerant|osmotolerant|JJ mutant|mutant|JJ
G2|g2|NN Replicate|replicate|VB 1|1|CD
G2|g2|NN Replicate|replicate|VB 2|2|CD
G3|g3|NN ,|,|, osmotolerant|osmotolerant|JJ mutant|mutant|JJ
G3|g3|NN Replicate|replicate|VB 1|1|CD
G3|g3|NN Replicate|replicate|VB 2|2|CD
G4H14|g4h14|NN
G4H14|g4h14|NN strain|strain|NN
G500|g500|CD _|_|NN 1|1|CD
G5|g5|NN DH10BGFP|dh10bgfp|NN _|_|CD Lux|lux|FW _|_|FW 3|3|CD
G5|g5|NN ,|,|, osmotolerant|osmotolerant|JJ mutant|mutant|JJ
G5|g5|NN Replicate|replicate|VB 1|1|CD
G5|g5|NN Replicate|replicate|VB 2|2|CD
G6|g6|NN DH10BGFP|dh10bgfp|NN _|_|CD pD864|pd864|NN _|_|CD LacZ|lacz|NN _|_|NN 3|3|CD
G6|g6|NN ,|,|, osmotolerant|osmotolerant|JJ mutant|mutant|JJ
G6|g6|NN Replicate|replicate|VB 1|1|CD
G6|g6|NN Replicate|replicate|VB 2|2|CD
gabT|gabt|NN KO|ko|NN rep1|rep1|NN
gabT|gabt|NN KO|ko|NN rep2|rep2|NN
gabT|gabt|NN KO|ko|NN rep3|rep3|NN
Galaxy1|galaxy1|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pHDB3|phdb3|NN _|_|CD 5|5|CD .|.|. txt|txt|NN -RSB-|-rsb-|-RRB-
Galaxy2|galaxy2|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pLCV1|plcv1|NN _|_|CD 5|5|CD .|.|. txt|txt|NN -RSB-|-rsb-|-RRB-
Galaxy3|galaxy3|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pLCV1|plcv1|NN _|_|NN 10|10|CD .|.|. txt|txt|NN -RSB-|-rsb-|-RRB-
Galaxy4|galaxy4|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pHDB3|phdb3|NN _|_|CD 20|20|CD .|.|. txt|txt|NN -RSB-|-rsb-|-RRB-
Galaxy5|galaxy5|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pLCV1|plcv1|NN _|_|CD 20|20|CD .|.|. txt|txt|NN -RSB-|-rsb-|-RRB-
Galaxy6|galaxy6|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pHDB3|phdb3|NN _|_|NN 10|10|CD .|.|. txt|txt|NN -RSB-|-rsb-|-RRB-
galE|gale|NN KO|ko|NN rep1|rep1|NN
galE|gale|NN KO|ko|NN rep2|rep2|NN
galE|gale|NN KO|ko|NN rep3|rep3|NN
galF|galf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
galF|galf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
galF|galf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
galF|galf|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
GATC|gatc|NN
GATC|gatc|NN software|software|NN for|for|IN read|read|NN mapping|mapping|NN on|on|IN MG1655|mg1655|NN
Gave|give|VBD a|a|DT pseudocount|pseudocount|NN of|of|IN 0.01|0.01|CD to|to|TO all|all|DT values|value|NNS of|of|IN 0|0|CD
GCOS|gcos|NN 1.0|1.0|CD
GCOS|gcos|NN was|be|VBD used|use|VBN to|to|TO obtain|obtain|VB detection|detection|NN calls|call|NNS for|for|IN each|each|DT microarray|microarray|NN .|.|. The|the|DT statistical|statistical|JJ difference|difference|NN for|for|IN mRNA|mrna|NN expression|expression|NN were|be|VBD analyzed|analyze|VBN using|use|VBG CarmaWeb|CarmaWeb|NNP .|.|. Affymetrix|Affymetrix|NNP GeneChip|GeneChip|NNP analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG MAS|MAS|NNP for|for|IN background|background|NN correction|correction|NN ,|,|, VSN|VSN|NNP for|for|IN normalization|normalization|NN ,|,|, MAS|MAS|NNP for|for|IN PM|PM|NNP correction|correction|NN and|and|CC Medianpolish|medianpolish|NN for|for|IN Expression|expression|NN .|.|. VSN|VSN|NNP normalized|normalize|VBD data|datum|NNS not|not|RB provided|provide|VBN by|by|IN submitter|submitter|NN .|.|.
GCRMA|gcrma|NN method|method|NN
GCRMA|gcrma|NN normalized|normalize|VBD
gcvR|gcvr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
gcvR|gcvr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
gcvR|gcvr|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
gcvR|gcvr|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
gcvT-ala-1|gcvt-ala-1|NN
gcvT-ala-2|gcvt-ala-2|NN
gcvT|gcvt|NN mutant|mutant|NN in|in|IN Ala|Ala|NNP media|media|NNS
gcvT|gcvt|NN mutant|mutant|NN in|in|IN Gln|gln|NN media|media|NNS
gDNA|gdna|NN 520|520|CD
gDNA|gdna|NN 521|521|CD
gDNA|gdna|NN _|_|CD A|a|DT _|_|NN cy5|cy5|NN
gDNA|gdna|NN B02|b02|NN
gDNA|gdna|NN B05|b05|NN
gDNA|gdna|NN _|_|NN B|b|NN _|_|CD cy3|cy3|NN
gDNA|gdna|NN C01|c01|NN
gDNA|gdna|NN C02|c02|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|SYM 520|520|CD
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|SYM 521|521|CD
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP B02|b02|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP B05|b05|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP C01|c01|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP C02|c02|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP F01|f01|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP F02|f02|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H01|h01|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H02|h02|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H03|h03|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H04|h04|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H05|h05|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H12|h12|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H23|h23|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP H27|h27|NN
gDNA|gdna|NN _|_|CD Ecoli|Ecoli|NNP _|_|SYM K12|k12|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP S04|s04|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP S05|s05|NN
gDNA|gdna|NN _|_|CD EColi|ecolus|NNS _|_|VBP S13|s13|NN
gDNA|gdna|NN F01|f01|NN
gDNA|gdna|NN F02|f02|NN
gDNA|gdna|NN from|from|IN E.coli|e.coli|JJ K12|k12|NN cyanine|cyanine|NN 3|3|CD
gDNA|gdna|NN H01|h01|NN
gDNA|gdna|NN H02|h02|NN
gDNA|gdna|NN H03|h03|NN
gDNA|gdna|NN H04|h04|NN
gDNA|gdna|NN H05|h05|NN
gDNA|gdna|NN H12|h12|NN
gDNA|gdna|NN H23|h23|NN
gDNA|gdna|NN H27|h27|NN
gDNA|gdna|NN K12|k12|NN
gDNA|gdna|NN S04|s04|NN
gDNA|gdna|NN S05|s05|NN
gDNA|gdna|NN S13|s13|NN
Gene|gene|NN annotation|annotation|NN was|be|VBD obtained|obtain|VBN from|from|IN the|the|DT EcoCyc|EcoCyc|NNP E.|E.|NNP coli|coli|NN Database|database|NN -LRB-|-lrb-|-LRB- https://ecocyc.org/|https://ecocyc.org/|NN -RRB-|-rrb-|-RRB- .|.|.
GeneChip|GeneChip|NNP Operating|Operating|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- MAS|MAS|NNP 5.0|5.0|CD -RRB-|-rrb-|-RRB- using|use|VBG Affymetrix|Affymetrix|NNP default|default|NN analysis|analysis|NN settings|setting|NNS and|and|CC global|global|JJ scaling|scaling|NN as|as|IN normalization|normalization|NN method|method|NN ,|,|, genes|gene|NNS with|with|IN a|a|DT p-value|p-value|NN of|of|IN less|less|JJR than|than|IN 0.0025|0.0025|CD or|or|CC greater|greater|JJR than|than|IN 0.9975|0.9975|CD were|be|VBD considered|consider|VBN statistically|statistically|RB significant|significant|JJ based|base|VBN on|on|IN Wilcoxon|Wilcoxon|NNP signed|sign|VBD rank|rank|JJ test|test|NN and|and|CC Tukey|tukey|NN Byweight|byweight|NN ,|,|, labeled|label|VBN as|as|IN I|I|PRP and|and|CC D|d|NN in|in|IN the|the|DT attached|attach|VBN txt|txt|NN file|file|NN .|.|. To|to|TO ensure|ensure|VB the|the|DT significance|significance|NN of|of|IN microarray|microarray|NN data|datum|NNS ,|,|, an|a|DT additional|additional|JJ criterion|criterion|NN was|be|VBD applied|apply|VBN to|to|TO only|only|RB select|select|VB the|the|DT genes|gene|NNS with|with|IN an|a|DT expression|expression|NN ratio|ratio|NN of|of|IN 2|2|CD or|or|CC high|high|JJ from|from|IN this|this|DT group|group|NN as|as|IN induced|induce|VBN and|and|CC repressed|repress|VBN genes|gene|NNS .|.|.
GeneChips|genechip|NNS were|be|VBD washed|wash|VBN and|and|CC stained|stain|VBN with|with|IN an|a|DT FS450|fs450|NN fluidics|fluidic|NNS machine|machine|NN and|and|CC scanned|scan|VBN using|use|VBG a|a|DT GeneChip|GeneChip|NNP Scanner|Scanner|NNP 3000|3000|CD
gene|gene|NN counting|counting|NN :|:|: HTSeq-Count|htseq-count|JJ 0.6.0|0.6.0|CD
Gene|gene|NN expression|expression|NN analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG a|a|DT strand-specific|strand-specific|JJ ,|,|, paired-end|paired-end|JJ RNA-seq|rna-seq|NN protocol|protocol|NN using|use|VBG the|the|DT dUTP|dutp|NN method|method|NN -LRB-|-lrb-|-LRB- Levin|Levin|NNP et|et|FW al.|al.|FW ,|,|, 2010|2010|CD -RRB-|-rrb-|-RRB- .|.|. Total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN and|and|CC purified|purify|VBN using|use|VBG the|the|DT Qiagen|Qiagen|NNP Rneasy|Rneasy|NNP Kit|kit|NN with|with|IN on-column|on-column|JJ DNase|dnase|NN treatment|treatment|NN .|.|.
Gene|Gene|NNP expression|expression|NN -LRB-|-lrb-|-LRB- based|base|VBN on|on|IN known|known|JJ genes|gene|NNS -RRB-|-rrb-|-RRB- was|be|VBD determined|determine|VBN using|use|VBG Cufflinks|Cufflinks|NNP 2.0.2|2.0.2|CD ,|,|, only|only|RB PF|pf|NN reads|read|VBZ were|be|VBD retained|retain|VBN
Gene|Gene|NNP expression|expression|NN data|datum|NNS -LRB-|-lrb-|-LRB- 3|3|CD biological|biological|JJ replicates|replicate|VBZ per|per|IN strain|strain|NN -RRB-|-rrb-|-RRB- were|be|VBD analyzed|analyze|VBN in|in|IN the|the|DT statistical|statistical|JJ software|software|NN program|program|NN R|r|NN -LRB-|-lrb-|-LRB- www.r-project.org|www.r-project.org|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT EdgeR|edger|NN package|package|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- .|.|. Data|datum|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT CQN|cqn|NN package|package|NN ,|,|, which|which|WDT accounts|account|VBZ for|for|IN both|both|DT gene|gene|NN length|length|NN and|and|CC GC|gc|NN content|content|JJ effects|effect|NNS -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB- .|.|. Differentially|differentially|RB expressed|express|VBN genes|gene|NNS were|be|VBD determined|determine|VBN by|by|IN comparing|compare|VBG expression|expression|NN values|value|NNS under|under|IN anaerobic|anaerobic|JJ and|and|CC aerobic|aerobic|JJ conditions|condition|NNS .|.|. Those|those|DT genes|gene|NNS with|with|IN adjusted|adjusted|JJ P|p|NN values|value|NNS less|less|JJR than|than|IN 0.01|0.01|CD -LRB-|-lrb-|-LRB- i.e.|i.e.|FW ,|,|, false|false|JJ discovery|discovery|NN rate|rate|NN less|less|JJR than|than|IN 1|1|CD %|%|NN -RRB-|-rrb-|-RRB- were|be|VBD identified|identify|VBN as|as|IN significantly|significantly|RB differentially|differentially|RB expressed|express|VBN genes|gene|NNS .|.|. Finally|finally|RB ,|,|, gene|gene|NN annotations|annotation|NNS were|be|VBD automatically|automatically|RB made|make|VBN using|use|VBG the|the|DT biomaRt|biomart|NN package|package|NN -LRB-|-lrb-|-LRB- 5|5|CD -RRB-|-rrb-|-RRB- together|together|RB with|with|IN the|the|DT annotation|annotation|NN files|file|VBZ available|available|JJ at|at|IN the|the|DT Ensembl|ensembl|NN database|database|NN -LRB-|-lrb-|-LRB- www.ensembl.org|www.ensembl.org|NN -RRB-|-rrb-|-RRB- and|and|CC gene|gene|NN set|set|NN enrichment|enrichment|NN analysis|analysis|NN -LRB-|-lrb-|-LRB- GSEA|gsea|NN -RRB-|-rrb-|-RRB- was|be|VBD performed|perform|VBN using|use|VBG the|the|DT piano|piano|NN package|package|NN -LRB-|-lrb-|-LRB- 6|6|CD -RRB-|-rrb-|-RRB- .|.|. All|all|DT R|r|NN packages|package|NNS used|use|VBN in|in|IN this|this|DT study|study|NN are|be|VBP available|available|JJ in|in|IN Bioconductor|Bioconductor|NNP -LRB-|-lrb-|-LRB- www.bioconductor.org|www.bioconductor.org|NN -RRB-|-rrb-|-RRB- .|.|.
gene|gene|NN expression|expression|NN sum|sum|NN normalized|normalize|VBD to|to|TO 1|1|CD at|at|IN each|each|DT time|time|NN point|point|NN
Gene|gene|NN expression|expression|NN was|be|VBD calculated|calculate|VBN as|as|IN reads|read|VBZ per|per|IN gene|gene|NN by|by|IN determining|determine|VBG the|the|DT number|number|NN of|of|IN reads|read|VBZ that|that|IN overlapped|overlap|VBD with|with|IN the|the|DT annotated|annotated|JJ gene|gene|NN loci|locus|NNS using|use|VBG HTSeq|htseq|NN -LRB-|-lrb-|-LRB- Anders|Anders|NNP et|et|FW al.|al.|FW ,|,|, 2015|2015|CD ,|,|, doi|doi|FW :|:|: 10.1093|10.1093|CD /|/|: bioinformatics/btu638|bioinformatics/btu638|CD -RRB-|-rrb-|-RRB- with|with|IN the|the|DT option|option|NN `|`|`` intersection-nonempty|intersection-nonempty|NN '|'|'' .|.|.
GenePix|GenePix|NNP Pro|pro|FW -LRB-|-lrb-|-LRB- v|v|LS 6.1|6.1|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN background|background|NN subtraction|subtraction|NN and|and|CC normalization|normalization|NN .|.|.
GenePix|genepix|NN software|software|NN -LRB-|-lrb-|-LRB- Axon|Axon|NNP Instruments|Instruments|NNP ,|,|, Union|Union|NNP City|City|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- version|version|NN 5.1|5.1|CD was|be|VBD used|use|VBN to|to|TO process|process|VB the|the|DT scanned|scan|VBN data|datum|NNS and|and|CC generate|generate|VB the|the|DT gpr|gpr|NN files|file|NNS .|.|.
generation|generation|NN of|of|IN coverage|coverage|NN graphs|graph|NNS representing|represent|VBG the|the|DT number|number|NN of|of|IN pAA|paa|NN plasmid-associated|plasmid-associated|JJ mapped|map|VBN reads|read|VBZ per|per|IN nucleotide|nucleotide|NN using|use|VBG READemption|reademption|NN 0.3.7|0.3.7|CD
Gene|Gene|NNP selection|selection|NN was|be|VBD done|do|VBN using|use|VBG the|the|DT False|False|NNP Discovery|Discovery|NNP Rate|Rate|NNP -LRB-|-lrb-|-LRB- FDR|FDR|NNP -RRB-|-rrb-|-RRB- correction|correction|NN procedure|procedure|NN for|for|IN adjusting|adjust|VBG genes|gene|NNS with|with|IN p-value|p-value|JJ smaller|smaller|JJR than|than|IN 0.05|0.05|CD and|and|CC Fold|Fold|NNP Change|Change|NNP greater|greater|JJR than|than|IN 2|2|CD .|.|.
Genes|gene|NNS from|from|IN the|the|DT amplified|amplify|VBN regions|region|NNS in|in|IN O500|o500|NN -LRB-|-lrb-|-LRB- 12-fold|12-fold|JJ -RRB-|-rrb-|-RRB- and|and|CC P500|p500|NN -LRB-|-lrb-|-LRB- two-fold|two-fold|JJ -RRB-|-rrb-|-RRB- strains|strain|NNS are|be|VBP significantly|significantly|RB over-expressed|over-expressed|JJ relative|relative|JJ to|to|TO the|the|DT reference|reference|NN :|:|: average|average|JJ log|log|NN Fold|Fold|NNP Change|Change|NNP for|for|IN concentrations|concentration|NNS is|be|VBZ +3.6|+3.6|CD and|and|CC +0.8|+0.8|CD -LRB-|-lrb-|-LRB- both|both|CC with|with|IN p-values|p-values|NN <|<|JJR 10-20|10-20|CD -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB .|.|.
GeneSpring|genespring|NN GX|GX|NNP v.|v.|CC 13.1|13.1|CD
Genes|gene|NNS with|with|IN BH|bh|NN -LRB-|-lrb-|-LRB- Benjamini|Benjamini|NNP and|and|CC Hochberg|Hochberg|NNP -RRB-|-rrb-|-RRB- adjusted|adjust|VBN p-values|p-value|NNS below|below|IN 0.05|0.05|CD threshold|threshold|NN were|be|VBD selected|select|VBN as|as|IN DE|de|NN genes|gene|NNS .|.|.
Genetic|Genetic|NNP background|background|NN :|:|: fnr|fnr|SYM -|-|:
genetic|genetic|JJ background|background|NN :|:|: O157|o157|NN H19|h19|NN
Genetic|Genetic|NNP background|background|NN :|:|: wt|wt|JJ
Genetic|Genetic|NNP background|background|NN :|:|: wt|wt|JJ
Genetic|Genetic|NNP background|background|NN :|:|: wtGrowth|wtgrowth|NN conditions|condition|NNS :|:|: aerobic|aerobic|JJ
genetic|genetic|JJ modification|modification|NN :|:|: empty|empty|JJ plasmid|plasmid|NN -LRB-|-lrb-|-LRB- LJ110/pTM30|lj110/ptm30|NN -RRB-|-rrb-|-RRB-
genetic|genetic|JJ modification|modification|NN :|:|: PdhR|pdhr|NN knockout|knockout|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- LJ110deltapdhR|lj110deltapdhr|NN -RRB-|-rrb-|-RRB-
genetic|genetic|JJ modification|modification|NN :|:|: PdhR|pdhr|NN overexpression|overexpression|NN strain|strain|NN -LRB-|-lrb-|-LRB- LJ110/pTM30PdhRhis|lj110/ptm30pdhrhis|NN -RRB-|-rrb-|-RRB-
genetic|genetic|JJ modification|modification|NN :|:|: wild|wild|JJ type|type|NN LJ110|lj110|NN
Gene|gene|NN wise|wise|JJ natural|natural|JJ spline|spline|NN interpolation|interpolation|NN of|of|IN temporal|temporal|JJ data|datum|NNS from|from|IN initial|initial|JJ time|time|NN points|point|NNS to|to|TO a|a|DT dataset|dataset|NN of|of|IN 10|10|CD minutes|minute|NNS steps|step|NNS -LRB-|-lrb-|-LRB- see|see|VB processed|process|VBN data|datum|NNS files|file|NNS -RRB-|-rrb-|-RRB- .|.|. Expression|expression|NN values|value|NNS at|at|IN the|the|DT time|time|NN points|point|NNS of|of|IN the|the|DT raw|raw|JJ data|datum|NNS are|be|VBP not|not|RB affected|affect|VBN by|by|IN the|the|DT interpolation|interpolation|NN .|.|.
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000752975|000752975|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000753215|000753215|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000753275|000753275|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000936225|000936225|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000936245|000936245|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000936475|000936475|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000937275|000937275|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000938695|000938695|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000938995|000938995|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000939195|000939195|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000939755|000939755|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000939955|000939955|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000941395|000941395|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000941895|000941895|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000946755|000946755|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000947315|000947315|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000951835|000951835|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000951875|000951875|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000951915|000951915|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965545|000965545|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965555|000965555|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965575|000965575|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965625|000965625|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965635|000965635|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965655|000965655|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965665|000965665|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965705|000965705|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000965715|000965715|CD
genome|genome|NN accession|accession|NN :|:|: GCA|gca|NN _|_|SYM 000966935|000966935|CD
genome|genome|NN accession|accession|NN :|:|: PVRW00000000|pvrw00000000|NN
Genome|Genome|NNP Build|Build|NNP :|:|:
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM1024v1|asm1024v1|NN -LRB-|-lrb-|-LRB- NCBI|NCBI|NNP E.|E.|NNP coli|coli|NN K12|k12|NN subst|subst|NN .|.|. W3110|w3110|NN genome|genome|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN :|:|: AP009048|ap009048|NN .1|.1|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM1938v1|asm1938v1|NN
genome|genome|NN build|build|VB :|:|: ASM584v1|asm584v1|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM584v1|asm584v1|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM584v1|asm584v1|NN ;|;|: Reference|Reference|NNP genome|genome|NN for|for|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN -LRB-|-lrb-|-LRB- RefSeq|refseq|NN NC|nc|NN _|_|SYM 000913|000913|CD -RRB-|-rrb-|-RRB- .|.|. Paper|Paper|NNP title|title|NN :|:|: Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN :|:|: a|a|DT cooperatively|cooperatively|RB developed|develop|VBN annotation|annotation|NN snapshot|snapshot|NN --|--|: 2005|2005|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM584v1|asm584v1|NN ,|,|, U00096|u00096|NN .2|.2|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM584v2|asm584v2|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM584v2|asm584v2|NN -LRB-|-lrb-|-LRB- Escherichia|escherichia|FW _|_|FW coli|coli|FW _|_|SYM str|str|FW _|_|FW k|k|NN _|_|SYM 12|12|CD _|_|SYM substr|substr|FW _|_|FW mg1655.GCA|mg1655.gca|NN _|_|SYM 000005845.2.24|000005845.2.24|CD .|.|. gtf|gtf|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ASM666v1|asm666v1|NN ;|;|: NC|NC|NNP _|_|NNP 002655.2|002655.2|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: ATCC8739|atcc8739|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: CFT073|cft073|NN -LRB-|-lrb-|-LRB- AE014075|ae014075|NN .1|.1|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: CFT073|CFT073|NNP E.|E.|NNP coli|coli|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: CP009273|cp009273|NN .1|.1|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: CP018801|cp018801|NN -LRB-|-lrb-|-LRB- https://www.ncbi.nlm.nih.gov/nuccore/CP018801|https://www.ncbi.nlm.nih.gov/nuccore/cp018801|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: DL4201|dl4201|NN _|_|NN in|in|IN _|_|NN lab|lab|NN _|_|CD reference|reference|NN _|_|NN genome|genome|NN -LRB-|-lrb-|-LRB- available|available|JJ on|on|IN series|series|NN record|record|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: E.coli|e.coli|NN K12|k12|NN BW25113|bw25113|NN
Genome|Genome|NNP build|build|VB :|:|: E.|e.|FW coli|coli|FW -LSB-|-lsb-|-LRB- K-12|k-12|NN MG1655|mg1655|NN strain|strain|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .3|.3|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: E.|e.|FW coli|coli|FW MG1655|mg1655|NN GenBank|genbank|NN :|:|: U00096|u00096|NN .2|.2|NN ,|,|, total|total|JJ length|length|NN :|:|: 4639675|4639675|CD bp|bp|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: E.|e.|FW coli|coli|FW :|:|: NC|NC|NNP _|_|NNP 000913|000913|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: E.|e.|FW coli|coli|FW strain|strain|NN BW25113|bw25113|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW B|b|NN str|str|NN .|.|. REL606|rel606|NN ;|;|: NC|NC|NNP _|_|NNP 012967.1|012967.1|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- DH10B|dh10b|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN NC000913|nc000913|NN .3|.3|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW K12|k12|NN str|str|NN MG1655|mg1655|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN substr|substr|NN .|.|. DH10B|dh10b|NN ASM1942v1|asm1942v1|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN ,|,|, substr|substr|NN .|.|. MG1655|mg1655|NN -LRB-|-lrb-|-LRB- assembly|assembly|NN ASM584v2|asm584v2|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN genome|genome|NN version|version|NN U00096|u00096|NN .2|.2|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 00091313-Feb-2011|00091313-feb-2011|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- NC000913|nc000913|NN .2|.2|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW strain|strain|NN K12|k12|NN sub-strain|sub-strain|JJ MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN accession|accession|NN no|no|DT .|.|. U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN ,|,|, NCBI|NCBI|NNP Reference|Reference|NNP Sequence|sequence|NN :|:|: NC|NC|NNP _|_|NNP 000913.3|000913.3|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .3|.3|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Escherichia|escherichia|FW coli|coli|FW W3110|w3110|NN MuSGS|musgs|NN -LRB-|-lrb-|-LRB- on|on|IN the|the|DT basis|basis|NN of|of|IN NC|NC|NNP _|_|SYM 007779.1|007779.1|CD -RRB-|-rrb-|-RRB- .|.|. FASTA|fasta|NN and|and|CC GFF|gff|NN are|be|VBP included|include|VBN on|on|IN series|series|NN record|record|NN .|.|.
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: FM180568|fm180568|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: FM180569|fm180569|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: FM180570|fm180570|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: gi|gi|NN ||||SYM 387825439|387825439|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: http://www.ncbi.nih.gov/nuccore/AP009048.1|http://www.ncbi.nih.gov/nuccore/ap009048.1|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: K12|k12|SYM -|-|: MG1655|mg1655|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: K-12|k-12|NN subst|subst|NN .|.|. MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913.3|000913.3|CD -RRB-|-rrb-|-RRB- /|/|: ASM584v1|asm584v1|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913.3|000913.3|CD -RRB-|-rrb-|-RRB- /|/|: ASM584v1|asm584v1|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 000913|000913|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 000913.2|000913.2|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC000913|nc000913|NN .2|.2|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC000913|nc000913|NN .2|.2|NN MG1655|mg1655|NN
genome|genome|NN build|build|VB :|:|: NC|NC|NNP _|_|NNP 000913.3|000913.3|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 000913.3|000913.3|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|SYM 000913.3|000913.3|CD E.|e.|FW coli|coli|FW K12|k12|NN substr|substr|NN .|.|. MG1655|mg1655|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 000913/ASM584v1|000913/asm584v1|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 002655|002655|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 002655.2|002655.2|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 007779.1|007779.1|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC007779|nc007779|NN .1|.1|NN -LRB-|-lrb-|-LRB- UCSC|ucsc|NN Archaeal|archaeal|NN Genome|Genome|NNP Browser|Browser|NNP -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 010473.1|010473.1|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 011741|011741|CD -LRB-|-lrb-|-LRB- E.coli|e.coli|NN strain|strain|NN IAI1|iai1|NN -RRB-|-rrb-|-RRB- ,|,|, NC|nc|NN _|_|SYM 000913.2|000913.2|CD -LRB-|-lrb-|-LRB- E.coli|e.coli|NN strain|strain|NN MG1655|mg1655|NN -RRB-|-rrb-|-RRB- ,|,|, TW09308|tw09308|NN -LRB-|-lrb-|-LRB- E.coli|e.coli|NN strain|strain|NN TW09308|tw09308|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC TW11588|tw11588|NN -LRB-|-lrb-|-LRB- E.coli|e.coli|NN strain|strain|NN TW11588|tw11588|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 011916.1|011916.1|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 012967.1|012967.1|CD plus|plus|CC small|small|JJ RNAs|rna|NNS as|as|IN annotated|annotated|JJ in|in|IN Rfam|Rfam|NNP 11.0|11.0|CD database|database|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 016856.1|016856.1|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 017644.1|017644.1|CD -LRB-|-lrb-|-LRB- Escherichia|escherichia|FW coli|coli|FW NA114|na114|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 018220|018220|CD and|and|CC NC|NC|NNP _|_|NNP 000913|000913|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 018658.1|018658.1|CD ,|,|, NC|NC|NNP _|_|NNP 018659.1|018659.1|CD ,|,|, NC|NC|NNP _|_|NNP 018660.1|018660.1|CD ,|,|, NC|NC|NNP _|_|NNP 018666.1|018666.1|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NCBI|ncbi|NN reference|reference|NN sequence|sequence|NN :|:|: NC|NC|NNP _|_|NNP 000913.2|000913.2|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NCBI|ncbi|NN reference|reference|NN sequence|sequence|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 017626.1|017626.1|CD -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: pPR9|ppr9|NN plasmid|plasmid|NN -LRB-|-lrb-|-LRB- ref|ref|NN is|be|VBZ Kashlec|Kashlec|NNP et|et|FW al.|al.|FW ,|,|, 1989|1989|CD ,|,|, PMID|PMID|NNP :|:|: 2547695|2547695|CD -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Reference|Reference|NNP genome|genome|NN for|for|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN -LRB-|-lrb-|-LRB- RefSeq|refseq|NN NC|nc|NN _|_|CD 000913.3|000913.3|CD -RRB-|-rrb-|-RRB- .|.|.
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Reference|Reference|NNP genome|genome|NN used|use|VBN :|:|: Escherichia|escherichia|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN ,|,|, version|version|NN :|:|: iGenome|iGenome|NNP
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: reference|reference|NN sequence|sequence|NN is|be|VBZ REL606|REL606|NNP
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: RefSeq|RefSeq|NNP NC|NC|NNP _|_|NNP 000913.3|000913.3|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Samples|sample|NNS from|from|IN strain|strain|NN DH10BGFP|dh10bgfp|NN were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN geneome|geneome|NN Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. DH10B|dh10b|NN ,|,|, assembly|assembly|NN ASM1942v1|asm1942v1|NN .31|.31|CD complemented|complement|VBN with|with|IN the|the|DT GFP|gfp|NN sequence|sequence|NN ,|,|, and|and|CC the|the|DT sequence|sequence|NN of|of|IN corresponding|corresponding|JJ synthetic|synthetic|JJ circuit|circuit|NN .|.|.
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Samples|sample|NNS from|from|IN strain|strain|NN MG1655GFP|mg1655gfp|NN were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN geneome|geneome|NN Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN ,|,|, assembly|assembly|NN ASM584v2|asm584v2|NN .31|.31|CD complemented|complement|VBN with|with|IN the|the|DT GFP|gfp|NN sequence|sequence|NN ,|,|, and|and|CC the|the|DT sequence|sequence|NN of|of|IN corresponding|corresponding|JJ synthetic|synthetic|JJ circuit|circuit|NN .|.|.
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: strain|strain|NN MG1655|mg1655|NN ,|,|, version|version|NN U00096|u00096|NN .2|.2|NN ,|,|, downloaded|download|VBN from|from|IN NCBI|NCBI|NNP
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: Streptococcus|streptococcus|NN pneumoniae|pneumoniae|FW D39|d39|NN -LRB-|-lrb-|-LRB- assembly|assembly|NN ASM1436v1|asm1436v1|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: The|the|DT reference|reference|NN genomes|genome|NNS used|use|VBN for|for|IN E.|e.|FW coli|coli|FW K12|k12|NN strain|strain|NN BW25113|bw25113|NN and|and|CC S.|S.|NNP coelicolor|coelicolor|VBP A3|a3|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- strain|strain|NN M145|m145|NN were|be|VBD U00096|u00096|NN .2|.2|NN and|and|CC AL645882|al645882|NN ,|,|, respectively|respectively|RB .|.|.
genome|genome|NN build|build|VB :|:|: U00096|u00096|NN .2|.2|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: U00096|u00096|NN .2|.2|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: U00096|u00096|NN .2|.2|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: U00096|u00096|NN .3|.3|NN
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: U00096|u00096|NN .3|.3|NN -LRB-|-lrb-|-LRB- E.|e.|FW coli|coli|FW K12|k12|NN -RRB-|-rrb-|-RRB- and|and|CC NC|nc|NN _|_|VBP 001604.1|001604.1|CD -LRB-|-lrb-|-LRB- T7|t7|NN -RRB-|-rrb-|-RRB- ,|,|, excluding|exclude|VBG ribosomal|ribosomal|JJ genes|gene|NNS ,|,|, and|and|CC with|with|IN recoded|recode|VBN gene|gene|NN 10|10|CD sequence|sequence|NN -LRB-|-lrb-|-LRB- Bull|bull|NN ,|,|, 2012|2012|CD ,|,|, PMCID|pmcid|NN :|:|: PMC3457771|pmc3457771|NN -RRB-|-rrb-|-RRB- in|in|IN place|place|NN of|of|IN wild-type|wild-type|JJ sequence|sequence|NN for|for|IN analysis|analysis|NN of|of|IN recoded|recode|VBN and|and|CC evolved|evolve|VBD strains|strain|NNS
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: UCSC|UCSC|NNP mm10|mm10|CD
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: W3110|w3110|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 007779|007779|CD -RRB-|-rrb-|-RRB-
Genome|Genome|NNP _|_|NNP build|build|VB :|:|: NC|NC|NNP _|_|NNP 000913|000913|CD
Genome|Genome|NNP mapping|mapping|NN using|use|VBG Bowtie|Bowtie|NNP ,|,|, version|version|NN 0.12.9|0.12.9|CD ,|,|, parameters|parameter|NNS for|for|IN samples|sample|NNS 1-5|1-5|CD :|:|: -|-|: v|v|LS 2|2|CD --|--|: best|best|JJS --|--|: strata|strata|SYM -|-|: m|m|NN 1|1|CD ,|,|, parameters|parameter|NNS for|for|IN samples|sample|NNS 6-9|6-9|CD :|:|: -|-|: v|v|LS 3|3|CD --|--|: best|best|JJS --|--|: strata|strata|SYM -|-|: m|m|NN 1|1|CD
Genome|Genome|NNP mapping|mapping|NN using|use|VBG Bowtie|Bowtie|NNP ,|,|, version|version|NN 1.1.2|1.1.2|CD ,|,|, parameters|parameter|NNS for|for|IN samples|sample|NNS 1-2|1-2|CD :|:|: -|-|: v|v|LS 2|2|CD --|--|: best|best|JJS --|--|: strata|strata|SYM -|-|: m|m|NN 1|1|CD
Genomic|genomic|JJ bacterial|bacterial|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN following|follow|VBG the|the|DT protocol|protocol|NN described|describe|VBN in|in|IN Maniatis|Maniatis|NNP Sambrook|Sambrook|NNP -LRB-|-lrb-|-LRB- Sambrook|Sambrook|NNP et|et|FW al.|al.|FW ,|,|, 1989|1989|CD -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN was|be|VBD sonicated|sonicate|VBN in|in|IN a|a|DT Bioruptor|Bioruptor|NNP -LRB-|-lrb-|-LRB- Diagenode|Diagenode|NNP ,|,|, Liege|Liege|NNP ,|,|, Belgium|Belgium|NNP -RRB-|-rrb-|-RRB- to|to|TO obtain|obtain|VB fragments|fragment|NNS of|of|IN approximately|approximately|RB 500|500|CD bp|bp|NN .|.|.
genomic|genomic|JJ dna|dna|NN
genomic|genomic|JJ DNA|dna|NN
Genomic|genomic|JJ DNA|dna|NN control|control|NN
Genomic|genomic|JJ DNA|dna|NN control|control|NN from|from|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS
Genomic|genomic|JJ DNA|dna|NN control|control|NN from|from|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 100ug/ml|100ug/ml|JJ rifampicin|rifampicin|NN
Genomic|genomic|JJ DNA|dna|NN control|control|NN from|from|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 20ug/ml|20ug/ml|JJ bicyclomycin|bicyclomycin|NN
Genomic|genomic|JJ DNA|dna|NN control|control|NN from|from|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS ,|,|, untreated|untreated|JJ
Genomic|genomic|JJ DNA|dna|NN control|control|NN from|from|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN HA3|ha3|NN :|:|: :|:|: nusG|nusg|NN cells|cell|NNS
Genomic|genomic|JJ DNA|dna|NN E.|e.|FW coli|coli|FW EDL933|edl933|NN
Genomic|genomic|JJ DNA|dna|NN Extraction|extraction|NN :|:|: Genomic|genomic|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN according|accord|VBG to|to|TO Current|current|JJ Protocols|protocol|NNS in|in|IN Molecular|molecular|JJ Biology|biology|NN .|.|. Protein-DNA|protein-dna|JJ complex|complex|NN isolation|isolation|NN :|:|: Protein-DNA|protein-dna|JJ complexes|complex|NNS were|be|VBD isolated|isolate|VBN by|by|IN phenol|phenol|NN extraction|extraction|NN with|with|IN 150|150|CD μL|μl|NN 10|10|CD mM|mm|NN Tris|Tris|NNP and|and|CC 500|500|CD μL|μl|NN 25:24:1|25:24:1|CD phenol|phenol|NN :|:|: chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN .|.|. A|a|DT white|white|JJ disk|disk|NN was|be|VBD readily|readily|RB discernible|discernible|JJ at|at|IN the|the|DT aqueous/organic|aqueous/organic|JJ interface|interface|NN .|.|. To|to|TO purify|purify|VB this|this|DT interface|interface|NN ,|,|, all|all|DT aqueous|aqueous|JJ and|and|CC organic|organic|JJ liquid|liquid|NN was|be|VBD removed|remove|VBN by|by|IN pipetting|pipetting|NN .|.|. A|a|DT second|second|JJ extraction|extraction|NN was|be|VBD performed|perform|VBN by|by|IN adding|add|VBG 500|500|CD μL|μl|NN 10|10|CD mM|mm|NN Tris|Tris|NNP and|and|CC 450|450|CD μL|μl|NN 24:1|24:1|CD chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN ,|,|, vortexing|vortexing|NN and|and|CC centrifuging|centrifuging|NN .|.|. Again|again|RB ,|,|, all|all|DT liquid|liquid|NN was|be|VBD removed|remove|VBN from|from|IN the|the|DT interface|interface|NN by|by|IN pipetting|pipetting|NN ,|,|, and|and|CC residual|residual|JJ liquid|liquid|NN was|be|VBD removed|remove|VBN .|.|. For|for|IN cross-link|cross-link|NN reversal|reversal|NN :|:|: the|the|DT interface|interface|NN was|be|VBD suspended|suspend|VBN in|in|IN 500|500|CD μL|μl|NN 10|10|CD mM|mm|NN Tris|Tris|NNP and|and|CC 50|50|CD μL|μl|NN 10|10|CD %|%|NN SDS|sds|NN ,|,|, and|and|CC placed|place|VBN at|at|IN ~|~|NN 100|100|CD ˚C|˚c|NN for|for|IN 30|30|CD minutes|minute|NNS .|.|. The|the|DT tubes|tube|NNS were|be|VBD placed|place|VBN on|on|IN ice|ice|NN ,|,|, then|then|RB moved|move|VBD to|to|TO 65|65|CD ˚C|˚c|NN for|for|IN 3|3|CD hours|hour|NNS following|follow|VBG addition|addition|NN of|of|IN 5|5|CD μL|μl|NN proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- 20|20|CD mg/mL|mg/ml|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN heat|heat|NN treatment|treatment|NN ,|,|, the|the|DT solutions|solution|NNS were|be|VBD phenol/chloroform|phenol/chloroform|NN extracted|extract|VBN and|and|CC ethanol|ethanol|NN precipitated|precipitate|VBD in|in|IN the|the|DT presence|presence|NN of|of|IN glycogen|glycogen|NN to|to|TO purify|purify|VB the|the|DT DNA|dna|NN .|.|. RNA|rna|NN extraction|extraction|NN :|:|: the|the|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- P/N|p/n|NN 74104|74104|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO isolate|isolate|VB total|total|JJ cellular|cellular|JJ RNA|rna|NN .|.|. Immediately|immediately|RB following|follow|VBG elution|elution|NN in|in|IN RNase-free|rnase-free|JJ water|water|NN ,|,|, residual|residual|JJ DNA|dna|NN was|be|VBD removed|remove|VBN by|by|IN treatment|treatment|NN with|with|IN DNaseI|dnasei|NN at|at|IN 37|37|CD °C|°c|NN for|for|IN 15|15|CD minutes|minute|NNS .|.|. The|the|DT samples|sample|NNS were|be|VBD treated|treat|VBN again|again|RB using|use|VBG the|the|DT RNeasy|RNeasy|NNP kit|kit|NN ,|,|, resuspended|resuspend|VBN in|in|IN 40|40|CD μl|μl|NN RNase-free|rnase-free|NN water|water|NN ,|,|, and|and|CC stored|store|VBD at|at|IN -20|-20|CD °C|°c|NN .|.|.
Genomic|genomic|JJ DNA|dna|NN from|from|IN EDL933|edl933|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 10828|10828|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 11109|11109|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 11117|11117|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 11128|11128|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 11619|11619|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 11711|11711|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 11788|11788|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 11845|11845|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 12009|12009|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN 13369|13369|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN ED71|ed71|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O111|o111|NN strain|strain|NN PMK5|pmk5|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 980551|980551|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 980706|980706|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 980938|980938|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 981456|981456|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 981795|981795|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 982243|982243|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 990281|990281|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O157|o157|NN strain|strain|NN 990570|990570|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN 11044|11044|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN 11368|11368|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN 11656|11656|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN 12719|12719|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN 12929|12929|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN 13065|13065|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN 13247|13247|CD
Genomic|genomic|JJ DNA|dna|NN from|from|IN O26|o26|NN strain|strain|NN ED411|ed411|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H6|h6|NN strain|strain|NN ICC219|icc219|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H6|h6|NN strain|strain|NN ICC221|icc221|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H6|h6|NN strain|strain|NN ICC222|icc222|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H7|h7|NN strain|strain|NN st58|st58|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H7|h7|NN strain|strain|NN st957|st957|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H7|h7|NN strain|strain|NN TB182A|tb182a|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H7|h7|NN strain|strain|NN WC211|wc211|NN
Genomic|genomic|JJ DNA|dna|NN from|from|IN O55|o55|NN :|:|: H7|h7|NN strain|strain|NN WC416|wc416|NN
Genomic|genomic|JJ DNA|dna|NN isolation|isolation|NN according|accord|VBG to|to|TO Grimberg|Grimberg|NNP et|et|FW al.|al.|FW .|.|. Nucleic|nucleic|JJ acids|acid|NNS research|research|NN 1989|1989|CD ,|,|, 17|17|CD -LRB-|-lrb-|-LRB- 21|21|CD -RRB-|-rrb-|-RRB- :|:|: 8893|8893|CD
Genomic|genomic|JJ DNA|dna|NN of|of|IN all|all|DT strains|strain|NNS -LRB-|-lrb-|-LRB- degraders|degrader|NNS and|and|CC non-degraders|non-degrader|NNS -RRB-|-rrb-|-RRB- isolated|isolate|VBN individually|individually|RB and|and|CC mixed|mix|VBN in|in|IN equal|equal|JJ ratio|ratio|NN -LRB-|-lrb-|-LRB- 500ng|500ng|CD each|each|DT -RRB-|-rrb-|-RRB-
Genomic|genomic|JJ DNA|dna|NN of|of|IN EDL933|edl933|NN
Genomic|genomic|JJ DNA|dna|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW DH5α|dh5α|NN
Genomic|genomic|JJ DNA|dna|NN of|of|IN mixed|mixed|JJ culture|culture|NN containing|contain|VBG only|only|RB non-degraders|non-degraders|JJ in|in|IN equal|equal|JJ ratio|ratio|NN
Genomic|genomic|JJ DNA|dna|NN of|of|IN mixed|mixed|JJ culture|culture|NN -LRB-|-lrb-|-LRB- Degraders|degrader|NNS and|and|CC non-degraders|non-degrader|NNS in|in|IN 2:1|2:1|CD ratio|ratio|NN -RRB-|-rrb-|-RRB-
Genomic|genomic|JJ DNA|dna|NN of|of|IN mixed|mixed|JJ culture|culture|NN -LRB-|-lrb-|-LRB- Degraders|degrader|NNS :|:|: NM-05|nm-05|NN ,|,|, IITR-02|iitr-02|NN ,|,|, RHA1|rha1|NN ;|;|: Non-degraders|non-degrader|NNS :|:|: DH5α|dh5α|NN ,|,|, BL21|bl21|NN and|and|CC K12|k12|NN in|in|IN equal|equal|JJ ratio|ratio|NN -RRB-|-rrb-|-RRB-
Genomic|genomic|JJ DNA|dna|NN purified|purify|VBN from|from|IN wild|wild|JJ type|type|NN bacteri|bacteri|NN
Genomic|genomic|JJ DNA|dna|NN purified|purify|VBN from|from|IN wild|wild|JJ type|type|NN bacteria|bacterium|NNS
Genomic|genomic|JJ DNA|dna|NN served|serve|VBD as|as|IN a|a|DT universal|universal|JJ reference|reference|NN
Genomic|genomic|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN by|by|IN standard|standard|JJ phenol-chloroform|phenol-chloroform|NN method|method|NN -LRB-|-lrb-|-LRB- Sambrook|Sambrook|NNP ,|,|, J|J|NNP ,|,|, Molecular|molecular|JJ Cloning|cloning|NN ,|,|, 3rd|3rd|JJ Edition|edition|NN -RRB-|-rrb-|-RRB-
Genomic|genomic|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN from|from|IN 4|4|CD bacteria|bacterium|NNS strains|strain|NNS .|.|. Strains|strain|NNS Fibrobacter|fibrobacter|JJ succinogenes|succinogene|NNS S85|s85|NN -LRB-|-lrb-|-LRB- ATCC|atcc|NN 19169|19169|CD -RRB-|-rrb-|-RRB- ,|,|, Ruminococcus|ruminococcus|NN albus|albus|NN 20|20|CD -LRB-|-lrb-|-LRB- ATCC|atcc|NN 27211|27211|CD -RRB-|-rrb-|-RRB- and|and|CC Bacteroides|bacteroide|NNS xylanisolvens|xylanisolven|NNS XB1A|xb1a|NN -LRB-|-lrb-|-LRB- DSM|DSM|NNP 18836T|18836T|NNP -RRB-|-rrb-|-RRB- were|be|VBD grown|grow|VBN 15|15|CD h|h|NN under|under|IN strictly|strictly|RB anaerobic|anaerobic|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- Hungate|Hungate|NNP ,|,|, 1950|1950|CD -RRB-|-rrb-|-RRB- in|in|IN a|a|DT complex|complex|JJ medium|medium|NN containing|contain|VBG 20|20|CD %|%|NN of|of|IN clarified|clarify|VBN rumen|ruman|NNS fluid|fluid|NN -LRB-|-lrb-|-LRB- Béra-Maillet|béra-maillet|JJ et|et|FW al.|al.|FW ,|,|, 2000|2000|CD -RRB-|-rrb-|-RRB- and|and|CC 0.2|0.2|CD g|g|NN of|of|IN cellobiose|cellobiose|NN -LRB-|-lrb-|-LRB- Sigma-Aldrich|sigma-aldrich|NN -RRB-|-rrb-|-RRB- as|as|IN carbon|carbon|NN source|source|NN ,|,|, at|at|IN 39|39|CD °C|°c|NN for|for|IN the|the|DT two|two|CD first|first|JJ ones|one|NNS and|and|CC 37|37|CD °C|°c|NN for|for|IN the|the|DT third|third|JJ one|one|CD .|.|. The|the|DT strain|strain|NN Escherichia|escherichia|FW coli|coli|FW K12|k12|NN -LRB-|-lrb-|-LRB- ATCC|atcc|NN 10798|10798|CD -RRB-|-rrb-|-RRB- was|be|VBD cultivated|cultivate|VBN 15|15|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN Luria-Bertani|luria-bertani|JJ medium|medium|NN under|under|IN shaking|shake|VBG and|and|CC aerobic|aerobic|JJ conditions|condition|NNS .|.|. -LRB-|-lrb-|-LRB-
Genomic|genomic|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN using|use|VBG an|a|DT SDS|sds|NN lysis/phenol/chloroform|lysis/phenol/chloroform|NN method|method|NN described|describe|VBN by|by|IN -LRB-|-lrb-|-LRB- Syn|syn|NN CK|ck|NN ,|,|, Swarup|Swarup|NNP S|s|NN -LRB-|-lrb-|-LRB- 2000|2000|CD -RRB-|-rrb-|-RRB- A|a|DT scalable|scalable|JJ protocol|protocol|NN for|for|IN the|the|DT isolation|isolation|NN of|of|IN large-sized|large-sized|JJ genomic|genomic|JJ DNA|dna|NN within|within|IN an|a|DT hour|hour|NN from|from|IN several|several|JJ bacteria|bacterium|NNS .|.|. Anal|Anal|NNP Biochem|Biochem|NNP 278|278|CD :|:|: 86-90|86-90|CD -RRB-|-rrb-|-RRB- with|with|IN slight|slight|JJ modifications|modification|NNS as|as|IN follows|follow|VBZ :|:|: subsequent|subsequent|JJ to|to|TO DNA|dna|NN precipitation|precipitation|NN ,|,|, spun|spin|VBD pellets|pellet|NNS were|be|VBD treated|treat|VBN with|with|IN 50μg|50μg|JJ mL-1|ml-1|NN DNAse-free|dnase-free|JJ RNAse|rnase|NN A|a|NN and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD min|min|NN .|.|. Samples|sample|NNS were|be|VBD then|then|RB re-extracted|re-extracted|JJ once|once|RB with|with|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN -LRB-|-lrb-|-LRB- 3:1|3:1|CD -RRB-|-rrb-|-RRB- ,|,|, once|once|RB with|with|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN -LRB-|-lrb-|-LRB- 1:1|1:1|CD -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN chloroform|chloroform|NN ,|,|, reprecipitated|reprecipitate|VBN and|and|CC then|then|RB resuspended|resuspend|VBD in|in|IN TE|TE|NNP ,|,|, pH|ph|NN 8.0|8.0|CD .|.|.
Genomic|genomic|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT Epicentre|Epicentre|NNP DNA|dna|NN extraction|extraction|NN kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocols|protocol|NNS .|.|.
Genomic|genomic|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN using|use|VBG Ultra|Ultra|NNP Clean|Clean|NNP Soil|Soil|NNP DNA|dna|NN -LRB-|-lrb-|-LRB- MoBio|mobio|NN Laboratories|Laboratories|NNPS ,|,|, Solana|Solana|NNP Beach|Beach|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|.
Genomic|genomic|JJ DNA|dna|NN was|be|VBD isolated|isolate|VBN by|by|IN lysozyme|lysozyme|NN and|and|CC proteinase|proteinase|NN K|k|NN treatment|treatment|NN .|.|.
Genomic|genomic|JJ DNA|dna|NN was|be|VBD isolated|isolate|VBN by|by|IN lysozyme|lysozyme|NN and|and|CC proteinase|proteinase|NN K|k|NN treatment|treatment|NN .|.|.
Genomic|genomic|JJ DNA|dna|NN was|be|VBD purified|purify|VBN from|from|IN exponentially|exponentially|RB growing|grow|VBG cells|cell|NNS by|by|IN lysis|lysis|NN in|in|IN lysozyme/mutanolysin|lysozyme/mutanolysin|NN ,|,|, incubation|incubation|NN in|in|IN proteinase|proteinase|NN K/SDS|k/sds|NN ,|,|, followed|follow|VBN by|by|IN a|a|DT standard|standard|JJ phenol/chloroform|phenol/chloroform|NN extraction|extraction|NN procedure|procedure|NN .|.|. Final|final|JJ pellets|pellet|NNS were|be|VBD dissolved|dissolve|VBN in|in|IN TE|TE|NNP -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN at|at|IN pH|ph|NN 8.0|8.0|CD ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- .|.|. Genomic|genomic|JJ DNA|dna|NN was|be|VBD digested|digest|VBN to|to|TO completion|completion|NN with|with|IN Sau3A1|sau3a1|NN -LRB-|-lrb-|-LRB- Promega|promega|NN -RRB-|-rrb-|-RRB- and|and|CC purified|purify|VBN by|by|IN phenol/chloroform|phenol/chloroform|NN extraction|extraction|NN .|.|. Synthesis|synthesis|NN and|and|CC degradation|degradation|NN of|of|IN RNA|rna|NN were|be|VBD stopped|stop|VBN by|by|IN adding|add|VBG 1/4|1/4|CD volume|volume|NN of|of|IN stop-solution|stop-solution|NN -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN ethanol/5|ethanol/5|CD %|%|NN phenol|phenol|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 4,000|4,000|CD rpm|rpm|NN ,|,|, 20|20|CD min|min|NN -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD °C|°c|NN and|and|CC resuspended|resuspend|VBN in|in|IN 0.5|0.5|CD mL|ml|NN of|of|IN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mg/mL|mg/ml|NN lysozyme|lysozyme|NN ,|,|, 10|10|CD %|%|NN SDS|sds|NN ,|,|, Tris-EDTA|tris-edta|JJ buffer|buffer|NN ,|,|, 3|3|CD M|m|NN sodium|sodium|NN acetate|acetate|NN ,|,|, pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- .|.|. Phenol|phenol|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD ml|ml|NN ,|,|, pH|ph|NN 4.5|4.5|CD -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN ,|,|, and|and|CC the|the|DT samples|sample|NNS were|be|VBD vortexed|vortex|VBN vigorously|vigorously|RB before|before|IN incubation|incubation|NN at|at|IN 64|64|CD °C|°c|NN for|for|IN 6|6|CD min|min|NN .|.|. After|after|IN placing|place|VBG the|the|DT samples|sample|NNS on|on|IN ice|ice|NN ,|,|, the|the|DT aqueous|aqueous|JJ layer|layer|NN was|be|VBD extracted|extract|VBN with|with|IN 1:1|1:1|CD phenol|phenol|NN :|:|: chloroform|chloroform|NN and|and|CC with|with|IN chloroform|chloroform|NN ,|,|, and|and|CC the|the|DT RNA|rna|NN was|be|VBD precipitated|precipitate|VBN with|with|IN ethanol|ethanol|NN at|at|IN -80|-80|CD °C|°c|NN .|.|. After|after|IN resuspension|resuspension|NN ,|,|, RNA|rna|NN concentration|concentration|NN and|and|CC purity|purity|NN was|be|VBD assessed|assess|VBN by|by|IN NanoDrop|NanoDrop|NNP ND-1000|ND-1000|NNP UV|uv|NN spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Nanodrop|Nanodrop|NNP Technologies|Technologies|NNPS ,|,|, Wilmingon|Wilmingon|NNP ,|,|, DE|de|NN -RRB-|-rrb-|-RRB- and|and|CC Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB .|.|.
Genomic|genomic|JJ DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG a|a|DT 20/G|20/g|NN genomic-tip|genomic-tip|JJ kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS and|and|CC was|be|VBD sonicated|sonicate|VBN to|to|TO an|a|DT average|average|JJ size|size|NN of|of|IN ~|~|NN 500|500|CD bp|bp|NN .|.|.
Genomic|genomic|JJ DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG the|the|DT Genomic-tip|genomic-tip|JJ 100/G|100/g|NN and|and|CC Genomic|genomic|JJ DNA|dna|NN buffer|buffer|NN set|set|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instruction|instruction|NN .|.|.
Genomic|genomic|JJ Library|Library|NNP of|of|IN E.|e.|FW coli|coli|FW was|be|VBD enriched|enriched|JJ via|via|IN serial|serial|NN transfers|transfer|NNS .|.|. The|the|DT cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ media|media|NNS -LRB-|-lrb-|-LRB- 5|5|CD g/L|g/l|NN glucose|glucose|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC in|in|IN increasing|increase|VBG concentration|concentration|NN of|of|IN n-butanol|n-butanol|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD ,|,|, 0.9|0.9|CD ,|,|, 1.3|1.3|CD and|and|CC 1.7|1.7|CD %|%|NN v/v|v/v|NN -RRB-|-rrb-|-RRB- .|.|.
genomic|genomic|JJ _|_|NN ref1|ref1|NN
genomic|genomic|JJ _|_|NN ref2|ref2|NN
genomic|genomic|JJ _|_|NN ref3|ref3|NN
genomic|genomic|JJ _|_|NN ref4|ref4|NN
genomic|genomic|JJ _|_|NN ref5|ref5|NN
genomic|genomic|JJ _|_|NN ref6|ref6|NN
Genomic|genomic|JJ response|response|NN analysis|analysis|NN of|of|IN E.coli|e.coli|NN during|during|IN coexpression|coexpression|NN of|of|IN a|a|DT bacteriocin|bacteriocin|NN release|release|NN protein|protein|NN
genotype|genotype|NN :|:|: 285c|285c|JJ rpoD|rpod|NN mutation|mutation|NN
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN scrambled|scramble|VBD site|site|NN 3|3|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN scrambled|scramble|VBD site|site|NN 3|3|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 1|1|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 2|2|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 2|2|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 3|3|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 3|3|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 4|4|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 4|4|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 5|5|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 5|5|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 6|6|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 7|7|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: AB1157|ab1157|NN ybbD|ybbd|NN :|:|: :|:|: parS|pars|NN site|site|NN 7|7|CD pUTC18|putc18|NN :|:|: :|:|: parB|parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: ArgR-8myc|argr-8myc|NN
genotype|genotype|NN :|:|: BW27784|bw27784|NN delta|delta|NN _|_|CD recD|recd|NN lacZ|lacz|NN :|:|: :|:|: XXX|xxx|NN mhpR|mhpr|NN :|:|: :|:|: XXX|XXX|NNP proA|proA|NNP :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN +|+|CC cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZX|laczx|NN -|-|:
genotype|genotype|NN :|:|: BW27784|bw27784|NN delta|delta|NN _|_|CD recD|recd|NN lacZ|lacz|NN :|:|: :|:|: XXX|xxx|NN mhpR|mhpr|NN :|:|: :|:|: XXX|XXX|NNP proA|proA|NNP :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN :|:|: :|:|: pal246|pal246|NN cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZX|laczx|NN -|-|:
genotype|genotype|NN :|:|: BW27784|bw27784|NN lacZ|lacz|NN :|:|: :|:|: XXX|xxx|NN mhpR|mhpr|NN :|:|: :|:|: XXX|XXX|NNP proA|proA|NNP :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN +|+|CC cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZX|laczx|NN -|-|:
genotype|genotype|NN :|:|: BW27784|bw27784|NN lacZ|lacz|NN :|:|: :|:|: XXX|xxx|NN mhpR|mhpr|NN :|:|: :|:|: XXX|XXX|NNP proA|proA|NNP :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN :|:|: :|:|: pal246|pal246|NN cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZX|laczx|NN -|-|:
genotype|genotype|NN :|:|: crpfis|crpfis|NN mutant|mutant|JJ background|background|NN
genotype|genotype|NN :|:|: crp|crp|NN mutant|mutant|JJ background|background|NN
genotype|genotype|NN :|:|: CV108|cv108|NN
genotype|genotype|NN :|:|: cya|cya|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: cya|cya|NN mutant|mutant|JJ background|background|NN
genotype|genotype|NN :|:|: del-fis|del-fis|JJ
genotype|genotype|NN :|:|: del-hns|del-hns|JJ
genotype|genotype|NN :|:|: del|del|DT rpoS|rpos|NN
genotype|genotype|NN :|:|: del|del|DT rsd|rsd|NN
genotype|genotype|NN :|:|: del|del|DT rsd|rsd|NN ;|;|: del|del|DT ssrS|ssrs|NN
genotype|genotype|NN :|:|: del|del|DT ssrS|ssrs|NN
genotype|genotype|NN :|:|: delta-cra|delta-cra|NN Knock-out|knock-out|JJ strain|strain|NN
genotype|genotype|NN :|:|: delta-crp|delta-crp|JJ Knock-out|knock-out|JJ strain|strain|NN
genotype|genotype|NN :|:|: delta|delta|NN dicF|dicf|NN ,|,|, lacIq|laciq|NN
genotype|genotype|NN :|:|: delta-fis|delta-fis|JJ
genotype|genotype|NN :|:|: deltahmp|deltahmp|JJ deltanrfA|deltanrfa|NN deltanorVW|deltanorvw|NN
genotype|genotype|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- hns|hn|VBZ
genotype|genotype|NN :|:|: delta-hns|delta-hn|NNS
genotype|genotype|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- nusG|nusg|NN
genotype|genotype|NN :|:|: delta|delta|NN _|_|CD ompR|ompr|NN
genotype|genotype|NN :|:|: delta-rac|delta-rac|JJ
genotype|genotype|NN :|:|: delta|delta|NN _|_|SYM recG263|recg263|NN :|:|: :|:|: KanR|kanr|NN lacZ|lacz|NN :|:|: :|:|: χχχ|χχχ|NN mhpR|mhpr|NN :|:|: :|:|: χχχ|χχχ|NN proA|proa|NN :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN +|+|CC cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZχ|laczχ|NN -|-|:
genotype|genotype|NN :|:|: delta|delta|NN _|_|SYM recG263|recg263|NN :|:|: :|:|: KanR|kanr|NN lacZ|lacz|NN :|:|: :|:|: χχχ|χχχ|NN mhpR|mhpr|NN :|:|: :|:|: χχχ|χχχ|NN proA|proa|NN :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN :|:|: :|:|: pal246|pal246|NN cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZχ|laczχ|NN -|-|:
genotype|genotype|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- rho|rho|NN
genotype|genotype|NN :|:|: DH1|dh1|NN ΔhisC|δhisc|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-rfp-tetR-zeocinr|Ptrc-rfp-tetR-zeocinr|NNP ΔgalK|ΔgalK|NNP :|:|: :|:|: PtetA-gfp-hisC-kanr|PtetA-gfp-hisC-kanr|NNP
genotype|genotype|NN :|:|: DH1|dh1|NN ΔhisC|δhisc|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-rfp-tetR-zeocinr|Ptrc-rfp-tetR-zeocinr|NNP ΔgalK|ΔgalK|NNP :|:|: :|:|: PtetA-gfp-kanr|PtetA-gfp-kanr|NNP
genotype|genotype|NN :|:|: dnaC2|dnac2|NN
genotype|genotype|NN :|:|: dnaC2|dnac2|NN ,|,|, pMQ430|pmq430|NN
Genotype|Genotype|NNP :|:|: E.|e.|FW coli|coli|FW K12|k12|NN
genotype|genotype|NN :|:|: E.|e.|FW coli|coli|FW -LSB-|-lsb-|-LRB- supE44|supe44|NN hsdS20|hsds20|NN -LRB-|-lrb-|-LRB- rB-mB|rb-mb|NN -|-|: -RRB-|-rrb-|-RRB- recA13|reca13|NN ara-14|ara-14|NN proA2|proa2|NN lacY1|lacy1|NN galK2|galk2|NN rpsL20|rpsl20|NN xyl-5|xyl-5|NN mtl-1|mtl-1|NN -RSB-|-rsb-|-RRB-
genotype|genotype|NN :|:|: ethanol-tolerant|ethanol-tolerant|JJ mutant|mutant|JJ E1|e1|NN of|of|IN IrrE|irre|NN
genotype|genotype|NN :|:|: EvgSc|evgsc|NN KO|ko|NN
genotype|genotype|NN :|:|: EvgSc|evgsc|NN ompR|ompr|NN KO|ko|NN
genotype|genotype|NN :|:|: ∆|∆|CD fadE|fade|NN with|with|IN overexpression|overexpression|NN of|of|IN `|`|`` tesA|tesa|NN and|and|CC MlfabH|mlfabh|NN via|via|IN an|a|DT IPTG-inudcible|iptg-inudcible|JJ promoter|promoter|NN
genotype|genotype|NN :|:|: ∆|∆|CD fadE|fade|NN with|with|IN overexpression|overexpression|NN of|of|IN `|`|`` tesA|tesa|NN via|via|IN an|a|DT IPTG-inudcible|iptg-inudcible|JJ promoter|promoter|NN
genotype|genotype|NN :|:|: fis|fi|NNS :|:|: :|:|: 3xFLAG|3xflag|NN
genotype|genotype|NN :|:|: fis|fis|NN mutant|mutant|JJ background|background|NN
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- fis|fi|VBZ :|:|: :|:|: frt-kan-frt|frt-kan-frt|JJ
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- hns|hn|NNS :|:|: :|:|: frt|frt|SYM -|-|: kan|kan|SYM -|-|: frt|frt|NN
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- matP|matp|NN :|:|: :|:|: frt-cam-frt|frt-cam-frt|JJ
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- mukB|mukb|NN :|:|: :|:|: frt|frt|SYM -|-|: kan|kan|NN
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- zapB|zapb|NN :|:|: :|:|: frt-kan-frt|frt-kan-frt|JJ
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN matP|matp|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- C20|c20|NN :|:|: :|:|: frt-cam-frt|frt-cam-frt|JJ
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN phi80|phi80|NN +|+|CC -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- hupA|hupa|NN :|:|: :|:|: frt|frt|SYM -|-|: kan|kan|SYM -|-|: frt|frt|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- hupB|hupb|NN :|:|: :|:|: frt-cam-frt|frt-cam-frt|JJ
genotype|genotype|NN :|:|: F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1phi80|rph-1phi80|NN +|+|CC -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- mukB|mukb|NN :|:|: :|:|: frt|frt|SYM -|-|: apra|apra|NN -LSB-|-lsb-|-LRB- delta|delta|NN -RSB-|-rsb-|-RRB- matP|matp|NN :|:|: :|:|: frt-cam-frt|frt-cam-frt|JJ
genotype|genotype|NN :|:|: F|f|NN -|-|: ,|,|, lambda|lambda|NN -|-|: ,|,|, rph-1|rph-1|NN
Genotype|Genotype|NNP :|:|: F|f|NN -|-|: ompT|ompt|NN hsdSB|hsdsb|NN -LRB-|-lrb-|-LRB- rB-mB|rb-mb|NN -|-|: -RRB-|-rrb-|-RRB- gal|gal|NN dcm|dcm|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: furfural-tolerant|furfural-tolerant|JJ mutant|mutant|JJ F1-37|f1-37|NN of|of|IN IrrE|irre|NN
genotype|genotype|NN :|:|: Fusion|fusion|NN of|of|IN venus|venus|NN to|to|TO the|the|DT 3|3|CD '|'|'' end|end|NN of|of|IN rpoC|rpoc|NN in|in|IN E.|e.|FW coli|coli|FW wild-type|wild-type|JJ MG1655|mg1655|NN
genotype|genotype|NN :|:|: gadE-8myc|gade-8myc|NN
genotype|genotype|NN :|:|: gadW-8myc|gadw-8myc|NN
genotype|genotype|NN :|:|: gadX-8myc|gadx-8myc|NN
genotype|genotype|NN :|:|: Galaxy1|galaxy1|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pHDB3|phdb3|NN _|_|CD 5|5|CD -RSB-|-rsb-|-RRB-
genotype|genotype|NN :|:|: Galaxy2|galaxy2|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pLCV1|plcv1|NN _|_|CD 5|5|CD -RSB-|-rsb-|-RRB-
genotype|genotype|NN :|:|: Galaxy3|galaxy3|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pLCV1|plcv1|NN _|_|NN 10|10|CD -RSB-|-rsb-|-RRB-
genotype|genotype|NN :|:|: Galaxy4|galaxy4|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pHDB3|phdb3|NN _|_|CD 20|20|CD -RSB-|-rsb-|-RRB-
genotype|genotype|NN :|:|: Galaxy5|galaxy5|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pLCV1|plcv1|NN _|_|CD 20|20|CD -RSB-|-rsb-|-RRB-
genotype|genotype|NN :|:|: Galaxy6|galaxy6|NN -|-|: -LSB-|-lsb-|-LRB- CV104|cv104|NN _|_|CD pHDB3|phdb3|NN _|_|NN 10|10|CD -RSB-|-rsb-|-RRB-
genotype|genotype|NN :|:|: GATC-cluster|gatc-cluster|NN :|:|: :|:|: hisA|hisA|NNP
genotype|genotype|NN :|:|: GATC-cluster|gatc-cluster|NN :|:|: :|:|: srlA|srla|NN
genotype|genotype|NN :|:|: GATC-cluster|gatc-cluster|NN :|:|: :|:|: ter|ter|NN
genotype|genotype|NN :|:|: GATC-cluster|gatc-cluster|NN :|:|: :|:|: tnaA|tnaa|NN
genotype|genotype|NN :|:|: gss|gss|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: hns|hn|NNS :|:|: :|:|: 3xFLAG|3xflag|NN
genotype|genotype|NN :|:|: lacZ|lacz|NN :|:|: :|:|: χχχ|χχχ|NN mhpR|mhpr|NN :|:|: :|:|: χχχ|χχχ|NN proA|proa|NN :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN +|+|CC cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZχ|laczχ|NN -|-|:
genotype|genotype|NN :|:|: lacZ|lacz|NN :|:|: :|:|: χχχ|χχχ|NN mhpR|mhpr|NN :|:|: :|:|: χχχ|χχχ|NN proA|proa|NN :|:|: :|:|: ISceIcs|isceic|NNS tsx|tsx|NN :|:|: :|:|: ISceIcs|isceic|NNS PBAD-sbcDC|pbad-sbcdc|NN lacZ|lacz|NN :|:|: :|:|: pal246|pal246|NN cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacIq|laciq|NN lacZχ|laczχ|NN -|-|:
genotype|genotype|NN :|:|: Lrp-8myc|lrp-8myc|JJ
genotype|genotype|NN :|:|: luxS|luxs|NN
genotype|genotype|NN :|:|: ∆|∆|CD mazEF|mazef|NN
genotype|genotype|NN :|:|: ∆|∆|SYM mazEFlexA3|mazeflexa3|NN
genotype|genotype|NN :|:|: mfd|mfd|SYM -|-|:
genotype|genotype|NN :|:|: Mfd|mfd|NN +|+|CC +|+|CC
genotype|genotype|NN :|:|: MG1655|mg1655|NN
genotype|genotype|NN :|:|: MG1655|mg1655|NN DdksA|ddksa|NN
genotype|genotype|NN :|:|: MG1655|mg1655|NN del|del|FW ssrS|ssrs|FW
genotype|genotype|NN :|:|: MG1655|mg1655|NN wild-type|wild-type|JJ
genotype|genotype|NN :|:|: mutant|mutant|JJ hhahha2|hhahha2|NN
genotype|genotype|NN :|:|: mutant|mutant|JJ hhs|hh|NNS
genotype|genotype|NN :|:|: mutant|mutant|JJ hns2|hns2|NN
genotype|genotype|NN :|:|: mutant|mutant|JJ hnshns2|hnshns2|NN
genotype|genotype|NN :|:|: n/a|n/a|NN
genotype|genotype|NN :|:|: ompR-8myc|ompr-8myc|NN
genotype|genotype|NN :|:|: ompR|ompr|NN deletion|deletion|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: ompR|ompr|NN KO|ko|NN
genotype|genotype|NN :|:|: Pck|pck|NN over-expressed|over-expressed|JJ
genotype|genotype|NN :|:|: pHDB3|phdb3|NN
genotype|genotype|NN :|:|: plasmid|plasmid|NN cured|cure|VBD strain|strain|NN
genotype|genotype|NN :|:|: pLCV1|plcv1|NN
genotype|genotype|NN :|:|: PNPase|pnpase|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: PurR-8myc|purr-8myc|NN
genotype|genotype|NN :|:|: RNase|rnase|NN II|ii|CD mutant|mutant|JJ
genotype|genotype|NN :|:|: RNase|rnase|NN R|r|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: rne-3071|rne-3071|NN -LRB-|-lrb-|-LRB- ts|t|NNS -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: rne|rne|NN wild-type|wild-type|JJ
genotype|genotype|NN :|:|: rng|rng|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: rng|rng|NN wild-type|wild-type|JJ
genotype|genotype|NN :|:|: rpoC|rpoc|NN K370|k370|NN _|_|CD A396dup|a396dup|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: rpoH-8myc|rpoh-8myc|NN
genotype|genotype|NN :|:|: rpoN|rpon|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- EcJR-8|ecjr-8|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: rpoS|rpos|NN
genotype|genotype|NN :|:|: rpoS|rpos|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: SgrR|sgrr|NN
genotype|genotype|NN :|:|: sgrS|sgrs|NN
genotype|genotype|NN :|:|: TolC|tolc|NN defective|defective|JJ -LRB-|-lrb-|-LRB- TolC|tolc|NN -|-|: -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: triclosan|triclosan|NN tolerant|tolerant|JJ mutant|mutant|JJ
genotype|genotype|NN :|:|: TrpR-8myc|trpr-8myc|NN
genotype|genotype|NN :|:|: tynA|tyna|NN -|-|:
genotype/varation|genotype/varation|NN :|:|: mutant|mutant|JJ
genotype/varation|genotype/varation|NN :|:|: wild-type|wild-type|JJ
genotype/variaion|genotype/variaion|NN :|:|: bla|bla|FW
genotype/variaion|genotype/variaion|NN :|:|: lacZ|lacz|NN
genotype/variaion|genotype/variaion|NN :|:|: mMaple3|mmaple3|NN
genotype/variaion|genotype/variaion|NN :|:|: Mut|mut|NN
genotype/variaion|genotype/variaion|NN :|:|: neo|neo|NN
genotype/variaion|genotype/variaion|NN :|:|: phoA|phoa|NN
genotype/variaion|genotype/variaion|NN :|:|: WT|WT|NNP
genotype/variaion|genotype/variaion|NN :|:|: WTKas|wtka|NNS
genotype/variation|genotype/variation|NN :|:|: 42|42|CD deletions|deletion|NNS
genotype/variation|genotype/variation|NN :|:|: 42|42|CD deletions|deletion|NNS ,|,|, ΔnusA|δnusa|NN *|*|SYM
genotype/variation|genotype/variation|NN :|:|: 42|42|CD deletions|deletion|NNS ,|,|, ΔnusG|δnusg|NN
genotype/variation|genotype/variation|NN :|:|: 43|43|CD deletions|deletion|NNS ,|,|, ΔnusA|δnusa|NN *|*|SYM
genotype/variation|genotype/variation|NN :|:|: 43|43|CD deletions|deletion|NNS ,|,|, ΔnusG|δnusg|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN deltamatP|deltamatp|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN matP-3xflag|matp-3xflag|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN mukB-3xflag|mukb-3xflag|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN mukB-3xflag|mukb-3xflag|NN deltamatP|deltamatp|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN mukBDA-3xflag|mukbda-3xflag|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN mukBEQ-3xflag|mukbeq-3xflag|NN
genotype/variation|genotype/variation|NN :|:|: AB1157|ab1157|NN mukBEQ-3xflag|mukbeq-3xflag|NN deltamatP|deltamatp|NN
genotype/variation|genotype/variation|NN :|:|: Adaptive|adaptive|JJ mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: adhE|adhe|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: AR1|ar1|NN -|-|: /|/|: AR2|ar2|SYM -|-|:
genotype/variation|genotype/variation|NN :|:|: aspC|aspc|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: coding|code|VBG for|for|IN QnrS1|qnrs1|NN
genotype/variation|genotype/variation|NN :|:|: Combined|combine|VBN input|input|NN
genotype/variation|genotype/variation|NN :|:|: cpxA|cpxa|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: cra-8myc-tagged|cra-8myc-tagged|JJ
genotype/variation|genotype/variation|NN :|:|: cra|cra|NN KO|ko|NN ;|;|: BW25113|bw25113|NN Dcra|dcra|NN
genotype/variation|genotype/variation|NN :|:|: cysA|cysa|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: cysG|cysg|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: cysH|cysh|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: cysQ|cysq|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: dcd|dcd|NN knockout|knockout|JJ
genotype/variation|genotype/variation|NN :|:|: delta|delta|NN _|_|SYM cra|cra|FW
genotype/variation|genotype/variation|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- cspABCEG|cspabceg|NN
genotype/variation|genotype/variation|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- cspABEG|cspabeg|NN
genotype/variation|genotype/variation|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- cspBG|cspbg|NN
genotype/variation|genotype/variation|NN :|:|: delta-gadE|delta-gade|NN
genotype/variation|genotype/variation|NN :|:|: delta-gadW|delta-gadw|NN
genotype/variation|genotype/variation|NN :|:|: delta-gadX|delta-gadx|NN
genotype/variation|genotype/variation|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- lacZ|lacz|NN ,|,|, -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- tonB|tonb|NN ,|,|, -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- feoA|feoa|NN ,|,|, -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- zupT|zupt|NN K12|k12|NN
genotype/variation|genotype/variation|NN :|:|: delta-oxyR|delta-oxyr|NN
genotype/variation|genotype/variation|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- perC|perc|NN :|:|: :|:|: kanR|kanr|NN ,|,|, coisogenic|coisogenic|JJ to|to|TO WT|wt|JJ
genotype/variation|genotype/variation|NN :|:|: delta|delta|NN ptsN|ptsn|NN
genotype/variation|genotype/variation|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- rnr|rnr|NN
genotype/variation|genotype/variation|NN :|:|: delta-soxR|delta-soxr|NN
genotype/variation|genotype/variation|NN :|:|: delta-soxS|delta-soxs|NN
genotype/variation|genotype/variation|NN :|:|: -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- tonB|tonb|NN ,|,|, -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- feoA|feoa|NN ,|,|, -LCB-|-lcb-|-LRB- delta|delta|NN -RCB-|-rcb-|-RRB- zupT|zupt|NN K12|k12|NN
genotype/variation|genotype/variation|NN :|:|: DH1DilvE|dh1dilve|NN :|:|: :|:|: -LRB-|-lrb-|-LRB- dsred.T3-cat|dsred.t3-cat|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: DH1DleuB|dh1dleub|NN :|:|: :|:|: -LRB-|-lrb-|-LRB- gfpuv5-Kmr|gfpuv5-kmr|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: DH1|dh1|NN -LRB-|-lrb-|-LRB- GB|gb|NN :|:|: AP012030|ap012030|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: dnaJ|dnaj|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: DnaK|dnak|NN deletant|deletant|JJ
genotype/variation|genotype/variation|NN :|:|: EDL|edl|NN 933|933|CD
genotype/variation|genotype/variation|NN :|:|: empty|empty|JJ vector|vector|NN -LRB-|-lrb-|-LRB- pCA24N|pca24n|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: entF|entf|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: expressing|express|VBG pFlagRhlBP238L|pflagrhlbp238l|NN
genotype/variation|genotype/variation|NN :|:|: expressing|express|VBG pFlagRhlBwt|pflagrhlbwt|NN
genotype/variation|genotype/variation|NN :|:|: fadR|fadr|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: fepA|fepa|NN knockout|knockout|JJ
genotype/variation|genotype/variation|NN :|:|: flhD|flhd|NN
genotype/variation|genotype/variation|NN :|:|: fliY|fliy|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: fur-8myc|fur-8myc|JJ
genotype/variation|genotype/variation|NN :|:|: fur-knockout|fur-knockout|JJ mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: gabT|gabt|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: galE|gale|NN knockout|knockout|JJ
genotype/variation|genotype/variation|NN :|:|: galT|galt|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: gcvT|gcvt|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: harboring|harbor|VBG ArcA-8myc|arca-8myc|JJ
genotype/variation|genotype/variation|NN :|:|: harboring|harbor|VBG Fnr-8myc|fnr-8myc|JJ
genotype/variation|genotype/variation|NN :|:|: hfq|hfq|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: Irp|irp|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: K100Q|k100q|NN
genotype/variation|genotype/variation|NN :|:|: K100R|k100r|NN
genotype/variation|genotype/variation|NN :|:|: K-12|k-12|NN delta-rnr|delta-rnr|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- JW5741-1|jw5741-1|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: K-12|k-12|NN wild|wild|JJ type|type|NN
genotype/variation|genotype/variation|NN :|:|: kefB|kefb|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: khc|khc|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: lacA|laca|NN knockout|knockout|JJ
genotype/variation|genotype/variation|NN :|:|: lacking|lack|VBG the|the|DT small|small|JJ RNA|rna|NN RyhB|ryhb|NN
genotype/variation|genotype/variation|NN :|:|: lacking|lack|VBG the|the|DT transcription|transcription|NN factor|factor|NN Fur|Fur|NNP
genotype/variation|genotype/variation|NN :|:|: lacking|lack|VBG the|the|DT transcription|transcription|NN factor|factor|NN Fur|Fur|NNP and|and|CC the|the|DT small|small|JJ RNA|rna|NN RyhB|ryhb|NN
genotype/variation|genotype/variation|NN :|:|: lplA|lpla|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: LuxS|luxs|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: marR|marr|NN deletion|deletion|NN and|and|CC coding|code|VBG for|for|IN QnrS1|qnrs1|NN
genotype/variation|genotype/variation|NN :|:|: MC4100|mc4100|NN ∆|∆|NN tig|tig|NN :|:|: :|:|: kan|kan|FW pTig-TEV-Avi|ptig-tev-avi|FW
genotype/variation|genotype/variation|NN :|:|: MG1655star|mg1655star|NN
genotype/variation|genotype/variation|NN :|:|: mgtA|mgta|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: mhpD|mhpd|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: mntR|mntr|NN KO|ko|NN ;|;|: BW25113|bw25113|NN DmntR|dmntr|NN
genotype/variation|genotype/variation|NN :|:|: mqsR/pBS|mqsr/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: mqsR|mqsr|NN
genotype/variation|genotype/variation|NN :|:|: mqsR/pBS|mqsr/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: mqsR|mqsr|NN 2-1|2-1|CD
genotype/variation|genotype/variation|NN :|:|: mutant|mutant|JJ M.HpyAVIB|m.hpyavib|NN
genotype/variation|genotype/variation|NN :|:|: nac|nac|NN KO|ko|NN ;|;|: BW25113|bw25113|NN Dnac|dnac|NN
genotype/variation|genotype/variation|NN :|:|: null|null|JJ polyphosphate|polyphosphate|NN metabolism|metabolism|NN
genotype/variation|genotype/variation|NN :|:|: overexpression|overexpression|NN of|of|IN arT|art|NN -LRB-|-lrb-|-LRB- pCA24N|pca24n|NN _|_|CD arT|art|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: overexpression|overexpression|NN of|of|IN dosP|dosp|NN -LRB-|-lrb-|-LRB- pCA24N|pca24n|NN _|_|CD dosP|dosp|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: overexpression|overexpression|NN of|of|IN empty|empty|JJ vector|vector|NN -LRB-|-lrb-|-LRB- pCA24N|pca24n|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: oxyR-8myc-tagged|oxyr-8myc-tagged|JJ
genotype/variation|genotype/variation|NN :|:|: PEN205|pen205|NN
genotype/variation|genotype/variation|NN :|:|: pFlag-only|pflag-only|NN control|control|NN
genotype/variation|genotype/variation|NN :|:|: pgi|pgi|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: PhoB|phob|NN _|_|CD FLAG|flag|NN
genotype/variation|genotype/variation|NN :|:|: PhoB|phob|NN knock-out|knock-out|JJ
genotype/variation|genotype/variation|NN :|:|: polyphosphate|polyphosphate|NN accumulation|accumulation|NN
genotype/variation|genotype/variation|NN :|:|: polyphosphate|polyphosphate|NN depleted|deplete|VBN levels|level|NNS
genotype/variation|genotype/variation|NN :|:|: ppk|ppk|NN knockout|knockout|JJ
genotype/variation|genotype/variation|NN :|:|: putP|putp|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: rfbA|rfba|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: rnc|rnc|SYM -|-|: deletion|deletion|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: sdhA|sdha|NN deletion|deletion|NN mutant|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: sdhC|sdhc|NN knockout|knockout|JJ
genotype/variation|genotype/variation|NN :|:|: Ser83Leu|ser83leu|NN substitution|substitution|NN in|in|IN GyrA|gyra|NN and|and|CC coding|code|VBG for|for|IN QnrS1|qnrs1|NN
genotype/variation|genotype/variation|NN :|:|: soxR-8myc-tagged|soxr-8myc-tagged|JJ
genotype/variation|genotype/variation|NN :|:|: soxS-8myc-tagged|soxs-8myc-tagged|JJ
genotype/variation|genotype/variation|NN :|:|: trpD|trpd|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: ugpC|ugpc|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: W3110|w3110|NN rpoC-6xHis|rpoc-6xhis|NN :|:|: :|:|: kan|kan|FW gal490|gal490|FW
genotype/variation|genotype/variation|NN :|:|: W3110|w3110|NN rpoC-6xHis|rpoc-6xhis|NN :|:|: :|:|: kan|kan|NN greA|grea|NN :|:|: :|:|: tet|tet|NN ,|,|, greB|greb|NN :|:|: :|:|: amp|amp|NN
genotype/variation|genotype/variation|NN :|:|: wild|wild|JJ type|type|NN
genotype/variation|genotype/variation|NN :|:|: wild-type|wild-type|JJ
genotype/variation|genotype/variation|NN :|:|: Wild-type|wild-type|JJ
genotype/variation|genotype/variation|NN :|:|: wild|wild|JJ type|type|NN -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB-
genotype/variation|genotype/variation|NN :|:|: wild|wild|JJ type|type|NN ;|;|: MG1655|mg1655|NN
genotype/variation|genotype/variation|NN :|:|: wild|wild|JJ type|type|NN M.HpyAVIB|m.hpyavib|NN
genotype/variation|genotype/variation|NN :|:|: Wild|Wild|NNP type|type|NN strain|strain|NN
genotype/variation|genotype/variation|NN :|:|: WT|WT|NNP
genotype/variation|genotype/variation|NN :|:|: wzc|wzc|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: ydcR|ydcr|NN -LRB-|-lrb-|-LRB- b1439|b1439|NN -RRB-|-rrb-|-RRB- MUTANT|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: yghD|yghd|NN knockout|knockout|NN
genotype/variation|genotype/variation|NN :|:|: yjiR|yjir|NN -LRB-|-lrb-|-LRB- b4340|b4340|NN -RRB-|-rrb-|-RRB- MUTANT|mutant|JJ
genotype/variation|genotype/variation|NN :|:|: ΔarcA|δarca|NN
genotype/variation|genotype/variation|NN :|:|: Δfnr|Δfnr|NNP
genotype/variation|genotype/variation|NN :|:|: Δfur|Δfur|NNP
genotype/variation|genotype/variation|NN :|:|: Δhns|δhns|NNS
genotype/variation|genotype/variation|NN :|:|: ΔmqsRA|δmqsra|NN
genotype/variation|genotype/variation|NN :|:|: Δrac|Δrac|NNP
genotype/variation|genotype/variation|NN :|:|: Δrac|Δrac|NNP ΔnusG|ΔnusG|NNP
genotype/variation|genotype/variation|NN :|:|: σ70|σ70|NN mutation|mutation|NN
genotype|genotype|NN :|:|: wildtype|wildtype|JJ
genotype|genotype|NN :|:|: wild|wild|JJ type|type|NN
genotype|genotype|NN :|:|: wild|wild|JJ _|_|NN type|type|NN
genotype|genotype|NN :|:|: wild-type|wild-type|JJ
genotype|genotype|NN :|:|: Wildtype|wildtype|JJ
genotype|genotype|NN :|:|: Wild-type|wild-type|JJ
genotype|genotype|NN :|:|: Wild|Wild|NNP Type|type|NN
genotype|genotype|NN :|:|: wild|wild|JJ type|type|NN IrrE|irre|NN
genotype|genotype|NN :|:|: Wild-type|wild-type|JJ strain|strain|NN
genotype|genotype|NN :|:|: Wildtype|wildtype|NN with|with|IN vector|vector|NN
genotype|genotype|NN :|:|: wt|wt|JJ
genotype|genotype|NN :|:|: WT|WT|NNP
genotype|genotype|NN :|:|: yajL|yajl|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: ybjN|ybjn|NN mutant|mutant|JJ
genotype|genotype|NN :|:|: ybjN|ybjn|NN over-expression|over-expression|NN
genotype|genotype|NN :|:|: ΔbolA|δbola|NN
genotype|genotype|NN :|:|: ΔrpoN|δrpon|NN
genotype|genotype|NN :|:|: ΔrpoS|δrpos|NN
genotype|genotype|NN :|:|: ΔseqA|δseqa|NN
genotype|genotype|NN :|:|: Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB-
genotype|genotype|NN :|:|: Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN
genotype|genotype|NN :|:|: Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN
genotyp/variation|genotyp/variation|NN :|:|: deltacrp|deltacrp|JJ JW5702-4|jw5702-4|NN background|background|NN with|with|IN a|a|DT K100Q|k100q|NN mutant|mutant|NN of|of|IN CRP|crp|NN -LRB-|-lrb-|-LRB- CRP|crp|NN Q|Q|NNP -RRB-|-rrb-|-RRB- inserted|insert|VBN into|into|IN paaH|paah|NN gene|gene|NN locus|locus|NN
genotyp/variation|genotyp/variation|NN :|:|: deltacrp|deltacrp|JJ JW5702-4|jw5702-4|NN background|background|NN with|with|IN a|a|DT K100R|k100r|NN mutant|mutant|NN of|of|IN CRP|crp|NN -LRB-|-lrb-|-LRB- CRP|crp|NN R|r|NN -RRB-|-rrb-|-RRB- inserted|insert|VBN into|into|IN paaH|paah|NN gene|gene|NN locus|locus|NN
genotyp/variation|genotyp/variation|NN :|:|: deltacrp|deltacrp|JJ JW5702-4|jw5702-4|NN background|background|NN with|with|IN a|a|DT wild|wild|JJ type|type|NN CRP|crp|NN -LRB-|-lrb-|-LRB- CRP|crp|NN N|n|NN -RRB-|-rrb-|-RRB- inserted|insert|VBN into|into|IN paaH|paah|NN gene|gene|NN locus|locus|NN
genotyp/variation|genotyp/variation|NN :|:|: wild|wild|JJ type|type|NN
Genowiz|genowiz|NN 4.0.5.6|4.0.5.6|CD normalized|normalize|VBD ,|,|, background|background|NN subtracted|subtract|VBD data|datum|NNS obtained|obtain|VBN from|from|IN log2|log2|NN of|of|IN processed|process|VBN Red|Red|NNP signal/processed|signal/processed|VBD Green|Green|NNP signal|signal|NN .|.|. Agilent|Agilent|NNP software|software|NN was|be|VBD used|use|VBN .|.|.
genoype|genoype|NN :|:|: dFNR|dfnr|NN
genoype|genoype|NN :|:|: Wild-Type|wild-type|JJ
Gentamicin-1|gentamicin-1|NN ,|,|, biological|biological|JJ rep1|rep1|NN
Gentamicin-2|gentamicin-2|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Gentamicin-3|gentamicin-3|NN ,|,|, biological|biological|JJ rep3|rep3|NN
gentamycin|gentamycin|NN concentration|concentration|NN -LRB-|-lrb-|-LRB- ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- :|:|: 25|25|CD
gentamycin|gentamycin|NN concentration|concentration|NN -LRB-|-lrb-|-LRB- ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- :|:|: 50|50|CD
gentamycin|gentamycin|NN concentration|concentration|NN -LRB-|-lrb-|-LRB- ug/ml|ug/ml|NN -RRB-|-rrb-|-RRB- :|:|: 75|75|CD
Germfree|germfree|JJ rat|rat|NN 's|'s|POS caecum|caecum|NN ,|,|, biological|biological|JJ rep1|rep1|NN
Germfree|germfree|JJ rat|rat|NN 's|'s|POS caecum|caecum|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Germfree|germfree|JJ rat|rat|NN 's|'s|POS caecum|caecum|NN ,|,|, biological|biological|JJ rep3|rep3|NN
get|get|VBP raw|raw|JJ counts|count|NNS for|for|IN reads|read|VBZ mapped|map|VBN with|with|IN htseq-count|htseq-count|JJ
GGG10|ggg10|NN ,|,|, steady-state|steady-state|JJ continuous|continuous|JJ cultured|culture|VBN experimental|experimental|JJ samples|sample|NNS at|at|IN 37|37|CD °C|°c|NN
GGG10|ggg10|NN ,|,|, steady-state|steady-state|JJ continuous|continuous|JJ cultured|culture|VBN experimental|experimental|JJ samples|sample|NNS at|at|IN 37|37|CD °C|°c|NN and|and|CC then|then|RB 15|15|CD minutes|minute|NNS heatshock|heatshock|NN at|at|IN 50|50|CD °C|°c|NN
GHA507|gha507|NN
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|NNP Exp|Exp|NNP
GLBRCE1|glbrce1|NN ,|,|, ACSH|ACSH|NNP ,|,|, Exp|Exp|NNP
GLBRCE1|GLBRCE1|NNP _|_|NNP ACSH|ACSH|NNP _|_|VBD Exp|Exp|NNP _|_|SYM rep318|rep318|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|NNP Exp|Exp|NNP _|_|SYM rep320|rep320|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|NNP Exp|Exp|NNP _|_|SYM rep327|rep327|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|NNP Stat|stat|NN
GLBRCE1|glbrce1|NN ,|,|, ACSH|ACSH|NNP ,|,|, Stat1|stat1|NN
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|SYM Stat1|stat1|NN _|_|CD rep318|rep318|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|SYM Stat1|stat1|NN _|_|CD rep320|rep320|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|SYM Stat1|stat1|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, ACSH|ACSH|NNP ,|,|, Stat2|stat2|NN
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|SYM Stat2|stat2|NN _|_|CD rep318|rep318|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|SYM Stat2|stat2|NN _|_|CD rep320|rep320|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|SYM Stat2|stat2|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|NNP Trans|Trans|NNP
GLBRCE1|glbrce1|NN ,|,|, ACSH|ACSH|NNP ,|,|, Trans|Trans|NNP
GLBRCE1|GLBRCE1|NNP _|_|NNP ACSH|ACSH|NNP _|_|VBD Trans|Trans|NNP _|_|SYM rep318|rep318|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|CD Trans|Trans|NNP _|_|SYM rep318|rep318|CD _|_|NN 2|2|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|CD Trans|Trans|NNP _|_|SYM rep320|rep320|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD ACSH|ACSH|NNP _|_|CD Trans|Trans|NNP _|_|SYM rep327|rep327|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD pBBR|pbbr|NN _|_|CD ACSH|ACSH|NNP _|_|NNP Exp|Exp|NNP
GLBRCE1|glbrce1|NN _|_|CD pBBR|pbbr|NN _|_|SYM ACSH|ACSH|NNP _|_|VBD Stat|stat|NN
GLBRCE1|glbrce1|NN _|_|CD pBBR|pbbr|NN _|_|CD ACSH|ACSH|NNP _|_|NNP Trans|Trans|NNP
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN ,|,|, Exp|exp|NN
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Exp|exp|NN _|_|CD rep318|rep318|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Exp|exp|NN _|_|CD rep318|rep318|NN _|_|NN 2|2|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Exp|exp|NN _|_|CD rep320|rep320|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Exp|exp|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN _|_|CD LT|lt|NN ,|,|, Exp|exp|NN
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Exp|exp|NN _|_|CD rep318|rep318|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Exp|exp|NN _|_|CD rep320|rep320|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Exp|exp|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN _|_|CD LT|lt|NN ,|,|, Stat1|stat1|NN
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Stat1|stat1|NN _|_|CD rep318|rep318|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Stat1|stat1|NN _|_|CD rep320|rep320|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Stat1|stat1|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN _|_|CD LT|lt|NN ,|,|, Stat2|stat2|NN
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|SYM Stat2|stat2|NN _|_|CD rep318|rep318|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|SYM Stat2|stat2|NN _|_|CD rep320|rep320|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|SYM Stat2|stat2|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN _|_|CD LT|lt|NN ,|,|, Trans|Trans|NNP
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Trans|Trans|NNP _|_|SYM rep318|rep318|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Trans|Trans|NNP _|_|SYM rep320|rep320|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Trans|Trans|NNP _|_|SYM rep327|rep327|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN ,|,|, Stat1|stat1|NN
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Stat1|stat1|NN _|_|CD rep318|rep318|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Stat1|stat1|NN _|_|CD rep320|rep320|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Stat1|stat1|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN ,|,|, Stat2|stat2|NN
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Stat2|stat2|NN _|_|CD rep327|rep327|NN _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN ,|,|, SynH|synh|NN ,|,|, Trans|Trans|NNP
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Trans|Trans|NNP _|_|SYM rep318|rep318|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Trans|Trans|NNP _|_|SYM rep320|rep320|CD _|_|NN 1|1|CD
GLBRCE1|glbrce1|NN _|_|CD SynH|synh|NN _|_|CD Trans|Trans|NNP _|_|SYM rep327|rep327|CD _|_|NN 1|1|CD
gluconate|gluconate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 091|091|CD
gluconate|gluconate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 092|092|CD
gluconate|gluconate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 093|093|CD
gluconate|gluconate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 094|094|CD
gluconate|gluconate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 095|095|CD
gluconate|gluconate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 096|096|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 168|168|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 168|168|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 168|168|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 168|168|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 24|24|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 24|24|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 24|24|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 24|24|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 336|336|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 336|336|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 336|336|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 336|336|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 3|3|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 3|3|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 3|3|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 3|3|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 48|48|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 48|48|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 48|48|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 48|48|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 4|4|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 4|4|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 4|4|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 4|4|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 5|5|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 5|5|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 5|5|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 5|5|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 6|6|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 6|6|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 6|6|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 6|6|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 8|8|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 1|1|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 8|8|CD hour|hour|NN time|time|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 8|8|CD hourt|hourt|NN ime|ime|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD
Glucose|glucose|NN time|time|NN course|course|NN ,|,|, 8|8|CD hourt|hourt|NN ime|ime|NN point|point|NN ,|,|, biological|biological|JJ replicate|replicate|VBP 3|3|CD ,|,|, rRNA|rrna|NN not|not|RB depleted|deplete|VBN
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 016|016|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 017|017|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 018|018|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 019|019|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 020|020|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 021|021|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 022|022|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 023|023|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 024|024|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 025|025|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 026|026|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 027|027|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 028|028|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 029|029|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 030|030|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 031|031|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 032|032|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 033|033|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 097|097|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 098|098|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 099|099|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 100|100|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 101|101|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 102|102|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|NN 103|103|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|VBD 104|104|CD
glucose|glucose|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 105|105|CD
Glutamate|glutamate|JJ addition|addition|NN
Glutamine|Glutamine|NNP addition|addition|NN
Glycerol|Glycerol|NNP replicate|replicate|VB 1|1|CD
Glycerol|Glycerol|NNP replicate|replicate|VB 2|2|CD
Glycerol|Glycerol|NNP replicate|replicate|VB 3|3|CD
Glycerol|glycerol|NN stocks|stock|NNS of|of|IN E.|e.|FW coli|coli|FW K12|k12|NN strain|strain|NN MG1655|mg1655|NN were|be|VBD inoculated|inoculate|VBN into|into|IN LB|lb|NN media|media|NNS grown|grow|VBN at|at|IN 37|37|CD ℃|℃|NN with|with|IN constant|constant|JJ agitation|agitation|NN overnight|overnight|JJ .|.|. Cultures|culture|NNS were|be|VBD diluted|dilute|VBN 1:100|1:100|CD into|into|IN fresh|fresh|JJ minimal|minimal|JJ medium|medium|NN and|and|CC then|then|RB cultured|culture|VBN at|at|IN 37|37|CD ℃|℃|CD to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN nm|nm|NN ~|~|NN 0.6|0.6|CD -RRB-|-rrb-|-RRB- .|.|.
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 034|034|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 035|035|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 036|036|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 037|037|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 038|038|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 039|039|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 040|040|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 041|041|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 042|042|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 043|043|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 044|044|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 045|045|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 046|046|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 047|047|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 048|048|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 049|049|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 050|050|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 052|052|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 053|053|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 054|054|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 055|055|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 056|056|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 057|057|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 058|058|CD
glycerol|glycerol|NN _|_|CD time|time|NN _|_|NN course|course|NN :|:|: MURI|MURI|NNP _|_|SYM 059|059|CD
Glycine|glycine|NN addition|addition|NN
go|go|VB to|to|TO the|the|DT directory|directory|NN :|:|:
GPR|gpr|NN files|file|NNS were|be|VBD analyzed|analyze|VBN further|further|RB with|with|IN Acuity|acuity|NN 4.0|4.0|CD software|software|NN -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Devices|Devices|NNPS ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- starting|start|VBG with|with|IN lowess|lowess|NN normalization|normalization|NN .|.|. Normalized|normalize|VBN log2|log2|NN ratio|ratio|NN data|datum|NNS from|from|IN biological|biological|JJ replicates|replicate|VBZ and|and|CC technical|technical|JJ replicates|replicate|VBZ -LRB-|-lrb-|-LRB- dye|dye|VB swap|swap|NN -RRB-|-rrb-|-RRB- were|be|VBD averaged|average|VBN and|and|CC the|the|DT statistical|statistical|JJ significance|significance|NN -LRB-|-lrb-|-LRB- p-value|p-value|NN -RRB-|-rrb-|-RRB- was|be|VBD calculated|calculate|VBN .|.|.
gpt|gpt|NN _|_|NN 0|0|CD _|_|NN Hx|hx|NN Rep1|rep1|NN
gpt|gpt|NN _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep2|rep2|JJ
gpt|gpt|NN _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep3|rep3|JJ
gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
gpt|gpt|NN _|_|CD 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
gpt|gpt|NN _|_|CD 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
gpt|gpt|NN _|_|CD 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
gpt|gpt|NN _|_|CD 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
gpt|gpt|NN _|_|CD 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
gpt|gpt|NN _|_|CD 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
gpt|gpt|NN _|_|CD 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
gpt|gpt|NN _|_|CD 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
gpt|gpt|NN _|_|CD 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
gpt|gpt|NN _|_|CD 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
gpt|gpt|NN _|_|CD 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
gpt|gpt|NN _|_|CD 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
gpt|gpt|NN strain|strain|NN with|with|IN hypoxanthine|hypoxanthine|NN
gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 120|120|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 15|15|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 30|30|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 45|45|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 60|60|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
gram|gram|NN status|status|NN :|:|: Gram-negative|gram-negative|JJ
graphics.off|graphics.off|NN -LRB-|-lrb-|-LRB- -RRB-|-rrb-|-RRB-
group|group|NN -LRB-|-lrb-|-LRB- hus/non-hus|hus/non-hus|JJ -RRB-|-rrb-|-RRB- :|:|: HUS|hus|NN
group|group|NN -LRB-|-lrb-|-LRB- hus/non-hus|hus/non-hus|JJ -RRB-|-rrb-|-RRB- :|:|: Non-HUS|non-hus|JJ
Grow|grow|VBP bacteria|bacterium|NNS overnight|overnight|JJ in|in|IN LB|lb|NN medium|medium|NN ,|,|, reinoculate|reinoculate|NN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN at|at|IN an|a|DT initial|initial|JJ OD600|od600|NN of|of|IN 0.005|0.005|CD .|.|. After|after|IN eight|eight|CD hours|hour|NNS growth|growth|NN at|at|IN 34|34|CD °C|°c|NN in|in|IN M9|m9|NN medium|medium|NN ,|,|, 2|2|CD mL|ml|NN of|of|IN RNA|rna|NN Protect|protect|VB Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO 1|1|CD ml|ml|NN bacterial|bacterial|JJ cultures|culture|NNS -LRB-|-lrb-|-LRB- at|at|IN OD600|od600|NN of|of|IN about|about|IN 0.5-0.8|0.5-0.8|CD -RRB-|-rrb-|-RRB- to|to|TO stabilize|stabilize|VB RNA|rna|NN .|.|. Centrifuge|Centrifuge|NNP for|for|IN 10|10|CD min|min|NN at|at|IN 4000|4000|CD g.|g.|NNP Decant|Decant|NNP the|the|DT supernatant|supernatant|NN .|.|.
growing|grow|VBG condition|condition|NN :|:|: M9|m9|NN minimal|minimal|JJ medium|medium|NN
Growing|grow|VBG t|t|NN =|=|JJ 1|1|CD hour|hour|NN
Grown|grow|VBN in|in|IN Davis|Davis|NNP 's|'s|POS Mineral|Mineral|NNP Salts|salt|NNS medium|medium|NN -LRB-|-lrb-|-LRB- Gibco|Gibco|NNP BRL|brl|NN Life|Life|NNP Technologies|Technologies|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- with|with|IN 0.1|0.1|CD %|%|NN D-glucose|d-glucose|NN at|at|IN 25|25|CD C|c|NN -LRB-|-lrb-|-LRB- 100|100|CD r.p.m.|r.p.m.|NN shaking|shake|VBG -RRB-|-rrb-|-RRB- until|until|IN an|a|DT OD|od|NN -LRB-|-lrb-|-LRB- 550|550|CD nm|nm|NN -RRB-|-rrb-|-RRB- of|of|IN 0.6|0.6|CD .|.|.
Grown|Grown|NNP in|in|IN glucose|glucose|NN M9|m9|NN media|media|NNS supplemented|supplement|VBN with|with|IN 0.55|0.55|CD M|m|NN NaCl|nacl|NN
Grown|Grown|NNP in|in|IN glucose|glucose|NN M9|m9|NN media|media|NNS with|with|IN or|or|CC without|without|IN supplementation|supplementation|NN of|of|IN 0.6|0.6|CD M|m|NN NaCl|nacl|NN
grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.0|1.0|CD in|in|IN DMEM|DMEM|NNP
grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.0|1.0|CD in|in|IN DMEM|dmem|NN with|with|IN 50|50|CD uM|um|NN epinephrine|epinephrine|NN
grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.0|1.0|CD in|in|IN DMEM|dmem|NN with|with|IN AI3|ai3|NN
grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.0|1.0|CD in|in|IN DMEM|dmem|NN with|with|IN AI3|ai3|NN signaling|signaling|NN molecule|molecule|NN
grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.0|1.0|CD in|in|IN DMEM|dmem|NN with|with|IN Epinephrine|epinephrine|NN
grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.0|1.0|CD in|in|IN LB|LB|NNP
Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN
growth|growth|NN condition|condition|NN :|:|: 16|16|CD µM|µm|NN IPTG|iptg|NN
growth|growth|NN condition|condition|NN :|:|: 25|25|CD μl|μl|NN into|into|IN K-medium|k-medium|NN
growth|growth|NN condition|condition|NN :|:|: 4|4|CD µM|µm|NN IPTG|iptg|NN
growth|growth|NN condition|condition|NN :|:|: 50|50|CD µl|µl|NN into|into|IN K-medium|k-medium|NN +|+|CC 0.3|0.3|CD M|m|NN NaCl|nacl|NN
growth|growth|NN condition|condition|NN :|:|: 75|75|CD µl|µl|NN into|into|IN K-medium|k-medium|NN +|+|CC 0.6|0.6|CD M|m|NN urea|urea|NN
growth|growth|NN condition|condition|NN :|:|: 8|8|CD µM|µm|NN IPTG|iptg|NN
growth|growth|NN condition|condition|NN :|:|: Adenine|Adenine|NNP
growth|growth|NN condition|condition|NN :|:|: Aerobic|aerobic|JJ
growth|growth|NN condition|condition|NN :|:|: Aerobic|Aerobic|NNP Cultures|Cultures|NNP
growth|growth|NN condition|condition|NN :|:|: anaerobic|anaerobic|JJ
growth|growth|NN condition|condition|NN :|:|: Anaerobic|anaerobic|JJ
growth|growth|NN condition|condition|NN :|:|: Anaerobic|anaerobic|JJ Cultures|culture|NNS
growth|growth|NN condition|condition|NN :|:|: early-exponential|early-exponential|JJ
growth|growth|NN condition|condition|NN :|:|: Exponential|Exponential|NNP +|+|CC O2|o2|CD
growth|growth|NN condition|condition|NN :|:|: glucose|glucose|NN
growth|growth|NN condition|condition|NN :|:|: Inside|inside|IN Acanthamoeba|acanthamoeba|NN
growth|growth|NN condition|condition|NN :|:|: LB|lb|NN at|at|IN 30|30|CD °C|°c|NN
growth|growth|NN condition|condition|NN :|:|: LB|lb|NN at|at|IN 37|37|CD °C|°c|NN
growth|growth|NN condition|condition|NN :|:|: LB|lb|NN broth|broth|NN alone|alone|RB -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB-
growth|growth|NN condition|condition|NN :|:|: LB|lb|NN broth|broth|NN supplemented|supplement|VBN with|with|IN cranberry|cranberry|NN PACs|pac|NNS -LRB-|-lrb-|-LRB- 100|100|CD µg/mL|µg/ml|NN -RRB-|-rrb-|-RRB-
growth|growth|NN condition|condition|NN :|:|: mid-exponential|mid-exponential|JJ
growth|growth|NN condition|condition|NN :|:|: MM|mm|NN +|+|CC 0.12|0.12|CD %|%|NN casaminoacids|casaminoacid|NNS +0.4|+0.4|CD %|%|NN glucose|glucose|NN at|at|IN 22|22|CD °C|°c|NN
growth|growth|NN condition|condition|NN :|:|: MM|mm|NN +|+|CC 0.12|0.12|CD %|%|NN casaminoacids|casaminoacid|NNS +0.4|+0.4|CD %|%|NN glucose|glucose|NN at|at|IN 30|30|CD °C|°c|NN
growth|growth|NN condition|condition|NN :|:|: normal|normal|JJ condtion|condtion|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN w/v|w/v|NN glucose|glucose|NN -RRB-|-rrb-|-RRB-
growth|growth|NN condition|condition|NN :|:|: osmotic|osmotic|JJ stress|stress|NN condtion|condtion|NN -LRB-|-lrb-|-LRB- 12|12|CD %|%|NN w/v|w/v|NN glucose|glucose|NN -RRB-|-rrb-|-RRB-
growth|growth|NN condition|condition|NN :|:|: Outside|outside|JJ Control|control|NN
Growth|growth|NN conditions|condition|NNS :|:|: aaerobic|aaerobic|JJ
Growth|growth|NN conditions|condition|NNS :|:|: aerobic|aerobic|JJ
Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ
Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO2|no2|NN
Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO3|no3|NN
growth|growth|NN conditions|condition|NNS :|:|: LB|lb|NN growth|growth|NN OD|od|NN 0,3|0,3|CD
growth|growth|NN conditions|condition|NNS :|:|: LB|lb|NN growth|growth|NN OD|od|NN 0,5|0,5|CD
growth|growth|NN conditions|condition|NNS :|:|: Minimal|minimal|JJ Medium|medium|NN A|a|DT supplemented|supplement|VBN with|with|IN casaminoacids|casaminoacid|NNS -LRB-|-lrb-|-LRB- 0,1|0,1|CD %|%|NN -RRB-|-rrb-|-RRB- and|and|CC succinate|succinate|NN -LRB-|-lrb-|-LRB- 0,2|0,2|CD %|%|NN -RRB-|-rrb-|-RRB- ,|,|, OD|od|NN 0,2|0,2|CD at|at|IN 40|40|CD °C|°c|NN
growth|growth|NN condition|condition|NN :|:|: Static|static|JJ +|+|CC O2|o2|CD
growth|growth|NN condition|condition|NN :|:|: stationary|stationary|JJ
growth|growth|NN condition|condition|NN :|:|: steady-state|steady-state|JJ continuous|continuous|JJ cultivation|cultivation|NN -LRB-|-lrb-|-LRB- dilution|dilution|NN rate|rate|NN of|of|IN 0.4|0.4|CD h-1|h-1|NN -RRB-|-rrb-|-RRB- ,|,|, aerobic|aerobic|JJ
growth|growth|NN condition|condition|NN :|:|: transition-to-stationary|transition-to-stationary|JJ
Growth|growth|NN curves|curve|NNS of|of|IN all|all|DT selected|select|VBN evolved|evolve|VBD colony|colony|NN types|type|NNS and|and|CC the|the|DT ancestor|ancestor|NN were|be|VBD obtained|obtain|VBN by|by|IN growing|grow|VBG them|they|PRP under|under|IN their|they|PRP$ evolved|evolve|VBN environmental|environmental|JJ conditions|condition|NNS in|in|IN LB|lb|NN medium|medium|NN until|until|IN Log-phase|log-phase|NN .|.|. For|for|IN this|this|DT ,|,|, optical|optical|JJ density|density|NN was|be|VBD recorded|record|VBN at|at|IN 600nm|600nm|CD at|at|IN a|a|DT value|value|NN of|of|IN 0.6|0.6|CD to|to|TO 0.7|0.7|CD .|.|.
grow|grow|VBP ||||SYM The|the|DT E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN bacterial|bacterial|JJ strains|strain|NNS used|use|VBN in|in|IN this|this|DT work|work|NN are|be|VBP the|the|DT following|following|NN :|:|: E.|e.|FW coli|coli|FW MG1655|mg1655|NN -LRB-|-lrb-|-LRB- F|f|NN -|-|: lambda|lambda|NN -|-|: ilvG|ilvg|NN -|-|: rfb-50|rfb-50|NN rph-1|rph-1|NN -RRB-|-rrb-|-RRB- ;|;|: MG1655|mg1655|NN hns|hn|NNS -LRB-|-lrb-|-LRB- hns|hn|NNS :|:|: :|:|: Kanr|kanr|NN -RRB-|-rrb-|-RRB- ;|;|: MG1655|mg1655|NN fis|fis|NN -LRB-|-lrb-|-LRB- fis|fis|NN :|:|: :|:|: Kanr|kanr|NN -RRB-|-rrb-|-RRB- ;|;|: MG1655|mg1655|NN hns-FLAG|hns-flag|NN -LRB-|-lrb-|-LRB- hns|hn|NNS :|:|: :|:|: 3xFLAG|3xflag|NN :|:|: :|:|: Kanr|kanr|NN -RRB-|-rrb-|-RRB- ;|;|: MG1655|mg1655|NN fis-FLAG|fis-flag|NN -LRB-|-lrb-|-LRB- fis|fis|NN :|:|: :|:|: 3xFLAG|3xflag|NN :|:|: :|:|: Kanr|kanr|NN -RRB-|-rrb-|-RRB- .|.|. Luria-Bertani|luria-bertani|JJ -LRB-|-lrb-|-LRB- 0.5|0.5|CD %|%|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- broth|broth|NN and|and|CC agar|agar|NN -LRB-|-lrb-|-LRB- 15|15|CD g/liter|g/liter|NN -RRB-|-rrb-|-RRB- were|be|VBD used|use|VBN for|for|IN routine|routine|JJ growth|growth|NN .|.|. Where|where|WRB needed|need|VBN ,|,|, ampicillin|ampicillin|NN ,|,|, kanamycin|kanamycin|NN ,|,|, and|and|CC chloramphenicol|chloramphenicol|NN were|be|VBD used|use|VBN at|at|IN final|final|JJ concentrations|concentration|NNS of|of|IN 100|100|CD ,|,|, 30|30|CD ,|,|, and|and|CC 30|30|CD ug/ml|ug/ml|NN respectively|respectively|RB .|.|.
growth|growth|NN environment|environment|NN :|:|: Aerobic|aerobic|JJ
growth|growth|NN environment|environment|NN :|:|: Anaerobic|anaerobic|JJ
growth|growth|NN media|media|NNS :|:|: DMEM|dmem|NN growth|growth|NN media|media|NNS
growth|growth|NN media|media|NNS :|:|: LB|lb|NN
growth|growth|NN media|media|NNS :|:|: LB|lb|NN ;|;|: 0.8|0.8|CD %|%|NN bile|bile|NN salts|salt|NNS
growth|growth|NN media|media|NNS :|:|: LB|lb|NN medium|medium|NN
growth|growth|NN medium|medium|NN :|:|: Combined|combine|VBN input|input|NN
growth|growth|NN medium|medium|NN :|:|: LB|lb|NN +|+|CC glycerol|glycerol|NN medium|medium|NN
growth|growth|NN medium|medium|NN :|:|: LB|lb|NN medium|medium|NN
growth|growth|NN medium|medium|NN :|:|: liquid|liquid|JJ culture|culture|NN
Growth|Growth|NNP medium|medium|NN :|:|: MOPS|mop|NNS minimal|minimal|JJ ,|,|, 0.4|0.4|CD %|%|NN glucose|glucose|NN ,|,|, 0.5|0.5|CD %|%|NN casamino|casamino|NN acids|acid|NNS
growth|growth|NN medium|medium|NN :|:|: MOPS|mop|NNS minimal|minimal|JJ glucose|glucose|NN media|media|NNS containing|contain|VBG 10|10|CD µM|µm|NN FeSO4|feso4|NN
growth|growth|NN medium|medium|NN :|:|: MOPS|mop|NNS minimal|minimal|JJ glucose|glucose|NN media|media|NNS containing|contain|VBG 1|1|CD µM|µm|NN FeSO4|feso4|NN
growth|growth|NN mode|mode|NN :|:|: planktonic|planktonic|JJ culture|culture|NN in|in|IN annular|annular|JJ reactor|reactor|NN
growth|growth|NN phase|phase|NN :|:|: 30|30|CD min|min|NN post|post|NN stationary|stationary|JJ
growth|growth|NN phase|phase|NN :|:|: Early|early|JJ exponential|exponential|JJ
growth|growth|NN phase|phase|NN :|:|: Early|early|JJ Exponential|exponential|JJ
growth|growth|NN phase|phase|NN :|:|: Exp|exp|NN
growth|growth|NN phase|phase|NN :|:|: Exp1|exp1|NN
growth|growth|NN phase|phase|NN :|:|: Exp2|exp2|NN
growth|growth|NN phase|phase|NN :|:|: Exp3|exp3|NN
growth|growth|NN phase|phase|NN :|:|: exponential|exponential|JJ
growth|growth|NN phase|phase|NN :|:|: Exponential|exponential|JJ
Growth|growth|NN phase|phase|NN :|:|: exponential|exponential|JJ
growth|growth|NN phase|phase|NN :|:|: exponential|exponential|JJ growth|growth|NN phase|phase|NN
growth|growth|NN phase|phase|NN :|:|: Exponential|Exponential|NNP Phase|phase|NN
growth|growth|NN phase|phase|NN :|:|: Late|late|JJ exponential/Early|exponential/early|JJ stationary|stationary|JJ -LRB-|-lrb-|-LRB- OD|od|JJ ~|~|NN 1.8|1.8|CD -RRB-|-rrb-|-RRB-
growth|growth|NN phase|phase|NN :|:|: late|late|JJ _|_|NN stationary|stationary|JJ
growth|growth|NN phase|phase|NN :|:|: Late|late|JJ Stationary|stationary|JJ
growth|growth|NN phase|phase|NN :|:|: logarithmic|logarithmic|JJ growth|growth|NN
growth|growth|NN phase|phase|NN :|:|: log|log|NN phase|phase|NN
growth|growth|NN phase|phase|NN :|:|: Log|log|VB phase|phase|NN OD|od|NN 0.4|0.4|CD
growth|growth|NN phase|phase|NN :|:|: Mid|Mid|NNP exponential|exponential|JJ
growth|growth|NN phase|phase|NN :|:|: Mid-Exponential|mid-exponential|JJ
growth|growth|NN phase|phase|NN :|:|: mid-log|mid-log|JJ
growth|growth|NN phase|phase|NN :|:|: mid-log|mid-log|JJ phase|phase|NN
growth|growth|NN phase|phase|NN :|:|: mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.3|0.3|CD -RRB-|-rrb-|-RRB-
Growth|Growth|NNP phase|phase|NN :|:|: OD600|od600|NN =|=|JJ 0.3|0.3|CD
growth|growth|NN phase|phase|NN :|:|: Stat|stat|NN
growth|growth|NN phase|phase|NN :|:|: stat|stat|NN 1|1|CD
growth|growth|NN phase|phase|NN :|:|: Stat1|stat1|NN
growth|growth|NN phase|phase|NN :|:|: stat|stat|NN 2|2|CD
growth|growth|NN phase|phase|NN :|:|: Stat2|stat2|NN
growth|growth|NN phase|phase|NN :|:|: stationary|stationary|JJ
growth|growth|NN phase|phase|NN :|:|: Stationary|stationary|JJ
growth|growth|NN phase|phase|NN :|:|: stationary|stationary|JJ growth|growth|NN phase|phase|NN
growth|growth|NN phase|phase|NN :|:|: Stationary|stationary|JJ phase|phase|NN
growth|growth|NN phase|phase|NN :|:|: stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- grown|grow|VBN to|to|TO an|a|DT OD600nm|od600nm|NN of|of|IN 0.9|0.9|CD -RRB-|-rrb-|-RRB-
growth|growth|NN phase|phase|NN :|:|: Trans|Trans|NNP
growth|growth|NN phase|phase|NN :|:|: transition|transition|NN
growth|growth|NN phase|phase|NN :|:|: transition|transition|NN growth|growth|NN phase|phase|NN
growth|growth|NN phase|phase|NN :|:|: Transition|transition|NN to|to|TO Stationary|stationary|JJ
growth|growth|NN protocol|protocol|NN :|:|: Bacteria|bacterium|NNS liquid|liquid|JJ culture|culture|NN
growth|growth|NN protocol|protocol|NN :|:|: biofilm|biofilm|NN grown|grow|VBN on|on|IN glass|glass|NN wool|wool|NN ,|,|, 37C|37c|NN
growth|growth|NN protocol|protocol|NN :|:|: control|control|NN
growth|growth|NN protocol|protocol|NN :|:|: Controls|Controls|NNP grown|grow|VBN to|to|TO an|a|DT optimal|optimal|JJ temperature|temperature|NN of|of|IN 37|37|CD °C|°c|NN
growth|growth|NN protocol|protocol|NN :|:|: grown|grow|VBN in|in|IN LB|lb|NN +|+|CC glycerol|glycerol|NN to|to|TO 0.8|0.8|CD OD|od|NN
growth|growth|NN protocol|protocol|NN :|:|: grown|grow|VBN in|in|IN LB|lb|NN to|to|TO 0.8|0.8|CD OD|od|NN
growth|growth|NN protocol|protocol|NN :|:|: heat|heat|NN shock|shock|NN
growth|growth|NN protocol|protocol|NN :|:|: in|in|IN the|the|DT caecal|caecal|JJ content|content|NN of|of|IN rats|rat|NNS associated|associate|VBN with|with|IN the|the|DT human|human|JJ microbiota|microbiota|NN
growth|growth|NN protocol|protocol|NN :|:|: logarithmic|logarithmic|JJ phase|phase|NN in|in|IN DMEM-MOPS|dmem-mops|NN
growth|growth|NN protocol|protocol|NN :|:|: Log-phase|log-phase|JJ culture|culture|NN -LRB-|-lrb-|-LRB- LB|lb|NN broth|broth|NN ,|,|, Miller|Miller|NNP formulation|formulation|NN -RRB-|-rrb-|-RRB- inoculated|inoculate|VBN with|with|IN one|one|CD blue|blue|JJ colony|colony|NN and|and|CC grown|grow|VBN for|for|IN 5|5|CD hr|hr|NN at|at|IN 37|37|CD degrees|degree|NNS celsius|celsius|NN
growth|growth|NN protocol|protocol|NN :|:|: Log-phase|log-phase|JJ culture|culture|NN -LRB-|-lrb-|-LRB- LB|lb|NN broth|broth|NN ,|,|, Miller|Miller|NNP formulation|formulation|NN -RRB-|-rrb-|-RRB- inoculated|inoculate|VBN with|with|IN one|one|CD pale|pale|JJ colony|colony|NN and|and|CC grown|grow|VBN for|for|IN 5|5|CD hr|hr|NN at|at|IN 37|37|CD degrees|degree|NNS celsius|celsius|NN
growth|growth|NN protocol|protocol|NN :|:|: steady|steady|JJ growth|growth|NN
growth|growth|NN protocol|protocol|NN :|:|: transition|transition|NN phase|phase|NN in|in|IN DMEM-MOPS|dmem-mops|NN
growth|growth|NN protocol|protocol|NN :|:|: Treatment|treatment|NN 1|1|CD -LRB-|-lrb-|-LRB- 58|58|CD °C|°c|NN F|f|NN =|=|JJ 2|2|CD -RRB-|-rrb-|-RRB-
growth|growth|NN protocol|protocol|NN :|:|: Treatment|treatment|NN 2|2|CD -LRB-|-lrb-|-LRB- 58|58|CD °C|°c|NN F|f|NN =|=|JJ 3|3|CD -RRB-|-rrb-|-RRB-
growth|growth|NN protocol|protocol|NN :|:|: Treatment|treatment|NN 3|3|CD -LRB-|-lrb-|-LRB- 60|60|CD °C|°c|NN F|f|NN =|=|JJ 3|3|CD -RRB-|-rrb-|-RRB-
growth|growth|NN protocol|protocol|NN :|:|: Treatment|treatment|NN 4|4|CD -LRB-|-lrb-|-LRB- core|core|NN temperature|temperature|NN of|of|IN 71|71|CD °C|°c|NN -RRB-|-rrb-|-RRB-
growth|growth|NN stage|stage|NN :|:|: log|log|NN phase|phase|NN
growth|growth|NN stage|stage|NN :|:|: log-phase|log-phase|JJ
growth|growth|NN stage|stage|NN :|:|: mid|mid|JJ exponetial|exponetial|JJ phase|phase|NN
growth|growth|NN stage|stage|NN :|:|: mid-log|mid-log|JJ phase|phase|NN
growth|growth|NN temperature|temperature|NN :|:|: 22|22|CD °C|°c|NN
growth|growth|NN temperature|temperature|NN :|:|: 30C|30c|CD
growth|growth|NN temperature|temperature|NN :|:|: 37|37|CD °C|°c|NN
growth|growth|NN time|time|NN :|:|: 7-day|7-day|JJ
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 10|10|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 14|14|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 168|168|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 24|24|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 26|26|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 27|27|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 28|28|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 29|29|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 3|3|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 336|336|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 4|4|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 48|48|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 5|5|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 5.5|5.5|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 6|6|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 6.5|6.5|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 7|7|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 8|8|CD
growth|growth|NN time|time|NN -LRB-|-lrb-|-LRB- hours|hour|NNS -RRB-|-rrb-|-RRB- :|:|: 9|9|CD
growth|growth|NN type|type|NN :|:|: amino|amino|NN acid|acid|NN starvation|starvation|NN
growth|growth|NN type|type|NN :|:|: log|log|NN phase|phase|NN
GSH-sepharose|gsh-sepharose|NN 4b|4b|NN purification|purification|NN
gss-1|gss-1|NN
gss-2|gss-2|NN
gss-3|gss-3|NN
GST|gst|NN control|control|NN Protoarray|Protoarray|NNP replicate|replicate|VB 1|1|CD
Guanosine|Guanosine|NNP addition|addition|NN
gut|gut|NN origin|origin|NN :|:|: Human|human|JJ colon|colon|NN
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|NN 1|1|CD
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|NN 2|2|CD
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|RB 3|3|CD
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|RB 4|4|CD
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|RB 5|5|CD
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|RB 6|6|CD
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|NN 7|7|CD
gyrase|gyrase|NN binding|binding|NN -LRB-|-lrb-|-LRB- ChIP-chip|chip-chip|NN -RRB-|-rrb-|-RRB- no.|no.|RB 8|8|CD
Gyrase|gyrase|NN Cleavage|cleavage|NN Sites|site|NNS -LRB-|-lrb-|-LRB- GCSs|gcss|NNS -RRB-|-rrb-|-RRB- were|be|VBD called|call|VBN using|use|VBG custom|custom|NN script|script|NN -LRB-|-lrb-|-LRB- GCSs_calling.py|gcss_calling.py|NN ,|,|, github|github|NN :|:|: https://github.com/sutormin94/Gyrase_Topo-seq|https://github.com/sutormin94/gyrase_topo-seq|NN -RRB-|-rrb-|-RRB- that|that|WDT takes|take|VBZ 4|4|CD files|file|NNS -LRB-|-lrb-|-LRB- tetrade|tetrade|NN -RRB-|-rrb-|-RRB- as|as|IN input|input|NN :|:|: +|+|CC A+IP|A+IP|NNP ,|,|, +|+|CC A-IP|a-ip|NN ,|,|, -|-|: A+IP|a+ip|NN ,|,|, -|-|: A-IP|a-ip|NN
gyrA|gyra|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
gyrA|gyra|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
gyrA|gyra|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
gyrA|gyra|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
gyrI|gyri|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
gyrI|gyri|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
gyrI|gyri|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
gyrI|gyri|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
H2O2|h2o2|NN
H500|h500|CD _|_|NN 1|1|CD
Harvested|harvest|VBN by|by|IN chloramphenicol|chloramphenicol|NN pre-treatment|pre-treatment|NN and|and|CC centrifugation|centrifugation|NN ;|;|: DSP|DSP|NNP treated|treat|VBN ex|ex|FW vivo|vivo|FW ;|;|: Affinity|affinity|NN purified|purify|VBN TF|tf|NN crosslinked|crosslink|VBD RNC|rnc|NN footprints|footprint|NNS
Harvested|harvest|VBN by|by|IN chloramphenicol|chloramphenicol|NN pre-treatment|pre-treatment|NN and|and|CC centrifugation|centrifugation|NN ;|;|: DSP|DSP|NNP treated|treat|VBN ex|ex|FW vivo|vivo|FW ;|;|: Total|total|JJ footprints|footprint|NNS
Harvested|harvest|VBN by|by|IN rapid|rapid|JJ filtration|filtration|NN ;|;|: DSP|DSP|NNP treated|treat|VBN ex|ex|FW vivo|vivo|FW ;|;|: Affinity|affinity|NN purified|purify|VBN TF|tf|NN crosslinked|crosslink|VBD RNC|rnc|NN footprints|footprint|NNS
Harvested|harvest|VBN by|by|IN rapid|rapid|JJ filtration|filtration|NN ;|;|: DSP|DSP|NNP treated|treat|VBN ex|ex|FW vivo|vivo|FW ;|;|: Total|total|JJ footprints|footprint|NNS
Harvested|harvest|VBN by|by|IN rapid|rapid|JJ filtration|filtration|NN ;|;|: EDC|edc|NN treated|treat|VBN ex|ex|FW vivo|vivo|FW ;|;|: Affinity|affinity|NN purified|purify|VBN TF|tf|NN crosslinked|crosslink|VBD RNC|rnc|NN footprints|footprint|NNS
Harvested|harvest|VBN by|by|IN rapid|rapid|JJ filtration|filtration|NN ;|;|: EDC|edc|NN treated|treat|VBN ex|ex|FW vivo|vivo|FW ;|;|: Total|total|JJ footprints|footprint|NNS
Harvested|harvest|VBN cells|cell|NNS -LRB-|-lrb-|-LRB- 4|4|CD ×|×|NN 6|6|CD ml|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD immediately|immediately|RB combined|combine|VBN with|with|IN 6|6|CD ml|ml|NN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS ,|,|, Grand|Grand|NNP Island|Island|NNP ,|,|, NY|NY|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- ,|,|, centrifuged|centrifuge|VBN for|for|IN 15|15|CD min|min|NN at|at|IN 12000|12000|CD r.p.m.|r.p.m.|NN ,|,|, washed|wash|VBN with|with|IN 1|1|CD ml|ml|NN RNAlater|rnalater|NN -LRB-|-lrb-|-LRB- 3|3|CD min|min|NN at|at|IN 15000|15000|CD r.p.m.|r.p.m.|NN -RRB-|-rrb-|-RRB- ,|,|, re-suspended|re-suspended|JJ in|in|IN 0.5|0.5|CD ml|ml|NN RNAlater|rnalater|NN and|and|CC stored|store|VBD at|at|IN −|−|CD 20|20|CD °C|°c|NN .|.|. For|for|IN RNA|rna|NN extraction|extraction|NN the|the|DT RiboPure-Bacteria|RiboPure-Bacteria|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. To|to|TO achieve|achieve|VB high|high|JJ RNA|rna|NN yields|yield|NNS several|several|JJ reactions|reaction|NNS for|for|IN each|each|DT sample|sample|NN were|be|VBD done|do|VBN in|in|IN parallel|parallel|NN and|and|CC pooled|pool|VBD at|at|IN the|the|DT end|end|NN of|of|IN the|the|DT procedure|procedure|NN .|.|. An|a|DT additional|additional|JJ DNase|dnase|NN treatment|treatment|NN step|step|NN with|with|IN TURBO|TURBO|NNP DNase|dnase|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- was|be|VBD included|include|VBN to|to|TO assure|assure|VB no|no|DT genomic|genomic|JJ DNA|dna|NN contamination|contamination|NN .|.|. Messenger|messenger|NN RNA|rna|NN was|be|VBD enriched|enrich|VBN using|use|VBG the|the|DT RiboMinus|RiboMinus|NNP Bacteria|bacterium|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
HB101|hb101|NN ,|,|, biological|biological|JJ rep2|rep2|NN
HB101|hb101|NN ,|,|, biological|biological|JJ rep3|rep3|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS and|and|CC Giardia|Giardia|NNP ,|,|, biological|biological|JJ rep1|rep1|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS and|and|CC Giardia|Giardia|NNP ,|,|, biological|biological|JJ rep2|rep2|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS and|and|CC Giardia|Giardia|NNP ,|,|, biological|biological|JJ rep3|rep3|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS ,|,|, biological|biological|JJ rep1|rep1|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS ,|,|, biological|biological|JJ rep2|rep2|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO C.|C.|NNP elegans|elegan|NNS ,|,|, biological|biological|JJ rep3|rep3|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO Giardia|Giardia|NNP ,|,|, biological|biological|JJ rep1|rep1|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO Giardia|Giardia|NNP ,|,|, biological|biological|JJ rep2|rep2|NN
HB101|hb101|NN ,|,|, exposed|expose|VBN to|to|TO Giardia|Giardia|NNP ,|,|, biological|biological|JJ rep3|rep3|NN
HCl|hcl|NN replicate|replicate|VBP 1|1|CD
HCl|hcl|NN replicate|replicate|VBP 3|3|CD
heat|heat|NN sensitivity|sensitivity|NN :|:|: resistant|resistant|JJ
heat|heat|NN sensitivity|sensitivity|NN :|:|: sensitive|sensitive|JJ
heat|heat|NN shock|shock|NN response|response|NN in|in|IN the|the|DT minimal|minimal|JJ medium|medium|NN
heat|heat|NN shock|shock|NN time|time|NN :|:|: 0|0|CD min|min|NN
heat|heat|NN shock|shock|NN time|time|NN :|:|: 10|10|CD min|min|NN
heat|heat|NN shock|shock|NN time|time|NN :|:|: 20|20|CD min|min|NN
heat|heat|NN shock|shock|NN time|time|NN :|:|: None|none|NN
HEK293T/17|hek293t/17|NN cells|cell|NNS -LRB-|-lrb-|-LRB- ATCC|atcc|NN CRL-11268|crl-11268|NN -RRB-|-rrb-|-RRB- were|be|VBD cultured|culture|VBN in|in|IN DMEM|dmem|NN -LRB-|-lrb-|-LRB- Mediatech|mediatech|NN -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 10|10|CD %|%|NN FBS|fbs|NN and|and|CC L-glutamine/penicillin/streptomycin|l-glutamine/penicillin/streptomycin|NN .|.|.
hfq-gln-1|hfq-gln-1|NN
hfq-gln-2|hfq-gln-2|NN
hfq|hfq|NN mutant|mutant|NN in|in|IN Ala|Ala|NNP media|media|NNS
hfq|hfq|NN mutant|mutant|NN in|in|IN Gln|gln|NN media|media|NNS
Hfq|hfq|NN mut|mut|NN exp|exp|NN mRNA|mrna|NN
Hfq|hfq|NN mut|mut|NN exp|exp|NN RPF|rpf|NN
Hfq|hfq|NN -|-|: RpoE|rpoe|NN overexpression|overexpression|NN -LRB-|-lrb-|-LRB- 20|20|CD min|min|NN -RRB-|-rrb-|-RRB-
hfq|hfq|NN +|+|CC Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 20|20|CD min|min|NN -RRB-|-rrb-|-RRB-
Hfr-2xSFX|hfr-2xsfx|NN -|-|:
High|High|NNP succinic|succinic|JJ acid|acid|NN tolerance|tolerance|NN E.coli|e.coli|NNS _|_|VBP rep|rep|NN Dn|dn|NN
High|High|NNP succinic|succinic|JJ acid|acid|NN tolerance|tolerance|NN E.coli|e.coli|NNS _|_|VBP rep|rep|NN Up|up|IN
HisC|hisc|NN rewired|rewire|VBD strain|strain|NN exponentially|exponentially|RB grown|grow|VBN in|in|IN the|the|DT absence|absence|NN of|of|IN histidine|histidine|NN
HisC|hisc|NN rewired|rewire|VBD strain|strain|NN exponentially|exponentially|RB grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN histidine|histidine|NN -LRB-|-lrb-|-LRB- 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB-
Hiseq|hiseq|JJ 2500|2500|CD Illumina|Illumina|NNP short|short|JJ reads|read|VBZ -LRB-|-lrb-|-LRB- 50|50|CD bp|bp|NN -RRB-|-rrb-|-RRB- were|be|VBD mapped|map|VBN back|back|RB to|to|TO the|the|DT Caulobacter|Caulobacter|NNP NA1000|na1000|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NCBI|ncbi|NN Reference|Reference|NNP Sequence|sequence|NN :|:|: NC-011916.1|nc-011916.1|NN -RRB-|-rrb-|-RRB- using|use|VBG Bowtie|Bowtie|NNP 1|1|CD -LRB-|-lrb-|-LRB- Langmead|Langmead|NNP et|et|FW al.|al.|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT following|follow|VBG command|command|NN :|:|: bowtie|bowtie|NN -|-|: m|m|NN 1|1|CD -|-|: n|n|NN 1|1|CD --|--|: best|best|JJS --|--|: strata|strata|SYM -|-|: p|p|NN 4|4|CD --|--|: chunkmbs|chunkmb|NNS 512|512|CD NA1000-bowtie|na1000-bowtie|NN --|--|: sam|sam|NN *|*|NN .|.|. fastq|fastq|NN >|>|JJR output.sam|output.sam|NN .|.|. Subsequently|subsequently|RB ,|,|, the|the|DT sequencing|sequencing|NN coverage|coverage|NN for|for|IN each|each|DT nucleotide|nucleotide|NN position|position|NN was|be|VBD computed|compute|VBN using|use|VBG BEDTools|bedtool|NNS -LRB-|-lrb-|-LRB- Quinlan|Quinlan|NNP &|&|CC Hall|Hall|NNP ,|,|, 2010|2010|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT following|follow|VBG command|command|NN :|:|: bedtools|bedtool|NNS genomecov|genomecov|NN -|-|: d|d|SYM -|-|: ibam|ibam|NN output.sorted.bam|output.sorted.bam|NN -|-|: g|g|NN NA1000.fna|na1000.fna|NN >|>|JJR coverage_output.txt|coverage_output.txt|NN .|.|. Finally|finally|RB ,|,|, the|the|DT ratio|ratio|NN between|between|IN the|the|DT number|number|NN of|of|IN reads|read|VBZ of|of|IN libraries|library|NNS generated|generate|VBN from|from|IN pMCS1-Tn5-ME-R6Kγ-kanR-ME|pmcs1-tn5-me-r6kγ-kanr-me|NN or|or|CC pMCS1-Tn5-ME-R6Kγ-kanR-parS456-ME|pmcs1-tn5-me-r6kγ-kanr-pars456-me|NN were|be|VBD calculated|calculate|VBN .|.|. Results|result|NNS were|be|VBD binned|bin|VBN over|over|IN 1|1|CD kb|kb|NN and|and|CC represented|represent|VBN as|as|IN a|a|DT log10|log10|NN scale|scale|NN .|.|.
His-tagged|his-tagged|JJ DNA|dna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN BW25113/pCA24N|bw25113/pca24n|NN -LRB-|-lrb-|-LRB- empty|empty|JJ vector|vector|NN -RRB-|-rrb-|-RRB- after|after|IN 24|24|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN at|at|IN 37oC|37oc|NN under|under|IN 2|2|CD mM|mm|NN IPTG|iptg|NN
His-tagged|his-tagged|JJ DNA|dna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN after|after|IN 24|24|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN at|at|IN 37oC|37oc|NN under|under|IN 2|2|CD mM|mm|NN IPTG|iptg|NN
His-tagged|his-tagged|JJ DNA|dna|NN extracted|extract|VBN from|from|IN planktonic|planktonic|JJ cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN BW25113|bw25113|NN /|/|: /|/|: pBAD-Myc-His|pbad-myc-his|NN C|c|NN -LRB-|-lrb-|-LRB- empty|empty|JJ vector|vector|NN -RRB-|-rrb-|-RRB- after|after|IN 24|24|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN with|with|IN induction|induction|NN of|of|IN 0.5|0.5|CD %|%|NN L-arabinose|l-arabinose|JJ suspension|suspension|NN cell|cell|NN
His-tagged|his-tagged|JJ DNA|dna|NN extracted|extract|VBN from|from|IN planktonic|planktonic|JJ cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN BW25113/pBAD-Myc-His|bw25113/pbad-myc-his|NN C-mqsA|c-mqsa|NN after|after|IN 24|24|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN with|with|IN induction|induction|NN of|of|IN 0.5|0.5|CD %|%|NN L-arabinose|l-arabinose|JJ suspension|suspension|NN cell|cell|NN
Histidine|histidine|NN addition|addition|NN
hlpA|hlpa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
hlpA|hlpa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
hlpA|hlpa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
hlpA|hlpa|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
HNCE3|hnce3|NN is|be|VBZ an|a|DT isogenic|isogenic|JJ mutant|mutant|JJ derived|derive|VBN from|from|IN hyper-resistant|hyper-resistant|JJ AG102|ag102|NN -LRB-|-lrb-|-LRB- marR1|marr1|NN -RRB-|-rrb-|-RRB- .|.|. It|it|PRP contains|contain|VBZ a|a|DT nonpolar|nonpolar|JJ mutation|mutation|NN at|at|IN the|the|DT acrA|acra|NN locus|locus|NN which|which|WDT allows|allow|VBZ read-through|read-through|NN for|for|IN acrB|acrb|NN expression|expression|NN and|and|CC results|result|VBZ in|in|IN a|a|DT multidrug|multidrug|JJ efflux|efflux|NN negative|negative|JJ phenotype|phenotype|NN .|.|.
HNCE4|hnce4|NN is|be|VBZ an|a|DT isogenic|isogenic|JJ mutant|mutant|JJ derived|derive|VBN from|from|IN drug|drug|NN sensitive|sensitive|JJ AG102MB|ag102mb|NN -LRB-|-lrb-|-LRB- marR1|marr1|NN ,|,|, AcrB|acrb|NN :|:|: :|:|: kan|kan|NN -RRB-|-rrb-|-RRB- .|.|. It|it|PRP contains|contain|VBZ an|a|DT additional|additional|JJ mutation|mutation|NN at|at|IN the|the|DT emrAB|emrab|NN locus|locus|NN -LRB-|-lrb-|-LRB- marR1|marr1|NN ,|,|, acrB|acrb|NN :|:|: :|:|: kan|kan|NN ,|,|, emrAB|emrab|NN :|:|: :|:|: cat|cat|NN -RRB-|-rrb-|-RRB- resulting|result|VBG in|in|IN a|a|DT multidrug|multidrug|JJ efflux|efflux|NN negative|negative|JJ phenotype|phenotype|NN .|.|.
hns|hn|NNS _|_|VBP 1|1|CD
Hns|hn|NNS --|--|: 120|120|CD min|min|NN
Hns|hn|VBZ -180|-180|CD min|min|NN
hns|hn|NNS _|_|VBP 2|2|CD
Hns|hn|NNS --|--|: 420|420|CD min|min|NN
Hns|hn|NNS --|--|: 60|60|CD min|min|NN
HNS|hns|SYM -|-|: Aerobic|aerobic|JJ A|a|NN
HNS|hns|SYM -|-|: Aerobic|aerobic|JJ B|b|NN
HNS|hns|SYM -|-|: Anaerobic|anaerobic|JJ A|a|NN
HNS|hns|SYM -|-|: Anaerobic|anaerobic|JJ B|b|NN
H-NS|h-ns|NN ChIP|chip|NN DNA|dna|NN from|from|IN MG1655|mg1655|NN cells|cell|NNS
HNS|hns|NN ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
HNS|hn|VBZ ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN Replicate|replicate|VB B|b|NN
H-NS|h-ns|NN ,|,|, EE|ee|NN
H-NS|h-ns|NN flag|flag|NN tagged|tag|VBD cells|cell|NNS with|with|IN bcm|bcm|NN treatment|treatment|NN
H-NS|h-ns|NN flag|flag|NN tagged|tag|VBD cells|cell|NNS without|without|IN bcm|bcm|NN treatment|treatment|NN
H-NS|h-ns|NN ,|,|, ME|me|NN
H-NS|h-ns|NN ,|,|, S|s|NN
H-NS|h-ns|NN ,|,|, TS|ts|NN
holD|hold|VBP __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
holD|hold|VBP __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
holD|hold|VBP __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
holD|hold|VBP upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
Hot|hot|JJ phenol|phenol|NN extraction|extraction|NN of|of|IN total|total|JJ RNA|rna|NN .|.|.
Hot|hot|JJ phenol|phenol|NN RNA|rna|NN extraction|extraction|NN as|as|IN described|describe|VBN in|in|IN Aiba|Aiba|NNP ,|,|, Adhya|Adhya|NNP and|and|CC Crombrugge|Crombrugge|NNP .|.|. J.|J.|NNP Bio|Bio|NNP Chem|Chem|NNP .|.|. 1981|1981|CD ,|,|, 256|256|CD :|:|: p11905-11910|p11905-11910|JJ
Hot|hot|JJ phenol|phenol|NN RNA|rna|NN extraction|extraction|NN as|as|IN described|describe|VBN in|in|IN Aiba|Aiba|NNP .|.|. Adhya|Adhya|NNP and|and|CC Crombrugghe|Crombrugghe|NNP .|.|. J.|J.|NNP Bio|Bio|NNP Chem|Chem|NNP .|.|. 1981|1981|CD ,|,|, 256|256|CD :|:|: p.|p.|NN 11905-11910|11905-11910|CD .|.|.
Hot|hot|JJ phenol|phenol|NN -LRB-|-lrb-|-LRB- Sharma|sharma|FW et|et|FW al.|al.|FW 2010|2010|CD ,|,|, Bloomberg|Bloomberg|NNP 1990|1990|CD ,|,|, EMBO|EMBO|NNP J|J|NNP -RRB-|-rrb-|-RRB-
HP1|hp1|NN
HP2|hp2|NN
HP3|hp3|NN
HP4|hp4|NN
HS15min|hs15min|NN _|_|CD r1|r1|NN _|_|CD HiSeq|hiseq|NN
HS15min|hs15min|NN _|_|CD r2|r2|NN _|_|CD HiSeq|hiseq|NN
HS15min|hs15min|NN _|_|CD r3|r3|NN _|_|SYM GAII|gaii|CD
HS30min|hs30min|NN _|_|CD r1|r1|NN _|_|CD HiSeq|hiseq|NN
HS30min|hs30min|NN _|_|CD r2|r2|NN _|_|CD HiSeq|hiseq|NN
HS60min|hs60min|NN _|_|CD r1|r1|NN _|_|CD HiSeq|hiseq|NN
HS60min|hs60min|NN _|_|CD r2|r2|NN _|_|CD HiSeq|hiseq|NN
hscA|hsca|VBP __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r1|r1|FW
hscA|hsca|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
hscA|hsca|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
hscA|hsca|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
HT873-Con1|ht873-con1|NN
HT873-Con2|ht873-con2|NN
HT873-Con3|ht873-con3|NN
HT873-PA1|ht873-pa1|NN
HT873-PA2|ht873-pa2|NN
HT873-PA3|ht873-pa3|NN
HT875-Con1|ht875-con1|NN
HT875-Con2|ht875-con2|NN
HT875-Con3|ht875-con3|NN
HT875-PA1|ht875-pa1|NN
HT875-PA2|ht875-pa2|NN
HT875-PA3|ht875-pa3|NN
HTseq-derived|htseq-derived|JJ raw|raw|JJ count|count|NN data|datum|NNS were|be|VBD used|use|VBN as|as|IN input|input|NN after|after|IN a|a|DT non-specific|non-specific|JJ filtering|filter|VBG step|step|NN that|that|WDT removed|remove|VBD residual|residual|JJ rRNAs|rrna|NNS and|and|CC tRNAs|trna|NNS and|and|CC low|low|JJ coverage|coverage|NN genes|gene|NNS with|with|IN fewer|fewer|JJR than|than|IN 2|2|CD counts|count|NNS per|per|IN million|million|CD -LRB-|-lrb-|-LRB- 16-20|16-20|CD reads|read|VBZ -RRB-|-rrb-|-RRB- in|in|IN more|more|JJR than|than|IN 25|25|CD %|%|NN of|of|IN the|the|DT dataset|dataset|NN .|.|.
HTSeq|htseq|NN is|be|VBZ used|use|VBN to|to|TO generate|generate|VB expression|expression|NN count|count|NN for|for|IN each|each|DT gene|gene|NN .|.|.
-LRB-|-lrb-|-LRB- http://david.abcc.ncifcrf.gov/home.jsp|http://david.abcc.ncifcrf.gov/home.jsp|NN -RRB-|-rrb-|-RRB-
Human|human|JJ
Human|human|JJ III|iii|CD versus|versus|CC MG1655|mg1655|CD technical|technical|JJ replicate|replicate|VB 1|1|CD
Human|Human|NNP III|III|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 2|2|CD
Human|Human|NNP II|II|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VB 1|1|CD
Human|Human|NNP II|II|NNP versus|versus|CC MG1655|MG1655|NNP technical|technical|JJ replicate|replicate|VBP 2|2|CD
Human|human|JJ intestinal|intestinal|JJ microbiota|microbiota|NN associated|associate|VBN rat|rat|NN 's|'s|POS caecum|caecum|NN ,|,|, biological|biological|JJ rep1|rep1|NN
Human|human|JJ intestinal|intestinal|JJ microbiota|microbiota|NN associated|associate|VBN rat|rat|NN 's|'s|POS caecum|caecum|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Human|human|JJ intestinal|intestinal|JJ microbiota|microbiota|NN associated|associate|VBN rat|rat|NN 's|'s|POS caecum|caecum|NN ,|,|, biological|biological|JJ rep3|rep3|NN
Human|human|JJ I|I|PRP versus|versus|CC MG1655|mg1655|NN technical|technical|JJ replicate|replicate|VB 1|1|CD
Human|Human|NNP I|I|PRP versus|versus|CC MG1655|mg1655|NN technical|technical|JJ replicate|replicate|VBP 2|2|CD
Human|human|JJ sewage|sewage|NN isolate|isolate|NN H1|h1|NN
Human|human|JJ sewage|sewage|NN isolate|isolate|NN H2|h2|NN
Human|human|JJ sewage|sewage|NN isolate|isolate|NN H3|h3|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 0|0|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 10|10|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 15|15|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 20|20|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 25|25|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 32.5|32.5|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 45|45|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- formamide|formamide|NN content|content|NN -RRB-|-rrb-|-RRB- :|:|: 5|5|CD %|%|NN formamide|formamide|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- total|total|JJ rna|rna|NN -RRB-|-rrb-|-RRB- :|:|: 50|50|CD ng|ng|NN
hybridization|hybridization|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- total|total|JJ rna|rna|NN -RRB-|-rrb-|-RRB- :|:|: 5|5|CD ng|ng|NN
Hydrocortisone|Hydrocortisone|NNP Treatment|treatment|NN
IA-co1|ia-co1|NN
IA-co2|ia-co2|NN
IAI1|iai1|NN batch|batch|NN
IAI1|iai1|NN chemostat|chemostat|NN
IAI1|iai1|NN starvation|starvation|NN
IAI1|iai1|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 1|1|CD
IAI1|iai1|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 2|2|CD
IAI1|iai1|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 1|1|CD
IAI1|iai1|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 2|2|CD
IAI1|iai1|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 1|1|CD
IAI1|iai1|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 2|2|CD
IA-log|ia-log|JJ
IA-starve|ia-starve|JJ
Identical|identical|JJ to|to|TO Channel|Channel|NNP 1|1|CD with|with|IN no|no|DT arabinose|arabinose|NN added|add|VBD
IE-co1|ie-co1|NN
IE-co2|ie-co2|NN
IE-log|ie-log|JJ
IE-starve|ie-starve|JJ
IFNB|ifnb|NN Multi|multi|JJ SeV0|sev0|NN Rep1|rep1|NN Plasmid|plasmid|NN
IFNB|ifnb|NN Multi|multi|JJ SeV10|sev10|NN Rep1|rep1|NN Plasmid|plasmid|NN
IFNB|ifnb|NN Single|single|JJ SeV10|sev10|NN Rep1|rep1|NN Plasmid|plasmid|NN
IHF|ihf|SYM -|-|: Anaerobic|anaerobic|JJ A|a|NN
IHF|ihf|SYM -|-|: Anaerobic|anaerobic|JJ B|b|NN
IHF|ihf|NN ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
IHF|ihf|VBP ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN Replicate|replicate|VB B|b|NN
IHF|ihf|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r1|r1|FW
IHF|ihf|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
IHF|ihf|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T2|t2|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T3|t3|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T3|t3|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T4|t4|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T4|t4|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T5|t5|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T5|t5|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T6|t6|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN H2|h2|NN _|_|CD T8|t8|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T2|t2|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T3|t3|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T3|t3|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T4|t4|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T4|t4|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T5|t5|NN .5|.5|CD _|_|NN r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T5|t5|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T6|t6|NN _|_|CD r1|r1|NN
ik|ik|NN _|_|NN L2|l2|NN _|_|CD T8|t8|NN _|_|CD r1|r1|NN
Illumina|Illumina|NNP Casava1|Casava1|NNP .7|.7|CD software|software|NN used|use|VBN for|for|IN basecalling|basecalling|NN .|.|.
Illumina|Illumina|NNP Casava|Casava|NNP 1.8.2|1.8.2|CD software|software|NN used|use|VBN for|for|IN basecalling|basecall|VBG with|with|IN default|default|NN parameter|parameter|NN .|.|.
Illumina|Illumina|NNP Casava|Casava|NNP 1.8|1.8|CD software|software|NN was|be|VBD used|use|VBN for|for|IN basecalling|basecalling|NN .|.|.
Illumina|Illumina|NNP Casava|Casava|NNP software|software|NN used|use|VBN for|for|IN basecalling|basecalling|NN .|.|.
Illumina|Illumina|NNP Casava|Casava|NNP v1|v1|NN .8|.8|CD used|use|VBN for|for|IN basecalling|basecalling|NN .|.|.
Illumina|Illumina|NNP fastq|fastq|NN files|file|NNS were|be|VBD submitted|submit|VBN to|to|TO the|the|DT galaxy|galaxy|NN pipeline|pipeline|NN =|=|JJ >|>|JJR grooming|grooming|NN =|=|JJ >|>|JJR mapping|mapping|NN to|to|TO NC|NC|NNP _|_|SYM 002655|002655|CD using|use|VBG bowtie2|bowtie2|NN -LRB-|-lrb-|-LRB- default|default|NN but|but|CC seed|seed|NN 19|19|CD nt|nt|NNS &|&|CC zero|zero|CD mismatches|mismatch|NNS within|within|IN seed|seed|NN -RRB-|-rrb-|-RRB-
Illumina|Illumina|NNP GAII|GAII|NNP reads|read|VBZ were|be|VBD filtered|filter|VBN by|by|IN SGA|SGA|NNP version|version|NN 0.9.9|0.9.9|CD with|with|IN the|the|DT following|follow|VBG options|option|NNS :|:|: sga|sga|NN preprocess|preprocess|NN -|-|: q|q|NN 10|10|CD -|-|: f|f|LS 10|10|CD -|-|: m|m|NN 25|25|CD -LRB-|-lrb-|-LRB- quality|quality|NN trim|trim|JJ 10|10|CD ,|,|, quality|quality|NN filter|filter|NN 10|10|CD ,|,|, minimal|minimal|JJ length|length|NN 25|25|CD -RRB-|-rrb-|-RRB-
Illumina|Illumina|NNP read|read|VB were|be|VBD aligned|align|VBN to|to|TO NC|NC|NNP _|_|SYM 000913|000913|CD using|use|VBG Bowtie|Bowtie|NNP 1|1|CD with|with|IN 2|2|CD mismatches|mismatch|NNS allowed|allow|VBD per|per|IN read|read|NN alignment|alignment|NN
Illumina|Illumina|NNP Ribozero|Ribozero|NNP rRNA|rrna|NN removal|removal|NN followed|follow|VBN by|by|IN NEB|NEB|NNP Next|next|JJ RNA|rna|NN library|library|NN Prep|Prep|NNP set|set|VBD .|.|.
Illumina|Illumina|NNP sequencing|sequencing|NN instruments|instrument|NNS generate|generate|VBP per-cycle|per-cycle|JJ BCL|BCL|NNP base|base|NN call|call|NN files|file|NNS as|as|IN primary|primary|JJ sequencing|sequencing|NN output|output|NN in|in|IN bcl2|bcl2|NN format|format|NN .|.|. Conversion|conversion|NN of|of|IN the|the|DT bcl2|bcl2|NN file|file|NN to|to|TO gzipped|gzipped|JJ fastq|fastq|NN files|file|NNS was|be|VBD performed|perform|VBN using|use|VBG the|the|DT bcl2fastq|bcl2fastq|NN script|script|NN v.|v.|CC 2.18.0.12|2.18.0.12|CD provided|provide|VBN by|by|IN Illumina|Illumina|NNP .|.|.
Image|image|NN analysis|analysis|NN was|be|VBD performed|perform|VBN with|with|IN GenePix|GenePix|NNP Pro|pro|FW 7|7|CD software|software|NN -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Device|device|NN -RRB-|-rrb-|-RRB- ,|,|, background|background|NN was|be|VBD defined|define|VBN with|with|IN the|the|DT ``|``|`` Local|local|JJ features|feature|NNS background|background|NN median|median|NN ''|''|'' method|method|NN .|.|. Quantile|quantile|JJ normalization|normalization|NN was|be|VBD applied|apply|VBN on|on|IN the|the|DT total|total|JJ number|number|NN of|of|IN spots|spot|NNS in|in|IN R|r|NN -LRB-|-lrb-|-LRB- version|version|NN 2.11.1|2.11.1|CD -RRB-|-rrb-|-RRB- with|with|IN the|the|DT LIMMA|LIMMA|NNP software|software|NN package|package|NN .|.|. Spots|spot|NNS corresponding|correspond|VBG to|to|TO the|the|DT E.|e.|FW coli|coli|FW MG1655|mg1655|NN K12|k12|NN species|species|NNS were|be|VBD extracted|extract|VBN .|.|.
Images|image|NNS Analysis|analysis|NN using|use|VBG Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP Version|Version|NNP 11.5|11.5|CD to|to|TO obtain|obtain|VB raw|raw|JJ data.Probe|data.probe|NN intensities|intensity|NNS generated|generate|VBN from|from|IN feature|feature|NN extraction|extraction|NN raw|raw|JJ data|datum|NNS were|be|VBD split|split|VBN based|base|VBN on|on|IN channel|channel|NN type|type|NN and|and|CC analysis|analysis|NN was|be|VBD performed|perform|VBN .|.|.
Images|image|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG a|a|DT combination|combination|NN of|of|IN GenePix|GenePix|NNP Pro|pro|FW 6.0|6.0|CD ,|,|, the|the|DT freely|freely|RB available|available|JJ TIGR|tigr|NN TM4|tm4|NN software|software|NN suite|suite|NN -LRB-|-lrb-|-LRB- www.tm4.org|www.tm4.org|NN -RRB-|-rrb-|-RRB- and|and|CC Microsoft|Microsoft|NNP Excel|Excel|NNP .|.|. Spots|spot|NNS with|with|IN an|a|DT intensity|intensity|NN :|:|: background|background|NN ratio|ratio|NN >|>|JJR 1.5|1.5|CD and|and|CC overall|overall|JJ intensity|intensity|NN >|>|JJR 350|350|CD in|in|IN the|the|DT reference|reference|NN channel|channel|NN and|and|CC an|a|DT intensity|intensity|NN :|:|: background|background|NN ratio|ratio|NN of|of|IN >|>|JJR 1.0|1.0|CD in|in|IN the|the|DT experimental|experimental|JJ channel|channel|NN were|be|VBD considered|consider|VBN acceptable|acceptable|JJ for|for|IN downstream|downstream|JJ processing|processing|NN .|.|. Local|local|JJ background|background|NN was|be|VBD subtracted|subtract|VBN for|for|IN each|each|DT spot|spot|NN ,|,|, the|the|DT corresponding|corresponding|JJ log2|log2|NN ratios|ratio|NNS were|be|VBD normalized|normalize|VBN using|use|VBG total|total|JJ intensity|intensity|NN normalization|normalization|NN ,|,|, and|and|CC replicate|replicate|VB spots|spot|NNS were|be|VBD averaged|average|VBN using|use|VBG TIGR|TIGR|NNP MIDAS|MIDAS|NNP .|.|. Genes|gene|NNS that|that|WDT had|have|VBD missing|missing|JJ data|datum|NNS -LRB-|-lrb-|-LRB- i.e.|i.e.|FW unacceptable|unacceptable|JJ spots|spot|NNS -RRB-|-rrb-|-RRB- for|for|IN more|more|JJR than|than|IN one-third|one-third|NN of|of|IN the|the|DT samples|sample|NNS were|be|VBD excluded|exclude|VBN from|from|IN the|the|DT downstream|downstream|JJ analysis|analysis|NN leaving|leave|VBG 3993|3993|CD ORFs|orf|NNS in|in|IN the|the|DT final|final|JJ data|data|NN set|set|NN .|.|. Each|each|DT sample|sample|NN was|be|VBD hybridized|hybridize|VBN twice|twice|RB and|and|CC the|the|DT results|result|NNS averaged|average|VBD in|in|IN Microsoft|Microsoft|NNP Excel|Excel|NNP after|after|IN processing|process|VBG with|with|IN MIDAS|MIDAS|NNP .|.|. A|a|DT strict|strict|JJ cutoff|cutoff|NN of|of|IN log2|log2|NN ratio|ratio|NN >|>|JJR 0.9|0.9|CD or|or|CC <|<|JJR 0.9|0.9|CD was|be|VBD applied|apply|VBN for|for|IN the|the|DT determination|determination|NN of|of|IN gene|gene|NN amplifications|amplification|NNS and|and|CC gene|gene|NN absences|absence|NNS ,|,|, respectively|respectively|RB .|.|.
Images|image|NNS were|be|VBD quantified|quantify|VBN and|and|CC normalized|normalize|VBN using|use|VBG extraction|extraction|NN protocol|protocol|NN GE2|ge2|NN _|_|NN 107|107|CD _|_|SYM Sept09|sept09|NN and|and|CC Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- version|version|NN 10.7.3.1|10.7.3.1|CD -RRB-|-rrb-|-RRB- .|.|.
Images|image|NNS were|be|VBD quantified|quantify|VBN using|use|VBG Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- 10.5.1.1|10.5.1.1|CD -RRB-|-rrb-|-RRB- and|and|CC obtained|obtain|VBN background|background|NN subtracted|subtract|VBN and|and|CC spatially|spatially|RB detrended|detrend|VBD Processed|processed|JJ Signal|signal|NN intensities|intensity|NNS .|.|.
Images|image|NNS were|be|VBD quantified|quantify|VBN using|use|VBG Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- version|version|NN 9.5.1.1|9.5.1.1|CD &|&|CC 10.5.1.1|10.5.1.1|CD -RRB-|-rrb-|-RRB- and|and|CC obtained|obtain|VBN background|background|NN subtracted|subtract|VBN and|and|CC spatially|spatially|RB detrended|detrend|VBD Processed|processed|JJ Signal|signal|NN intensities|intensity|NNS .|.|.
Images|image|NNS were|be|VBD quantified|quantify|VBN using|use|VBG Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- .|.|. Feature|feature|NN extracted|extract|VBN raw|raw|JJ data|datum|NNS was|be|VBD analyzed|analyze|VBN using|use|VBG GeneSpring|GeneSpring|NNP GX|GX|NNP Version|Version|NNP software|software|NN from|from|IN Agilent|Agilent|NNP .|.|. Normalization|normalization|NN of|of|IN the|the|DT data|datum|NNS was|be|VBD done|do|VBN in|in|IN GeneSpring|GeneSpring|NNP GX|GX|NNP using|use|VBG the|the|DT 75th|75th|JJ percentile|percentile|NN shift|shift|NN
Images|image|NNS were|be|VBD quantified|quantify|VBN using|use|VBG GenePix|GenePix|NNP Pro|pro|FW software|software|NN
Image|image|NN was|be|VBD analized|analize|VBN with|with|IN Genepix|Genepix|NNP 6|6|CD pro|pro|JJ followed|follow|VBN by|by|IN background|background|NN substration|substration|NN and|and|CC global|global|JJ LOWESS|lowess|NN normalization|normalization|NN in|in|IN R|r|NN environment|environment|NN -LRB-|-lrb-|-LRB- KTH|kth|NN package|package|NN -RRB-|-rrb-|-RRB- .|.|. Spots|spot|NNS with|with|IN signal|signal|NN to|to|TO noise|noise|NN ratio|ratio|NN lower|lower|JJR that|that|IN 3|3|CD and/or|and/or|CC relative|relative|JJ standard|standard|JJ deviation|deviation|NN between|between|IN parallel|parallel|JJ spots|spot|NNS greater|greater|JJR than|than|IN 20|20|CD %|%|NN were|be|VBD removed|remove|VBN .|.|.
Immediately|immediately|RB after|after|IN turning|turn|VBG off|off|RP oxygen|oxygen|NN
Immunoprecipitated|immunoprecipitate|VBN DNA|dna|NN
imp|imp|NN mutation|mutation|NN :|:|: contains|contain|VBZ a|a|DT 23|23|CD codon|codon|NN deletion|deletion|NN allele|allele|NN in|in|IN imp|imp|NN -LRB-|-lrb-|-LRB- increased|increase|VBN membrane|membrane|NN permeability|permeability|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN the|the|DT 93th|93th|JJ codon|codon|NN of|of|IN fabI|fabi|NN ,|,|, NTG|NTG|NNP treatment|treatment|NN ;|;|: fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN Gly|gly|NN -LRB-|-lrb-|-LRB- the|the|DT 93th|93th|JJ codon|codon|NN -RRB-|-rrb-|-RRB- of|of|IN fabI|fabi|NN with|with|IN Val|val|NN ,|,|, NTG|NTG|NNP treatment|treatment|NN to|to|TO be|be|VB high|high|JJ resistance|resistance|NN to|to|TO triclosan|triclosan|NN
imp|imp|NN mutation|mutation|NN :|:|: contains|contain|VBZ a|a|DT 23|23|CD codon|codon|NN deletion|deletion|NN allele|allele|NN in|in|IN imp|imp|NN -LRB-|-lrb-|-LRB- increased|increase|VBN membrane|membrane|NN permeability|permeability|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN the|the|DT 94th|94th|JJ codon|codon|NN of|of|IN fabI|fabi|NN ,|,|, NTG|NTG|NNP treatment|treatment|NN ;|;|: fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN Gly|gly|NN -LRB-|-lrb-|-LRB- the|the|DT 94th|94th|JJ codon|codon|NN -RRB-|-rrb-|-RRB- of|of|IN fabI|fabi|NN with|with|IN Val|val|NN ,|,|, NTG|NTG|NNP treatment|treatment|NN to|to|TO be|be|VB high|high|JJ resistance|resistance|NN to|to|TO triclosan|triclosan|NN
imp|imp|NN mutation|mutation|NN :|:|: contains|contain|VBZ a|a|DT 23|23|CD codon|codon|NN detion|detion|NN allele|allele|NN in|in|IN imp|imp|NN -LRB-|-lrb-|-LRB- increased|increase|VBN membrane|membrane|NN permeability|permeability|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN the|the|DT 93th|93th|JJ codon|codon|NN of|of|IN fabI|fabi|NN ;|;|: fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN Gly|gly|NN -LRB-|-lrb-|-LRB- the|the|DT 93th|93th|JJ codon|codon|NN -RRB-|-rrb-|-RRB- of|of|IN fabI|fabi|NN with|with|IN Val|val|NN
imp|imp|NN mutation|mutation|NN :|:|: contains|contain|VBZ a|a|DT 23|23|CD codon|codon|NN detion|detion|NN allele|allele|NN in|in|IN imp|imp|NN -LRB-|-lrb-|-LRB- increased|increase|VBN membrane|membrane|NN permeability|permeability|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN the|the|DT 94th|94th|JJ codon|codon|NN of|of|IN fabI|fabi|NN ;|;|: fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN Gly|gly|NN -LRB-|-lrb-|-LRB- the|the|DT 94th|94th|JJ codon|codon|NN -RRB-|-rrb-|-RRB- of|of|IN fabI|fabi|NN with|with|IN Val|val|NN
incubated|incubate|VBN with|with|IN :|:|: Drosophila|drosophila|FW immune|immune|JJ proteins|protein|NNS
incubated|incubate|VBN with|with|IN :|:|: GST|gst|NN alone|alone|RB -LRB-|-lrb-|-LRB- 3|3|CD μM|μm|NN ;|;|: control|control|NN -RRB-|-rrb-|-RRB-
Incubation|incubation|NN and|and|CC RNA|rna|NN harvesting|harvesting|NN were|be|VBD carried|carry|VBN out|out|RP for|for|IN all|all|DT samples|sample|NNS simultaneously|simultaneously|RB and|and|CC under|under|IN RNase-free|rnase-free|JJ conditions|condition|NNS to|to|TO minimize|minimize|VB biological|biological|JJ variability|variability|NN in|in|IN gene|gene|NN expression|expression|NN between|between|IN each|each|DT sample|sample|NN .|.|. Bacterial|bacterial|JJ concentrations|concentration|NNS were|be|VBD equalized|equalize|VBN to|to|TO the|the|DT same|same|JJ density|density|NN -LRB-|-lrb-|-LRB- by|by|IN OD600|od600|NN -RRB-|-rrb-|-RRB- .|.|.
incubation|incubation|NN condition|condition|NN :|:|: In|in|IN the|the|DT dark|dark|NN ,|,|, 5h|5h|NN ,|,|, 20|20|CD °C|°c|NN ,|,|, 150|150|CD rpm|rpm|NN
incubation|incubation|NN duration|duration|NN :|:|: 10|10|CD min|min|NN
incubation|incubation|NN medium|medium|NN :|:|: 10|10|CD mM|mm|NN NaCl|nacl|NN
incubation|incubation|NN medium|medium|NN :|:|: 10|10|CD mM|mm|NN NaCl|nacl|NN +|+|CC 100mg/l|100mg/l|CD TiO2|tio2|NN nanoparticles|nanoparticle|NNS
Incubation|incubation|NN temperature|temperature|NN =|=|JJ 37C|37c|NN
incubation|incubation|NN time|time|NN :|:|: 0|0|CD min|min|NN
incubation|incubation|NN time|time|NN :|:|: 10|10|CD min|min|NN
incubation|incubation|NN time|time|NN :|:|: 5|5|CD hr|hr|NN
incubation|incubation|NN time|time|NN :|:|: n/a|n/a|NN
Index|Index|NNP and|and|CC sort|sort|NN alignments|alignment|NNS with|with|IN samtools|samtool|NNS version|version|NN 1.2|1.2|CD
Index|Index|NNP sequences|sequence|NNS accompanying|accompany|VBG with|with|IN reads|read|VBZ were|be|VBD compared|compare|VBN with|with|IN pre-designed|pre-designed|JJ barcodes|barcode|NNS ,|,|, allowing|allow|VBG two|two|CD base|base|NN mismatches|mismatch|NNS at|at|IN most|most|JJS .|.|.
Indices|Indices|NNPS corresponding|correspond|VBG to|to|TO the|the|DT same|same|JJ sample|sample|NN were|be|VBD merged|merge|VBN ,|,|, and|and|CC then|then|RB uploaded|upload|VBD to|to|TO a|a|DT cloud-based|cloud-based|JJ variant|variant|NN of|of|IN Galaxy|Galaxy|NNP named|name|VBD RNA23|RNA23|NNP Rocket|Rocket|NNP
individual|individual|NN :|:|: CF|cf|NN patient|patient|NN
Individual|Individual|NNP clones|clone|NNS of|of|IN E.|e.|FW coli|coli|FW DH1|dh1|NN were|be|VBD grown|grow|VBN in|in|IN M9|M9|NNP MOPS|MOPS|NNP media|media|NNS in|in|IN 300|300|CD mL|ml|NN media|media|NNS in|in|IN 1|1|CD L|l|NN baffled|baffle|VBD flasks|flask|NNS
Individual|Individual|NNP colonies|colony|NNS were|be|VBD inoculated|inoculate|VBN into|into|IN MOPS|MOPS|NNP EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN -LRB-|-lrb-|-LRB- Teknova|teknova|NN ,|,|, CA|CA|NNP ,|,|, M2105|m2105|NN -RRB-|-rrb-|-RRB- with|with|IN 0.2|0.2|CD %|%|NN glycerol|glycerol|NN carbon|carbon|NN source|source|NN and|and|CC 50|50|CD μg/mL|μg/ml|NN kanamycin|kanamycin|NN -LRB-|-lrb-|-LRB- Gold|gold|NN Biotechnology|biotechnology|NN ,|,|, MO|MO|NNP ,|,|, K-120-5|k-120-5|NN -RRB-|-rrb-|-RRB- and|and|CC grown|grow|VBN overnight|overnight|JJ for|for|IN 16|16|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN and|and|CC 1000|1000|CD RPM|RPM|NNP in|in|IN V-bottom|V-bottom|NNP 96-well|96-well|JJ plates|plate|NNS -LRB-|-lrb-|-LRB- Nunc|Nunc|NNP ,|,|, Roskilde|Roskilde|NNP ,|,|, Denmark|Denmark|NNP ,|,|, 249952|249952|CD -RRB-|-rrb-|-RRB- in|in|IN an|a|DT ELMI|ELMI|NNP Digital|Digital|NNP Thermos|Thermos|NNP Microplates|Microplates|NNP shaker|shaker|NN incubator|incubator|NN -LRB-|-lrb-|-LRB- Elmi|Elmi|NNP Ltd|Ltd|NNP ,|,|, Riga|Riga|NNP ,|,|, Latvia|Latvia|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT following|follow|VBG day|day|NN ,|,|, cultures|culture|NNS were|be|VBD diluted|dilute|VBN 178-fold|178-fold|JJ -LRB-|-lrb-|-LRB- two|two|CD serial|serial|JJ dilutions|dilution|NNS of|of|IN 15|15|CD µL|µl|NN into|into|IN 185|185|CD µL|µl|NN -RRB-|-rrb-|-RRB- into|into|IN EZ|ez|NN Rich|rich|JJ glycerol|glycerol|NN with|with|IN kanamycin|kanamycin|NN ,|,|, and|and|CC grown|grow|VBN under|under|IN the|the|DT same|same|JJ ELMI|elmi|NN shaker|shaker|NN incubator|incubator|NN conditions|condition|NNS for|for|IN three|three|CD hours|hour|NNS .|.|. Cells|cell|NNS were|be|VBD diluted|dilute|VBN 658-fold|658-fold|JJ -LRB-|-lrb-|-LRB- 4.56|4.56|CD µL|µl|NN into|into|IN 3|3|CD mL|ml|NN -RRB-|-rrb-|-RRB- into|into|IN culture|culture|NN tubes|tube|NNS -LRB-|-lrb-|-LRB- Falcon|Falcon|NNP 14|14|CD mL|ml|NN round-bottom|round-bottom|JJ polypropylene|polypropylene|NN tubes|tube|NNS ;|;|: Corning|Corning|NNP ,|,|, MA|MA|NNP ,|,|, 352059|352059|CD -RRB-|-rrb-|-RRB- containing|contain|VBG EZ|ez|NN Rich|rich|JJ glycerol|glycerol|NN with|with|IN kanamycin|kanamycin|NN and|and|CC inducers|inducer|NNS .|.|. For|for|IN Erlenmeyer|Erlenmeyer|NNP flask|flask|NN assays|assay|NNS -LRB-|-lrb-|-LRB- Pyrex|pyrex|NN 250|250|CD mL|ml|NN ;|;|: Cole-Palmer|Cole-Palmer|NNP ,|,|, IL|il|NN ,|,|, 4980-250|4980-250|CD -RRB-|-rrb-|-RRB- ,|,|, cells|cell|NNS were|be|VBD diluted|dilute|VBN 658-fold|658-fold|JJ -LRB-|-lrb-|-LRB- 76|76|CD µL|µl|NN into|into|IN 50|50|CD mL|ml|NN -RRB-|-rrb-|-RRB- into|into|IN EZ|ez|NN Rich|rich|JJ glycerol|glycerol|NN with|with|IN kanamycin|kanamycin|NN and|and|CC inducers|inducer|NNS .|.|. Eight|eight|CD inducer|inducer|NN combinations|combination|NNS were|be|VBD used|use|VBN that|that|IN cover|cover|VBP the|the|DT presence|presence|NN or|or|CC absence|absence|NN of|of|IN 0.5|0.5|CD mM|mm|NN IPTG|iptg|NN ,|,|, 10|10|CD ng/mL|ng/ml|NN aTc|atc|NN ,|,|, and|and|CC 5|5|CD mM|mm|NN L-arabinose|l-arabinose|NN .|.|. Culture|culture|NN tubes|tube|NNS were|be|VBD then|then|RB grown|grow|VBN in|in|IN an|a|DT Innova|Innova|NNP 44|44|CD shaker|shaker|NN -LRB-|-lrb-|-LRB- Eppendorf|eppendorf|NN ,|,|, CT|ct|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN and|and|CC 250|250|CD rpm|rpm|NN for|for|IN five|five|CD hours|hour|NNS .|.|.
Individual|Individual|NNP colonies|colony|NNS were|be|VBD inoculated|inoculate|VBN into|into|IN MOPS|MOPS|NNP EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN -LRB-|-lrb-|-LRB- Teknova|teknova|NN ,|,|, CA|CA|NNP ,|,|, M2105|m2105|NN -RRB-|-rrb-|-RRB- with|with|IN 0.2|0.2|CD %|%|NN glycerol|glycerol|NN carbon|carbon|NN source|source|NN and|and|CC 50|50|CD μg/mL|μg/ml|NN kanamycin|kanamycin|NN -LRB-|-lrb-|-LRB- Gold|gold|NN Biotechnology|biotechnology|NN ,|,|, MO|MO|NNP ,|,|, K-120-5|k-120-5|NN -RRB-|-rrb-|-RRB- and|and|CC grown|grow|VBN overnight|overnight|JJ for|for|IN 16|16|CD hours|hour|NNS at|at|IN 37|37|CD °C|°c|NN and|and|CC 1000|1000|CD RPM|RPM|NNP in|in|IN V-bottom|V-bottom|NNP 96-well|96-well|JJ plates|plate|NNS -LRB-|-lrb-|-LRB- Nunc|Nunc|NNP ,|,|, Roskilde|Roskilde|NNP ,|,|, Denmark|Denmark|NNP ,|,|, 249952|249952|CD -RRB-|-rrb-|-RRB- in|in|IN an|a|DT ELMI|ELMI|NNP Digital|Digital|NNP Thermos|Thermos|NNP Microplates|Microplates|NNP shaker|shaker|NN incubator|incubator|NN -LRB-|-lrb-|-LRB- Elmi|Elmi|NNP Ltd|Ltd|NNP ,|,|, Riga|Riga|NNP ,|,|, Latvia|Latvia|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT following|follow|VBG day|day|NN ,|,|, cultures|culture|NNS were|be|VBD diluted|dilute|VBN 178-fold|178-fold|JJ -LRB-|-lrb-|-LRB- two|two|CD serial|serial|JJ dilutions|dilution|NNS of|of|IN 15|15|CD µL|µl|NN into|into|IN 185|185|CD µL|µl|NN -RRB-|-rrb-|-RRB- into|into|IN EZ|ez|NN Rich|rich|JJ glycerol|glycerol|NN with|with|IN kanamycin|kanamycin|NN ,|,|, and|and|CC grown|grow|VBN under|under|IN the|the|DT same|same|JJ ELMI|elmi|NN shaker|shaker|NN incubator|incubator|NN conditions|condition|NNS for|for|IN three|three|CD hours|hour|NNS .|.|. For|for|IN culture|culture|NN tube|tube|NN assays|assay|NNS -LRB-|-lrb-|-LRB- Falcon|Falcon|NNP 14|14|CD mL|ml|NN round-bottom|round-bottom|JJ polypropylene|polypropylene|NN tubes|tube|NNS ;|;|: Corning|Corning|NNP ,|,|, MA|MA|NNP ,|,|, 352059|352059|CD -RRB-|-rrb-|-RRB- ,|,|, cells|cell|NNS were|be|VBD diluted|dilute|VBN 658-fold|658-fold|JJ -LRB-|-lrb-|-LRB- 4.56|4.56|CD µL|µl|NN into|into|IN 3|3|CD mL|ml|NN -RRB-|-rrb-|-RRB- into|into|IN EZ|ez|NN Rich|rich|JJ glycerol|glycerol|NN with|with|IN kanamycin|kanamycin|NN and|and|CC inducers|inducer|NNS .|.|. For|for|IN Erlenmeyer|Erlenmeyer|NNP flask|flask|NN assays|assay|NNS -LRB-|-lrb-|-LRB- Pyrex|pyrex|NN 250|250|CD mL|ml|NN ;|;|: Cole-Palmer|Cole-Palmer|NNP ,|,|, IL|il|NN ,|,|, 4980-250|4980-250|CD -RRB-|-rrb-|-RRB- ,|,|, cells|cell|NNS were|be|VBD diluted|dilute|VBN 658-fold|658-fold|JJ -LRB-|-lrb-|-LRB- 76|76|CD µL|µl|NN into|into|IN 50|50|CD mL|ml|NN -RRB-|-rrb-|-RRB- into|into|IN EZ|ez|NN Rich|rich|JJ glycerol|glycerol|NN with|with|IN kanamycin|kanamycin|NN and|and|CC inducers|inducer|NNS .|.|. Eight|eight|CD inducer|inducer|NN combinations|combination|NNS were|be|VBD used|use|VBN that|that|IN cover|cover|VBP the|the|DT presence|presence|NN or|or|CC absence|absence|NN of|of|IN 0.5|0.5|CD mM|mm|NN IPTG|iptg|NN ,|,|, 10|10|CD ng/mL|ng/ml|NN aTc|atc|NN ,|,|, and|and|CC 5|5|CD mM|mm|NN L-arabinose|l-arabinose|NN .|.|. Culture|culture|NN tubes|tube|NNS and|and|CC Erlenmeyer|Erlenmeyer|NNP flasks|flask|NNS were|be|VBD then|then|RB grown|grow|VBN in|in|IN an|a|DT Innova|Innova|NNP 44|44|CD shaker|shaker|NN -LRB-|-lrb-|-LRB- Eppendorf|eppendorf|NN ,|,|, CT|ct|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN and|and|CC 250|250|CD rpm|rpm|NN for|for|IN five|five|CD hours|hour|NNS .|.|.
individual|individual|NN :|:|: healthy|healthy|JJ child|child|NN
Indole|Indole|NNP treated|treat|VBN at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 0h|0h|NN
Indole|indole|FW treated|treat|VBN at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 10h|10h|JJ
Indole|indole|FW treated|treat|VBN at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 16h|16h|JJ
Indole|indole|FW treated|treat|VBN at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 5h|5h|JJ
Indole|indole|FW treated|treat|VBN at|at|IN specific|specific|JJ growth|growth|NN rate|rate|NN 0.5h-1|0.5h-1|JJ 8h|8h|NN
Induced|induce|VBN from|from|IN E.|e.|FW coli|coli|FW strain|strain|NN 3538|3538|CD with|with|IN mitomycin|mitomycin|NN C|c|NN
induced/non-induced|induced/non-induced|JJ :|:|: Induced|induce|VBN
induced/non-induced|induced/non-induced|JJ :|:|: Non-induced|non-induced|JJ
induction|induction|NN :|:|: 0.2|0.2|CD %|%|NN arabinose|arabinose|NN
induction|induction|NN :|:|: induced|induce|VBN 50|50|CD µM|µm|NN IPTG|iptg|NN
induction|induction|NN :|:|: None|none|NN
Infected|infected|JJ kidney|kidney|NN solutions|solution|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 5000xg|5000xg|CD for|for|IN 10|10|CD min|min|NN to|to|TO separate|separate|JJ bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- pellet|pellet|NN -RRB-|-rrb-|-RRB- from|from|IN kidney|kidney|NN -LRB-|-lrb-|-LRB- surface|surface|NN of|of|IN RNA-later|rna-later|NN solution|solution|NN -RRB-|-rrb-|-RRB- cells|cell|NNS .|.|. The|the|DT kidney|kidney|NN cells|cell|NNS were|be|VBD evacuated|evacuate|VBN from|from|IN the|the|DT top|top|NN of|of|IN the|the|DT solution|solution|NN ,|,|, and|and|CC the|the|DT remaining|remain|VBG solution|solution|NN was|be|VBD spun|spin|VBN once|once|RB more|more|RBR at|at|IN 12000xg|12000xg|CD for|for|IN 10|10|CD min|min|NN ,|,|, followed|follow|VBN by|by|IN disposal|disposal|NN of|of|IN the|the|DT supernatant|supernatant|NN .|.|. Pelleted|pelleted|JJ cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN TE|TE|NNP buffer|buffer|NN and|and|CC treated|treat|VBN with|with|IN lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- at|at|IN 1mg/ml|1mg/ml|CD final|final|JJ concentration|concentration|NN for|for|IN 5|5|CD min|min|NN ,|,|, and|and|CC samples|sample|NNS of|of|IN 3-5|3-5|CD infected|infected|JJ mice|mouse|NNS were|be|VBD pooled|pool|VBN together|together|RB for|for|IN each|each|DT infection|infection|NN group|group|NN .|.|. Nucleic|nucleic|JJ acids|acid|NNS were|be|VBD extracted|extract|VBN via|via|IN the|the|DT RNA|rna|NN extraction|extraction|NN protocol|protocol|NN and|and|CC products|product|NNS of|of|IN the|the|DT RNAeasy|RNAeasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. Following|follow|VBG column|column|NN purification|purification|NN ,|,|, RNA|rna|NN samples|sample|NNS were|be|VBD treated|treat|VBN with|with|IN DNAse|dnase|NN Turbo|Turbo|NNP -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD min|min|NN at|at|IN 37C|37c|NN ,|,|, followed|follow|VBN by|by|IN quantification|quantification|NN of|of|IN RNA|rna|NN using|use|VBG a|a|DT spectrophotometer|spectrophotometer|NN .|.|. Remaining|remain|VBG polyadenylated|polyadenylated|JJ eukaryotic|eukaryotic|JJ RNA|rna|NN was|be|VBD depleted|deplete|VBN from|from|IN the|the|DT samples|sample|NNS following|follow|VBG the|the|DT MicroEnrich|MicroEnrich|NNP -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- protocol|protocol|NN and|and|CC resuspended|resuspend|VBN in|in|IN 20|20|CD l|l|NN of|of|IN TE|TE|NNP buffer|buffer|NN .|.|. RNA|rna|NN was|be|VBD quantified|quantify|VBN spectrophotometrically|spectrophotometrically|RB and|and|CC equal|equal|JJ amounts|amount|NNS -LRB-|-lrb-|-LRB- ~|~|CD 300-500ng|300-500ng|JJ -RRB-|-rrb-|-RRB- of|of|IN KMD|kmd|NN and|and|CC PC1012|pc1012|NN RNA|rna|NN samples|sample|NNS were|be|VBD subjected|subject|VBN to|to|TO the|the|DT MessageAmp|MessageAmp|NNP -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- RNA|rna|NN amplification|amplification|NN protocol|protocol|NN .|.|. Resultant|resultant|JJ amplified|amplify|VBN RNA|rna|NN was|be|VBD quantified|quantify|VBN and|and|CC equal|equal|JJ amounts|amount|NNS were|be|VBD used|use|VBN in|in|IN the|the|DT Affymetrix|Affymetrix|NNP protocol|protocol|NN for|for|IN prokaryotic|prokaryotic|JJ cDNA|cdna|NN synthesis|synthesis|NN and|and|CC biotin|biotin|NN labeling|labeling|NN .|.|.
infection|infection|NN :|:|: T7|t7|NN
infinity|infinity|NN .|.|. These|these|DT values|value|NNS were|be|VBD eliminated|eliminate|VBN using|use|VBG the|the|DT find|find|VB ,|,|, imag|imag|NN ,|,|, and|and|CC isfinite|isfinite|NN functions|function|NNS in|in|IN Matlab|Matlab|NNP .|.|.
inhibitor|inhibitor|NN :|:|: 20uM|20um|NN ME0052|me0052|NN
inhibitor|inhibitor|NN :|:|: 20uM|20um|NN ME0053|me0053|NN
inhibitor|inhibitor|NN :|:|: 20uM|20um|NN ME0054|me0054|NN
inhibitor|inhibitor|NN :|:|: 20uM|20um|NN ME0055|me0055|NN
Initial|initial|JJ data|data|NN analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT GeneChip|GeneChip|NNP ®|®|NNP Operating|Operating|NNP Software|Software|NNP .|.|. Microarray|microarray|NN quality|quality|NN control|control|NN parameters|parameter|NNS were|be|VBD as|as|IN follow|follow|VB :|:|: noise|noise|NN -LRB-|-lrb-|-LRB- RawQ|rawq|NN -RRB-|-rrb-|-RRB- less|less|JJR than|than|IN 5|5|CD ,|,|, background|background|NN signal|signal|NN less|less|JJR than|than|IN 40|40|CD -LRB-|-lrb-|-LRB- 100|100|CD target|target|NN intensity|intensity|NN for|for|IN array|array|NN scaling|scaling|NN -RRB-|-rrb-|-RRB- ,|,|, consistent|consistent|JJ numbers|number|NNS of|of|IN genes|gene|NNS detected|detect|VBN as|as|IN present|present|JJ across|across|IN arrays|array|NNS .|.|.
in|in|IN Microsoft|Microsoft|NNP Excel|Excel|NNP ,|,|, containing|contain|VBG the|the|DT following|follow|VBG information|information|NN for|for|IN each|each|DT of|of|IN the|the|DT 14,352|14,352|CD entries|entry|NNS :|:|: block|block|NN
In|in|IN order|order|NN to|to|TO distinguish|distinguish|VB between|between|IN 3|3|CD '|'|'' ends|end|NNS of|of|IN transient|transient|JJ products|product|NNS of|of|IN RNA|rna|NN metabolism|metabolism|NN and|and|CC stable|stable|JJ 3|3|CD '|'|'' ends|end|VBZ ,|,|, we|we|PRP developed|develop|VBD an|a|DT algorithm|algorithm|NN to|to|TO call|call|VB coverage|coverage|NN peaks|peak|NNS .|.|. The|the|DT algorithm|algorithm|NN will|will|MD be|be|VB discussed|discuss|VBN in|in|IN detail|detail|NN in|in|IN an|a|DT upcoming|upcoming|JJ manuscript|manuscript|NN ,|,|, and|and|CC the|the|DT scripts|script|NNS used|use|VBN are|be|VBP available|available|JJ upon|upon|IN request|request|NN from|from|IN the|the|DT authors|author|NNS .|.|. In|in|IN short|short|RB ,|,|, positions|position|NNS in|in|IN the|the|DT E.|e.|FW coli|coli|FW genome|genome|NN were|be|VBD considered|consider|VBN in|in|IN descending|descend|VBG order|order|NN of|of|IN coverage|coverage|NN and|and|CC assigned|assign|VBN a|a|DT p-value|p-value|NN based|base|VBN on|on|IN a|a|DT Poisson|Poisson|NNP distribution|distribution|NN parameterized|parameterize|VBN by|by|IN the|the|DT mean|mean|NN coverage|coverage|NN of|of|IN all|all|DT covered|cover|VBN bases|basis|NNS in|in|IN the|the|DT genome|genome|NN .|.|. Peaks|peak|NNS were|be|VBD rejected|reject|VBN if|if|IN their|they|PRP$ p-values|p-value|NNS exceeded|exceed|VBD 1e-4|1e-4|NN or|or|CC if|if|IN there|there|EX existed|exist|VBD a|a|DT >|>|JJR 10-bp|10-bp|JJ window|window|NN containing|contain|VBG the|the|DT peak|peak|NN in|in|IN which|which|WDT all|all|DT positions|position|NNS were|be|VBD within|within|IN 2-fold|2-fold|JJ coverage|coverage|NN of|of|IN the|the|DT peak|peak|JJ position|position|NN .|.|. Parameters|parameter|NNS were|be|VBD chosen|choose|VBN based|base|VBN on|on|IN analysis|analysis|NN of|of|IN annotated|annotated|JJ 3|3|CD '|'|'' ends|end|VBZ as|as|RB well|well|RB as|as|IN qualitative|qualitative|JJ analysis|analysis|NN of|of|IN peaks|peak|NNS .|.|. This|this|DT resulted|result|VBD in|in|IN 20,019|20,019|CD peaks|peak|NNS .|.|.
In|in|IN order|order|NN to|to|TO generate|generate|VB the|the|DT VBNC|vbnc|JJ state|state|NN in|in|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN ,|,|, 20|20|CD mL|ml|NN of|of|IN the|the|DT exponential-phase|exponential-phase|NN cell|cell|NN suspensions|suspension|NNS in|in|IN a|a|DT 50|50|CD mL|ml|NN sterile|sterile|JJ glass|glass|NN tube|tube|NN was|be|VBD treated|treat|VBN by|by|IN HPCD|hpcd|NN at|at|IN 5|5|CD MPa|mpa|NN and|and|CC 25|25|CD ℃|℃|NN for|for|IN 40|40|CD min|min|NN .|.|.
INPUT|INPUT|NNP ChIP|chip|NN DNA|dna|NN from|from|IN ∆|∆|CD hns|hn|NNS /|/|: ∆|∆|SYM stpA|stpa|NN ,|,|, no|no|DT antibody|antibody|NN control|control|NN
INPUT|INPUT|NNP ChIP|chip|NN DNA|dna|NN from|from|IN PK9416|pk9416|NN ,|,|, no|no|DT ArcA|arca|NN control|control|NN
INPUT|INPUT|NNP ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherchia|Escherchia|NNP coli|coli|NN MG1655|mg1655|NN K-12|k-12|NN ,|,|, no|no|DT antibody|antibody|NN control|control|NN
INPUT|INPUT|NNP ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherchia|Escherchia|NNP coli|coli|NN MG1655|mg1655|NN K-12|k-12|NN ,|,|, no|no|DT antibody|antibody|NN control|control|NN ,|,|, Replicate|replicate|VB B|b|NN
INPUT|input|VBP ChIP|chip|NN DNA|dna|NN from|from|IN WTPK4854|wtpk4854|NN ,|,|, no|no|DT antibody|antibody|NN control|control|NN
Input|Input|NNP ChIP-Seq|ChIP-Seq|NNP
INPUT|INPUT|NNP _|_|SYM ChIP-seq|ChIP-seq|NNP _|_|NNP Aerobic|Aerobic|NNP _|_|SYM WIG.wig|WIG.wig|NNP :|:|: U00096|u00096|NN .2|.2|NN
INPUT|input|VBP _|_|SYM ChIP-seq|ChIP-seq|NNP _|_|SYM Anaerobic|anaerobic|JJ _|_|NN WIG.wig|wig.wig|NN :|:|: U00096|u00096|NN .2|.2|NN
input|input|NN DNA|dna|NN
INPUT|input|NN DNA|dna|NN B|b|NN
Input|input|NN DNA|dna|NN from|from|IN DdksA|ddksa|NN cells|cell|NNS
Input|Input|NNP DNA|dna|NN from|from|IN E.|E.|NNP Coli|Coli|NNP MG1655|MG1655|NNP
Input|Input|NNP DNA|dna|NN from|from|IN E.|E.|NNP Coli|Coli|NNP MG1655|MG1655|NNP ΔseqA|ΔseqA|NNP
Input|Input|NNP DNA|dna|NN from|from|IN heat-shocked|heat-shocked|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
Input|Input|NNP DNA|dna|NN from|from|IN MDS42|mds42|NN cells|cell|NNS
Input|Input|NNP DNA|dna|NN from|from|IN MDS42|mds42|NN ΔnusA|δnusa|NN *|*|SYM cells|cell|NNS
Input|Input|NNP DNA|dna|NN from|from|IN MDS42|mds42|NN ΔnusG|δnusg|NN cells|cell|NNS
Input|Input|NNP DNA|dna|NN from|from|IN MG1655|mg1655|NN cells|cell|NNS
Input|Input|NNP DNA|dna|NN from|from|IN MG1655|mg1655|NN Δhns|δhns|NN cells|cell|NNS
Input|Input|NNP DNA|dna|NN from|from|IN mid-exponential|mid-exponential|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
Input|Input|NNP DNA|dna|NN from|from|IN mid-exponential|mid-exponential|JJ condition|condition|NN with|with|IN rifampicin|rifampicin|NN treatment|treatment|NN
Input|Input|NNP DNA|dna|NN from|from|IN nitrogen-limiting|nitrogen-limiting|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
Input|Input|NNP DNA|dna|NN from|from|IN SeqA|seqa|NN ChIP|chip|NN supernatant|supernatant|JJ
Input|input|NN DNA|dna|NN from|from|IN starved|starve|VBN DdksA|ddksa|NN cells|cell|NNS
Input|Input|NNP DNA|dna|NN from|from|IN starved|starve|VBN wt|wt|JJ cells|cell|NNS
Input|input|NN DNA|dna|NN from|from|IN stationary|stationary|JJ condition|condition|NN without|without|IN rifampicin|rifampicin|NN treatment|treatment|NN
Input|Input|NNP DNA|dna|NN from|from|IN wt|wt|JJ cells|cell|NNS
Input|input|NN DNA|dna|NN from|from|IN ΔseqA-SeqA|δseqa-seqa|NN ChIP|chip|NN supernatant|supernatant|JJ
Input|input|NN DNA|dna|NN from|from|IN σ32|σ32|NN ChIP|chip|NN supernatant|supernatant|JJ
Input|input|NN ∆|∆|CD fur|fur|NN Anaerobic|anaerobic|JJ
Input|input|NN _|_|CD hns-F|hns-f|NN _|_|SYM bcm|bcm|SYM -|-|: #|#|# 1|1|CD
Input|Input|NNP _|_|SYM hns-F|hns-f|JJ _|_|NN bcm|bcm|NN +|+|CC #|#|# 1|1|CD
Input|Input|NNP _|_|SYM hns-F|hns-f|JJ _|_|NN bcm|bcm|NN -|-|: #|#|# 2|2|CD
Input|Input|NNP _|_|SYM hns-F|hns-f|JJ _|_|NN bcm|bcm|NN +|+|CC #|#|# 2|2|CD
Input|Input|NNP ParC-flag|ParC-flag|NNP 1|1|CD
Input|Input|NNP ParE-flag|ParE-flag|NNP 1|1|CD
Input|Input|NNP ParE-flag|ParE-flag|NNP 2|2|CD
Input|Input|NNP ParE-flag|ParE-flag|NNP G1|g1|NN
Input|Input|NNP ParE-flag|ParE-flag|NNP G2|g2|NN
Input|Input|NNP ParE-flag|ParE-flag|NNP S20min|S20min|NNP
Input|Input|NNP ParE-flag|ParE-flag|NNP S40min|s40min|NN
input|input|NN signal|signal|NN frequency|frequency|NN :|:|: 1/1200|1/1200|CD Hz|hz|NN
input|input|NN signal|signal|NN frequency|frequency|NN :|:|: 1/2400|1/2400|CD Hz|hz|NN
input|input|NN signal|signal|NN frequency|frequency|NN :|:|: 1/3600|1/3600|CD Hz|hz|NN
input|input|NN signal|signal|NN frequency|frequency|NN :|:|: 1/600|1/600|CD Hz|hz|NN
input|input|NN signal|signal|NN frequency|frequency|NN :|:|: 1/900|1/900|CD Hz|hz|NN
intensities|intensity|NNS ,|,|, respectively|respectively|RB .|.|. In|in|IN some|some|DT cases|case|NNS ,|,|, when|when|WRB the|the|DT intensity|intensity|NN of|of|IN the|the|DT background|background|NN was|be|VBD higher|higher|JJR
Intensity|intensity|NN measures|measure|NNS in|in|IN wild|wild|JJ type|type|NN strain|strain|NN ,|,|, replicate|replicate|VBP 1|1|CD
Intensity|intensity|NN measures|measure|NNS in|in|IN wild|wild|JJ type|type|NN strain|strain|NN ,|,|, replicate|replicate|VB 2|2|CD
Intensity|intensity|NN measures|measure|NNS in|in|IN yajL|yajl|NN mutant|mutant|JJ strain|strain|NN ,|,|, replicate|replicate|VBP 1|1|CD
Intensity|intensity|NN measures|measure|NNS in|in|IN yajL|yajl|NN mutant|mutant|JJ strain|strain|NN ,|,|, replicate|replicate|VB 2|2|CD
In|in|IN the|the|DT 15|15|CD ml|ml|NN centrifuge|centrifuge|NN tube|tube|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP ,|,|, 430791|430791|CD -RRB-|-rrb-|-RRB- ,|,|, the|the|DT overnight|overnight|JJ culture|culture|NN was|be|VBD diluted|dilute|VBN to|to|TO 2|2|CD ml|ml|NN in|in|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN containing|contain|VBG Ampicillin|ampicillin|NN -LRB-|-lrb-|-LRB- 50|50|CD ng/μl|ng/μl|NN -RRB-|-rrb-|-RRB- ,|,|, Chloramphenicol|chloramphenicol|NN -LRB-|-lrb-|-LRB- 170|170|CD ng/μl|ng/μl|NN -RRB-|-rrb-|-RRB- and|and|CC IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mM|mm|NN -RRB-|-rrb-|-RRB- to|to|TO reach|reach|VB OD600|od600|NN =|=|JJ 0.01|0.01|CD .|.|. The|the|DT LED|LED|NNP tube|tube|NN was|be|VBD screwed|screw|VBN into|into|IN the|the|DT centrifuge|centrifuge|NN tube|tube|NN and|and|CC connected|connect|VBN with|with|IN the|the|DT control|control|NN box|box|NN .|.|. Then|then|RB the|the|DT power|power|NN of|of|IN the|the|DT control|control|NN box|box|NN was|be|VBD turned|turn|VBN on|on|RB and|and|CC the|the|DT LED|lead|VBN frequency|frequency|NN input|input|NN was|be|VBD generated|generate|VBN .|.|. At|at|IN last|last|JJ ,|,|, the|the|DT 15|15|CD ml|ml|NN centrifuge|centrifuge|NN tube|tube|NN with|with|IN LED|lead|VBN tube|tube|NN was|be|VBD put|put|VBN into|into|IN the|the|DT Thermomixer|Thermomixer|NNP comfort|comfort|NN -LRB-|-lrb-|-LRB- Eppendorf|eppendorf|NN -RRB-|-rrb-|-RRB- and|and|CC shaken|shake|VBN at|at|IN 650|650|CD rpm|rpm|NN and|and|CC 37|37|CD °C|°c|NN for|for|IN 10|10|CD hours|hour|NNS .|.|.
In|in|FW vitro|vitro|FW RNA|rna|NN preparation|preparation|NN :|:|: The|the|DT 5.7|5.7|CD kb|kb|NN RNA|rna|NN was|be|VBD purified|purify|VBN from|from|IN the|the|DT digested|digest|VBN DNA|dna|NN ,|,|, NTPs|ntp|NNS ,|,|, abortive|abortive|JJ oligo-RNA|oligo-rna|JJ products|product|NNS ,|,|, and|and|CC proteins|protein|NNS by|by|IN Acidic|acidic|JJ phenol|phenol|NN extraction|extraction|NN ,|,|, G50|g50|NN spin|spin|NN column|column|NN ,|,|, followed|follow|VBN by|by|IN EtOH|etoh|NN precipitation|precipitation|NN .|.|.
In|in|FW vitro|vitro|FW transcription|transcription|NN reactions|reaction|NNS were|be|VBD performed|perform|VBN in|in|IN a|a|DT final|final|JJ volume|volume|NN of|of|IN 50|50|CD µl|µl|NN .|.|. Each|each|DT reaction|reaction|NN contained|contain|VBD 2|2|CD µl|µl|NN E.|e.|FW coli|coli|FW RNA|rna|NN Polymerase|polymerase|NN Holoenzyme|holoenzyme|NN -LRB-|-lrb-|-LRB- NEB|neb|NN ,|,|, cat|cat|NN .|.|. M0551S|m0551s|NN -RRB-|-rrb-|-RRB- ,|,|, 5|5|CD µl|µl|NN E.|e.|FW coli|coli|FW RNA|rna|NN Polymerase|polymerase|NN Buffer|buffer|NN -LRB-|-lrb-|-LRB- 10X|10x|NN -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD µl|µl|NN SUPERase|superase|NN •|•|SYM In|in|IN ™|™|CD RNase|rnase|NN Inhibitor|inhibitor|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, cat|cat|NN .|.|. AM2696|am2696|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC 500|500|CD ng|ng|NN template|template|NN DNA|dna|NN .|.|. Reactions|reaction|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS to|to|TO allow|allow|VB formation|formation|NN of|of|IN the|the|DT RNA|rna|NN Polymerase-DNA|polymerase-dna|JJ binary|binary|JJ complex|complex|NN .|.|. Transcription|transcription|NN was|be|VBD started|start|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD µl|µl|NN NTPs|ntp|NNS -LRB-|-lrb-|-LRB- 25|25|CD mM|mm|NN each|each|DT -RRB-|-rrb-|-RRB- ,|,|, and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 5|5|CD minutes|minute|NNS .|.|. Transcription|transcription|NN was|be|VBD stopped|stop|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD µl|µl|NN DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- 50|50|CD U/µl|u/µl|NN -RRB-|-rrb-|-RRB- and|and|CC Actinomycin|actinomycin|NN D|d|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP ,|,|, cat|cat|NN .|.|. A1410|a1410|NN ,|,|, dissolved|dissolve|VBN in|in|IN DMSO|dmso|NN to|to|TO 5|5|CD μg/μl|μg/μl|NN -RRB-|-rrb-|-RRB- to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 25|25|CD ng/μl|ng/μl|NN .|.|. Reactions|reaction|NNS were|be|VBD diluted|dilute|VBN by|by|IN addition|addition|NN of|of|IN 50|50|CD μl|μl|NN E.|e.|FW coli|coli|FW RNA|rna|NN Polymerase|polymerase|NN Buffer|buffer|NN 1X|1x|NN .|.|. DMS|dms|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP ,|,|, cat|cat|NN .|.|. D186309|d186309|NN -RRB-|-rrb-|-RRB- was|be|VBD diluted|dilute|VBN 1:6|1:6|CD in|in|IN 100|100|CD %|%|NN Ethanol|ethanol|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1.76|1.76|CD M.|m.|NN Diluted|Diluted|NNP DMS|DMS|NNP was|be|VBD added|add|VBN to|to|TO reactions|reaction|NNS to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 100|100|CD mM|mm|NN .|.|. For|for|IN control|control|NN samples|sample|NNS ,|,|, an|a|DT equal|equal|JJ volume|volume|NN of|of|IN a|a|DT 1:6|1:6|CD dilution|dilution|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN in|in|IN 100|100|CD %|%|NN Ethanol|ethanol|NN was|be|VBD added|add|VBN .|.|. Samples|sample|NNS were|be|VBD incubated|incubate|VBN with|with|IN moderate|moderate|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 800|800|CD RPM|rpm|NN -RRB-|-rrb-|-RRB- at|at|IN 25|25|CD °C|°c|NN for|for|IN 2|2|CD minutes|minute|NNS ,|,|, after|after|IN which|which|WDT reactions|reaction|NNS were|be|VBD immediately|immediately|RB transferred|transfer|VBN to|to|TO ice|ice|NN .|.|. Two|two|CD volumes|volume|NNS of|of|IN ice-cold|ice-cold|JJ RNA|rna|NN Binding|binding|NN Buffer|buffer|NN from|from|IN RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD kit|kit|NN -LRB-|-lrb-|-LRB- Zymo|Zymo|NNP Research|Research|NNP ,|,|, cat|cat|NN .|.|. R1014|r1014|NN -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN DTT|dtt|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP ,|,|, cat|cat|NN .|.|. 43815|43815|CD -RRB-|-rrb-|-RRB- to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.7|0.7|CD M|m|NN ,|,|, were|be|VBD added|add|VBN to|to|TO quench|quench|VB DMS|DMS|NNP ,|,|, and|and|CC samples|sample|NNS were|be|VBD vigorously|vigorously|RB vortexed|vortex|VBN for|for|IN 10|10|CD seconds|seconds|NNS .|.|.
in|in|FW vivo|vivo|FW
In|in|FW vivo|vivo|FW RNA|rna|NN preparation|preparation|NN :|:|: The|the|DT cells|cell|NNS in|in|IN 200|200|CD ml|ml|NN culture|culture|NN were|be|VBD harvested|harvest|VBN and|and|CC resuspended|resuspend|VBN with|with|IN a|a|DT solution|solution|NN containing|contain|VBG 0.5|0.5|CD %|%|NN SDS|sds|NN ,|,|, 20|20|CD mM|mm|NN sodium|sodium|NN acetate|acetate|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.5|5.5|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC 10|10|CD mM|mm|NN EDTA|edta|NN .|.|. The|the|DT suspended|suspend|VBN cells|cell|NNS were|be|VBD mixed|mix|VBN with|with|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN pre-warmed|pre-warmed|JJ saturated|saturated|JJ phenol|phenol|NN -LRB-|-lrb-|-LRB- 20|20|CD mM|mm|NN sodium|sodium|NN acetate|acetate|NN ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN pH|ph|NN 5.5|5.5|CD -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN for|for|IN 5|5|CD min|min|NN at|at|IN 60|60|CD C|c|NN .|.|. The|the|DT mixture|mixture|NN was|be|VBD centrifuged|centrifuge|VBN ,|,|, and|and|CC RNA|rna|NN and|and|CC DNA|dna|NN were|be|VBD precipitated|precipitate|VBN with|with|IN ethanol|ethanol|NN from|from|IN the|the|DT supernatant|supernatant|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD dissolved|dissolve|VBN in|in|IN DNase|dnase|NN I|i|CD buffer|buffer|NN with|with|IN 10U|10u|NN of|of|IN DNaseI|dnasei|NN and|and|CC incubated|incubate|VBN for|for|IN 30|30|CD min|min|NN .|.|. RNA|rna|NN was|be|VBD separated|separate|VBN from|from|IN the|the|DT digested|digest|VBN DNA|dna|NN by|by|IN acidic|acidic|JJ phenol|phenol|NN extraction|extraction|NN followed|follow|VBN by|by|IN G-50|G-50|NNP Micro|Micro|NNP column|column|NN -LRB-|-lrb-|-LRB- GE|GE|NNP Healthcare|Healthcare|NNP -RRB-|-rrb-|-RRB- purification|purification|NN ,|,|, and|and|CC then|then|RB precipitated|precipitate|VBD with|with|IN ethanol|ethanol|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD dissolved|dissolve|VBN in|in|IN diethylpyrocarbonate-treated|diethylpyrocarbonate-treated|JJ water|water|NN and|and|CC used|use|VBN for|for|IN cDNA|cdna|NN synthesis|synthesis|NN .|.|.
Ionic|Ionic|NNP silver|silver|NN stock|stock|NN solutions|solution|NNS were|be|VBD prepared|prepare|VBN from|from|IN AgNO3|agno3|NN powder|powder|NN -LRB-|-lrb-|-LRB- Fisher|Fisher|NNP Scientific|Scientific|NNP Bioblock|Bioblock|NNP -RRB-|-rrb-|-RRB- as|as|IN previously|previously|RB described|describe|VBN -LRB-|-lrb-|-LRB- Saulou|Saulou|NNP ,|,|, Jamme|Jamme|NNP et|et|FW al.|al.|FW ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN in|in|IN darkness|darkness|NN .|.|. The|the|DT final|final|JJ tested|test|VBN concentrations|concentration|NNS -LRB-|-lrb-|-LRB- 5.0|5.0|CD ,|,|, 6.5|6.5|CD ,|,|, and|and|CC 8.5|8.5|CD µM|µm|NN -RRB-|-rrb-|-RRB- were|be|VBD obtained|obtain|VBN by|by|IN diluting|dilute|VBG the|the|DT corresponding|corresponding|JJ AgNO3|agno3|NN stock|stock|NN solution|solution|NN directly|directly|RB into|into|IN the|the|DT M9|m9|NN growth|growth|NN medium|medium|NN .|.|. Control|Control|NNP experiment|experiment|NN was|be|VBD simultaneously|simultaneously|RB performed|perform|VBN by|by|IN adding|add|VBG deionised|deionised|JJ water|water|NN into|into|IN the|the|DT M9|m9|NN broth|broth|NN .|.|. In|in|IN both|both|DT cases|case|NNS ,|,|, a|a|DT stabilization|stabilization|NN period|period|NN of|of|IN 24|24|CD h|h|NN -LRB-|-lrb-|-LRB- at|at|IN 37|37|CD °C|°c|NN and|and|CC 120|120|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- was|be|VBD carried|carry|VBN out|out|RP before|before|IN cell|cell|NN inoculation|inoculation|NN .|.|.
Ion|Ion|NNP Xpress|Xpress|NNP barcoded|barcode|VBD libraries|library|NNS were|be|VBD constructed|construct|VBN using|use|VBG the|the|DT Ribo-Zero|Ribo-Zero|NNP Magnatic|Magnatic|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Gram-negative|gram-negative|JJ bacteria|bacterium|NNS ,|,|, Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- and|and|CC IonXpress|ionxpress|NN RNA-seq|rna-seq|NN v2|v2|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- kits|kit|NNS according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS directions|direction|NNS .|.|.
ip|ip|NN antibody|antibody|NN :|:|: affinity|affinity|NN purified|purify|VBN anti-Fur|anti-fur|JJ antibody|antibody|NN
IP|IP|NNP ∆|∆|NNP fur|fur|NN Anaerobic|anaerobic|JJ
IPOD|ipod|NN _|_|NN early|early|JJ _|_|CD log|log|NN _|_|NN 1|1|CD
IPOD|ipod|NN _|_|RB early|early|JJ _|_|NN log|log|NN _|_|NN 2|2|CD
IPOD|ipod|VBD _|_|RB late|late|JJ _|_|NN log|log|NN _|_|NN 1|1|CD
IPOD|ipod|NN _|_|CD late|late|JJ _|_|NN log|log|NN _|_|NN 2|2|CD
IPOD|ipod|VBD _|_|SYM MDS42|mds42|NN
IP|IP|NNP ParC-flag|ParC-flag|NNP 1|1|CD
IP|IP|NNP ParE-flag|ParE-flag|NNP 1|1|CD
IP|IP|NNP ParE-flag|ParE-flag|NNP 2|2|CD
IP|IP|NNP ParE-flag|ParE-flag|NNP G1|g1|NN
IP|IP|NNP ParE-flag|ParE-flag|NNP G2|g2|NN
IP|IP|NNP ParE-flag|ParE-flag|NNP S20min|S20min|NNP
IP|IP|NNP ParE-flag|ParE-flag|NNP S40min|S40min|NNP
Irp|Irp|NNP mutant|mutant|NN in|in|IN Ala|Ala|NNP media|media|NNS
Irp|irp|NN mutant|mutant|NN in|in|IN Gln|gln|NN media|media|NNS
isolate|isolate|NN :|:|: bovine|bovine|JJ isolate|isolate|NN of|of|IN e|e|SYM coli|coli|FW o157|o157|FW :|:|: H7|h7|NN FRIK2000|frik2000|NN lineage|lineage|NN II|ii|CD
isolate|isolate|NN :|:|: bovine|bovine|JJ isolate|isolate|NN of|of|IN e|e|SYM coli|coli|FW o157|o157|FW :|:|: H7|h7|NN FRIK966|frik966|NN lineage|lineage|NN II|ii|CD
isolate|isolate|NN :|:|: clinical|clinical|JJ isolate|isolate|JJ e|e|SYM coli|coli|FW o157|o157|FW :|:|: H7|h7|NN lineage|lineage|NN I|I|PRP
isolated|isolate|VBN by|by|IN chloroform|chloroform|NN extraction|extraction|NN and|and|CC precipitation|precipitation|NN by|by|IN isopropanol|isopropanol|NN .|.|. Precipitated|precipitate|VBN RNA|rna|NN
Isolated|isolate|VBN from|from|IN feces|fece|NNS of|of|IN a|a|DT HUS|hus|NN patient|patient|NN from|from|IN an|a|DT outbreak|outbreak|NN in|in|IN China|China|NNP in|in|IN 1999|1999|CD
Isolate|Isolate|NNP :|:|: EDL933|edl933|NN
Isolate|isolate|VB G|g|NN 1/2|1/2|CD of|of|IN Symbioflor2|symbioflor2|NN probiotic|probiotic|JJ product|product|NN from|from|IN Symbiopharm|Symbiopharm|NNP
Isolate|isolate|VB G|g|NN 3/10|3/10|CD of|of|IN Symbioflor2|symbioflor2|NN probiotic|probiotic|JJ probiotic|probiotic|JJ from|from|IN Symbiopharm|Symbiopharm|NNP
Isolate|isolate|VB G|g|NN 3/10|3/10|CD of|of|IN Symbioflor2|symbioflor2|NN probiotic|probiotic|JJ product|product|NN from|from|IN Symbiopharm|Symbiopharm|NNP
Isolate|isolate|VB G|g|NN 4/9|4/9|CD of|of|IN Symbioflor2|symbioflor2|NN probiotic|probiotic|JJ product|product|NN from|from|IN Symbiopham|Symbiopham|NNP
Isolate|isolate|VB G|g|NN 4/9|4/9|CD of|of|IN Symbioflor2|symbioflor2|NN probiotic|probiotic|JJ product|product|NN from|from|IN Symbiopharm|Symbiopharm|NNP
Isolate|isolate|VB G5|g5|NN of|of|IN Symbioflor2|symbioflor2|NN probiotic|probiotic|JJ product|product|NN from|from|IN Symbiopharm|Symbiopharm|NNP
Isolate|isolate|VB :|:|: MDS42|mds42|NN
Isolate|isolate|VB :|:|: MG1655|mg1655|NN
isolate|isolate|NN :|:|: UR40|ur40|NN
Isolate|isolate|VB W3110|w3110|NN of|of|IN K-12|k-12|NN strain|strain|NN
isolation|isolation|NN source|source|NN :|:|: Mixed|mixed|JJ culture|culture|NN
isolation|isolation|NN source|source|NN :|:|: Pure|pure|JJ culture|culture|NN
Isoleucine|isoleucine|NN addition|addition|NN
IspG1|ispg1|NN
IspG1|ispg1|NN strain|strain|NN
Iterative|iterative|JJ alignment|alignment|NN ,|,|, Min-leght|min-leght|NN =|=|JJ 20|20|CD ,|,|, step|step|NN =|=|JJ 5|5|CD ,|,|, bowtie2|bowtie2|NN --|--|: very-sensitive|very-sensitive|JJ
Jaguar|Jaguar|NNP
JCB570|jcb570|NN
JM109-1|jm109-1|NN ,|,|, biological|biological|JJ rep1|rep1|NN
JM109-2|jm109-2|NN ,|,|, biological|biological|JJ rep2|rep2|NN
JM109-3|jm109-3|NN ,|,|, biological|biological|JJ rep3|rep3|NN
JM109|jm109|NN GLY-1|gly-1|NN ,|,|, biological|biological|JJ rep1|rep1|NN
JM109|jm109|NN GLY-2|gly-2|NN ,|,|, biological|biological|JJ rep2|rep2|NN
JM109|jm109|NN GLY-3|gly-3|NN ,|,|, biological|biological|JJ rep3|rep3|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB-
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, LB|LB|NNP ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, LB|LB|NNP ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, LB|LB|NNP ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, LB|LB|NNP ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, LB|LB|NNP ,|,|, transition|transition|NN phase|phase|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, Min|min|NN Glucose|glucose|NN ,|,|, exponential|exponential|JJ phase|phase|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, Min|Min|NNP Glucose|Glucose|NNP ,|,|, exponential|exponential|JJ phase|phase|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, Min|min|NN Glucose|glucose|NN ,|,|, stationary|stationary|JJ phase|phase|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, Min|Min|NNP Glucose|Glucose|NNP ,|,|, stationary|stationary|JJ phase|phase|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP ,|,|, exponential|exponential|JJ phase|phase|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP ,|,|, exponential|exponential|JJ phase|phase|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP ,|,|, stationary|stationary|JJ phase|phase|NN
JO2057|jo2057|NN WT|WT|NNP ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP ,|,|, stationary|stationary|JJ phase|phase|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO2057|jo2057|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- ,|,|, transition|transition|NN phase|phase|NN
JO2081|jo2081|NN -LRB-|-lrb-|-LRB- hupA|hupa|NN -RRB-|-rrb-|-RRB-
JO2081|jo2081|NN -LRB-|-lrb-|-LRB- hupA|hupa|NN -RRB-|-rrb-|-RRB- ,|,|, exponential|exponential|JJ phase|phase|NN
JO2081|jo2081|NN hupA|hupa|NN ,|,|, LB|lb|NN ,|,|, exponential|exponential|JJ phase|phase|NN
JO2081|jo2081|NN hupA|hupa|NN ,|,|, LB|lb|NN ,|,|, stationary|stationary|JJ phase|phase|NN
JO2081|jo2081|NN hupA|hupa|NN ,|,|, LB|lb|NN ,|,|, transition|transition|NN phase|phase|NN
JO2081|jo2081|NN -LRB-|-lrb-|-LRB- hupA|hupa|NN -RRB-|-rrb-|-RRB- ,|,|, stationary|stationary|JJ phase|phase|NN
JO2081|jo2081|NN -LRB-|-lrb-|-LRB- hupA|hupa|NN -RRB-|-rrb-|-RRB- ,|,|, transition|transition|NN phase|phase|NN
JO2083|jo2083|NN -LRB-|-lrb-|-LRB- hupB|hupb|NN -RRB-|-rrb-|-RRB-
JO2083|jo2083|NN -LRB-|-lrb-|-LRB- hupB|hupb|NN -RRB-|-rrb-|-RRB- ,|,|, exponential|exponential|JJ phase|phase|NN
JO2083|jo2083|NN hupB|hupb|NN ,|,|, LB|lb|NN ,|,|, exponential|exponential|JJ phase|phase|NN
JO2083|jo2083|NN hupB|hupb|NN ,|,|, LB|lb|NN ,|,|, stationary|stationary|JJ phase|phase|NN
JO2083|jo2083|NN hupB|hupb|NN ,|,|, LB|lb|NN ,|,|, transition|transition|NN phase|phase|NN
JO2083|jo2083|NN -LRB-|-lrb-|-LRB- hupB|hupb|NN -RRB-|-rrb-|-RRB- ,|,|, stationary|stationary|JJ phase|phase|NN
JO2083|jo2083|NN -LRB-|-lrb-|-LRB- hupB|hupb|NN -RRB-|-rrb-|-RRB- ,|,|, transition|transition|NN phase|phase|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB-
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, LB|lb|NN ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, LB|lb|NN ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, LB|lb|NN ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, LB|lb|NN ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, LB|lb|NN ,|,|, transition|transition|NN phase|phase|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, Min|min|NN Glucose|glucose|NN ,|,|, exponential|exponential|JJ phase|phase|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, Min|min|NN Glucose|glucose|NN ,|,|, exponential|exponential|JJ phase|phase|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, Min|min|NN Glucose|glucose|NN ,|,|, stationary|stationary|JJ phase|phase|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, Min|min|NN Glucose|glucose|NN ,|,|, stationary|stationary|JJ phase|phase|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP exponential|exponential|JJ phase|phase|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP exponential|exponential|JJ phase|phase|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP stationary|stationary|JJ phase|phase|NN
JO3020|jo3020|NN hupAB|hupab|NN ,|,|, Min|Min|NNP Glycerol|Glycerol|NNP stationary|stationary|JJ phase|phase|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition1|repetition1|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, repetition2|repetition2|NN
JO3020|jo3020|NN -LRB-|-lrb-|-LRB- hupAB|hupab|NN -RRB-|-rrb-|-RRB- ,|,|, transition|transition|NN phase|phase|NN
JQ004|jq004|NN -LRB-|-lrb-|-LRB- rraA|rraa|NN -RRB-|-rrb-|-RRB-
K100Q|k100q|NN
K100Q|k100q|NN rep|rep|NN 1|1|CD
K100Q|k100q|NN rep|rep|NN 2|2|CD
K100Q|k100q|NN rep|rep|NN 3|3|CD
K100R|k100r|NN
K100R|k100r|NN rep|rep|NN 1|1|CD
K100R|k100r|NN rep|rep|NN 2|2|CD
K100R|k100r|NN rep|rep|NN 3|3|CD
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 2.5|2.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 3.5|3.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 3|3|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 4.5|4.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 4|4|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 5.5|5.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 5|5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 6|6|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.2|0.2|CD percent|percent|NN glucose|glucose|NN ,|,|, 8|8|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 2.5|2.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 3.5|3.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 3|3|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 4.5|4.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 4|4|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 5.5|5.5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 5|5|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 6|6|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN EMG2|emg2|NN on|on|IN LB|lb|NN with|with|IN 0.4|0.4|CD percent|percent|NN glucose|glucose|NN ,|,|, 8|8|CD hours|hour|NNS post-incubation|post-incubation|JJ
K12|k12|NN MG1655|mg1655|NN with|with|IN 10|10|CD mM|mm|NN of|of|IN heptanoic|heptanoic|JJ acid|acid|NN
K12|k12|NN MG1655|mg1655|NN without|without|IN heptanoic|heptanoic|JJ acid|acid|NN
K12|k12|NN strain|strain|NN MG1655|mg1655|NN ,|,|, 100|100|CD mcg/ml|mcg/ml|NN bicyclomycin|bicyclomycin|NN 20|20|CD min|min|NN ,|,|, exponential|exponential|JJ phase|phase|NN
K12|k12|NN strain|strain|NN MG1655|mg1655|NN ,|,|, 10|10|CD mcg/ml|mcg/ml|NN bicyclomycin|bicyclomycin|NN 20|20|CD min|min|NN ,|,|, exponential|exponential|JJ phase|phase|NN
K12|k12|NN strain|strain|NN MG1655|mg1655|NN ,|,|, 25|25|CD mcg/ml|mcg/ml|NN bicyclomycin|bicyclomycin|NN 20|20|CD min|min|NN ,|,|, exponential|exponential|JJ phase|phase|NN
K12|k12|NN strain|strain|NN MG1655|mg1655|NN ,|,|, control|control|NN sample|sample|NN ,|,|, exponential|exponential|JJ phase|phase|NN
K-12|k-12|NN strain|strain|NN _|_|RB wild|wild|JJ type|type|NN
K-12|k-12|NN strain|strain|NN ,|,|, wild|wild|JJ type|type|NN
K12|k12|NN WT|wt|JJ 3110|3110|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC ctrl|ctrl|NN
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 3|3|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 4|4|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pBglJ|pbglj|NN
K12Δ|k12δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pBglJ|pbglj|NN
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
K12Δ|k12δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 3|3|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 4|4|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pLeuO|pleuo|NN
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pLeuO|pleuo|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pLeuO|pleuo|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pLeuO|pleuo|NN ,|,|, biological|biological|JJ replicate|replicate|VB 3|3|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- +|+|CC pLeuO|pleuo|NN ,|,|, biological|biological|JJ replicate|replicate|VB 4|4|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC ctrl|ctrl|NN
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 3|3|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 4|4|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC pBglJ|pbglj|NN
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 3|3|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔleuO|δleuo|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 4|4|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC ctrl|ctrl|NN
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 3|3|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC ctrl|ctrl|NN ,|,|, biological|biological|JJ replicate|replicate|VB 4|4|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC pBglJ|pbglj|NN
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 1|1|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 2|2|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 3|3|CD
K12|k12|NN Δ|δ|NN -LRB-|-lrb-|-LRB- yjjP-yjjQ-bglJ|yjjp-yjjq-bglj|NN -RRB-|-rrb-|-RRB- ΔrcsB|δrcsb|NN +|+|CC pBglJ|pbglj|NN ,|,|, biological|biological|JJ replicate|replicate|VB 4|4|CD
KCN|kcn|NN
kefB|kefb|NN KO|ko|NN rep1|rep1|NN
kefB|kefb|NN KO|ko|NN rep2|rep2|NN
kefB|kefb|NN KO|ko|NN rep3|rep3|NN
khc|khc|NN KO|ko|NN rep1|rep1|NN
khc|khc|NN KO|ko|NN rep2|rep2|NN
khc|khc|NN KO|ko|NN rep3|rep3|NN
KMD|kmd|NN 1|1|CD
KMD|kmd|NN 2|2|CD
KMD|kmd|NN 3|3|CD
KSL2000|ksl2000|NN ,|,|, 0.1|0.1|CD %|%|NN arabinose|arabinose|NN
KSL2000|ksl2000|NN ,|,|, no|no|DT arabinose|arabinose|NN
KSL2000|ksl2000|NN plus|plus|CC pTrc99A|ptrc99a|NN
KSL2000|ksl2000|NN plus|plus|CC pTrc99A-RraA|ptrc99a-rraa|NN
KSL2000-Rne|ksl2000-rne|NN depletion|depletion|NN
KSL2000-RraA|ksl2000-rraa|NN overexpression|overexpression|NN
KSL2009|ksl2009|NN ,|,|, 0.1|0.1|CD %|%|NN arabinose|arabinose|NN
KSL2009|ksl2009|NN ,|,|, no|no|DT arabinose|arabinose|NN
KSL2009-N-Rne|ksl2009-n-rne|NN depletion|depletion|NN
KSL2009|ksl2009|NN plus|plus|CC pTrc99A|ptrc99a|NN
KSL2009|ksl2009|NN plus|plus|CC pTrc99A-RraA|ptrc99a-rraa|NN
KSL2009-RraA|ksl2009-rraa|NN overexpression|overexpression|NN
lacA|laca|NN KO|ko|NN LB|lb|NN rep1|rep1|NN
lacA|laca|NN KO|ko|NN LB|lb|NN rep2|rep2|NN
lacA|laca|NN KO|ko|NN M9|m9|NN rep1|rep1|NN
lacA|laca|NN KO|ko|NN M9|m9|NN rep2|rep2|NN
LA-co1|la-co1|NN
LA-co2|la-co2|NN
lactate|lactate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 085|085|CD
lactate|lactate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 086|086|CD
lactate|lactate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 087|087|CD
lactate|lactate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 088|088|CD
lactate|lactate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 089|089|CD
lactate|lactate|NN _|_|NN growth|growth|NN :|:|: MURI|MURI|NNP _|_|SYM 090|090|CD
Lactobacillus|lactobacillus|NN acidophilus|acidophilus|NN
lacZ|lacz|NN _|_|NN 0|0|CD min|min|NN
lacZ|lacz|NN _|_|CD 10|10|CD min|min|NN
lacZ|lacz|NN _|_|CD 15|15|CD min|min|NN
lacZ|lacz|NN _|_|NN 1|1|CD min|min|NN
lacZ|lacz|NN _|_|NN 2|2|CD min|min|NN
lacZ|lacz|NN _|_|CD 4|4|CD min|min|NN
lacZ|lacz|NN _|_|CD 6|6|CD min|min|NN
lacZ|lacz|NN _|_|CD 8|8|CD min|min|NN
lacZ|lacz|NN _|_|CD K12|k12|NN _|_|NN 0|0|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD K12|k12|NN _|_|NN 120|120|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD K12|k12|NN _|_|CD 30|30|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD K12|k12|NN _|_|NN 60|60|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD K12|k12|NN _|_|NN 90|90|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|NN 0|0|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|NN 0|0|CD _|_|NN r2|r2|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|NN 120|120|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|CD 30|30|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|CD 30|30|CD _|_|NN r2|r2|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|NN 60|60|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|NN 60|60|CD _|_|NN r2|r2|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|NN 90|90|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD MG1063|mg1063|NN _|_|NN 90|90|CD _|_|NN r2|r2|NN
lacZ|lacz|NN _|_|CD W1863|w1863|NN _|_|NN 0|0|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD W1863|w1863|NN _|_|CD 30|30|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD W1863|w1863|NN _|_|NN 60|60|CD _|_|NN r1|r1|NN
lacZ|lacz|NN _|_|CD W1863|w1863|NN _|_|NN 90|90|CD _|_|NN r1|r1|NN
LA-log|la-log|NN
LA-log-tr|la-log-tr|NN
Lambda|Lambda|NNP phage|phage|NN
LA-starve|la-starve|JJ
late|late|JJ log|log|NN phase|phase|NN grown|grow|VBN e|e|SYM coli|coli|NNS 966|966|CD into|into|IN RNAprotect|rnaprotect|NN solution|solution|NN ,|,|, RNA|rna|NN extracted|extract|VBN with|with|IN qiagen|qiagen|NN RNA|rna|NN bacteria|bacterium|NNS kits|kit|NNS
late|late|JJ log|log|NN phase|phase|NN grown|grow|VBN e|e|SYM coli|coli|FW EDL933|edl933|FW into|into|IN RNAprotect|rnaprotect|NN solution|solution|NN ,|,|, RNA|rna|NN extracted|extract|VBN with|with|IN qiagen|qiagen|NN RNA|rna|NN bacteria|bacterium|NNS kits|kit|NNS
late|late|JJ stationary|stationary|JJ culture|culture|NN
LA|LA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl1|repl1|NN
LA|LA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl2|repl2|NN
LA|LA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl3|repl3|NN
LA|LA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl4|repl4|NN
LA|LA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl5|repl5|NN
LA|LA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl1|repl1|NN
LA|LA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl2|repl2|NN
LA|LA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl3|repl3|NN
LA|LA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl4|repl4|NN
LA|LA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl5|repl5|NN
LA|LA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl1|repl1|NN
LA|LA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl2|repl2|NN
LA|LA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl3|repl3|NN
LA|LA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl4|repl4|NN
LA|LA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl5|repl5|NN
LA|LA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl1|repl1|NN
LA|LA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl2|repl2|NN
LA|LA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl3|repl3|NN
LA|LA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl4|repl4|NN
LA|LA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl5|repl5|NN
LB|lb|NN 0.4|0.4|CD B1|b1|NN TEX|tex|NN neg|neg|NN L1|l1|NN GA|ga|NN
LB|lb|NN 0.4|0.4|CD B1|b1|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN GA|ga|NN
LB|lb|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP neg|neg|NNP L1|l1|NN HS1|hs1|NN
LB|lb|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP neg|neg|NNP L1|l1|NN HS2|hs2|NN
LB|lb|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN HS1|hs1|NN
LB|lb|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN HS2|hs2|NN
LB|lb|NN 2.0|2.0|CD B1|b1|NN TEX|tex|NN neg|neg|NN L1|l1|NN GA|ga|NN
LB|lb|NN 2.0|2.0|CD B1|b1|NN TEX|TEX|NNP neg|neg|NNP L2|l2|NN HS2|hs2|NN
LB|lb|NN 2.0|2.0|CD B1|b1|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN GA|ga|NN
LB|lb|NN 2.0|2.0|CD B1|b1|NN TEX|TEX|NNP pos|po|VBZ L2|l2|NN HS2|hs2|NN
LB|lb|NN 2.0|2.0|CD B2|b2|NN TEX|TEX|NNP neg|neg|NNP L1|l1|NN HS1|hs1|NN
LB|lb|NN 2.0|2.0|CD B2|b2|NN TEX|TEX|NNP neg|neg|NNP L1|l1|NN HS2|hs2|NN
LB|lb|NN 2.0|2.0|CD B2|b2|NN TEX|TEX|NNP neg|neg|NNP L2|l2|NN HS2|hs2|NN
LB|lb|NN 2.0|2.0|CD B2|b2|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN HS1|hs1|NN
LB|lb|NN 2.0|2.0|CD B2|b2|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN HS2|hs2|NN
LB|lb|NN 2.0|2.0|CD B2|b2|NN TEX|TEX|NNP pos|po|VBZ L2|l2|NN HS2|hs2|NN
LB|lb|NN ,|,|, 37|37|CD °C|°c|NN ,|,|, 220|220|CD rpm|rpm|NN ,|,|, OD600|od600|NN =|=|JJ 0.5|0.5|CD ,|,|, 2.0|2.0|CD ,|,|, 2.0|2.0|CD +6|+6|CD h|h|NN
LB|lb|NN -LRB-|-lrb-|-LRB- 5|5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD inoculated|inoculate|VBN by|by|IN a|a|DT frozen|frozen|JJ stock|stock|NN of|of|IN WT|WT|NNP or|or|CC perC-mutant|perc-mutant|JJ strain|strain|NN and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN 225|225|CD rpm|rpm|NN shaking|shake|VBG .|.|. Flasks|flask|NNS containing|contain|VBG low-glucose|low-glucose|JJ DMEM|dmem|NN were|be|VBD inoculated|inoculate|VBN 1:100|1:100|CD with|with|IN the|the|DT overnight|overnight|JJ culture|culture|NN and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN 225|225|CD rpm|rpm|NN shaking|shake|VBG to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN 0.3-0.5|0.3-0.5|CD -RRB-|-rrb-|-RRB- .|.|.
LB|LB|NNP agar|agar|NN plates|plate|NNS ,|,|, 37|37|CD °C|°c|NN for|for|IN 18|18|CD h|h|NN
LB|lb|NN ,|,|, biological|biological|JJ rep1|rep1|NN
LB|lb|NN ,|,|, biological|biological|JJ rep2|rep2|NN
LB|lb|NN ,|,|, biological|biological|JJ rep3|rep3|NN
LB|lb|NN +|+|CC glycerol|glycerol|NN ,|,|, biological|biological|JJ rep1|rep1|NN
LB|lb|NN +|+|CC glycerol|glycerol|NN ,|,|, biological|biological|JJ rep2|rep2|NN
LB|lb|NN +|+|CC glycerol|glycerol|NN ,|,|, biological|biological|JJ rep3|rep3|NN
LB-grown|lb-grown|JJ overnight|overnight|JJ cultures|culture|NNS were|be|VBD pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN ,|,|, washed|wash|VBN ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN M9-glutamine|m9-glutamine|NN of|of|IN M9-alanine|m9-alanine|NN media|media|NNS .|.|. Cultures|culture|NNS were|be|VBD shaken|shake|VBN at|at|IN 250|250|CD rpm|rpm|NN at|at|IN 37C|37c|NN .|.|. Samples|sample|NNS were|be|VBD taken|take|VBN in|in|IN mid-exponential|mid-exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.15|0.15|CD for|for|IN glutamine|glutamine|NN and|and|CC OD600|od600|NN =|=|JJ 0.2|0.2|CD for|for|IN alanine|alanine|NN on|on|IN an|a|DT Ultraspec|ultraspec|JJ 3100|3100|CD pro|pro|NN -RRB-|-rrb-|-RRB- after|after|IN ~|~|NN 5|5|CD generations|generation|NNS of|of|IN growth|growth|NN in|in|IN the|the|DT media|media|NNS .|.|.
LB|LB|NNP media|media|NNS
LB|lb|NN medium|medium|NN ,|,|, 180|180|CD rpm|rpm|NN shaking|shake|VBG ,|,|, at|at|IN 37|37|CD °C|°c|NN ,|,|, between|between|IN exponential|exponential|JJ and|and|CC stationary|stationary|JJ phase|phase|NN
LB|lb|NN medium|medium|NN ,|,|, 37|37|CD °C|°c|NN ,|,|, airated|airate|VBN ,|,|, constant|constant|JJ pH|ph|NN 7.5|7.5|CD
LB|lb|NN medium|medium|NN at|at|IN 37ºC|37ºc|NN with|with|IN 200rpm|200rpm|JJ agitation|agitation|NN .|.|.
LB|lb|NN mRNA|mrna|NN
LB|lb|NN mRNA|mrna|NN biological|biological|JJ replicate|replicate|VBP
LB|lb|NN mRNA|mrna|NN technical|technical|JJ replicate|replicate|VB
LBO|LBO|NNP
LB|lb|NN -LRB-|-lrb-|-LRB- OD|od|NN =|=|JJ 0.87|0.87|CD -RRB-|-rrb-|-RRB-
LB|LB|NNP RPF|RPF|NNP
LB|LB|NNP RPF|RPF|NNP biological|biological|JJ replicate|replicate|VB
LBTMP50|lbtmp50|NN _|_|CD 10|10|CD min|min|NN
LBTMP50|lbtmp50|NN _|_|NN 120|120|CD min|min|NN
LBTMP50|lbtmp50|NN _|_|CD 30|30|CD min|min|NN
LBTMP50|lbtmp50|NN _|_|CD 60|60|CD min|min|NN
LC1|lc1|NN
ldrA|ldra|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
ldrA|ldra|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
ldrA|ldra|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
ldrA|ldra|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
LE-co1|le-co1|NN
LE-co2|le-co2|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1637|tls1637|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1638|tls1638|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1639|tls1639|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1640|tls1640|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1641|tls1641|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1642|tls1642|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELAb|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1643|tls1643|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1644|tls1644|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1645|tls1645|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1646|tls1646|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1647|tls1647|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1648|tls1648|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1649|tls1649|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LELab|lelab|NN _|_|CD ChIP|chip|NN _|_|SYM seq|seq|FW _|_|FW TLS1650|tls1650|NN _|_|NN anti|anti|JJ _|_|CD FLAG|flag|NN
LE-log|le-log|JJ
LE-log-tr|le-log-tr|NN
LE-starve|le-starve|JJ
-|-|: Leu|leu|NN t|t|NN =|=|JJ 0|0|CD
-|-|: Leu|leu|NN t|t|NN =|=|JJ 0|0|CD charged|charge|VBN
-|-|: Leu|leu|NN t|t|NN =|=|JJ 0|0|CD total|total|JJ
-|-|: Leu|leu|NN t|t|NN =|=|JJ 17|17|CD
-|-|: Leu|leu|NN t|t|NN =|=|JJ 17|17|CD charged|charge|VBN
-|-|: Leu|leu|NN t|t|NN =|=|JJ 17|17|CD total|total|JJ
-|-|: Leu|leu|NN t|t|NN =|=|JJ 2|2|CD
-|-|: Leu|leu|NN t|t|NN =|=|JJ 2|2|CD charged|charge|VBN
-|-|: Leu|leu|NN t|t|NN =|=|JJ 2|2|CD total|total|JJ
-|-|: Leu|leu|NN t|t|NN =|=|JJ 32|32|CD
-|-|: Leu|leu|NN t|t|NN =|=|JJ 32|32|CD charged|charge|VBN
-|-|: Leu|leu|NN t|t|NN =|=|JJ 32|32|CD total|total|JJ
-|-|: Leu|leu|NN t|t|NN =|=|JJ 7|7|CD
-|-|: Leu|leu|NN t|t|NN =|=|JJ 7|7|CD charged|charge|VBN
-|-|: Leu|leu|NN t|t|NN =|=|JJ 7|7|CD total|total|JJ
lexA|lexa|NN 10|10|CD '|'|'' after|after|IN UV|uv|NN vs.|vs.|CC 0|0|CD '|'|'' ,|,|, MG1655|mg1655|NN
lexA|lexa|NN 10|10|CD min|min|NN after|after|IN UV|uv|NN treatment|treatment|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
lexA|lexa|NN 20|20|CD '|'|'' after|after|IN NOuv|NOuv|NNP vs.|vs.|CC 0|0|CD '|'|'' ,|,|, MG1655|mg1655|NN
lexA|lexa|NN 20|20|CD '|'|'' after|after|IN UV|uv|NN vs.|vs.|CC 0|0|CD '|'|'' ,|,|, MG1655|mg1655|NN
lexA|lexa|NN 20|20|CD min|min|NN after|after|IN NOuv|NOuv|NNP ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
lexA|lexa|NN 20|20|CD min|min|NN after|after|IN UV|uv|NN treatment|treatment|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
lexA|lexa|NN 40|40|CD '|'|'' after|after|IN UV|uv|NN vs.|vs.|CC 0|0|CD '|'|'' ,|,|, MG1655|mg1655|NN
lexA|lexa|NN 40|40|CD min|min|NN after|after|IN UV|uv|NN treatment|treatment|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
lexA|lexa|NN 5|5|CD '|'|'' after|after|IN UV|uv|NN vs.|vs.|CC 0|0|CD '|'|'' ,|,|, MG1655|mg1655|NN
lexA|lexa|NN 5|5|CD min|min|NN after|after|IN UV|uv|NN treatment|treatment|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
lexA|lexa|NN 60|60|CD '|'|'' after|after|IN NOuv|NOuv|NNP vs.|vs.|CC 0|0|CD '|'|'' ,|,|, MG1655|mg1655|NN
lexA|lexa|NN 60|60|CD '|'|'' after|after|IN UV|uv|NN vs.|vs.|CC 0|0|CD '|'|'' ,|,|, MG1655|mg1655|NN
lexA|lexa|NN 60|60|CD min|min|NN after|after|IN NOuv|NOuv|NNP ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
lexA|lexa|NN 60|60|CD min|min|NN after|after|IN UV|uv|NN treatment|treatment|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN ,|,|, 2|2|CD ug|ug|NN pdN6|pdn6|NN
lexA|lexa|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r1|r1|FW
lexA|lexa|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r2|r2|FW
lexA|lexa|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
lexA|lexa|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
lexA|lexa|NN vs.|vs.|CC wt|wt|JJ ,|,|, before|before|IN UV|uv|NN treatment|treatment|NN ,|,|, MG1655|mg1655|NN
L-form|l-form|NN ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN +|+|CC Sucrose|sucrose|NN +|+|CC MgSO4|mgso4|NN +|+|CC Pen|pen|NN G|g|NN ,|,|, rep|rep|NN 1|1|CD
L-form|l-form|NN ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN +|+|CC Sucrose|sucrose|NN +|+|CC MgSO4|mgso4|NN +|+|CC Pen|pen|NN G|g|NN ,|,|, rep|rep|NN 2|2|CD
L-form|l-form|NN ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN +|+|CC Sucrose|sucrose|NN +|+|CC MgSO4|mgso4|NN +|+|CC Pen|pen|NN G|g|NN ,|,|, rep|rep|NN 3|3|CD
L-form|l-form|JJ colony|colony|NN morphology|morphology|NN
Libraries|Libraries|NNPS for|for|IN Illumina|Illumina|NNP HiSeq|HiSeq|NNP 1000|1000|CD sequencing|sequencing|NN using|use|VBG the|the|DT Truseq|Truseq|NNP kit|kit|NN were|be|VBD prepared|prepare|VBN using|use|VBG protocols|protocol|NNS recommended|recommend|VBN by|by|IN the|the|DT manufacturer|manufacturer|NN .|.|.
Libraries|Libraries|NNPS of|of|IN RNA|rna|NN fractions|fraction|NNS were|be|VBD constructed|construct|VBN with|with|IN the|the|DT ScriptSeq|ScriptSeq|NNP V2|v2|NN RNA-Seq|rna-seq|NN Library|Library|NNP Prep|Prep|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturers|manufacturer|NNS guidelines|guideline|NNS .|.|.
Libraries|Libraries|NNPS were|be|VBD constructed|construct|VBN by|by|IN vertis|vertis|NN Biotechnologie|Biotechnologie|NNP AG|AG|NNP ,|,|, Germany|Germany|NNP -LRB-|-lrb-|-LRB- www.vertis-biotech.com|www.vertis-biotech.com|NNP -RRB-|-rrb-|-RRB- as|as|IN a|a|DT service|service|NN that|that|WDT included|include|VBD treating|treat|VBG an|a|DT aliquot|aliquot|NN of|of|IN each|each|DT RNA|rna|NN sample|sample|NN with|with|IN TAP|tap|NN .|.|. The|the|DT 5|5|CD '|'|'' -|-|: sequencing|sequencing|NN adaptor|adaptor|NN was|be|VBD ligated|ligate|VBN to|to|TO transcripts|transcript|NNS prior|prior|RB to|to|TO fragmentation|fragmentation|NN ,|,|, thereby|thereby|RB allowing|allow|VBG the|the|DT 5|5|CD '|'|'' ends|end|NNS of|of|IN both|both|DT long|long|JJ and|and|CC short|short|JJ transcripts|transcript|NNS to|to|TO be|be|VB detected|detect|VBN .|.|. Each|each|DT of|of|IN the|the|DT 4|4|CD libraries|library|NNS was|be|VBD constructed|construct|VBN using|use|VBG a|a|DT different|different|JJ barcode|barcode|NN .|.|.
Libraries|Libraries|NNPS were|be|VBD prepared|prepared|JJ according|accord|VBG to|to|TO Illumina|Illumina|NNP 's|'s|POS instructions|instruction|NNS accompanying|accompany|VBG the|the|DT DNA|dna|NN Sample|sample|NN Kit|kit|NN -LRB-|-lrb-|-LRB- FC-104-5001|fc-104-5001|NN -RRB-|-rrb-|-RRB- .|.|. Briefly|briefly|RB ,|,|, DNA|dna|NN was|be|VBD end-repaired|end-repaired|JJ using|use|VBG a|a|DT combination|combination|NN of|of|IN T4|t4|NN DNA|dna|NN polymerase|polymerase|NN ,|,|, E.|e.|FW coli|coli|FW DNA|dna|NN Pol|pol|NN I|I|PRP large|large|JJ fragment|fragment|NN -LRB-|-lrb-|-LRB- Klenow|klenow|NN polymerase|polymerase|NN -RRB-|-rrb-|-RRB- and|and|CC T4|t4|NN polynucleotide|polynucleotide|NN kinase|kinase|NN .|.|. The|the|DT blunt|blunt|JJ ,|,|, phosphorylated|phosphorylated|JJ ends|end|NNS were|be|VBD treated|treat|VBN with|with|IN Klenow|Klenow|NNP fragment|fragment|NN -LRB-|-lrb-|-LRB- 32|32|CD to|to|TO 52|52|CD exo|exo|NN minus|minus|NN -RRB-|-rrb-|-RRB- and|and|CC dATP|datp|NN to|to|TO yield|yield|VB a|a|DT protruding|protrude|VBG 3|3|LS -|-|: `|`|`` A|a|DT '|'|'' base|base|NN for|for|IN ligation|ligation|NN of|of|IN Illumina|Illumina|NNP 's|'s|POS adapters|adapter|NNS which|which|WDT have|have|VBP a|a|DT single|single|JJ `|`|`` T|t|NN '|'|'' base|base|NN overhang|overhang|NN at|at|IN the|the|DT 3|3|CD '|'|'' end|end|NN .|.|. After|after|IN adapter|adapter|NN ligation|ligation|NN DNA|dna|NN was|be|VBD PCR|pcr|NN amplified|amplify|VBN with|with|IN Illumina|Illumina|NNP primers|primer|NNS for|for|IN 15|15|CD cycles|cycle|NNS and|and|CC library|library|NN fragments|fragment|NNS of|of|IN ~|~|NN 250|250|CD bp|bp|NN -LRB-|-lrb-|-LRB- insert|insert|NN plus|plus|CC adaptor|adaptor|NN and|and|CC PCR|pcr|NN primer|primer|NN sequences|sequence|NNS -RRB-|-rrb-|-RRB- were|be|VBD band|band|NN isolated|isolate|VBN from|from|IN an|a|DT agarose|agarose|NN gel|gel|NN .|.|. The|the|DT purified|purify|VBN DNA|dna|NN was|be|VBD captured|capture|VBN on|on|IN an|a|DT Illumina|Illumina|NNP flow|flow|NN cell|cell|NN for|for|IN cluster|cluster|NN generation|generation|NN .|.|. Libraries|library|NNS were|be|VBD sequenced|sequence|VBN on|on|IN the|the|DT Genome|Genome|NNP Analyzer|Analyzer|NNP following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocols|protocol|NNS .|.|.
Libraries|Libraries|NNPS were|be|VBD prepared|prepared|JJ according|accord|VBG to|to|TO Illumina|Illumina|NNP 's|'s|POS instructions|instruction|NNS accompanying|accompany|VBG the|the|DT genomic|genomic|JJ DNA|dna|NN Sample|sample|NN Kit|kit|NN .|.|. Briefly|briefly|RB ,|,|, cDNA|cdna|NN was|be|VBD sonicated|sonicate|VBN in|in|IN a|a|DT biorupter|biorupter|NN sonicator|sonicator|NN ,|,|, cleaned|clean|VBN up/concentrated|up/concentrated|VBN through|through|IN a|a|DT Qiagen|Qiagen|NNP PCR|pcr|NN column|column|NN ,|,|, and|and|CC end-repaired|end-repaired|JJ .|.|. The|the|DT blunt|blunt|JJ DNA|dna|NN was|be|VBD treated|treat|VBN with|with|IN Klenow|Klenow|NNP fragment|fragment|NN -LRB-|-lrb-|-LRB- exo|exo|NN minus|minus|NN -RRB-|-rrb-|-RRB- to|to|TO add|add|VB an|a|DT A-overhang|a-overhang|NN ,|,|, and|and|CC ligated|ligate|VBN to|to|TO the|the|DT relevant|relevant|JJ Illumina|Illumina|NNP adapter|adapter|NN sequence|sequence|NN -LRB-|-lrb-|-LRB- either|either|CC with|with|IN our|we|PRP$ without|without|IN a|a|DT barcode|barcode|NN -RRB-|-rrb-|-RRB- .|.|. Adaptered-DNA|adaptered-dna|NN was|be|VBD then|then|RB size-selected|size-selected|JJ on|on|IN a|a|DT agarose|agarose|NN gel|gel|NN and|and|CC PCR|pcr|NN amplified|amplify|VBD .|.|. The|the|DT purified|purify|VBN PCR|pcr|NN was|be|VBD captured|capture|VBN on|on|IN an|a|DT Illumina|Illumina|NNP flow|flow|NN cell|cell|NN for|for|IN cluster|cluster|NN generation|generation|NN .|.|. Libraries|library|NNS were|be|VBD sequenced|sequence|VBN on|on|IN the|the|DT Genome|Genome|NNP Analyzer|Analyzer|NNP following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocols|protocol|NNS .|.|.
Libraries|Libraries|NNPS were|be|VBD prepared|prepared|JJ according|accord|VBG to|to|TO Illumina|Illumina|NNP 's|'s|POS instructions|instruction|NNS accompanying|accompany|VBG the|the|DT genomic|genomic|JJ DNA|dna|NN Sample|sample|NN Kit|kit|NN .|.|. Briefly|briefly|RB ,|,|, gDNA|gdna|NN was|be|VBD sonicated|sonicate|VBN in|in|IN a|a|DT biorupter|biorupter|NN sonicator|sonicator|NN ,|,|, cleaned|clean|VBN up/concentrated|up/concentrated|VBN through|through|IN a|a|DT Qiagen|Qiagen|NNP PCR|pcr|NN column|column|NN ,|,|, and|and|CC end-repaired|end-repaired|JJ .|.|. The|the|DT blunt|blunt|JJ DNA|dna|NN was|be|VBD treated|treat|VBN with|with|IN Klenow|Klenow|NNP fragment|fragment|NN -LRB-|-lrb-|-LRB- exo|exo|NN minus|minus|NN -RRB-|-rrb-|-RRB- to|to|TO add|add|VB an|a|DT A-overhang|a-overhang|NN ,|,|, and|and|CC ligated|ligate|VBN to|to|TO the|the|DT relevant|relevant|JJ Illumina|Illumina|NNP adapter|adapter|NN sequence|sequence|NN -LRB-|-lrb-|-LRB- either|either|CC with|with|IN our|we|PRP$ without|without|IN a|a|DT barcode|barcode|NN -RRB-|-rrb-|-RRB- .|.|. Adaptered-DNA|adaptered-dna|NN was|be|VBD then|then|RB size-selected|size-selected|JJ on|on|IN a|a|DT agarose|agarose|NN gel|gel|NN and|and|CC PCR|pcr|NN amplified|amplify|VBD .|.|. The|the|DT purified|purify|VBN PCR|pcr|NN was|be|VBD captured|capture|VBN on|on|IN an|a|DT Illumina|Illumina|NNP flow|flow|NN cell|cell|NN for|for|IN cluster|cluster|NN generation|generation|NN .|.|. Libraries|library|NNS were|be|VBD sequenced|sequence|VBN on|on|IN the|the|DT Genome|Genome|NNP Analyzer|Analyzer|NNP following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocols.library|protocols.library|JJ strategy|strategy|NN
Libraries|Libraries|NNPS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS
Library|Library|NNP constructed|construct|VBN using|use|VBG KAPA|KAPA|NNP Kit|kit|NN .|.|.
library|library|NN construction|construction|NN followed|follow|VBD Illumina|Illumina|NNP manufacturer|manufacturer|NN protocol|protocol|NN for|for|IN bacteria|bacterium|NNS using|use|VBG the|the|DT Nextera|Nextera|NNP XT|XT|NNP DNA|DNA|NNP Library|Library|NNP Preparation|Preparation|NNP Kit|kit|NN
Library|Library|NNP construction|construction|NN was|be|VBD based|base|VBN on|on|IN the|the|DT method|method|NN described|describe|VBN by|by|IN Rhee|Rhee|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- doi|doi|FW :|:|: 10.1016|10.1016|CD /|/|: j.cell|j.cell|JJ .2011.11.013|.2011.11.013|NN -RRB-|-rrb-|-RRB- .|.|.
Library|Library|NNP construction|construction|NN was|be|VBD performed|perform|VBN as|as|IN described|describe|VBN in|in|IN Oh|oh|UH et|et|FW al.|al.|FW 2011|2011|CD ,|,|, Cell|cell|NN 147|147|CD -LRB-|-lrb-|-LRB- 6|6|CD -RRB-|-rrb-|-RRB- :|:|: 1295-1308|1295-1308|CD -LRB-|-lrb-|-LRB- PMCID|pmcid|NN :|:|: PMC3277850|pmc3277850|NN -RRB-|-rrb-|-RRB- .|.|. Briefly|briefly|RB ,|,|, fragments|fragment|NNS of|of|IN total|total|NN mRNA|mrna|NN or|or|CC ribosome|ribosome|NN protected|protect|VBD mRNA|mrna|NN fragments|fragment|NNS were|be|VBD size|size|NN selected|select|VBN via|via|IN gel|gel|NN purification|purification|NN ,|,|, and|and|CC ligated|ligate|VBN to|to|TO a|a|DT 5|5|CD '|'|'' adenylated|adenylate|VBN DNA|dna|NN oligo|oligo|JJ .|.|. After|after|IN reverse|reverse|JJ transcription|transcription|NN ,|,|, the|the|DT single|single|JJ stranded|stranded|JJ DNA|dna|NN was|be|VBD circularized|circularize|VBN and|and|CC amplified|amplify|VBN by|by|IN PCR|pcr|NN .|.|.
Library|Library|NNP construction|construction|NN was|be|VBD performed|perform|VBN as|as|IN described|describe|VBN in|in|IN Parkhomchuk|Parkhomchuk|NNP et|et|FW al.|al.|FW 2009|2009|CD ,|,|, Nucleic|Nucleic|NNP Acids|Acids|NNP Res|Res|NNP 37|37|CD :|:|: e123|e123|NN .|.|. Briefly|briefly|RB ,|,|, ribosome-depleted|ribosome-depleted|JJ RNA|rna|NN was|be|VBD fragmented|fragmented|JJ and|and|CC used|use|VBN as|as|IN template|template|NN for|for|IN cDNA|cdna|NN synhtesis|synhtesis|NN .|.|. dUTP|dutp|NN was|be|VBD included|include|VBN in|in|IN the|the|DT second|second|JJ strand|strand|NN synthesis|synthesis|NN reaction|reaction|NN in|in|IN addition|addition|NN to|to|TO dTTP|dttp|NN to|to|TO chemically|chemically|RB mark|mark|VB the|the|DT second|second|JJ strand|strand|NN .|.|. cDNAs|cdna|NNS were|be|VBD size-selected|size-selected|JJ and|and|CC ligated|ligate|VBN to|to|TO sequencing|sequencing|NN adapters|adapter|NNS followed|follow|VBN by|by|IN dUTP|dutp|NN cleavage|cleavage|NN to|to|TO generate|generate|VB adapter-ligated|adapter-ligated|JJ single-stranded|single-stranded|JJ cDNAs|cdna|NNS .|.|.
Library|Library|NNP construction|construction|NN was|be|VBD performed|perform|VBN by|by|IN processing|processing|NN in|in|FW vitro|vitro|FW samples|sample|NNS to|to|TO generate|generate|VB a|a|DT library|library|NN of|of|IN short|short|JJ inserts|insert|NNS -LRB-|-lrb-|-LRB- the|the|DT DNA|dna|NN Colonies|colony|NNS Template|Template|NNP Library|Library|NNP -RRB-|-rrb-|-RRB- by|by|IN Fasteris|Fasteris|NNP SA|SA|NNP ,|,|, Switzerland|Switzerland|NNP
Library|Library|NNP minipreps|miniprep|NNS were|be|VBD performed|perform|VBN with|with|IN the|the|DT Zyppy|Zyppy|NNP Miniprep|Miniprep|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Zymo|Zymo|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC quantified|quantify|VBN using|use|VBG the|the|DT Qubit|Qubit|NNP dsDNA|dsDNA|NNP BR|BR|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT Nanodrop|Nanodrop|NNP spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB-
Library|Library|NNP preparation|preparation|NN was|be|VBD performed|perform|VBN by|by|IN vertis|vertis|NN Biotechnologie|Biotechnologie|NNP AG|AG|NNP ,|,|, according|accord|VBG to|to|TO the|the|DT following|follow|VBG protocol|protocol|NN :|:|: RNA|rna|NN samples|sample|NNS were|be|VBD first|first|JJ treated|treat|VBN with|with|IN rDNase|rdnase|NN .|.|. From|from|IN the|the|DT total|total|JJ RNA|rna|NN samples|sample|NNS ,|,|, ribosomal|ribosomal|JJ RNA|rna|NN molecules|molecule|NNS were|be|VBD depleted|deplete|VBN using|use|VBG the|the|DT Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Bacteria|bacterium|NNS ,|,|, Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|. the|the|DT rRNA|rrna|NN depleted|deplete|VBN RNA|rna|NN samples|sample|NNS were|be|VBD fragmented|fragmented|JJ with|with|IN ultrasound|ultrasound|NN -LRB-|-lrb-|-LRB- 2|2|CD pulses|pulse|NNS of|of|IN 30|30|CD sec|sec|NN at|at|IN 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|. Firststrand|Firststrand|NNP cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD primed|prime|VBN with|with|IN a|a|DT N6|n6|NN randomized|randomize|VBD primer|primer|NN .|.|. Then|then|RB ,|,|, Illumina|Illumina|NNP TruSeq|TruSeq|NNP sequencing|sequencing|NN adapters|adapter|NNS were|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 5|5|CD '|'|'' and|and|CC 3|3|CD '|'|'' ends|end|NNS of|of|IN the|the|DT cDNA|cdna|NN .|.|. The|the|DT cDNA|cdna|NN was|be|VBD finally|finally|RB amplified|amplify|VBN with|with|IN PCR|pcr|NN -LRB-|-lrb-|-LRB- 16-18|16-18|CD cycles|cycle|NNS ,|,|, depending|depend|VBG on|on|IN sample|sample|NN -RRB-|-rrb-|-RRB- using|use|VBG a|a|DT proof|proof|NN reading|reading|NN enzyme|enzyme|NN .|.|. Aliquots|aliquot|NNS of|of|IN each|each|DT library|library|NN were|be|VBD analyzed|analyze|VBN by|by|IN capillary|capillary|JJ electrophoresis|electrophoresis|NN .|.|.
Library|Library|NNP preparation|preparation|NN was|be|VBD performed|perform|VBN by|by|IN vertis|vertis|NN Biotechnologie|Biotechnologie|NNP AG|AG|NNP ,|,|, according|accord|VBG to|to|TO the|the|DT following|follow|VBG protocol|protocol|NN :|:|: the|the|DT DNA|dna|NN samples|sample|NNS were|be|VBD treated|treat|VBN with|with|IN ultrasound|ultrasound|NN -LRB-|-lrb-|-LRB- 3-5|3-5|CD pulses|pulse|NNS of|of|IN 30|30|CD sec|sec|NN at|at|IN 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN end-repair|end-repair|NN ,|,|, TruSeq|truseq|NN sequencing|sequencing|NN adapters|adapter|NNS were|be|VBD ligated|ligate|VBN to|to|TO the|the|DT DNA|dna|NN fragments|fragment|NNS .|.|. Finally|finally|RB ,|,|, the|the|DT DNA|dna|NN was|be|VBD PCR-amplified|pcr-amplified|JJ to|to|TO about|about|RB 20-30|20-30|CD ng/μl|ng/μl|NN using|use|VBG a|a|DT high|high|JJ fidelity|fidelity|NN DNA|dna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- 9-11|9-11|CD cycles|cycle|NNS ,|,|, depending|depend|VBG on|on|IN the|the|DT sample|sample|NN -RRB-|-rrb-|-RRB- .|.|. Aliquots|aliquot|NNS of|of|IN the|the|DT PCR|pcr|NN amplified|amplify|VBD libraries|library|NNS were|be|VBD examined|examine|VBN by|by|IN capillary|capillary|JJ electrophoresis|electrophoresis|NN .|.|.
Library|Library|NNP preparation|preparation|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT Nextera|Nextera|NNP XT|XT|NNP kit|kit|NN from|from|IN Illumina|Illumina|NNP -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP FC-131-1096|fc-131-1096|NN -RSB-|-rsb-|-RRB- starting|start|VBG from|from|IN 1|1|CD ng|ng|NN of|of|IN total|total|JJ cDNA|cdna|NN .|.|. The|the|DT original|original|JJ protocol|protocol|NN was|be|VBD modified|modify|VBN where|where|WRB 3|3|CD min|min|NN tagmentation|tagmentation|NN and|and|CC 13|13|CD cycles|cycle|NNS of|of|IN step-limited|step-limited|JJ PCR|pcr|NN were|be|VBD used|use|VBN .|.|. Ampure|ampure|JJ beads|bead|NNS from|from|IN Beckman|Beckman|NNP Coulter|Coulter|NNP -LSB-|-lsb-|-LRB- Cat|Cat|NNP No|No|NNP A63880|a63880|NN -RSB-|-rsb-|-RRB- were|be|VBD used|use|VBN for|for|IN library|library|NN purification|purification|NN .|.|. Library|Library|NNP quality|quality|NN assessment|assessment|NN and|and|CC quantification|quantification|NN was|be|VBD performed|perform|VBN with|with|IN Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP and|and|CC Agilent|Agilent|NNP high|high|JJ sensitivity|sensitivity|NN DNA|dna|NN analysis|analysis|NN kit|kit|NN -LSB-|-lsb-|-LRB- Cat|cat|NN No|no|DT 5067-4626|5067-4626|CD -RSB-|-rsb-|-RRB- .|.|. Finally|finally|RB all|all|DT 90|90|CD samples|sample|NNS were|be|VBD pooled|pool|VBN together|together|RB in|in|IN the|the|DT same|same|JJ reaction|reaction|NN tube|tube|NN at|at|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD nM|nm|NN .|.|.
Library|Library|NNP preparation|preparation|NN was|be|VBD performed|perform|VBN with|with|IN TruSeq|TruSeq|NNP Stranded|Stranded|NNP Total|Total|NNP RNA|rna|NN HT|ht|NN Sample|Sample|NNP Prep|Prep|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|. Libraries|library|NNS were|be|VBD sequenced|sequence|VBN with|with|IN 50|50|CD bp|bp|NN single|single|JJ read|read|NN configuration|configuration|NN on|on|IN a|a|DT HiSeq|hiseq|JJ 2500|2500|CD system|system|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|.
Library|Library|NNP preparation|preparation|NN were|be|VBD performed|perform|VBN with|with|IN Epicentre|Epicentre|NNP ScriptseqTM|ScriptseqTM|NNP v2|v2|NN RNA-Seq|rna-seq|NN Library|Library|NNP preparation|preparation|NN kit|kit|NN with|with|IN 50|50|CD ng|ng|NN of|of|IN depleted|deplete|VBN RNA|rna|NN ;|;|: Strand|Strand|NNP orientated|orientate|VBD RNA-Seq|rna-seq|JJ
Library|Library|NNP strategy|strategy|NN :|:|: 3C-seq|3c-seq|JJ
library|library|NN strategy|strategy|NN :|:|: 3|3|CD '|'|'' -|-|: end|end|NN RNA-seq|rna-seq|NN
library|library|NN strategy|strategy|NN :|:|: ChIP-exo|ChIP-exo|NNP
Library|Library|NNP strategy|strategy|NN :|:|: ChIP-exo|ChIP-exo|NNP
library|library|NN strategy|strategy|NN :|:|: ChIP-seq|chip-seq|NN -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
library|library|NN strategy|strategy|NN :|:|: DMS-seq|dms-seq|JJ
Library|Library|NNP strategy|strategy|NN :|:|: REC-Seq|rec-seq|NN
Library|Library|NNP strategy|strategy|NN :|:|: Ribo-Seq|Ribo-Seq|NNP
Library|Library|NNP strategy|strategy|NN :|:|: RIBO-seq|ribo-seq|JJ
library|library|NN strategy|strategy|NN :|:|: Ribosome|Ribosome|NNP profiling|profile|VBG
library|library|NN strategy|strategy|NN :|:|: Selective|selective|JJ ribosome|ribosome|NN profiling|profile|VBG
library|library|NN strategy|strategy|NN :|:|: SPET-seq|spet-seq|JJ
ligation|ligation|NN ,|,|, rt-PCR|rt-pcr|NN ,|,|, PCR|pcr|NN
LIMS477|lims477|NN _|_|CD S1|s1|NN _|_|CD T10|t10|NN
LIMS477|lims477|NN _|_|CD S1|s1|NN _|_|CD T3|t3|NN
LIMS477|lims477|NN _|_|CD S1|s1|NN _|_|CD T6|t6|NN
LIMS477|lims477|NN _|_|CD S2|s2|NN _|_|CD T4|t4|NN
LIMS477|lims477|NN _|_|CD S2|s2|NN _|_|CD T6|t6|NN
LIMS477|lims477|NN _|_|CD S2|s2|NN _|_|CD T8|t8|NN
LIMS477|lims477|NN _|_|CD S3|s3|NN _|_|CD T11|t11|NN
LIMS477|lims477|NN _|_|CD S3|s3|NN _|_|CD T3|t3|NN
LIMS477|lims477|NN _|_|CD S3|s3|NN _|_|CD T6|t6|NN
LIMS477|lims477|NN _|_|CD S5|s5|NN _|_|CD T4|t4|NN
LIMS477|lims477|NN _|_|CD S5|s5|NN _|_|CD T6|t6|NN
LIMS477|lims477|NN _|_|CD S5|s5|NN _|_|CD T8|t8|NN
LIMS484|lims484|NN _|_|CD S1|s1|NN _|_|CD T3|t3|NN
LIMS484|lims484|NN _|_|CD S1|s1|NN _|_|CD T6|t6|NN
LIMS484|lims484|NN _|_|CD S1|s1|NN _|_|CD T8|t8|NN
LIMS484|lims484|NN _|_|CD S2|s2|NN _|_|CD T2|t2|NN
LIMS484|lims484|NN _|_|CD S2|s2|NN _|_|CD T6|t6|NN
LIMS484|lims484|NN _|_|CD S2|s2|NN _|_|CD T8|t8|NN
LIMS484|lims484|NN _|_|CD S5|s5|NN _|_|CD T2|t2|NN
LIMS484|lims484|NN _|_|CD S5|s5|NN _|_|CD T6|t6|NN
LIMS484|lims484|NN _|_|CD S5|s5|NN _|_|CD T8|t8|NN
LIMS484|lims484|NN _|_|CD S6|s6|NN _|_|CD T4|t4|NN
LIMS484|lims484|NN _|_|CD S6|s6|NN _|_|CD T6|t6|NN
LIMS484|lims484|NN _|_|CD S6|s6|NN _|_|CD T8|t8|NN
Linearly|linearly|RB scaled|scale|VBN so|so|IN that|that|IN intensity|intensity|NN values|value|NNS in|in|IN gDNA|gdna|NN _|_|CD A|a|DT _|_|NN cy5|cy5|NN ,|,|, cDNA|cdna|NN _|_|NN A|a|NN _|_|NN cy3|cy3|NN ,|,|, gDNA|gdna|NN _|_|NN B|b|NN _|_|CD cy3|cy3|NN ,|,|, and|and|CC cDNA|cdna|NN _|_|NN B|b|NN _|_|CD cy5|cy5|NN are|be|VBP comparable|comparable|JJ
Linearly|linearly|RB scaled|scale|VBN so|so|IN that|that|IN intensity|intensity|NN values|value|NNS in|in|IN Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|NN control|control|NN _|_|CD A|a|DT _|_|NN cy3|cy3|NN ,|,|, Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|CD A|a|DT _|_|NN cy5|cy5|NN ,|,|, Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|NN control|control|NN _|_|NN B|b|NN _|_|CD cy3|cy3|NN ,|,|, Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|NN B|b|NN _|_|CD cy5|cy5|NN ,|,|, Beta|beta|NN _|_|CD ChIP|chip|NN _|_|NN control|control|NN _|_|CD A|a|DT _|_|NN cy3|cy3|NN ,|,|, Beta|beta|NN _|_|NN ChIP|chip|NN _|_|CD A|a|DT _|_|NN cy5|cy5|NN ,|,|, Beta|beta|NN _|_|NN ChIP|chip|NN _|_|CD control|control|NN _|_|NN B|b|NN _|_|CD cy3|cy3|NN ,|,|, Beta|beta|NN _|_|NN ChIP|chip|NN _|_|NN B|b|NN _|_|CD cy5|cy5|NN are|be|VBP comparable|comparable|JJ
LJ110|lj110|NN del|del|FW pdhr|pdhr|FW LBo|lbo|FW
LJ110|lj110|NN del|del|FW pdhr|pdhr|FW MMAcetat|mmacetat|NN
LJ110|lj110|NN del|del|FW pdhr|pdhr|FW MMPyruvat|mmpyruvat|NN
LJ110|lj110|NN LBo|lbo|NN
LJ110|lj110|NN MMAcetat|mmacetat|NN
LJ110|lj110|NN MMPyruvat|mmpyruvat|NN
LJ110|lj110|NN pTM30|ptm30|NN LBo|lbo|NN
LJ110|lj110|NN pTM30|ptm30|NN MMAcetat|mmacetat|NN
LJ110|lj110|NN pTM30|ptm30|NN MMPyruvat|mmpyruvat|NN
LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN LBo|lbo|NN
LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN MMAcetat|mmacetat|NN
LJ110|lj110|NN pTM30pdhr|ptm30pdhr|NN MMPyruvat|mmpyruvat|NN
Local|local|JJ Background|background|NN Substracted|Substracted|NNP Signal|Signal|NNP Corrected|Corrected|NNP for|for|IN unequal|unequal|JJ Dye|dye|NN incorporation|incorporation|NN or|or|CC unequal|unequal|JJ load|load|NN of|of|IN labelled|label|VBN product|product|NN
location|location|NN :|:|: Earth|Earth|NNP
location|location|NN :|:|: Space|Space|NNP
Log10|log10|NN mRNA|mrna|NN concentration|concentration|NN -LRB-|-lrb-|-LRB- pM|pm|NN -RRB-|-rrb-|-RRB- data|datum|NNS are|be|VBP provided|provide|VBN as|as|IN a|a|DT supplementary|supplementary|JJ file|file|NN .|.|. Expression|expression|NN levels|level|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT quantile|quantile|JJ normalization|normalization|NN method|method|NN -LRB-|-lrb-|-LRB- Bolstad|Bolstad|NNP et|et|FW al.|al.|FW ,|,|, 2003|2003|CD -RRB-|-rrb-|-RRB- .|.|.
log10|log10|NN mRNA|mrna|NN concentration|concentration|NN -LRB-|-lrb-|-LRB- pM|pm|NN -RRB-|-rrb-|-RRB- data|datum|NNS are|be|VBP provided|provide|VBN as|as|IN a|a|DT supplementary|supplementary|JJ file|file|NN on|on|IN the|the|DT SERIES|series|NN record|record|NN .|.|.
log2|log2|NN ratio|ratio|NN of|of|IN isolate/control|isolate/control|JJ
Logarithmic|logarithmic|JJ phase|phase|NN sample|sample|NN 1|1|CD
Logarithmic|logarithmic|JJ phase|phase|NN sample|sample|NN 2|2|CD
Logarithmic|logarithmic|JJ phase|phase|NN sample|sample|NN 3|3|CD
Logarithmic|logarithmic|JJ phase|phase|NN sample|sample|NN 4|4|CD
LogData|logdata|NN =|=|JJ createData|createdata|NN -LRB-|-lrb-|-LRB- Data|data|NN ,|,|, n.rep|n.rep|NN =|=|JJ 1|1|CD ,|,|, log.trans|log.trans|VBZ =|=|JJ TRUE|true|JJ -RRB-|-rrb-|-RRB-
log|log|VBP phase|phase|NN 1|1|CD
log|log|NN phase|phase|NN 2|2|CD
log|log|VBP phase|phase|NN 3|3|CD
log|log|NN phase|phase|NN 4|4|CD
log|log|VBP phase|phase|NN 5|5|CD
Log-phase|log-phase|NN cultures|culture|NNS -LRB-|-lrb-|-LRB- LB|lb|NN broth|broth|NN ,|,|, Miller|Miller|NNP formulation|formulation|NN -RRB-|-rrb-|-RRB- inoculated|inoculate|VBN with|with|IN either|either|CC blue|blue|JJ or|or|CC pale|pale|JJ colonies|colony|NNS were|be|VBD grown|grow|VBN for|for|IN 5|5|CD hr|hr|NN at|at|IN 37|37|CD degrees|degree|NNS celsius|celsius|NN .|.|. Cells|cell|NNS were|be|VBD pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC flash|flash|NN frozen|freeze|VBN on|on|IN dry|dry|JJ ice|ice|NN .|.|.
lon|lon|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r1|r1|NN
lon|lon|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r2|r2|NN
lon|lon|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r3|r3|NN
lon|lon|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
LOWESS|lowess|NN normalised|normalised|JJ data|datum|NNS that|that|WDT represents|represent|VBZ the|the|DT average|average|NN of|of|IN the|the|DT three|three|CD replicate|replicate|VBP experiments|experiment|NNS
LOWESS|lowess|NN normalized|normalize|VBD ,|,|, background|background|NN subtracted|subtract|VBD data|datum|NNS obtained|obtain|VBN from|from|IN log2|log2|NN of|of|IN processed|process|VBN Red|Red|NNP signal/processed|signal/processed|VBD Green|Green|NNP signal|signal|NN .|.|. Agilent|Agilent|NNP software|software|NN GX|GX|NNP 7.3|7.3|CD was|be|VBD used|use|VBN .|.|.
LOWESS|lowess|NN normalized|normalize|VBD ,|,|, background|background|NN subtracted|subtract|VBD data|datum|NNS obtained|obtain|VBN from|from|IN signals|signal|NNS .|.|. Agilent|Agilent|NNP GeneSpring|GeneSpring|NNP GX|GX|NNP 7.3|7.3|CD was|be|VBD used|use|VBN .|.|.
LOWESS|lowess|NN normalized|normalize|VBD data|datum|NNS obtained|obtain|VBN from|from|IN log2|log2|NN of|of|IN processed|process|VBN Red|red|JJ signal|signal|NN -LRB-|-lrb-|-LRB- treated|treat|VBN -RRB-|-rrb-|-RRB- /|/|: processed|process|VBN Green|Green|NNP signal|signal|NN -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB- are|be|VBP given|give|VBN in|in|IN the|the|DT data|datum|NNS table|table|NN below|below|IN .|.|. All|all|DT microarray|microarray|NN data|datum|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG R|r|NN software|software|NN and|and|CC Limma|limma|NN package|package|NN -LRB-|-lrb-|-LRB- part|part|NN of|of|IN Bioconductor|Bioconductor|NNP -RRB-|-rrb-|-RRB- .|.|. All|all|PDT the|the|DT probes|probe|NNS encoding|encode|VBG for|for|IN positive|positive|JJ and|and|CC negative|negative|JJ controls|control|NNS were|be|VBD not|not|RB used|use|VBN and|and|CC have|have|VBP been|be|VBN removed|remove|VBN .|.|. Only|only|RB raw|raw|JJ data|datum|NNS superior|superior|JJ to|to|TO background|background|NN values|value|NNS and|and|CC with|with|IN homogeneous|homogeneous|JJ fluorescent|fluorescent|JJ signals|signal|NNS were|be|VBD considered|consider|VBN -LRB-|-lrb-|-LRB- H|h|NN <|<|JJR 0.2|0.2|CD -RRB-|-rrb-|-RRB- .|.|. Red|Red|NNP and|and|CC green|green|JJ signal|signal|NN heterogeneity|heterogeneity|NN was|be|VBD estimated|estimate|VBN as|as|IN followed|follow|VBN :|:|: H|h|NN =|=|JJ ||||NN -LRB-|-lrb-|-LRB- trimmed|trimmed|RBR mean|mean|VB of|of|IN raw|raw|JJ intensity|intensity|NN -|-|: median|median|NN of|of|IN raw|raw|JJ intensity|intensity|NN -RRB-|-rrb-|-RRB- ||||SYM /|/|: ||||SYM -LRB-|-lrb-|-LRB- 0.5|0.5|CD *|*|SYM -LRB-|-lrb-|-LRB- trimmed|trimmed|RBR mean|mean|VB of|of|IN raw|raw|JJ intensity|intensity|NN +|+|CC median|median|NN of|of|IN raw|raw|JJ intensity|intensity|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. After|after|IN LOWESS|lowess|NN normalization|normalization|NN ,|,|, the|the|DT differences|difference|NNS between|between|IN the|the|DT four|four|CD heat-treatments|heat-treatment|NNS were|be|VBD tested|test|VBN by|by|IN Analysis|analysis|NN of|of|IN Variance|variance|NN -LRB-|-lrb-|-LRB- ANOVA|anova|NN -RRB-|-rrb-|-RRB- followed|follow|VBN by|by|IN a|a|DT priori|priori|FW tests|test|NNS -LRB-|-lrb-|-LRB- P-value|p-value|JJ <|<|VBG 0.0001|0.0001|CD and|and|CC P-value|p-value|JJ FDR|FDR|NNP after|after|IN Benjamini|Benjamini|NNP Yekutieli|Yekutieli|NNP adjustment|adjustment|NN <|<|JJR 0.01|0.01|CD -RRB-|-rrb-|-RRB- .|.|. Six|six|CD contrasts|contrast|VBZ -LRB-|-lrb-|-LRB- Contrast1|contrast1|NN :|:|: T1|t1|NN vs|vs|CC T2|t2|NN ,|,|, Contrast2|contrast2|NN :|:|: T1|t1|NN vs|vs|CC T3|t3|NN ,|,|, Contrast3|contrast3|NN :|:|: T1|t1|NN vs|vs|CC T4|t4|NN ,|,|, Contrast4|contrast4|NN :|:|: T2|t2|NN vs|vs|CC T3|t3|NN ,|,|, Contrast5|contrast5|NN :|:|: T2|t2|NN vs|vs|CC T4|t4|NN ,|,|, Contrast6|contrast6|NN :|:|: T3|t3|NN vs|vs|CC T4|t4|NN -RRB-|-rrb-|-RRB- were|be|VBD performed|perform|VBN .|.|. Normalized|normalize|VBN Log2|log2|NN ratio|ratio|NN between|between|IN treatments|treatment|NNS and|and|CC the|the|DT results|result|NNS of|of|IN the|the|DT statistical|statistical|JJ analysis|analysis|NN have|have|VBP been|be|VBN linked|link|VBN as|as|IN a|a|DT supplementary|supplementary|JJ file|file|NN on|on|IN the|the|DT Series|Series|NNP record|record|NN .|.|.
Lowess|lowess|NN normalized|normalize|VBD data|datum|NNS .|.|. Resultant|resultant|JJ data|datum|NNS is|be|VBZ log2|log2|NN normalized|normalize|VBD .|.|.
Lowly|Lowly|NNP expressed|express|VBD genes|gene|NNS -LRB-|-lrb-|-LRB- <|<|JJR 1|1|CD read|read|NN per|per|IN million|million|CD -RRB-|-rrb-|-RRB- were|be|VBD removed|remove|VBN .|.|.
Low|low|JJ quality|quality|NN reads|read|VBZ were|be|VBD trimmed|trim|VBN with|with|IN CutAdapt|cutadapt|JJ
LP1|lp1|NN
LP2|lp2|NN
LP3|lp3|NN
LP4|lp4|NN
lplA|lpla|NN KO|ko|NN rep1|rep1|NN
lplA|lpla|NN KO|ko|NN rep2|rep2|NN
lplA|lpla|NN KO|ko|NN rep3|rep3|NN
lrp-gln-1|lrp-gln-1|NN
lrp-gln-2|lrp-gln-2|NN
Lrp|lrp|VBP _|_|SYM Leu|Leu|NNP _|_|SYM 1|1|CD
Lrp|Lrp|NNP _|_|NNP Leu|Leu|NNP _|_|NNP 2|2|CD
Lrp|Lrp|NNP _|_|NNP Leu|Leu|NNP _|_|SYM 3|3|CD
lrp|lrp|SYM -|-|: +|+|CC Leu|Leu|NNP vs.|vs.|FW lrp|lrp|SYM -|-|: -|-|: Leu|leu|NN
lrp|lrp|NN -|-|: -|-|: Leu|leu|NN vs.|vs.|CC wt|wt|JJ -|-|: Leu|leu|NN
lrp|lrp|NN -|-|: +|+|CC Leu|Leu|NNP vs.|vs.|FW wt|wt|JJ -|-|: Leu|leu|NN
Lrp|lrp|NN _|_|CD NH4Cl|nh4cl|NN _|_|NN 1|1|CD
Lrp|Lrp|NNP _|_|SYM NH4Cl|nh4cl|NN _|_|NN 2|2|CD
Lrp|Lrp|NNP _|_|SYM NH4Cl|nh4cl|NN _|_|NN 3|3|CD
L-threonine|l-threonine|NN producing|produce|VBG strain|strain|NN
L-threonine|l-threonine|NN producing|produce|VBG strain|strain|NN vs|vs|CC control|control|NN strain|strain|NN
L|l|NN ,|,|, TP1|tp1|NN
L|l|NN ,|,|, TP2|tp2|NN
L|l|NN ,|,|, TP3|tp3|NN
L|l|NN ,|,|, TP4|tp4|NN
luc2|luc2|NN _|_|CD U|U|NNP _|_|NNP N0000|N0000|NNP _|_|VBD r1|r1|NN
luc2|luc2|NN _|_|CD U|U|NNP _|_|NNP N0000|N0000|NNP _|_|VBD r2|r2|NN
luc2|luc2|NN _|_|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r1|r1|NN
luc2|luc2|NN _|_|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r2|r2|NN
luciferase|luciferase|NN 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
luciferase|luciferase|NN no|no|DT drug|drug|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0000|N0000|NNP _|_|NNP r1|r1|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0000|N0000|NNP _|_|NNP r2|r2|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0000|N0000|NNP _|_|NNP r3|r3|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r1|r1|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r2|r2|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r3|r3|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r2|r2|NN
luc|luc|NN ___|___|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r3|r3|NN
luc|luc|NN upregulation|upregulation|NN ,|,|, 0.000|0.000|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
luc|luc|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
luc|luc|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
Luria|Luria|NNP broth|broth|NN -LRB-|-lrb-|-LRB- LB|lb|NN -RRB-|-rrb-|-RRB- medium|medium|NN under|under|IN aeration|aeration|NN ,|,|, exponential|exponential|JJ phase|phase|NN OD600|od600|NN =|=|JJ 0.3|0.3|CD .|.|.
luxS|luxs|NN mutants|mutant|NNS ,|,|, 10|10|CD %|%|NN H2O2|h2o2|NN
luxS|luxs|NN mutants|mutant|NNS ,|,|, 30|30|CD %|%|NN H2O2|h2o2|NN
luxS|luxs|NN mutants|mutant|NNS ,|,|, without|without|IN H2O2|h2o2|NN
Lysates|lysate|NNS were|be|VBD diluted|dilute|VBN with|with|IN 1|1|CD ml|ml|NN of|of|IN TES|tes|NN buffer|buffer|NN and|and|CC 100|100|CD μl|μl|NN of|of|IN ANTI-FLAG|anti-flag|NN ®|®|CD M2|m2|NN affinity|affinity|NN gel|gel|NN -LRB-|-lrb-|-LRB- Sigma-Aldrich|sigma-aldrich|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN .|.|. Immunoprecipitation|immunoprecipitation|NN was|be|VBD performed|perform|VBN for|for|IN 1.5-2|1.5-2|CD hours|hour|NNS at|at|IN room|room|NN temperature|temperature|NN with|with|IN moderate|moderate|JJ mixing|mix|VBG ,|,|, then|then|RB affinity|affinity|NN gel|gel|NN was|be|VBD washed|wash|VBN 4|4|CD times|time|NNS by|by|IN repeating|repeat|VBG steps|step|NNS of|of|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 1.5|1.5|CD minute|minute|NN ,|,|, 1000xg|1000xg|NN at|at|IN room|room|NN temperature|temperature|NN -RRB-|-rrb-|-RRB- and|and|CC resuspention|resuspention|NN -LRB-|-lrb-|-LRB- x2|x2|NN with|with|IN 1|1|CD ml|ml|NN of|of|IN TESS|TESS|NNP buffer|buffer|NN ,|,|, x1|x1|NN with|with|IN 1|1|CD ml|ml|NN of|of|IN TES|tes|NN buffer|buffer|NN ,|,|, x1|x1|NN with|with|IN 1|1|CD ml|ml|NN of|of|IN TE|TE|NNP buffer|buffer|NN -RRB-|-rrb-|-RRB- .|.|.
Lysine|Lysine|NNP addition|addition|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t0|t0|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t0|t0|NN ,|,|, rep2|rep2|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t10|t10|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t10|t10|NN ,|,|, rep2|rep2|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t2|t2|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t2|t2|NN ,|,|, rep2|rep2|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t4|t4|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t4|t4|NN ,|,|, rep2|rep2|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t6|t6|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t6|t6|NN ,|,|, rep2|rep2|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t8|t8|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN wild|wild|JJ type|type|NN at|at|IN t8|t8|NN ,|,|, rep2|rep2|NN
M1655|m1655|NN with|with|IN deletion|deletion|NN in|in|IN soxR|soxr|NN at|at|IN t0|t0|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN with|with|IN deletion|deletion|NN in|in|IN soxR|soxr|NN at|at|IN t10|t10|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN with|with|IN deletion|deletion|NN in|in|IN soxR|soxr|NN at|at|IN t2|t2|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN with|with|IN deletion|deletion|NN in|in|IN soxR|soxr|NN at|at|IN t4|t4|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN with|with|IN deletion|deletion|NN in|in|IN soxR|soxr|NN at|at|IN t6|t6|NN ,|,|, rep1|rep1|NN
M1655|m1655|NN with|with|IN deletion|deletion|NN in|in|IN soxR|soxr|NN at|at|IN t8|t8|NN ,|,|, rep1|rep1|NN
M63|m63|NN 0.4|0.4|CD B1|b1|NN TEX|tex|NN neg|neg|NN L1|l1|NN GA|ga|NN
M63|m63|NN 0.4|0.4|CD B1|b1|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN GA|ga|NN
M63|m63|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP neg|neg|NNP L1|l1|NN HS1|hs1|NN
M63|m63|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP neg|neg|NNP L1|l1|NN HS2|hs2|NN
M63|m63|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN HS1|hs1|NN
M63|m63|NN 0.4|0.4|CD B2|b2|NN TEX|TEX|NNP pos|po|VBZ L1|l1|NN HS2|hs2|NN
M9|m9|NN defined|define|VBN medium|medium|NN -LRB-|-lrb-|-LRB- 0.6|0.6|CD %|%|NN Na2HPO4|na2hpo4|NN ,|,|, 0.3|0.3|CD %|%|NN KH2PO4|kh2po4|NN ,|,|, 0.05|0.05|CD %|%|NN NaCl|nacl|NN ,|,|, 0.01|0.01|CD %|%|NN NH4Cl|nh4cl|NN ,|,|, 0.1|0.1|CD mM|mm|NN CaCl2|cacl2|NN ,|,|, 1|1|CD mM|mm|NN MgSO4|mgso4|NN ,|,|, 5|5|CD x|x|CC 10|10|CD −|−|NN 4|4|CD %|%|NN Thiamin|thiamin|NN -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 0.5|0.5|CD %|%|NN glucose|glucose|NN and|and|CC 0.1|0.1|CD %|%|NN amino|amino|NN acids|acid|NNS was|be|VBD used|use|VBN for|for|IN RNA-seq|rna-seq|NN experiments|experiment|NNS .|.|.
M9|m9|NN mineral|mineral|NN medium|medium|NN containing|contain|VBG -LRB-|-lrb-|-LRB- D|d|NN -RRB-|-rrb-|-RRB- -|-|: xylose|xylose|NN as|as|IN the|the|DT only|only|JJ carbon|carbon|NN source|source|NN -LRB-|-lrb-|-LRB- 100|100|CD ml|ml|NN in|in|IN 500|500|CD ml|ml|NN shake|shake|NN flasks|flask|NNS -RRB-|-rrb-|-RRB- was|be|VBD inoculated|inoculate|VBN from|from|IN exponentially|exponentially|RB growing|grow|VBG wild-type|wild-type|JJ cells|cell|NNS or|or|CC synthetic|synthetic|JJ cells|cell|NNS -LRB-|-lrb-|-LRB- cultivated|cultivate|VBN on|on|IN xylose|xylose|NN M9|m9|NN medium|medium|NN -RRB-|-rrb-|-RRB- to|to|TO adjust|adjust|VB an|a|DT OD|od|NN of|of|IN ~|~|NN 0.1|0.1|CD .|.|. Cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN under|under|IN shaking|shake|VBG until|until|IN OD|od|NN reached|reach|VBD ~|~|NN 1|1|CD .|.|. Then|then|RB they|they|PRP were|be|VBD split|split|VBN into|into|IN two|two|CD 50|50|CD ml|ml|NN aliquots|aliquot|NNS and|and|CC further|further|JJ cultivated|cultivate|VBN in|in|IN 250|250|CD ml|ml|NN shake|shake|NN flasks|flask|NNS in|in|IN the|the|DT presence|presence|NN or|or|CC absence|absence|NN of|of|IN 10|10|CD mM|mm|NN glycolaldehyde|glycolaldehyde|NN .|.|. After|after|IN 30|30|CD min|min|NN of|of|IN incubation|incubation|NN ,|,|, 1|1|CD ml|ml|NN of|of|IN the|the|DT cell|cell|NN suspension|suspension|NN was|be|VBD withdrawn|withdraw|VBN and|and|CC centrifuged|centrifuge|VBN at|at|IN 1500|1500|CD x|x|CC g|g|NN -LRB-|-lrb-|-LRB- Eppendorf|eppendorf|NN 5415D|5415d|NN -RRB-|-rrb-|-RRB- for|for|IN 5|5|CD min|min|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD removed|remove|VBN and|and|CC the|the|DT cell|cell|NN pellets|pellet|NNS were|be|VBD directly|directly|RB subject|subject|JJ to|to|TO RNA|rna|NN extraction|extraction|NN .|.|. Experiment|experiment|NN were|be|VBD repeated|repeat|VBN three|three|CD times|time|NNS .|.|.
M9|m9|NN minimal|minimal|JJ complete|complete|JJ media|media|NNS ,|,|, cultures|culture|NNS grown|grow|VBN aerobically|aerobically|RB at|at|IN 30|30|CD degrees|degree|NNS C|c|NN in|in|IN a|a|DT gyratory|gyratory|JJ water|water|NN bath|bath|NN shaking|shake|VBG at|at|IN 240|240|CD rpm|rpm|NN
M9TMP5|m9tmp5|NN _|_|CD 10|10|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|NN 120|120|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD 30|30|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD 60|60|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD 90|90|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD AdAA|adaa|NN _|_|NN 10|10|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD AdAA|adaa|NN _|_|NN 120|120|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD AdAA|adaa|NN _|_|CD 30|30|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD AdAA|adaa|NN _|_|NN 60|60|CD min|min|NN
M9TMP5|m9tmp5|NN _|_|CD AdAA|adaa|NN _|_|NN 90|90|CD min|min|NN
M9|m9|NN _|_|CD TMP5|tmp5|NN _|_|NN THY|thy|NN _|_|CD Ad|ad|NN _|_|SYM AA|aa|SYM _|_|SYM 10|10|CD min|min|NN
M9|m9|NN _|_|CD TMP5|tmp5|NN _|_|CD THY|THY|NNP _|_|SYM Ad|ad|FW _|_|FW AA|aa|NN _|_|NN 120|120|CD min|min|NN
M9|m9|NN _|_|CD TMP5|tmp5|NN _|_|CD THY|THY|NNP _|_|SYM Ad|ad|FW _|_|FW AA|aa|NN _|_|SYM 30|30|CD min|min|NN
M9|m9|NN _|_|CD TMP5|tmp5|NN _|_|CD THY|THY|NNP _|_|SYM Ad|ad|FW _|_|FW AA|aa|NN _|_|NN 60|60|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD AA|aa|NN _|_|NN 10|10|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD AA|aa|NN _|_|NN 120|120|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD AA|aa|NN _|_|SYM 30|30|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD AA|aa|NN _|_|NN 60|60|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD Ad|ad|NN _|_|SYM 10|10|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD Ad|ad|NN _|_|NN 120|120|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD Ad|ad|NN _|_|SYM 30|30|CD min|min|NN
M9TMP|m9tmp|NN _|_|CD Ad|ad|NN _|_|SYM 60|60|CD min|min|NN
MACE|MACE|NNP software|software|NN -LRB-|-lrb-|-LRB- https://code.google.com/p/chip-exo/|https://code.google.com/p/chip-exo/|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO detect|detect|VB peaks|peak|NNS with|with|IN aligned|align|VBN output|output|NN from|from|IN bowtie|bowtie|NN mapping|mapping|NN .|.|.
MACS|mac|NNS v2|v2|VBP .0.10.20131216|.0.10.20131216|CD was|be|VBD used|use|VBN for|for|IN peak|peak|JJ calling|call|VBG with|with|IN parameters|parameter|NNS --|--|: llocal|llocal|JJ =|=|JJ 10000|10000|CD -|-|: g|g|NN 4639675|4639675|CD --|--|: bw|bw|NN 300|300|CD -|-|: p|p|NN 0.05|0.05|CD --|--|: slocal|slocal|JJ =|=|JJ 1000|1000|CD --|--|: keep-dup|keep-dup|NN =|=|JJ 20|20|CD
Mapped|map|VBD R1|r1|NN reads|read|VBZ in|in|IN single-end|single-end|JJ mode|mode|NN using|use|VBG Bowtie2|bowtie2|NN 2.1.0|2.1.0|CD with|with|IN the|the|DT --|--|: k|k|NN 1|1|CD option|option|NN
Mapped|Mapped|NNP read|read|VBD counts|count|NNS were|be|VBD analyzed|analyze|VBN for|for|IN differential|differential|JJ expression|expression|NN -LRB-|-lrb-|-LRB- false|false|JJ discovery|discovery|NN rate|rate|NN of|of|IN <|<|JJR 0.01|0.01|CD ,|,|, fold-change|fold-change|JJ >|>|RBR 2|2|LS -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT baySeq|bayseq|NN package|package|NN in|in|IN R|r|NN -LRB-|-lrb-|-LRB- Hardcastle|hardcastle|NN and|and|CC Kelly|Kelly|NNP ,|,|, 2010|2010|CD ,|,|, BMC|BMC|NNP Bioinformatics|Bioinformatics|NNPS -RRB-|-rrb-|-RRB- .|.|. Within|within|IN baySeq|bayseq|NN ,|,|, two-way|two-way|JJ comparisons|comparison|NNS using|use|VBG quantile|quantile|JJ normalization|normalization|NN were|be|VBD made|make|VBN for|for|IN all|all|DT three|three|CD biological|biological|JJ replicate|replicate|VBP transcriptomes|transcriptome|NNS over|over|IN time|time|NN for|for|IN HgCl2|hgcl2|NN exposure|exposure|NN or|or|CC PMA|pma|NN exposure|exposure|NN versus|versus|CC the|the|DT unexposed|unexposed|JJ control|control|NN .|.|.
Mapped|map|VBD reads|read|VBZ per|per|IN annotated|annotated|JJ gene|gene|NN were|be|VBD counted|count|VBN by|by|IN Bam2readcount|bam2readcount|NN .|.|.
Mapped|map|VBD reads|read|VBZ were|be|VBD counted|count|VBN using|use|VBG the|the|DT Python|Python|NNP package|package|NN HTSeq|htseq|NN -LRB-|-lrb-|-LRB- v.|v.|CC 0.6.1|0.6.1|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT following|follow|VBG parameters|parameter|NNS ;|;|: htseq-count|htseq-count|NN -|-|: m|m|NN union|union|NN -|-|: r|r|NN pos|pos|SYM -|-|: i|i|FW gene|gene|NN _|_|NN name|name|NN -|-|: a|a|DT 10|10|CD
Mapped|map|VBD reads|read|VBZ were|be|VBD quality|quality|JJ checked|check|VBN with|with|IN SAMstat|samstat|NN -LRB-|-lrb-|-LRB- version|version|NN 1.08|1.08|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC transcripts|transcript|NNS were|be|VBD assembled|assemble|VBN in|in|IN Cufflinks|Cufflinks|NNP -LRB-|-lrb-|-LRB- version|version|NN 2.0.2|2.0.2|CD -RRB-|-rrb-|-RRB-
mapping|mapping|NN :|:|: bowtie|bowtie|NN -LRB-|-lrb-|-LRB- Galaxy|galaxy|NN Version|version|NN 1.1.2|1.1.2|CD -RRB-|-rrb-|-RRB- ;|;|: 28|28|CD nt|nt|NNS seed|seed|NN length|length|NN ,|,|, maximal|maximal|JJ two|two|CD mismatches|mismatch|NNS in|in|IN the|the|DT seed|seed|NN ,|,|, a|a|DT maximal|maximal|JJ threshold|threshold|NN of|of|IN 70|70|CD for|for|IN the|the|DT sum|sum|NN of|of|IN the|the|DT quality|quality|NN values|value|NNS at|at|IN mismatched|mismatched|JJ positions|position|NNS .|.|.
mapping|mapping|NN of|of|IN non-rRNA|non-rrna|JJ and|and|CC tRNA|trna|NN reads|read|VBZ to|to|TO E.|e.|FW coli|coli|FW O104|o104|NN :|:|: H4|h4|NN chromosome|chromosome|NN and|and|CC plasmids|plasmid|NNS using|use|VBG READemption|reademption|NN 0.3.7|0.3.7|CD and|and|CC segemehl|segemehl|NN 0.2.0|0.2.0|CD
mapping|mapping|NN of|of|IN reads|read|VBZ to|to|TO E.|e.|FW coli|coli|FW O104|o104|NN :|:|: H4|h4|NN rRNAs|rrna|NNS and|and|CC tRNAs|trna|NNS using|use|VBG READemption|reademption|NN 0.3.7|0.3.7|CD and|and|CC segemehl|segemehl|NN 0.2.0|0.2.0|CD
Mapping|mapping|NN of|of|IN the|the|DT trimmed|trimmed|RBR reads|read|VBZ to|to|TO the|the|DT reference|reference|NN sequences|sequence|NNS was|be|VBD also|also|RB performed|perform|VBN with|with|IN the|the|DT CLC|clc|NN Genomics|genomic|NNS Workbench|workbench|JJ 9.0|9.0|CD using|use|VBG the|the|DT `|`|`` Map|map|NN Reads|read|VBZ to|to|TO Reference|Reference|NNP '|'|POS tool|tool|NN with|with|IN standard|standard|JJ parameters|parameter|NNS .|.|.
Mapping|mapping|NN was|be|VBD performed|perform|VBN using|use|VBG BWA|BWA|NNP tool|tool|NN -LRB-|-lrb-|-LRB- version|version|NN 0.5.9|0.5.9|CD -RRB-|-rrb-|-RRB- against|against|IN the|the|DT reference|reference|NN genome|genome|NN
Map|map|NN reads|read|VBZ to|to|TO theEscherichia|theescherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN genome|genome|NN ,|,|, Bowtie|Bowtie|NNP 2|2|CD
Map|map|NN RNA-Seq|rna-seq|NN reads|read|VBZ to|to|TO reference|reference|VB genomes|genome|NNS using|use|VBG Bowtie|Bowtie|NNP -LRB-|-lrb-|-LRB- Langmead|Langmead|NNP et|et|FW al.|al.|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- with|with|IN alignment|alignment|NN parameters|parameter|NNS -LRB-|-lrb-|-LRB- -|-|: n|n|NN 2-e|2-e|JJ 70-l|70-l|JJ 28|28|CD --|--|: best|best|JJS -RRB-|-rrb-|-RRB-
Map|map|NN to|to|TO MG1655|mg1655|NN reference|reference|NN using|use|VBG BWA|BWA|NNP 0.7.4|0.7.4|CD -LRB-|-lrb-|-LRB- bwa|bwa|NN mem|mem|NN ,|,|, default|default|NN parameters|parameter|NNS -RRB-|-rrb-|-RRB-
map|map|NN trimmed|trim|VBD reads|read|VBZ to|to|TO reference|reference|NN sequence|sequence|NN in|in|IN indexes|index|NNS file|file|VBP with|with|IN bowtie2|bowtie2|NN
Marvinbryantia|marvinbryantia|NN formatexigens|formatexigen|NNS DSM|DSM|NNP 14469|14469|CD
MAS|MAS|NNP 5.0|5.0|CD
MAS5|mas5|NN .0|.0|CD
MAS|mas|NN 5.0|5.0|CD Expression|expression|NN Analysis|analysis|NN Default|Default|NNP Setting|Setting|NNP
MAS|MAS|NNP 5.0|5.0|CD Expression|expression|NN Analysis|analysis|NN Default|Default|NNP Setting|Setting|NNP .|.|.
MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN Kit|kit|NN
MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN Kit|kit|NN per|per|IN manufacturers|manufacturer|NNS protocol|protocol|NN
material|material|NN type|type|NN :|:|: whole|whole|JJ _|_|JJ organism|organism|NN
MATLAB|MATLAB|NNP v.|v.|CC R2012b|r2012b|NN program|program|NN using|use|VBG GCRMA|GCRMA|NNP algorithm|algorithm|NN
MatP|matp|NN 37|37|CD °C|°c|NN
∆|∆|CD mazEF|mazef|NN 0|0|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
∆|∆|CD mazEF|mazef|NN 0|0|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
∆|∆|CD mazEF|mazef|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
∆|∆|CD mazEF|mazef|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
∆|∆|CD mazEF|mazef|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep3|rep3|NN
∆|∆|CD mazEF|mazef|NN 10|10|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
∆|∆|CD mazEF|mazef|NN 10|10|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
∆|∆|CD mazEFlexA3|mazeflexa3|NN 0|0|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
∆|∆|CD mazEFlexA3|mazeflexa3|NN 0|0|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
∆|∆|CD mazEFlexA3|mazeflexa3|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
∆|∆|CD mazEFlexA3|mazeflexa3|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
∆|∆|CD mazEFlexA3|mazeflexa3|NN 10|10|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
∆|∆|CD mazEFlexA3|mazeflexa3|NN 10|10|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
mazF|mazf|NN _|_|CD chpA|chpa|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
MazF|mazf|NN _|_|NN mRNA|mrna|NN _|_|SYM 5m|5m|FW _|_|FW rep1|rep1|NN
MazF|mazf|NN _|_|NN mRNA|mrna|NN _|_|SYM 5m|5m|FW _|_|FW rep2|rep2|NN
MazF|mazf|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 30m|30m|FW _|_|FW rep1|rep1|NN
MazF|mazf|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 30m|30m|FW _|_|FW rep2|rep2|NN
MazF|mazf|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 5m|5m|FW _|_|FW rep1|rep1|NN
MazF|mazf|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 5m|5m|FW _|_|FW rep2|rep2|NN
MazF|mazf|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 60m|60m|FW _|_|FW rep1|rep1|NN
MazF|mazf|NN _|_|CD totalRNA|totalrna|NN _|_|SYM 60m|60m|FW _|_|FW rep2|rep2|NN
mazF|mazf|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r1|r1|NN
mazF|mazf|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r2|r2|NN
mazF|mazf|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
MBC|mbc|NN of|of|IN CYA|CYA|NNP ,|,|, biological|biological|JJ rep1|rep1|NN
MBC|mbc|NN of|of|IN CYA|CYA|NNP ,|,|, biological|biological|JJ rep2|rep2|NN
MBC|mbc|NN of|of|IN CYA|CYA|NNP ,|,|, biological|biological|JJ rep3|rep3|NN
MBC|mbc|NN of|of|IN OLA|OLA|NNP ,|,|, biological|biological|JJ rep1|rep1|NN
MBC|mbc|NN of|of|IN OLA|OLA|NNP ,|,|, biological|biological|JJ rep2|rep2|NN
MBC|mbc|NN of|of|IN OLA|OLA|NNP ,|,|, biological|biological|JJ rep3|rep3|NN
mcrB|mcrb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
mcrB|mcrb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
mcrB|mcrb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
mcrB|mcrb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
mcrC|mcrc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
mcrC|mcrc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
mcrC|mcrc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
mcrC|mcrc|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
MC|MC|NNP _|_|NNP Val|val|NN _|_|SYM G1|g1|NN
MC|MC|NNP _|_|NNP Val|val|NN _|_|SYM G2|g2|NN
MC|MC|NNP _|_|NNP Val|val|NN _|_|SYM G3|g3|NN
MC|MC|NNP _|_|NNP Val|val|NN _|_|CD G5|g5|NN
MDS42|mds42|NN
MDS42|mds42|NN 1|1|CD
MDS42|mds42|NN 2|2|CD
MDS42|mds42|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN
MDS42|mds42|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN 1|1|CD
MDS42|mds42|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN 2|2|CD
MDS42|mds42|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
MDS42|mds42|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
MDS42|mds42|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
MDS42|mds42|NN ,|,|, biological|biological|JJ rep|rep|NN 4|4|CD
MDS42|mds42|NN ,|,|, biological|biological|JJ rep|rep|NN 5|5|CD
MDS42|mds42|NN ,|,|, biological|biological|JJ rep|rep|NN 6|6|CD
MDS42|mds42|NN ,|,|, biological|biological|JJ rep|rep|NN 7|7|CD
MDS42|mds42|NN DNA|dna|NN isolated|isolate|VBN from|from|IN early-phase|early-phase|JJ DNA-protein|dna-protein|JJ complexes|complex|NNS
MDS42|mds42|NN exponentially|exponentially|RB grown|grow|VBN in|in|IN the|the|DT minimal|minimal|JJ medium|medium|NN
MDS42|mds42|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
MDS42|mds42|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
MDS42|mds42|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
MDS42|mds42|NN RNAP|rnap|NN 1|1|CD
MDS42|mds42|NN RNAP|rnap|NN 2|2|CD
MDS42|mds42|NN ΔnusA|δnusa|NN *|*|SYM
MDS42|mds42|NN ΔnusA|δnusa|NN *|*|SYM 1|1|CD
MDS42|mds42|NN ΔnusA|δnusa|NN *|*|SYM 2|2|CD
MDS42|mds42|NN ΔnusA|δnusa|NN *|*|SYM RNAP|rnap|NN 1|1|CD
MDS42|mds42|NN ΔnusA|δnusa|NN *|*|SYM RNAP|rnap|NN 2|2|CD
MDS42|mds42|NN ΔnusG|δnusg|NN
MDS42|mds42|NN ΔnusG|δnusg|NN 1|1|CD
MDS42|mds42|NN ΔnusG|δnusg|NN 2|2|CD
MDS42|mds42|NN ΔnusG|δnusg|NN RNAP|rnap|NN 1|1|CD
MDS42|mds42|NN ΔnusG|δnusg|NN RNAP|rnap|NN 2|2|CD
ME0052|me0052|NN
ME0053|me0053|NN
ME0054|me0054|NN
ME0055|me0055|NN
media|media|NNS :|:|: Defined|define|VBN MOPS|mop|NNS Minimal|minimal|JJ +|+|CC 0.4|0.4|CD %|%|NN Glycerol|glycerol|NN
media|media|NNS :|:|: Defined|define|VBN MOPS|mop|NNS Minimal|minimal|JJ +|+|CC 0.4|0.4|CD %|%|NN Glycerol|glycerol|NN +0.5|+0.5|CD %|%|NN 2-DG|2-dg|JJ
media|media|NNS :|:|: Defined|define|VBN MOPS|mop|NNS Minimal|minimal|JJ +|+|CC 0.4|0.4|CD %|%|NN Glycerol|glycerol|NN +0.5|+0.5|CD %|%|NN aMG|amg|NN
media|media|NNS :|:|: Defined|define|VBN MOPS|mop|NNS Rich|rich|JJ +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN
media|media|NNS :|:|: Defined|define|VBN MOPS|mop|NNS Rich|rich|JJ +|+|CC 0.4|0.4|CD %|%|NN Glycerol|glycerol|NN
media|media|NNS :|:|: Defined|define|VBN MOPS|mop|NNS Rich|rich|JJ +|+|CC 0.4|0.4|CD %|%|NN Glycerol|glycerol|NN +0.5|+0.5|CD %|%|NN aMG|amg|NN
media|media|NNS :|:|: fully|fully|RB supplemented|supplement|VBN MOPS|mop|NNS glucose|glucose|NN media|media|NNS
media|media|NNS :|:|: LB|lb|NN
media|media|NNS :|:|: LB|lb|NN +|+|CC 0.5|0.5|CD %|%|NN aMG|amg|NN
media|media|NNS :|:|: LB|lb|NN broth|broth|NN
media|media|NNS :|:|: M9|m9|NN
media|media|NNS :|:|: MEM-HEPES|mem-hepes|NN supplemented|supplement|VBN with|with|IN 0.1|0.1|CD %|%|NN Glucose|glucose|NN and|and|CC 250nM|250nm|NN Fe|Fe|NNP -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB- 2|2|CD
Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN
Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN +2.5|+2.5|CD mM|mm|NN sodium|sodium|NN nitrite|nitrite|JJ
media|media|NNS :|:|: MOPS|MOPS|NNP EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Media|Media|NNP
Median|median|JJ of|of|IN intensity|intensity|NN data|datum|NNS was|be|VBD extracted|extract|VBN ,|,|, LOESS|LOESS|NNP normalized|normalize|VBD and|and|CC an|a|DT ANOVA|ANOVA|NNP model|model|NN was|be|VBD fit|fit|VBN using|use|VBG the|the|DT MAANOVA|MAANOVA|NNP package|package|NN in|in|IN R|r|NN .|.|. The|the|DT Log|log|NN -LRB-|-lrb-|-LRB- Cy5/Cy3|cy5/cy3|NN -RRB-|-rrb-|-RRB- values|value|NNS were|be|VBD extracted|extract|VBN from|from|IN the|the|DT VG|vg|NN matrix|matrix|NN of|of|IN the|the|DT model|model|NN fit|fit|NN .|.|.
media|media|NNS :|:|: Tryptone|tryptone|NN broth|broth|NN buffered|buffer|VBD to|to|TO pH|ph|NN 7|7|CD supplemented|supplement|VBN with|with|IN 22|22|CD mM|mm|NN glucose|glucose|NN
medium|medium|NN :|:|: ACSH|ACSH|NNP
medium|medium|NN :|:|: defined|define|VBN mineral|mineral|JJ medium|medium|NN with|with|IN 1|1|CD g/l|g/l|NN glucose|glucose|NN
medium|medium|NN :|:|: LB|lb|NN
medium|medium|NN :|:|: M63|m63|NN
medium|medium|NN :|:|: M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN and|and|CC 5|5|CD %|%|NN LB|lb|NN
medium|medium|NN :|:|: MOPS|mop|NNS
medium|medium|NN :|:|: Neidhardt|Neidhardt|NNP 's|'s|POS EZ|EZ|NNP Rich|Rich|NNP Defined|Defined|NNP Medium|medium|NN -LRB-|-lrb-|-LRB- Teknova|Teknova|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB-
medium|medium|NN :|:|: SB|sb|NN broth|broth|NN
medium|medium|NN :|:|: SynH|synh|NN
medium|medium|NN :|:|: SynH|synh|NN _|_|NN Acids|acid|NNS _|_|VBP Amides|amide|NNS
medium|medium|NN :|:|: SynH|synh|NN _|_|CD LT|lt|NN
medium|medium|NN :|:|: SynH|synh|NN +|+|CC LTs|lts|NN
medium|medium|NN :|:|: SynH|synh|NN w/o|w/o|NN osmoprotectants|osmoprotectant|NNS
medium|medium|NN :|:|: SynH|synh|NN w/o|w/o|NN osmoprotectants|osmoprotectant|NNS +|+|CC LTs|lt|NNS
menB|menb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
menB|menb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
menB|menb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
menB|menb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
menC|menc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
menC|menc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
menC|menc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
menC|menc|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
Merge|merge|VBP the|the|DT replicates|replicate|VBZ for|for|IN each|each|DT sample|sample|NN .|.|. For|for|IN example|example|NN ,|,|, for|for|IN sample|sample|NN HS15min|hs15min|NN ,|,|, merge|merge|VBP HS15min_r1.HiSeq.fastq.gz|hs15min_r1.hiseq.fastq.gz|NN ,|,|, HS15min_r2.HiSeq.fastq.gz|hs15min_r2.hiseq.fastq.gz|NN and|and|CC HS15min_r3.HiSeq.fastq.gz|hs15min_r3.hiseq.fastq.gz|NN to|to|TO one|one|CD fastq|fastq|NN file|file|NN
metabolic|metabolic|JJ response|response|NN :|:|: BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- is|be|VBZ very|very|RB susceptible|susceptible|JJ to|to|TO heptanoic|heptanoic|JJ acid|acid|NN ,|,|, because|because|IN several|several|JJ acid|acid|NN resistance|resistance|NN systems|system|NNS stay|stay|VBP inactive|inactive|JJ under|under|IN this|this|DT stress|stress|NN condition|condition|NN
metabolic|metabolic|JJ response|response|NN :|:|: K12|k12|NN MG1655|mg1655|NN activates|activate|VBZ various|various|JJ acid|acid|NN resistance|resistance|NN systems|system|NNS under|under|IN heptanoic|heptanoic|JJ acid|acid|NN stress|stress|NN
Metabolome|metabolome|NN data|datum|NNS for|for|IN these|these|DT cultures|culture|NNS are|be|VBP also|also|RB provided|provide|VBN in|in|IN the|the|DT supplementary|supplementary|JJ file|file|NN \|\|SYM
Methionine|Methionine|NNP addition|addition|NN
Methylation|methylation|NN in|in|IN 0|0|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
Methylation|methylation|NN in|in|IN 0|0|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
Methylation|methylation|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
Methylation|methylation|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
mev|mev|NN data|datum|NNS obtained|obtain|VBN from|from|IN the|the|DT feature|feature|NN extraction|extraction|NN file|file|NN used|use|VBN ,|,|, no|no|DT further|further|JJ normalization|normalization|NN needed|need|VBD
mfd|mfd|NN _|_|NN 1|1|CD
MFD|mfd|NN +|+|CC +|+|CC _|_|SYM 1|1|CD
mfd|mfd|NN _|_|NN 2|2|CD
MFD|mfd|NN +|+|CC +|+|CC _|_|SYM 2|2|CD
mfd|mfd|NN _|_|NN 3|3|CD
mg1655|mg1655|NN
MG1655|mg1655|NN
MG1655|mg1655|NN 1|1|CD
MG1655|mg1655|NN _|_|NN 1|1|CD
MG1655|mg1655|NN 2|2|CD
MG1655|mg1655|NN _|_|NN 2|2|CD
MG1655|mg1655|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN
MG1655|mg1655|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN 1|1|CD
MG1655|mg1655|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN 2|2|CD
MG1655|mg1655|NN 2|2|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN _|_|CD 3|3|CD
MG1655|mg1655|NN 4|4|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN 6|6|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN 8|8|CD '|'|'' post|post|JJ rif|rif|NN
MG1655-aMG|mg1655-amg|NN _|_|NN 1|1|CD
MG1655|mg1655|NN +|+|CC aMG|amg|NN _|_|NN 1|1|CD
MG1655-aMG|mg1655-amg|NN _|_|NN 2|2|CD
MG1655|mg1655|NN +|+|CC aMG|amg|NN _|_|NN 2|2|CD
MG1655-aMG|mg1655-amg|NN _|_|CD 3|3|CD
MG1655|mg1655|NN +|+|CC aMG|amg|NN _|_|CD 3|3|CD
MG1655|mg1655|NN at|at|IN 30|30|CD Degrees|degree|NNS
MG1655|mg1655|NN batch|batch|NN
MG1655|mg1655|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
MG1655|mg1655|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
MG1655|mg1655|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
MG1655|mg1655|NN ,|,|, biological|biological|JJ rep|rep|NN 4|4|CD
MG1655|mg1655|NN ,|,|, biological|biological|JJ rep|rep|NN 5|5|CD
MG1655|mg1655|NN ,|,|, biological|biological|JJ rep|rep|NN 6|6|CD
MG1655|mg1655|NN ,|,|, biological|biological|JJ rep|rep|NN 7|7|CD
MG1655|mg1655|NN chemostat|chemostat|NN
MG1655|mg1655|NN ∆|∆|CD cspABCEG|cspabceg|NN
MG1655|mg1655|NN ∆|∆|CD cspABEG|cspabeg|NN
MG1655|mg1655|NN ∆|∆|CD cspBG|cspbg|NN
MG1655|mg1655|NN DNA|dna|NN isolated|isolate|VBN from|from|IN early-phase|early-phase|JJ DNA-protein|dna-protein|JJ complexes|complex|NNS
MG1655|mg1655|NN DNA|dna|NN isolated|isolate|VBN from|from|IN late-phase|late-phase|JJ DNA-protein|dna-protein|JJ complexes|complex|NNS
MG1655|mg1655|NN exponentially|exponentially|RB grown|grow|VBN in|in|IN the|the|DT minimal|minimal|JJ medium|medium|NN
MG1655|mg1655|NN ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, LB|lb|NN
MG1655|mg1655|NN G181D|g181d|NN NusA|nusa|NN BR1|br1|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN G181D|g181d|NN NusA|nusa|NN BR2|br2|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN G181D|g181d|NN NusA|nusa|NN BR|br|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN G181D|g181d|NN NusA|nusa|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN genomic|genomic|JJ DNA|dna|NN
MG1655|mg1655|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
MG1655|mg1655|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
MG1655|mg1655|NN ,|,|, heat|heat|NN shock|shock|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
MG1655|mg1655|NN H-NS|h-ns|NN 1|1|CD
MG1655|mg1655|NN H-NS|h-ns|NN 2|2|CD
MG1655|mg1655|NN hns-FLAG|hns-flag|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN liquid|liquid|JJ LB|lb|NN medium|medium|NN with|with|IN and|and|CC without|without|IN bicyclomycin|bicyclomycin|NN -LRB-|-lrb-|-LRB- BCM|bcm|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD degree|degree|NN with|with|IN shaking|shake|VBG at|at|IN 200rpm|200rpm|JJ
MG1655|mg1655|NN HPA|hpa|NN 0mM|0mm|NN
MG1655|mg1655|NN HPA|hpa|NN 10mM|10mm|NN
MG1655|mg1655|NN _|_|CD LB|lb|NN
MG1655|mg1655|NN _|_|CD LB1|lb1|NN
MG1655|mg1655|NN _|_|CD LB2|lb2|NN
MG1655|mg1655|NN _|_|CD minus|minus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 1|1|CD
MG1655|mg1655|NN _|_|CD minus|minus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 2|2|CD
MG1655|mg1655|NN _|_|CD minus|minus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 3|3|CD
MG1655|mg1655|NN pCA24N|pca24n|NN and|and|CC MG1655|mg1655|NN pCA24N-Mfd|pca24n-mfd|NN cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO an|a|DT OD560|od560|NN of|of|IN approximately|approximately|RB 0.25|0.25|CD and|and|CC treated|treat|VBN with|with|IN 100|100|CD μM|μm|NN IPTG|iptg|NN for|for|IN 1|1|CD hour|hour|NN .|.|.
MG1655|mg1655|NN PhtpG|phtpg|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74/pTG2|lacx74/ptg2|NN -LRB-|-lrb-|-LRB- vector|vector|NN carrying|carrying|NN inducible|inducible|JJ Ptrc|ptrc|NN :|:|: :|:|: rpoH|rpoh|NN -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN PhtpG|phtpg|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74/ptrc99A|lacx74/ptrc99a|NN -LRB-|-lrb-|-LRB- control|control|NN vector|vector|NN -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN _|_|NN plus|plus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 1|1|CD
MG1655|mg1655|NN _|_|NN plus|plus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 2|2|CD
MG1655|mg1655|NN _|_|NN plus|plus|CC _|_|SYM aMG|aMG|NNP _|_|SYM 3|3|CD
MG1655|mg1655|NN R258C|r258c|NN NusA|nusa|NN BR1|br1|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN R258C|r258c|NN NusA|nusa|NN BR2|br2|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN R258C|r258c|NN NusA|nusa|NN BR|br|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN R258C|r258c|NN NusA|nusa|NN ,|,|, treated|treat|VBN
MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN MCM|mcm|NN 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN
MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN MCM|mcm|NN 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN 8|8|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN
MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN 2|2|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN 4|4|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN 6|6|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN -LRB-|-lrb-|-LRB- Repaired|repair|VBN NCM|NCM|NNP 3416|3416|CD -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glucose|glucose|NN 8|8|CD '|'|'' post|post|JJ rif|rif|NN
MG1655|mg1655|NN RNA|rna|NN
MG1655|mg1655|NN RNAP|rnap|NN 1|1|CD
MG1655|mg1655|NN RNAP|rnap|NN 2|2|CD
MG1655|mg1655|NN ∆|∆|CD rnr|rnr|NN
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74|lacx74|NN
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74|lacx74|NN hfq1|hfq1|NN :|:|: :|:|: omega|omega|NN -LRB-|-lrb-|-LRB- Km|km|NN ;|;|: BclI|bcli|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- hfq|hfq|SYM -|-|: -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74|lacx74|NN hfq1|hfq1|NN :|:|: :|:|: omega|omega|NN -LRB-|-lrb-|-LRB- Km|km|NN ;|;|: BclI|bcli|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- hfq|hfq|SYM -|-|: -RRB-|-rrb-|-RRB- /|/|: pLC245|plc245|NN -LRB-|-lrb-|-LRB- vector|vector|NN carrying|carrying|NN inducible|inducible|JJ Ptrc|ptrc|NN :|:|: :|:|: rpoE|rpoe|NN -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74|lacx74|NN hfq2|hfq2|NN :|:|: :|:|: omega|omega|NN -LRB-|-lrb-|-LRB- Km|km|NN ;|;|: KpnI|kpni|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- hfq|hfq|NN +|+|CC -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74|lacx74|NN hfq2|hfq2|NN :|:|: :|:|: omega|omega|NN -LRB-|-lrb-|-LRB- Km|km|NN ;|;|: KpnI|kpni|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- hfq|hfq|NN +|+|CC -RRB-|-rrb-|-RRB- /|/|: pLC245|plc245|NN -LRB-|-lrb-|-LRB- vector|vector|NN carrying|carrying|NN inducible|inducible|JJ Ptrc|ptrc|NN :|:|: :|:|: rpoE|rpoe|NN -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74|lacx74|NN hfq2|hfq2|NN :|:|: :|:|: omega|omega|NN -LRB-|-lrb-|-LRB- Km|km|NN ;|;|: KpnI|kpni|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- hfq|hfq|NN +|+|CC -RRB-|-rrb-|-RRB- /|/|: ptrc99A|ptrc99a|NN -LRB-|-lrb-|-LRB- control|control|NN vector|vector|NN -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74|lacx74|NN nadB|nadb|NN :|:|: :|:|: Tn10|tn10|NN drseA|drsea|NN
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74/pLC245|lacx74/plc245|NN -LRB-|-lrb-|-LRB- vector|vector|NN carrying|carrying|NN inducible|inducible|JJ Ptrc|ptrc|NN :|:|: :|:|: rpoE|rpoe|NN -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN rpoHp3|rpohp3|NN :|:|: :|:|: lacZ|lacz|NN delta|delta|NN lacX74/ptrc99A|lacx74/ptrc99a|NN -LRB-|-lrb-|-LRB- control|control|NN vector|vector|NN -RRB-|-rrb-|-RRB-
MG1655|mg1655|NN rpoS|rpos|NN mutants|mutant|NNS
MG1655|mg1655|NN ,|,|, SD197|sd197|NN ,|,|, SB227|sb227|NN ,|,|, SF301|sf301|NN and|and|CC SS046|ss046|NN
MG1655|mg1655|NN ,|,|, SD197|sd197|NN ,|,|, SB227|sb227|NN ,|,|, SF301|sf301|NN and|and|CC SS046|ss046|NN
MG1655|mg1655|NN _|_|CD standard|standard|JJ _|_|NN condition|condition|NN _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|CD standard|standard|JJ _|_|NN condition|condition|NN _|_|CD rep2|rep2|NN
MG1655star-glucose|mg1655star-glucose|JJ
MG1655star-mannose|mg1655star-mannose|JJ
MG1655star-mucus-P1|mg1655star-mucus-p1|NN
MG1655star-mucus-P2|mg1655star-mucus-p2|NN
MG1655|mg1655|NN starvation|starvation|NN
MG1655|mg1655|NN ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, LB|lb|NN
MG1655|mg1655|NN strain|strain|NN of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN
MG1655|mg1655|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 1|1|CD
MG1655|mg1655|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 2|2|CD
MG1655|mg1655|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 1|1|CD
MG1655|mg1655|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 2|2|CD
MG1655|mg1655|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 1|1|CD
MG1655|mg1655|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 2|2|CD
MG1655|mg1655|NN _|_|NN under|under|IN _|_|CD ColdShock|ColdShock|NNP _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|CD ColdShock|ColdShock|NNP _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NN HeatShock|heatshock|NN _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NNP Low|Low|NNP _|_|NNP pH|ph|NN _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NN minimal|minimal|JJ _|_|NN C&N|c&n|NN _|_|NN source|source|NN _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NN minimal|minimal|JJ _|_|NN C&N|c&n|NN _|_|NN source|source|NN _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NN minimal|minimal|JJ _|_|NN C|c|NN _|_|NN source|source|NN _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NN minimal|minimal|JJ _|_|NN C|c|NN _|_|NN source|source|NN _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NN minimal|minimal|JJ _|_|CD N|n|NN _|_|NN source|source|NN _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NN minimal|minimal|JJ _|_|CD N|n|NN _|_|NN source|source|NN _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NNP Osmotic|Osmotic|NNP _|_|NNP Stress|stress|NN _|_|NN rep1|rep1|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|CD Osmotic|osmotic|JJ _|_|NN Stress|stress|NN _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NNP Oxidative|oxidative|JJ _|_|NN Stress|stress|NN _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|NN under|under|IN _|_|NNP Oxidative|oxidative|JJ _|_|NN Stress|stress|NN _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|CD UV|uv|NN _|_|NN Treatment|treatment|NN _|_|CD rep1|rep1|NN
MG1655|mg1655|NN _|_|CD UV|uv|NN _|_|NN Treatment|treatment|NN _|_|CD rep2|rep2|NN
MG1655|mg1655|NN _|_|NN vector|vector|NN _|_|NN 1|1|CD
MG1655|mg1655|NN _|_|NN vector|vector|NN _|_|NN 2|2|CD
MG1655|mg1655|NN wild|wild|JJ type|type|NN
MG1655|mg1655|NN WT|WT|NNP NusA|NusA|NNP BR1|br1|NN ,|,|, control|control|NN
MG1655|MG1655|NNP WT|WT|NNP NusA|nusa|NN BR2|br2|NN ,|,|, control|control|NN
MG1655|mg1655|NN WT|WT|NNP NusA|NusA|NNP BR|BR|NNP ,|,|, control|control|NN
MG1655|mg1655|NN WT|WT|NNP NusA|NusA|NNP ,|,|, control|control|NN
MG1655|mg1655|NN Δhns|δhns|NNS RNAP|rnap|NN 1|1|CD
MG1655|mg1655|NN Δhns|δhns|NNS RNAP|rnap|NN 2|2|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- levels|level|NNS -RRB-|-rrb-|-RRB- :|:|: baseMg|basemg|NN
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- levels|level|NNS -RRB-|-rrb-|-RRB- :|:|: highMg|highmg|NN
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- levels|level|NNS -RRB-|-rrb-|-RRB- :|:|: lowMg|lowmg|NN
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 0.005|0.005|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 0.01|0.01|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 0.02|0.02|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 0.04|0.04|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 0.08|0.08|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 0.8|0.8|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 200|200|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 400|400|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 50|50|CD
mg|mg|NN +2|+2|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 8|8|CD
MG6|mg6|NN _|_|NN replicated|replicate|VBN
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 106|106|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 107|107|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 108|108|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 109|109|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 110|110|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 111|111|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 112|112|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 113|113|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|VBD 114|114|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 115|115|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 116|116|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 117|117|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 118|118|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 119|119|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 120|120|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 121|121|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 122|122|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 123|123|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|VBD 124|124|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 125|125|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 126|126|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 127|127|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 128|128|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 129|129|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 130|130|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 131|131|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 132|132|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 133|133|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 134|134|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 135|135|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|VBD 136|136|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 137|137|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 138|138|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 139|139|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 140|140|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB high|high|JJ :|:|: MURI|MURI|NNP _|_|SYM 141|141|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 142|142|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 143|143|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 144|144|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 145|145|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 146|146|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 147|147|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|VBD 148|148|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|VBD 149|149|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 150|150|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 151|151|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 152|152|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 153|153|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|VBD 154|154|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|VBD 155|155|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 156|156|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 157|157|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|VBD 158|158|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 159|159|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 160|160|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 161|161|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 162|162|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 163|163|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 164|164|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 165|165|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|VBD 166|166|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 167|167|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 168|168|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 169|169|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 170|170|CD
MgSO4|mgso4|NN _|_|CD stress|stress|NN _|_|RB low|low|JJ :|:|: MURI|MURI|NNP _|_|SYM 171|171|CD
mgtA|mgta|NN KO|ko|NN rep1|rep1|NN
mgtA|mgta|NN KO|ko|NN rep2|rep2|NN
mgtA|mgta|NN KO|ko|NN rep3|rep3|NN
mhpD|mhpd|NN KO|ko|NN rep1|rep1|NN
mhpD|mhpd|NN KO|ko|NN rep2|rep2|NN
mhpD|mhpd|NN KO|ko|NN rep3|rep3|NN
MIC|mic|NN of|of|IN OLA|OLA|NNP ,|,|, biological|biological|JJ rep1|rep1|NN
MIC|mic|NN of|of|IN OLA|OLA|NNP ,|,|, biological|biological|JJ rep2|rep2|NN
MIC|mic|NN of|of|IN OLA|OLA|NNP ,|,|, biological|biological|JJ rep3|rep3|NN
Microarray|microarray|NN analysis|analysis|NN including|include|VBG pre-processing|pre-processing|JJ ,|,|, normalisation|normalisation|NN anmd|anmd|NN statistical|statistical|JJ analysis|analysis|NN were|be|VBD performed|perform|VBN using|use|VBG R|r|NN -LRB-|-lrb-|-LRB- R|r|NN ,|,|, 2007|2007|CD -RRB-|-rrb-|-RRB- version|version|NN 2.6|2.6|CD and|and|CC Bioconductor|Bioconductor|NNP -LRB-|-lrb-|-LRB- Gentleman|Gentleman|NNP et|et|FW al.|al.|FW 2004|2004|CD ,|,|, Genome|Genome|NNP Biol|Biol|NNP .|.|. 5|5|CD :|:|: R80|r80|NN -RRB-|-rrb-|-RRB- version|version|NN 2.1|2.1|CD as|as|IN previously|previously|RB described|describe|VBN by|by|IN Morris|Morris|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- 2009|2009|CD ,|,|, Physiol|Physiol|NNP .|.|. Genomics|genomic|NNS 39:28-37|39:28-37|CD -RRB-|-rrb-|-RRB- .|.|. Propagating|propagate|VBG uncertainty|uncertainty|NN in|in|IN microarray|microarray|NN analysis|analysis|NN -LRB-|-lrb-|-LRB- puma|puma|NN -RRB-|-rrb-|-RRB- method|method|NN was|be|VBD used|use|VBN to|to|TO estimate|estimate|VB fold|fold|JJ changes|change|NNS and|and|CC P-like|p-like|JJ values|value|NNS of|of|IN differential|differential|JJ gene|gene|NN expression|expression|NN analysis|analysis|NN -LRB-|-lrb-|-LRB- Pearson|Pearson|NNP et|et|FW al.|al.|FW 2009|2009|CD ,|,|, BMC|BMC|NNP Bioinformatics|Bioinformatics|NNPS 10:211|10:211|CD -RRB-|-rrb-|-RRB- .|.|.
Microarray|Microarray|NNP data|data|NN analyses|analysis|NNS were|be|VBD performed|perform|VBN using|use|VBG Acuity|acuity|NN 4.0|4.0|CD software|software|NN .|.|. Slides|slide|NNS were|be|VBD normalized|normalize|VBN using|use|VBG standard|standard|JJ ratio-based|ratio-based|JJ methods|method|NNS .|.|. Data|datum|NNS were|be|VBD analyzed|analyze|VBN based|base|VBN upon|upon|IN Log|log|NN ratio|ratio|NN -LRB-|-lrb-|-LRB- 635/532|635/532|CD -RRB-|-rrb-|-RRB- values|value|NNS .|.|. Genes|gene|NNS were|be|VBD included|include|VBN in|in|IN the|the|DT final|final|JJ dataset|dataset|NN that|that|WDT exhibit|exhibit|VBP significance|significance|NN based|base|VBN upon|upon|IN a|a|DT very|very|RB conservative|conservative|JJ FDR|FDR|NNP less|less|JJR than|than|IN 2.5|2.5|CD %|%|NN -LSB-|-lsb-|-LRB- 27|27|CD -RSB-|-rsb-|-RRB- and|and|CC at|at|IN least|least|JJS 2.0-fold|2.0-fold|JJ comparative|comparative|JJ regulation|regulation|NN .|.|.
Microarray|Microarray|NNP data|data|NN analysis|analysis|NN was|be|VBD performed|perform|VBN with|with|IN free|free|JJ software|software|NN genArise|genarise|NN ,|,|, developed|develop|VBN in|in|IN the|the|DT Computing|Computing|NNP Unit|unit|NN of|of|IN Cellular|cellular|JJ Physiology|Physiology|NNP Institute|Institute|NNP of|of|IN UNAM|UNAM|NNP -LRB-|-lrb-|-LRB- http://www.ifc.unam.mx/genarise/|http://www.ifc.unam.mx/genarise/|NN -RRB-|-rrb-|-RRB- .|.|. GenArise|GenArise|NNP carry|carry|VBP out|out|RP a|a|DT number|number|NN of|of|IN transformations|transformation|NNS :|:|: background|background|NN correction|correction|NN ,|,|, normalization|normalization|NN ,|,|, intensity|intensity|NN filter|filter|NN ,|,|, replicates|replicate|VBZ analysis|analysis|NN and|and|CC selecting|select|VBG differentially|differentially|RB expressed|express|VBN genes|gene|NNS .|.|. The|the|DT goal|goal|NN of|of|IN genArise|genarise|NN is|be|VBZ to|to|TO identify|identify|VB which|which|WDT genes|gene|NNS show|show|VBP good|good|JJ evidence|evidence|NN of|of|IN being|be|VBG differentially|differentially|RB expressed|express|VBN .|.|. The|the|DT software|software|NN identifies|identify|VBZ differential|differential|JJ expressed|express|VBN genes|gene|NNS by|by|IN calculating|calculate|VBG an|a|DT intensity-dependent|intensity-dependent|JJ z-score|z-score|NN .|.|. Using|use|VBG a|a|DT sliding|slide|VBG window|window|NN algorithm|algorithm|NN to|to|TO calculate|calculate|VB the|the|DT mean|mean|NN and|and|CC standard|standard|JJ deviation|deviation|NN within|within|IN a|a|DT window|window|NN surrounding|surround|VBG each|each|DT data|datum|NNS point|point|NN ,|,|, and|and|CC define|define|VB a|a|DT z-score|z-score|NN where|where|WRB z|z|SYM measures|measure|VBZ the|the|DT number|number|NN of|of|IN standard|standard|JJ deviations|deviation|NNS a|a|DT data|data|NN is|be|VBZ from|from|IN the|the|DT mean|mean|NN .|.|.
Microarray|Microarray|NNP data|datum|NNS normalization|normalization|NN
Microarray|Microarray|NNP data|datum|NNS were|be|VBD processed|process|VBN using|use|VBG a|a|DT custom|custom|NN R|r|NN software|software|NN for|for|IN the|the|DT finite|finite|JJ hybridisation|hybridisation|NN -LRB-|-lrb-|-LRB- FH|fh|NN -RRB-|-rrb-|-RRB- model|model|NN -LRB-|-lrb-|-LRB- Ono|Ono|NNP et|et|FW al.|al.|FW ,|,|, 2008|2008|CD ,|,|, Bioinformatics|Bioinformatics|NNP 24|24|CD ,|,|, p1278|p1278|NN -RRB-|-rrb-|-RRB- .|.|.
Microarray|Microarray|NNP data|datum|NNS were|be|VBD processed|process|VBN using|use|VBG custom|custom|NN scripts|script|NNS written|write|VBN in|in|IN R|r|NN based|base|VBN on|on|IN the|the|DT finite|finite|JJ hybridisation|hybridisation|NN -LRB-|-lrb-|-LRB- FH|fh|NN -RRB-|-rrb-|-RRB- model|model|NN -LRB-|-lrb-|-LRB- Ono|Ono|NNP et|et|FW al|al|FW ,|,|, 2008|2008|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT thermodynamic|thermodynamic|JJ model|model|NN of|of|IN non-specific|non-specific|JJ binding|binding|NN -LRB-|-lrb-|-LRB- NSB|nsb|NN -RRB-|-rrb-|-RRB- on|on|IN short|short|JJ nucleotide|nucleotide|NN microarrays|microarray|NNS -LRB-|-lrb-|-LRB- Furusawa|Furusawa|NNP et|et|FW al|al|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- .|.|.
Microarray|Microarray|NNP data|datum|NNS were|be|VBD processed|process|VBN using|use|VBG custom|custom|NN scripts|script|NNS written|write|VBN in|in|IN R|r|NN based|base|VBN on|on|IN the|the|DT finite|finite|JJ hybridisation|hybridisation|NN -LRB-|-lrb-|-LRB- FH|fh|NN -RRB-|-rrb-|-RRB- model|model|NN -LRB-|-lrb-|-LRB- Ono|Ono|NNP et|et|FW al|al|FW ,|,|, 2008|2008|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT thermodynamic|thermodynamic|JJ model|model|NN of|of|IN non-specific|non-specific|JJ binding|binding|NN -LRB-|-lrb-|-LRB- NSB|nsb|NN -RRB-|-rrb-|-RRB- on|on|IN short|short|JJ nucleotide|nucleotide|NN microarrays|microarray|NNS -LRB-|-lrb-|-LRB- Furusawa|Furusawa|NNP et|et|FW al|al|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT log10|log10|NN mRNA|mrna|NN concentration|concentration|NN -LRB-|-lrb-|-LRB- pM|pm|NN -RRB-|-rrb-|-RRB- data|datum|NNS are|be|VBP provided|provide|VBN as|as|IN a|a|DT supplementary|supplementary|JJ file|file|NN on|on|IN the|the|DT SERIES|series|NN record|record|NN .|.|.
Microarray|Microarray|NNP data|datum|NNS were|be|VBD processed|process|VBN using|use|VBG custom|custom|NN scripts|script|NNS written|write|VBN in|in|IN R|r|NN based|base|VBN on|on|IN the|the|DT finite|finite|JJ hybridisation|hybridisation|NN -LRB-|-lrb-|-LRB- FH|fh|NN -RRB-|-rrb-|-RRB- model|model|NN -LRB-|-lrb-|-LRB- Ono|Ono|NNP et|et|FW al|al|FW -LRB-|-lrb-|-LRB- 2008|2008|CD -RRB-|-rrb-|-RRB- An|a|DT improved|improve|VBN physico-chemical|physico-chemical|JJ model|model|NN of|of|IN hybridization|hybridization|NN on|on|IN high-density|high-density|JJ oligonucleotide|oligonucleotide|NN microarrays|microarray|NNS .|.|. Bioinformatics|bioinformatic|NNS 24|24|CD :|:|: 1278-1285|1278-1285|CD .|.|. -RRB-|-rrb-|-RRB- and|and|CC the|the|DT thermodynamic|thermodynamic|JJ model|model|NN of|of|IN non-specific|non-specific|JJ binding|binding|NN -LRB-|-lrb-|-LRB- NSB|nsb|NN -RRB-|-rrb-|-RRB- on|on|IN short|short|JJ nucleotide|nucleotide|NN microarrays|microarray|NNS -LRB-|-lrb-|-LRB- Furusawa|Furusawa|NNP et|et|FW al|al|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- .|.|.
Microarray|Microarray|NNP normalization|normalization|NN is|be|VBZ carried|carry|VBN out|out|RP using|use|VBG maanova|maanova|NN function|function|NN in|in|IN R|r|NN program|program|NN version|version|NN 2.2.1|2.2.1|CD .|.|. Eight|eight|CD arrays|array|NNS in|in|IN one|one|CD slide|slide|NN were|be|VBD globally|globally|RB normalized|normalize|VBN using|use|VBG glowess|glowess|NN method|method|NN .|.|.
Microarray|Microarray|NNP suit|suit|NN 5.0|5.0|CD -LRB-|-lrb-|-LRB- Affymetrix|Affymetrix|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO average|average|VB the|the|DT scans|scan|NNS and|and|CC process|process|NN the|the|DT data|datum|NNS ,|,|, further|further|RB data|data|NN analysis|analysis|NN was|be|VBD conducted|conduct|VBN using|use|VBG Affymetrix|Affymetrix|NNP ®|®|NNP Data|Data|NNP Mining|Mining|NNP Tool|Tool|NNP -LRB-|-lrb-|-LRB- DMT|DMT|NNP 3.0|3.0|CD -RRB-|-rrb-|-RRB- .|.|.
Microarray|Microarray|NNP suite|suite|NN 5.0|5.0|CD
Microcin|microcin|NN B17|b17|NN Rep|Rep|NNP 1|1|CD +|+|CC A-IP|a-ip|JJ
Microcin|microcin|NN B17|b17|NN Rep|Rep|NNP 1|1|CD +|+|CC A+IP|A+IP|NNP
Microcin|Microcin|NNP B17|B17|NNP Rep|Rep|NNP 2|2|CD +|+|CC A-IP|a-ip|JJ
Microcin|microcin|NN B17|b17|NN Rep|Rep|NNP 2|2|CD +|+|CC A+IP|A+IP|NNP
Microcin|Microcin|NNP B17|B17|NNP Rep|Rep|NNP 3|3|CD +|+|CC A-IP|a-ip|JJ
Microcin|microcin|NN B17|b17|NN Rep|Rep|NNP 3|3|CD +|+|CC A+IP|A+IP|NNP
Microcin|Microcin|NNP _|_|NNP IN|in|IN _|_|CD 50mkM|50mkm|NN _|_|NN 3|3|CD
Microcin|microcin|NN _|_|CD IN|in|IN _|_|CD Mu|mu|NN _|_|CD 10mkM|10mkm|NN _|_|NN 1|1|CD
Microcin|microcin|NN _|_|CD IN|in|IN _|_|CD Mu|mu|NN _|_|NN 10mkM|10mkm|NN _|_|NN 2|2|CD
Microcin|microcin|NN _|_|CD IP|IP|NNP _|_|NNP 50mkM|50mkM|NNP _|_|SYM 3|3|CD
MIcrocin|microcin|NN _|_|CD IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 10mkM|10mkm|NN _|_|NN 1|1|CD
Microcin|microcin|NN _|_|CD IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 10mkM|10mkm|NN _|_|NN 2|2|CD
Mid|Mid|NNP log|log|NN _|_|SYM cra|cra|FW KO|ko|FW _|_|SYM glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN aerobic|aerobic|JJ
Mid|Mid|NNP log|log|NN _|_|SYM cra|cra|FW KO|ko|FW _|_|SYM glc|glc|NN minimal|minimal|JJ media|media|NNS +|+|CC L-tryptophan|l-tryptophan|JJ _|_|NN aerobic|aerobic|JJ
Mid|Mid|NNP log|log|NN cultures|culture|NNS were|be|VBD treated|treat|VBN with|with|IN Qiagen|Qiagen|NNP RNA|rna|NN Protect|protect|VB reagent|reagent|NN following|follow|VBG the|the|DT vendor|vendor|NN 's|'s|POS protocol|protocol|NN .|.|. Cells|cell|NNS were|be|VBD centrifuged|centrifuge|VBN and|and|CC stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN for|for|IN <|<|JJR 30|30|CD days|day|NNS prior|prior|RB to|to|TO use|use|VB .|.|.
Mid|Mid|NNP log|log|NN _|_|CD mntR|mntr|NN KO|KO|NNP _|_|NNP glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN aerobic|aerobic|JJ
Mid|Mid|NNP log|log|NN _|_|CD mntR|mntr|NN KO|KO|NNP _|_|NNP glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN anaerobic|anaerobic|JJ
Mid|Mid|NNP log|log|NN _|_|CD nac|nac|NN KO|KO|NNP _|_|NNP glc|glc|NN minimal|minimal|JJ media|media|NNS +|+|CC adenine|adenine|JJ _|_|NN aerobic|aerobic|JJ
Mid|Mid|NNP log|log|NN _|_|CD nac|nac|NN KO|KO|NNP _|_|NNP glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN aerobic|aerobic|JJ
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS +|+|CC adenine|adenine|JJ _|_|NN aerobic|aerobic|JJ
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN aerobic|aerobic|JJ rep1|rep1|NN
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN aerobic|aerobic|JJ rep2|rep2|NN
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN aerobic|aerobic|JJ rep3|rep3|NN
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN anaerobic|anaerobic|JJ rep1|rep1|NN
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN anaerobic|anaerobic|JJ rep2|rep2|NN
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS _|_|NN anaerobic|anaerobic|JJ rep3|rep3|NN
Mid|Mid|NNP log|log|NN _|_|NN wildtype|wildtype|JJ _|_|NN glc|glc|NN minimal|minimal|JJ media|media|NNS +|+|CC L-tryptophan|l-tryptophan|JJ _|_|NN aerobic|aerobic|JJ
minD|mind|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
minD|mind|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
minD|mind|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
minD|mind|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
minE|mine|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r1|r1|NN
minE|mine|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|NNP r2|r2|NN
minE|mine|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
minE|mine|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
MiSeq|miseq|NN for|for|IN base|base|NN calling|call|VBG
Mixed|Mixed|NNP model|model|NN analysis|analysis|NN was|be|VBD conducted|conduct|VBN as|as|IN previously|previously|RB described|describe|VBN -LRB-|-lrb-|-LRB- Madsen|Madsen|NNP ,|,|, et|et|FW al.|al.|FW ,|,|, 2006|2006|CD -RRB-|-rrb-|-RRB- excluding|exclude|VBG slide|slide|NN region|region|NN and|and|CC slide-by-region|slide-by-region|NN interaction|interaction|NN effects|effect|NNS .|.|. The|the|DT value|value|NN column|column|NN was|be|VBD not|not|RB used|use|VBN for|for|IN analysis|analysis|NN or|or|CC in|in|IN publication|publication|NN .|.|. The|the|DT normalized|normalize|VBN values|value|NNS for|for|IN duplicate|duplicate|VBP spots|spot|NNS were|be|VBD averaged|average|VBN within|within|IN each|each|DT array|array|NN to|to|TO produce|produce|VB one|one|CD normalized|normalize|VBD measure|measure|NN of|of|IN expression|expression|NN for|for|IN each|each|DT of|of|IN the|the|DT probe|probe|NN sequences|sequence|NNS and|and|CC each|each|DT of|of|IN the|the|DT RNA|rna|NN samples|sample|NNS .|.|. -LSB-|-lsb-|-LRB- mean|mean|VB log|log|NN transformed|transform|VBN median|median|JJ centered|centered|JJ lowess|lowess|NN normalized|normalize|VBD signal|signal|NN intensity|intensity|NN -RSB-|-rsb-|-RRB-
MMAcetat|mmacetat|NN
mMaple3|mmaple3|NN _|_|NN 0|0|CD min|min|NN
mMaple3|mmaple3|NN _|_|CD 10|10|CD min|min|NN
mMaple3|mmaple3|NN _|_|CD 15|15|CD min|min|NN
mMaple3|mmaple3|NN _|_|NN 1|1|CD min|min|NN
mMaple3|mmaple3|NN _|_|NN 2|2|CD min|min|NN
mMaple3|mmaple3|NN _|_|CD 4|4|CD min|min|NN
mMaple3|mmaple3|NN _|_|CD 6|6|CD min|min|NN
mMaple3|mmaple3|NN _|_|CD 8|8|CD min|min|NN
MMPyruvat|mmpyruvat|NN
mntR|mntr|NN KO|ko|NN
mntR|mntr|NN KO|ko|SYM -|-|: O2|o2|CD
Mock|mock|JJ community|community|NN
molecule|molecule|NN subtype|subtype|NN :|:|: DMS-modified|dms-modified|JJ mRNA|mrna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: In|in|FW vitro|vitro|FW synthesized|synthesize|VBN RNase|rnase|NN P|p|NN -LRB-|-lrb-|-LRB- rnpB|rnpb|NN -RRB-|-rrb-|-RRB- RNA|rna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: mRNA|mrna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: nascent|nascent|JJ 3|3|CD '|'|'' RNA|rna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: ribosome-depeleted|ribosome-depeleted|JJ RNA|rna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: ribosome|ribosome|NN protected|protect|VBD mRNA|mrna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: Ribosome|ribosome|NN protected|protect|VBD mRNA|mrna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: rRNA-depleted|rrna-depleted|JJ total|total|JJ RNA|rna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: total|total|JJ RNA|rna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: Total|total|JJ RNA|rna|NN
molecule|molecule|NN subtype|subtype|NN :|:|: Total|total|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- Cytosolic|cytosolic|JJ fraction|fraction|NN -RRB-|-rrb-|-RRB-
molecule|molecule|NN subtype|subtype|NN :|:|: Total|total|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- Nucleoid|nucleoid|NN fraction|fraction|NN -RRB-|-rrb-|-RRB-
molecule|molecule|NN subtype|subtype|NN :|:|: total|total|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- ribosome-depleted|ribosome-depleted|JJ -RRB-|-rrb-|-RRB-
molecule|molecule|NN subtype|subtype|NN :|:|: total|total|JJ RNA|rna|NN ,|,|, rRNA|rrna|NN depleted|deplete|VBD
Monoclonal|monoclonal|JJ antibody|antibody|NN for|for|IN HA|HA|NNP -LRB-|-lrb-|-LRB- 12CA5|12ca5|NN -RRB-|-rrb-|-RRB-
Monoclonal|monoclonal|JJ antibody|antibody|NN for|for|IN NusA|nusa|NN -LRB-|-lrb-|-LRB- 1NA1|1na1|NN -RRB-|-rrb-|-RRB-
Monoclonal|monoclonal|JJ antibody|antibody|NN for|for|IN RNA|rna|NN polymerase|polymerase|NN Beta|beta|NN '|'|'' subunit|subunit|NN -LRB-|-lrb-|-LRB- NT73|nt73|NN -RRB-|-rrb-|-RRB-
Monoclonal|monoclonal|JJ antibody|antibody|NN for|for|IN Sigma70|sigma70|NN -LRB-|-lrb-|-LRB- 2G10|2g10|NN -RRB-|-rrb-|-RRB-
morphology|morphology|NN :|:|: a|a|DT
morphology|morphology|NN :|:|: b|b|NN
morphology|morphology|NN :|:|: c|c|NN
morphology|morphology|NN :|:|: Coliform|coliform|NN
morphology|morphology|NN :|:|: Filamented|filamented|JJ
morphology|morphology|NN :|:|: Reverted|revert|VBN -LRB-|-lrb-|-LRB- reverted|revert|VBD back|back|RB from|from|IN a|a|DT Filamented|filamented|JJ shape|shape|NN into|into|IN a|a|DT coli|coli|NN shape|shape|NN -RRB-|-rrb-|-RRB-
morphology|morphology|NN :|:|: Transition|transition|NN -LRB-|-lrb-|-LRB- from|from|IN Coli|Coli|NNP into|into|IN Filamented|Filamented|NNP -RRB-|-rrb-|-RRB-
mouse|mouse|NN feces|fece|VBZ
Mouse|Mouse|NNP kidneys|kidney|NNS were|be|VBD homogonized|homogonize|VBN in|in|IN RNALater|rnalater|NN solution|solution|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- and|and|CC bacterial|bacterial|JJ titers|titer|NNS were|be|VBD taken|take|VBN .|.|. Samples|sample|NNS were|be|VBD pooled|pool|VBN ,|,|, and|and|CC centrifuged|centrifuge|VBD as|as|IN described|describe|VBN below|below|IN
M-P0h|m-p0h|NN _|_|CD r1|r1|NN _|_|CD HiSeq|hiseq|NN
M-P0h|m-p0h|NN _|_|CD r2|r2|NN _|_|CD HiSeq|hiseq|NN
M-P2h|m-p2h|NN _|_|CD r1|r1|NN _|_|CD HiSeq|hiseq|NN
M-P2h|m-p2h|NN _|_|CD r2|r2|NN _|_|CD HiSeq|hiseq|NN
M-P4h|m-p4h|NN _|_|CD r1|r1|NN _|_|CD HiSeq|hiseq|NN
M-P4h|m-p4h|NN _|_|CD r2|r2|NN _|_|CD HiSeq|hiseq|NN
M-P4h|m-p4h|NN _|_|CD r3|r3|NN _|_|CD HiSeq|hiseq|NN
mRNA|mrna|NN
mRNA|mrna|NN fragments|fragment|NNS were|be|VBD size|size|NN selected|select|VBN via|via|IN gel|gel|NN purification|purification|NN ,|,|, and|and|CC ligated|ligate|VBN to|to|TO 5|5|CD '|'|'' adenylated|adenylate|VBN DNA|dna|NN oligo|oligo|JJ .|.|. After|after|IN reverse|reverse|JJ transcription|transcription|NN ,|,|, the|the|DT single|single|JJ stranded|stranded|JJ DNA|dna|NN was|be|VBD circularized|circularize|VBN ,|,|, and|and|CC PCR|pcr|NN amplified|amplify|VBD -LRB-|-lrb-|-LRB- Oh|oh|UH et|et|FW al.|al.|FW ,|,|, 2011|2011|CD ;|;|: Li|Li|NNP et|et|FW al.|al.|FW ,|,|, 2014|2014|CD ;|;|: Rouskin|Rouskin|NNP et|et|FW al.|al.|FW ,|,|, 2014|2014|CD -RRB-|-rrb-|-RRB- .|.|.
mRNA-seq|mrna-seq|NN 10|10|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
mRNA-seq|mrna-seq|NN 2|2|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
mRNA-seq|mrna-seq|NN 30|30|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
mRNA-seq|mrna-seq|NN 37|37|CD °C|°c|NN in|in|IN WT|wt|JJ with|with|IN control|control|NN plasmid|plasmid|NN
mRNA-seq|mrna-seq|NN 37|37|CD °C|°c|NN in|in|IN WT|wt|JJ with|with|IN plasmid|plasmid|NN expressing|express|VBG mini-ORF|mini-orf|NN CUA|cua|NN
mRNA-seq|mrna-seq|NN 37|37|CD °C|°c|NN in|in|IN WT|wt|JJ with|with|IN plasmid|plasmid|NN expressing|express|VBG mini-ORF|mini-orf|NN CUG|cug|NN
mRNA-seq|mrna-seq|NN 3|3|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
mRNA-seq|mrna-seq|NN 4|4|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
mRNA-seq|mrna-seq|NN 6|6|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
mRNA-seq|mrna-seq|NN 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD cspABEG|cspabeg|NN cells|cell|NNS
mRNA-seq|mrna-seq|NN 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
mRNA-seq|mrna-seq|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN ∆|∆|CD cspABCEG|cspabceg|NN cells|cell|NNS
mRNA-seq|mrna-seq|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS _|_|VBP 1|1|CD
mRNA-seq|mrna-seq|NN at|at|IN 37|37|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS _|_|VBP 2|2|CD
mRNA-seq|mrna-seq|NN in|in|IN rich|rich|JJ defined|define|VBN media|media|NNS
mRNA-seq|mrna-seq|NN MicL-S|micl-s|NN t0|t0|NN
mRNA-seq|mrna-seq|NN MicL-S|micl-s|NN t10|t10|NN
mRNA-seq|mrna-seq|NN MicL-S|micl-s|NN t20|t20|NN
mRNA-seq|mrna-seq|NN MicL-S|micl-s|NN t4|t4|NN
mRNA-seq|mrna-seq|NN MicL|micl|NN t0|t0|NN
mRNA-seq|mrna-seq|NN MicL|micl|NN t10|t10|NN
mRNA-seq|mrna-seq|NN MicL|micl|NN t20|t20|NN
mRNA-seq|mrna-seq|NN MicL|micl|NN t4|t4|NN
mRNA-seq|mrna-seq|NN Vector|Vector|NNP t0|t0|NN
mRNA-seq|mrna-seq|NN Vector|Vector|NNP t20|t20|NN
mRNA-seq|mrna-seq|NN with|with|IN barcode|barcode|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP TruSeq|TruSeq|NNP Index|Index|NNP 1-5|1-5|CD -RRB-|-rrb-|-RRB-
mRNA-seq|mrna-seq|NN WT|wt|JJ t10|t10|NN
mRNA-seq|mrna-seq|NN WT|wt|JJ t4|t4|NN
mrna|mrna|NN synthesis|synthesis|NN :|:|: in|in|FW vitro|vitro|FW MgCl2|mgcl2|NN
mrna|mrna|NN synthesis|synthesis|NN :|:|: in|in|FW vitro|vitro|FW MgCl2|mgcl2|NN +|+|CC GreAB|greab|NN
mrna|mrna|NN synthesis|synthesis|NN :|:|: in|in|FW vitro|vitro|FW MnCl2|mncl2|NN
mrna|mrna|NN synthesis|synthesis|NN :|:|: in|in|FW vitro|vitro|FW MnCl2|mncl2|NN +|+|CC GreAB|greab|NN
mrna|mrna|NN synthesis|synthesis|NN :|:|: in|in|FW vivo|vivo|FW
MT|MT|NNP _|_|SYM 12h|12h|CD _|_|CD rep1|rep1|NN
MT|mt|NNS _|_|VBP 12h|12h|JJ _|_|NN rep2|rep2|NN
MT|mt|NNS _|_|VBP 24h|24h|JJ _|_|NN rep1|rep1|NN
MT|mt|NNS _|_|VBP 24h|24h|JJ _|_|NN rep2|rep2|NN
MT|mt|NNS _|_|VBP 48h|48h|JJ _|_|NN rep1|rep1|NN
MT|mt|NNS _|_|VBP 48h|48h|JJ _|_|NN rep2|rep2|NN
MT|mt|NNS _|_|VBP 6h|6h|JJ _|_|NN rep1|rep1|NN
MT|mt|NNS _|_|VBP 6h|6h|JJ _|_|NN rep2|rep2|NN
MukB|mukb|NN 22|22|CD °C|°c|NN
MukB|mukb|NN 37|37|CD °C|°c|NN
MukBDA|mukbda|NN 22|22|CD °C|°c|NN
MukB|mukb|NN deltamatP|deltamatp|NN 22|22|CD °C|°c|NN
MukBEQ|mukbeq|NN 22|22|CD °C|°c|NN
MukBEQ|mukbeq|NN deltamatP|deltamatp|NN 22|22|CD °C|°c|NN
murI|muri|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r1|r1|FW
murI|muri|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
murI|muri|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
murI|muri|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
musgs|musg|NNS presence|presence|NN :|:|: -|-|:
musgs|musg|NNS presence|presence|NN :|:|: MuSGS|musgs|NN
mutant|mutant|JJ
Mutant|mutant|JJ B8|b8|NN _|_|NN 0.8|0.8|CD %|%|NN Bu|bu|NN _|_|CD 1.5|1.5|CD h|h|NN _|_|CD rep1|rep1|NN
Mutant|mutant|JJ B8|b8|NN _|_|NN 0.8|0.8|CD %|%|NN Bu|bu|NN _|_|CD 1.5|1.5|CD h|h|NN _|_|CD rep2|rep2|NN
Mutant|mutant|JJ B8|b8|NN _|_|NN 0.8|0.8|CD %|%|NN Bu|bu|NN _|_|CD 1.5|1.5|CD h|h|NN _|_|CD rep3|rep3|NN
Mutant|mutant|JJ B8|b8|NN ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN ,1.5|,1.5|CD h|h|NN ,|,|, replicate|replicate|VB 1|1|CD
Mutant|mutant|JJ B8|b8|NN ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN ,1.5|,1.5|CD h|h|NN ,|,|, replicate|replicate|VB 2|2|CD
Mutant|mutant|JJ B8|b8|NN ,|,|, 0.8|0.8|CD %|%|NN butanol|butanol|NN ,1.5|,1.5|CD h|h|NN ,|,|, replicate|replicate|VB 3|3|CD
mutant|mutant|JJ E1|e1|NN ,|,|, biological|biological|JJ rep1|rep1|NN
mutant|mutant|JJ E1|e1|NN ,|,|, biological|biological|JJ rep2|rep2|NN
mutant|mutant|JJ E1|e1|NN ,|,|, biological|biological|JJ rep3|rep3|NN
mutant|mutant|JJ E.|e.|FW coli|coli|FW ,|,|, after|after|IN butanol|butanol|NN treatment|treatment|NN
mutant|mutant|JJ E.|e.|FW coli|coli|FW ,|,|, before|before|IN butanol|butanol|NN treatment|treatment|NN
Mutant|mutant|JJ E.|e.|FW coli|coli|FW O157|o157|NN treated|treat|VBN with|with|IN 6|6|CD ug/ml|ug/ml|NN triclosan|triclosan|NN for|for|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Mutant|mutant|JJ E.|e.|FW coli|coli|FW O157|o157|NN treated|treat|VBN with|with|IN 6|6|CD ug/ml|ug/ml|NN triclosan|triclosan|NN for|for|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Mutant|mutant|JJ E.|e.|FW coli|coli|FW O157|o157|NN treated|treat|VBN with|with|IN 6|6|CD ug/ml|ug/ml|NN triclosan|triclosan|NN for|for|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
Mutant|mutant|JJ E.|e.|FW coli|coli|FW O157|o157|NN untreated|untreated|JJ ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Mutant|mutant|JJ E.|e.|FW coli|coli|FW O157|o157|NN untreated|untreated|JJ ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Mutant|mutant|JJ E.|e.|FW coli|coli|FW O157|o157|NN untreated|untreated|JJ ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T0|t0|NN RNA|rna|NN rep|rep|NN 1|1|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T0|t0|NN RNA|rna|NN rep|rep|NN 2|2|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T0|t0|NN RP|rp|NN rep|rep|NN 1|1|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T0|t0|NN RP|rp|NN rep|rep|NN 2|2|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T1|t1|NN RNA|rna|NN rep|rep|NN 1|1|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T1|t1|NN RNA|rna|NN rep|rep|NN 2|2|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T1|t1|NN RP|rp|NN rep|rep|NN 1|1|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T1|t1|NN RP|rp|NN rep|rep|NN 2|2|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T2|t2|NN RNA|rna|NN rep|rep|NN 1|1|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T2|t2|NN RNA|rna|NN rep|rep|NN 2|2|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T2|t2|NN RP|rp|NN rep|rep|NN 1|1|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- EP61|ep61|NN -RRB-|-rrb-|-RRB- T2|t2|NN RP|rp|NN rep|rep|NN 2|2|CD
Mutant|mutant|JJ -LRB-|-lrb-|-LRB- RL2325|rl2325|NN -RRB-|-rrb-|-RRB- RNA-seq|rna-seq|NN
mutant|mutant|JJ SdiA1E11|sdia1e11|NN
MutRep1|mutrep1|NN _|_|NN 0|0|CD min|min|NN
MutRep1|mutrep1|NN _|_|CD 10|10|CD min|min|NN
MutRep1|mutrep1|NN _|_|CD 15|15|CD min|min|NN
MutRep1|mutrep1|NN _|_|CD 20|20|CD min|min|NN
MutRep1|mutrep1|NN _|_|NN 2|2|CD min|min|NN
MutRep1|mutrep1|NN _|_|CD 4|4|CD min|min|NN
MutRep1|mutrep1|NN _|_|CD 6|6|CD min|min|NN
MutRep1|mutrep1|NN _|_|CD 8|8|CD min|min|NN
MutRep2|mutrep2|NN _|_|NN 0|0|CD min|min|NN
MutRep2|mutrep2|NN _|_|CD 10|10|CD min|min|NN
MutRep2|mutrep2|NN _|_|CD 15|15|CD min|min|NN
MutRep2|mutrep2|NN _|_|CD 20|20|CD min|min|NN
MutRep2|mutrep2|NN _|_|NN 2|2|CD min|min|NN
MutRep2|mutrep2|NN _|_|CD 4|4|CD min|min|NN
MutRep2|mutrep2|NN _|_|CD 6|6|CD min|min|NN
MutRep2|mutrep2|NN _|_|CD 8|8|CD min|min|NN
MW30|mw30|NN -LRB-|-lrb-|-LRB- rpoS|rpos|NN -RRB-|-rrb-|-RRB-
MW30|mw30|NN -LRB-|-lrb-|-LRB- rpoS|rpos|NN -RRB-|-rrb-|-RRB- ,|,|, LB|lb|NN ,|,|, exponential|exponential|JJ phase|phase|NN
MW30|mw30|NN rpoS|rpos|NN ,|,|, LB|lb|NN ,|,|, exponential|exponential|JJ phase|phase|NN
MW30|mw30|NN -LRB-|-lrb-|-LRB- rpoS|rpos|NN -RRB-|-rrb-|-RRB- ,|,|, LB|lb|NN ,|,|, stationary|stationary|JJ phase|phase|NN
MW30|mw30|NN rpoS|rpos|NN ,|,|, LB|lb|NN ,|,|, stationary|stationary|JJ phase|phase|NN
MY4|my4|NN _|_|NN replicated|replicate|VBN
N172-1|n172-1|NN
N172-2|n172-2|NN
N30-1|n30-1|NN
N30-2|n30-2|NN
N30-3|n30-3|NN
N30-4|n30-4|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pBADRNE|pbadrne|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pBAD-RNE|pbad-rne|NN w/out|w/out|NN Arabinose|arabinose|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pNRNE5|pnrne5|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pRNG3|prng3|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- rng|rng|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- rng|rng|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- LB|lb|NN at|at|IN 30|30|CD C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- pPM30|ppm30|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- pRNG3|prng3|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pBADRNE|pbadrne|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN Trial|trial|NN B|b|NN *|*|SYM
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pBAD-RNE|pbad-rne|NN w/out|w/out|NN Arabinose|arabinose|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS Trial|trial|NN A|a|DT
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pNRNE5|pnrne5|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN Trial|trial|NN A|a|NN *|*|SYM
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pNRNE5|pnrne5|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN Trial|trial|NN B|b|NN *|*|SYM
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pRNG3|prng3|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN Trial|trial|NN A|a|NN *|*|SYM
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rne|rne|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- pRNG3|prng3|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN Trial|trial|NN B|b|NN *|*|SYM
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rng|rng|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS C|c|NN Trial|trial|NN B|b|NN
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- rng|rng|NN deletion|deletion|NN -RRB-|-rrb-|-RRB- LB|lb|NN at|at|IN 30|30|CD C|c|NN Trial|trial|NN A|a|NN *|*|SYM
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- pRNG3|prng3|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS Trial|trial|NN A|a|DT *|*|SYM
N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- vs|vs|CC N3433|n3433|NN -LRB-|-lrb-|-LRB- wt|wt|JJ -RRB-|-rrb-|-RRB- pRNG3|prng3|NN in|in|IN LB|lb|NN at|at|IN 30|30|CD degrees|degree|NNS Trial|trial|NN B|b|NN *|*|SYM
N/A|N/A|NNP
na|na|TO +1|+1|NN -LRB-|-lrb-|-LRB- levels|level|NNS -RRB-|-rrb-|-RRB- :|:|: baseNa|basena|NN
na|na|TO +1|+1|NN -LRB-|-lrb-|-LRB- levels|level|NNS -RRB-|-rrb-|-RRB- :|:|: highNa|highna|NN
na|na|TO +1|+1|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 100|100|CD
na|na|TO +1|+1|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 200|200|CD
na|na|TO +1|+1|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 300|300|CD
na|na|TO +1|+1|NN -LRB-|-lrb-|-LRB- mm|mm|NN -RRB-|-rrb-|-RRB- :|:|: 5|5|CD
Nac|Nac|NNP _|_|SYM ChIPSeq|chipseq|NN
nac|nac|NN KO|ko|NN
nac|nac|NN KO|ko|NN +|+|CC ade|ade|NN
NaCl|nacl|NN replicate|replicate|VBP 1|1|CD
NaCl|nacl|NN replicate|replicate|VBP 2|2|CD
NaCl|nacl|NN replicate|replicate|VBP 3|3|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 061|061|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 063|063|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 064|064|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 065|065|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 066|066|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 067|067|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 068|068|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 069|069|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 070|070|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 071|071|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 072|072|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 073|073|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 074|074|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 075|075|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 076|076|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 077|077|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 079|079|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 080|080|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 081|081|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 082|082|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 083|083|CD
NaCl|nacl|NN _|_|CD stress|stress|NN :|:|: MURI|MURI|NNP _|_|SYM 084|084|CD
Nac|Nac|NNP _|_|SYM RNASeq|rnaseq|NN
NaOH|naoh|NN replicate|replicate|VBP 1|1|CD
NaOH|naoh|NN replicate|replicate|VBP 3|3|CD
narXL|narxl|NN anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN
narXLP|narxlp|NN anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN
narXLP|narxlp|NN rep|rep|NN 1|1|CD
narXLP|narxlp|NN rep|rep|NN 2|2|CD
narXLP|narxlp|NN rep|rep|NN 3|3|CD
narXL|narxl|NN rep|rep|NN 1|1|CD
narXL|narxl|NN rep|rep|NN 2|2|CD
narXL|narxl|NN rep|rep|NN 3|3|CD
narXL|narxl|NN rep|rep|NN 4|4|CD
n-Butanol|n-butanol|NN -LRB-|-lrb-|-LRB- 0.8|0.8|CD %|%|NN ,|,|, v/v|v/v|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN at|at|IN 0.8|0.8|CD OD660|od660|NN and|and|CC further|further|JJ incubated|incubate|VBN for|for|IN 1.5|1.5|CD h.|h.|NN
neo|neo|NN _|_|NN 0|0|CD min|min|NN
neo|neo|NN _|_|CD 10|10|CD min|min|NN
neo|neo|NN _|_|CD 15|15|CD min|min|NN
neo|neo|NN _|_|NN 1|1|CD min|min|NN
neo|neo|NN _|_|NN 2|2|CD min|min|NN
neo|neo|NN _|_|NN 4|4|CD min|min|NN
neo|neo|NN _|_|NN 6|6|CD min|min|NN
neo|neo|NN _|_|NN 8|8|CD min|min|NN
Next|Next|NNP ,|,|, a|a|DT linear|linear|JJ model|model|NN was|be|VBD built|build|VBN for|for|IN each|each|DT comparison|comparison|NN using|use|VBG the|the|DT R|r|NN LIMMA|limma|NN package|package|NN and|and|CC statistics|statistics|NNS for|for|IN differential|differential|JJ expression|expression|NN analysis|analysis|NN were|be|VBD computed|compute|VBN .|.|. To|to|TO filter|filter|NN for|for|IN differential|differential|JJ expression|expression|NN ,|,|, two|two|CD fold|fold|JJ or|or|CC three-fold|three-fold|JJ change|change|NN with|with|IN a|a|DT FDR|FDR|NNP ≤|≤|SYM 0.05|0.05|CD were|be|VBD used|use|VBN as|as|IN the|the|DT threshold|threshold|NN .|.|.
Next|Next|NNP ,|,|, data|datum|NNS were|be|VBD normalized|normalize|VBN ,|,|, by|by|IN averaging|average|VBG the|the|DT log|log|NN ratios|ratio|NNS resulting|result|VBG from|from|IN all|all|DT spots|spot|NNS printed|print|VBN by|by|IN a|a|DT
NEXTflexRapid|nextflexrapid|NN Directional|directional|JJ RNA-Seq|rna-seq|NN library|library|NN kit|kit|NN
NFNT|nfnt|JJ
ngs|ng|NNS platform|platform|NN :|:|: Illumina|Illumina|NNP HiSeq|HiSeq|NNP
ngs|ng|NNS platform|platform|NN :|:|: Illumina|Illumina|NNP MiSeq|MiSeq|NNP
NimbleScan|NimbleScan|NNP software|software|NN package|package|NN ,|,|, version|version|NN 2.5|2.5|CD -LRB-|-lrb-|-LRB- Roche|Roche|NNP NimbleGen|NimbleGen|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO extract|extract|VB the|the|DT scanned|scan|VBN data|datum|NNS ,|,|, which|which|WDT was|be|VBD subsequently|subsequently|RB qunatile|qunatile|JJ normalized|normalize|VBN using|use|VBG the|the|DT statistical|statistical|JJ program|program|NN R|r|NN .|.|. The|the|DT sample|sample|NN data|datum|NNS table|table|NN contains|contain|VBZ the|the|DT log2|log2|NN ratio|ratio|NN of|of|IN the|the|DT IP/Input|ip/input|NN after|after|IN data|datum|NNS was|be|VBD quantile|quantile|JJ normalized|normalize|VBN .|.|.
Nineteen|nineteen|CD hours|hour|NNS after|after|IN experiment|experiment|NN start|start|NN ,|,|, antibiotic|antibiotic|JJ -LRB-|-lrb-|-LRB- Gentamicin|gentamicin|NN Sulfate|sulfate|NN -LRB-|-lrb-|-LRB- MP|mp|NN Biomedical|biomedical|NN ,|,|, Cat|Cat|NNP No.|No.|NNP 1676045|1676045|CD ,|,|, Santa|Santa|NNP Ana|Ana|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- was|be|VBD introducing|introduce|VBG into|into|IN the|the|DT cultures|culture|NNS .|.|. Antibiotic|antibiotic|JJ concentration|concentration|NN varied|vary|VBD from|from|IN one|one|CD sample|sample|NN to|to|TO the|the|DT next|next|JJ from|from|IN 0|0|CD to|to|TO 150|150|CD ug/mL|ug/ml|NN in|in|IN 25|25|CD ug/mL|ug/ml|NN steps|step|NNS .|.|. Thirty|thirty|CD hours|hour|NNS later|later|RB ,|,|, samples|sample|NNS were|be|VBD fixed|fix|VBN in|in|IN RNA|rna|NN Later|later|RB II|ii|CD -LRB-|-lrb-|-LRB- -LRB-|-lrb-|-LRB- ACROS|ACROS|NNP ,|,|, Cat|Cat|NNP .|.|. No.|no.|NN 41678|41678|CD ,|,|, New|New|NNP Jersey|Jersey|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS were|be|VBD stored|store|VBN at|at|IN -75|-75|CD C|c|NN until|until|IN return|return|NN to|to|TO Earth|Earth|NNP for|for|IN analyses|analysis|NNS .|.|.
NN2|nn2|NN _|_|CD 0018|0018|CD _|_|NN 1|1|CD
NN2|nn2|NN _|_|CD 0018|0018|CD _|_|NN 2|2|CD
-LRB-|-lrb-|-LRB- -|-|: NO|no|NN -RRB-|-rrb-|-RRB- 1|1|CD
-LRB-|-lrb-|-LRB- +|+|CC NO|no|NN -RRB-|-rrb-|-RRB- 1|1|CD
-LRB-|-lrb-|-LRB- -|-|: NO|no|NN -RRB-|-rrb-|-RRB- 2|2|CD
-LRB-|-lrb-|-LRB- +|+|CC NO|no|NN -RRB-|-rrb-|-RRB- 2|2|CD
-LRB-|-lrb-|-LRB- -|-|: NO|no|NN -RRB-|-rrb-|-RRB- 3|3|CD
-LRB-|-lrb-|-LRB- +|+|CC NO|no|NN -RRB-|-rrb-|-RRB- 3|3|CD
No|no|DT further|further|JJ treatment|treatment|NN was|be|VBD applied|apply|VBN .|.|.
no|no|DT inhibitor|inhibitor|NN :|:|: equivalent|equivalent|JJ volume|volume|NN of|of|IN DMSO|dmso|NN added|add|VBD
Non-challenged|non-challenged|JJ Library|Library|NNP
Non-crosslinked|non-crosslinked|JJ DNA|dna|NN
None|none|NN
non-sorted|non-sorted|JJ E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN culture|culture|NN 1|1|CD
non-sorted|non-sorted|JJ E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN culture|culture|NN 2|2|CD
Non-treated|non-treated|JJ ,|,|, fur|fur|NN mutant|mutant|JJ sample|sample|NN at|at|IN T0|t0|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Non-treated|non-treated|JJ ,|,|, fur|fur|NN mutant|mutant|JJ sample|sample|NN at|at|IN T0|t0|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Non-treated|non-treated|JJ ,|,|, WT|wt|JJ control|control|NN at|at|IN T0|t0|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Non-treated|non-treated|JJ ,|,|, WT|wt|JJ control|control|NN at|at|IN T0|t0|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Non-treatment|non-treatment|JJ
NorflIP|norflip|NN Input|input|NN ParC-flag|parc-flag|NN 1|1|CD
NorflIP|norflip|NN Input|input|NN ParC-flag|parc-flag|NN 2|2|CD
NorflIP|norflip|NN Input|input|NN ParE-flag|pare-flag|NN 1|1|CD
NorflIP|norflip|NN IP|IP|NNP ParC-flag|ParC-flag|NNP 1|1|CD
NorflIP|norflip|NN IP|IP|NNP ParC-flag|ParC-flag|NNP 2|2|CD
NorflIP|norflip|NN IP|IP|NNP ParE-flag|ParE-flag|NNP 1|1|CD
NormalData|normaldata|NN =|=|JJ transform.madata|transform.madata|NN -LRB-|-lrb-|-LRB- LogData|LogData|NNP ,|,|, method|method|NN =|=|JJ c|c|NN -LRB-|-lrb-|-LRB- \|\|CD
Normalisation|normalisation|NN :|:|: Counts|count|NNS were|be|VBD normalised|normalise|VBN by|by|IN applying|apply|VBG a|a|DT single|single|JJ ,|,|, sample-specific|sample-specific|JJ scaling|scaling|NN factor|factor|NN .|.|. To|to|TO calculate|calculate|VB this|this|DT scaling|scaling|NN factor|factor|NN ,|,|, we|we|PRP implemented|implement|VBD the|the|DT median|median|NN of|of|IN ratios|ratio|NNS normalisation|normalisation|NN of|of|IN DESeq|deseq|NN software|software|NN -LRB-|-lrb-|-LRB- Anders|Anders|NNP ,|,|, S.|S.|NNP and|and|CC Huber|Huber|NNP ,|,|, W.|W.|NNP -LRB-|-lrb-|-LRB- 2010|2010|CD -RRB-|-rrb-|-RRB- Differential|differential|JJ expression|expression|NN analysis|analysis|NN for|for|IN sequence|sequence|NN count|count|NN data|datum|NNS .|.|. Genome|Genome|NNP Biol|Biol|NNP ,|,|, 11|11|CD ,|,|, R106|r106|NN -RRB-|-rrb-|-RRB- using|use|VBG R.|R.|NNP
Normalization|normalization|NN factors|factor|NNS were|be|VBD calculated|calculate|VBN using|use|VBG a|a|DT non-linear|non-linear|JJ Loess|loess|JJ model|model|NN using|use|VBG csaw|csaw|NN -LRB-|-lrb-|-LRB- Bioconductor|bioconductor|NN -RRB-|-rrb-|-RRB-
Normalization|normalization|NN is|be|VBZ performed|perform|VBN by|by|IN TREBAX|trebax|NN ,|,|, using|use|VBG MA-plots|ma-plot|NNS .|.|. MA-plots|ma-plot|NNS can|can|MD reveal|reveal|VB the|the|DT spot|spot|NN artifacts|artifact|NNS globally|globally|RB and|and|CC show|show|VB the|the|DT intensity-dependent|intensity-dependent|JJ logarithmic|logarithmic|JJ ratio|ratio|NN of|of|IN raw|raw|JJ microarray|microarray|NN data|datum|NNS .|.|. In|in|IN MA-plots|ma-plot|NNS ,|,|, we|we|PRP calculate|calculate|VBP two|two|CD parameters|parameter|NNS ,|,|, average|average|NN of|of|IN logarithmic|logarithmic|JJ transferred|transfer|VBN intensity|intensity|NN As|as|IN =|=|JJ -LRB-|-lrb-|-LRB- log|log|NN -LRB-|-lrb-|-LRB- Ts|ts|NN -RRB-|-rrb-|-RRB- +|+|CC log|log|NN -LRB-|-lrb-|-LRB- Rs|rs|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- /|/|: 2|2|CD and|and|CC logarithmic|logarithmic|JJ ratio|ratio|NN of|of|IN intensity|intensity|NN Ms|ms|NN =|=|JJ log|log|NN -LRB-|-lrb-|-LRB- Ts/Rs|ts/rs|NNS -RRB-|-rrb-|-RRB- Here|here|RB ,|,|, Ts|t|NNS and|and|CC Rs|rs|NN are|be|VBP the|the|DT intensity|intensity|NN of|of|IN target|target|NN and|and|CC control|control|NN experiments|experiment|NNS for|for|IN sth|sth|NN spot|spot|NN ,|,|, respectively.By|respectively.by|NN plotting|plot|VBG values|value|NNS of|of|IN As|as|IN on|on|IN the|the|DT abscissa|abscissa|NN and|and|CC Ms|ms|NN on|on|IN the|the|DT ordinate|ordinate|NN of|of|IN a|a|DT coordinate|coordinate|JJ system|system|NN ,|,|, it|it|PRP is|be|VBZ possible|possible|JJ to|to|TO evaluate|evaluate|VB the|the|DT bias|bias|NN error|error|NN with|with|IN respects|respects|NNS to|to|TO the|the|DT average|average|JJ logarithmic|logarithmic|JJ intensities|intensity|NNS .|.|. Normalized|normalize|VBN log|log|NN ratio|ratio|NN M|m|NN ''|''|'' s|s|NNS is|be|VBZ estimated|estimate|VBN as|as|IN the|the|DT difference|difference|NN between|between|IN Ms|Ms|NNP and|and|CC baseline|baseline|NN M|m|NN 's|'s|POS .|.|. Here|here|RB ,|,|, using|use|VBG a|a|DT relation|relation|NN between|between|IN Ms|Ms|NNP and|and|CC As|as|IN ,|,|, -LRB-|-lrb-|-LRB- Ms|ms|NN =|=|JJ f|f|FW -LRB-|-lrb-|-LRB- As|as|IN -RRB-|-rrb-|-RRB- +|+|CC es|e|NNS ,|,|, es|e|NNS is|be|VBZ the|the|DT difference|difference|NN between|between|IN Ms|Ms|NNP and|and|CC f|f|FW -LRB-|-lrb-|-LRB- As|as|IN -RRB-|-rrb-|-RRB- for|for|IN gene|gene|NN s|s|NNS -RRB-|-rrb-|-RRB- by|by|IN MA|MA|NNP plot|plot|NN ;|;|: the|the|DT baseline|baseline|NN for|for|IN sth|sth|NN spot|spot|NN is|be|VBZ estimated|estimate|VBN by|by|IN M|m|NN '|'|'' =|=|JJ f|f|FW -LRB-|-lrb-|-LRB- A|a|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT genes|gene|NNS whose|whose|WP$ signal|signal|NN intensity|intensity|NN is|be|VBZ regarded|regard|VBN as|as|IN zero|zero|CD are|be|VBP eliminated|eliminate|VBN in|in|IN the|the|DT present|present|JJ analysis|analysis|NN .|.|. With|with|IN this|this|DT methodology|methodology|NN ,|,|, it|it|PRP is|be|VBZ assumed|assume|VBN that|that|IN there|there|EX is|be|VBZ no|no|DT large|large|JJ error|error|NN due|due|JJ to|to|TO expression|expression|NN intensity|intensity|NN in|in|IN the|the|DT majority|majority|NN of|of|IN the|the|DT spots|spot|NNS and|and|CC that|that|IN expression|expression|NN change|change|NN does|do|VBZ not|not|RB occur|occur|VB on|on|IN the|the|DT majority|majority|NN of|of|IN the|the|DT spots|spot|NNS .|.|.
normalization|normalization|NN of|of|IN graphs|graph|NNS to|to|TO the|the|DT total|total|JJ number|number|NN of|of|IN mapped|map|VBN reads|read|VBZ per|per|IN library|library|NN using|use|VBG READemption|reademption|NN 0.3.7|0.3.7|CD
normalization|normalization|NN subtracting|subtract|VBG array-median|array-median|JJ log2|log2|NN ratio|ratio|NN .|.|.
normalized|normalize|VBD as|as|IN described|describe|VBN before|before|IN -LRB-|-lrb-|-LRB- Tong|Tong|NNP et|et|FW al.|al.|FW 2004|2004|CD BBRC|BBRC|NNP -RRB-|-rrb-|-RRB- .|.|. Briefly|briefly|RB ,|,|, spots|spot|NNS were|be|VBD excluded|exclude|VBN from|from|IN
Normalized|Normalized|NNP decay|decay|NN values|value|NNS with|with|IN average|average|NN of|of|IN stable|stable|JJ genes|gene|NNS ssrA|ssra|NN ,|,|, ssrS|ssrs|NN ,|,|, and|and|CC rnpB|rnpb|NN
Normalized|normalize|VBN FPKM|fpkm|NN values|value|NNS were|be|VBD generated|generate|VBN from|from|IN the|the|DT raw|raw|JJ gene|gene|NN counts|count|NNS by|by|IN custom|custom|NN scripts|script|NNS that|that|WDT calculated|calculate|VBD and|and|CC applied|apply|VBD a|a|DT trimmed|trimmed|RBR mean|mean|VB of|of|IN M-values|m-value|NNS -LRB-|-lrb-|-LRB- TMM|tmm|NN -RRB-|-rrb-|-RRB- factor|factor|NN using|use|VBG edgeR|edger|NN version|version|NN 3.8.6|3.8.6|CD .|.|.
Normalized|normalize|VBN log|log|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- ratio|ratio|NN of|of|IN Cy5/Cy3|cy5/cy3|NN ,|,|, normalized|normalize|VBD using|use|VBG lowess|lowess|JJ
normalized|normalize|VBD using|use|VBG lcDNA|lcdna|NN
normalizing|normalizing|NN :|:|: convert|convert|VB counts|count|NNS in|in|IN RPKM|rpkm|NN using|use|VBG Excel|Excel|NNP
norm.temp|norm.temp|NN <|<|JJR -|-|: cbind|cbind|NN -LRB-|-lrb-|-LRB- NormalData|NormalData|NNP $|$|$ metarow|metarow|JJ ,|,|, NormalData|NormalData|NNP $|$|$ metacol|metacol|JJ ,|,|, NormalData|NormalData|NNP $|$|$ row|row|NN ,|,|, NormalData|NormalData|NNP $|$|$ col|col|CD ,|,|, NormalData|NormalData|NNP $|$|$ geneID|geneid|JJ ,|,|, NormalData|NormalData|NNP $|$|$ data|datum|NNS -RRB-|-rrb-|-RRB-
No|no|DT specific|specific|JJ treatment|treatment|NN was|be|VBD done|do|VBN .|.|. Samples|sample|NNS were|be|VBD collected|collect|VBN in|in|IN the|the|DT mid-log|mid-log|JJ growth|growth|NN phase|phase|NN for|for|IN expression|expression|NN analysis|analysis|NN
no|no|DT treatment|treatment|NN
No|No|NNP treatment|treatment|NN
No|No|NNP treatment|treatment|NN -LRB-|-lrb-|-LRB- control|control|NN sample|sample|NN -RRB-|-rrb-|-RRB- .|.|.
No|no|DT treatment|treatment|NN ,|,|, just|just|RB comparison|comparison|NN of|of|IN RNAs|rna|NNS from|from|IN wild|wild|JJ type|type|NN and|and|CC mutant|mutant|NN .|.|.
No|no|DT treatment|treatment|NN were|be|VBD studied|study|VBN in|in|IN this|this|DT experience|experience|NN
No|no|DT triclosan|triclosan|NN treatment|treatment|NN
nrdA|nrda|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
nrdA|nrda|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
nrdA|nrda|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
nrdA|nrda|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
nrdB|nrdb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
nrdB|nrdb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
nrdB|nrdb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1.5|1.5|CD '|'|'' post|post|JJ rif|rif|NN
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3|3|CD '|'|'' post|post|JJ rif|rif|NN
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6|6|CD '|'|'' post|post|JJ rif|rif|NN
NsrR|nsrr|NN _|_|NN ChIPSeq|chipseq|NN _|_|CD rep1|rep1|NN
NsrR|nsrr|NN _|_|NN ChIPSeq|chipseq|NN _|_|CD rep2|rep2|NN
NsrR|nsrr|NN _|_|NN ChIPSeq|chipseq|NN _|_|CD rep3|rep3|NN
NsrR|nsrr|NN _|_|CD Flagtag|Flagtag|NNP _|_|CD rep1|rep1|NN
NsrR|nsrr|NN _|_|CD Flagtag|Flagtag|NNP _|_|CD rep2|rep2|NN
NsrR|nsrr|NN _|_|CD Flagtag|Flagtag|NNP _|_|CD rep3|rep3|NN
NsrR|nsrr|NN _|_|NN input|input|NN
NTG-treated|ntg-treated|JJ E.|e.|FW coli|coli|FW imp|imp|FW fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- -LSB-|-lsb-|-LRB- E.|e.|FW coli|coli|FW IFN4|ifn4|NN -RSB-|-rsb-|-RRB-
NTG-treated|ntg-treated|JJ E.|e.|FW coli|coli|FW imp|imp|FW fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- -LSB-|-lsb-|-LRB- E.|e.|FW coli|coli|FW IFN5|ifn5|NN -RSB-|-rsb-|-RRB-
ntg|ntg|NN treatment|treatment|NN :|:|: yes|yes|UH
NtrC|ntrc|NN _|_|NN ChIPSeq|chipseq|NN
nucleic|nucleic|JJ _|_|NN acid|acid|NN _|_|NN extraction|extraction|NN ||||SYM ChIP|chip|NN was|be|VBD performed|perform|VBN as|as|IN previously|previously|RB described|describe|VBN -LRB-|-lrb-|-LRB- Grainger|Grainger|NNP et|et|FW al|al|FW ,|,|, 2004|2004|CD -RRB-|-rrb-|-RRB- with|with|IN some|some|DT modifications|modification|NNS to|to|TO the|the|DT protdegree|protdegree|NN Col.|Col.|NNP Cells|cell|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB at|at|IN 37degree|37degree|CD C|c|NN to|to|TO the|the|DT desired|desire|VBN OD600|od600|NN and|and|CC formaldehyde|formaldehyde|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD %|%|NN .|.|. After|after|IN 20|20|CD min|min|NN of|of|IN incubation|incubation|NN ,|,|, glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD M|m|NN to|to|TO quench|quench|VB the|the|DT reaction|reaction|NN and|and|CC incubated|incubate|VBN for|for|IN a|a|DT further|further|JJ 5|5|CD min|min|NN .|.|. Cross-linked|cross-linked|JJ cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC washed|wash|VBN twice|twice|RB with|with|IN ice-cold|ice-cold|JJ TBS|tbs|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 1|1|CD ml|ml|NN of|of|IN lysis|lysis|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|tris|NN -LSB-|-lsb-|-LRB- pH|ph|NN 8.0|8.0|CD -RSB-|-rsb-|-RRB- ,|,|, 20|20|CD %|%|NN sucrose|sucrose|NN ,|,|, 50|50|CD mM|mm|NN NaCl|nacl|NN ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 20|20|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN and|and|CC 0.1|0.1|CD mg/ml|mg/ml|NN RNase|rnase|NN A|a|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN at|at|IN 37degree|37degree|CD C|c|NN for|for|IN 30|30|CD min|min|NN .|.|. Following|follow|VBG lysis|lysis|NN ,|,|, 3|3|CD ml|ml|NN immunoprecipitation|immunoprecipitation|NN -LRB-|-lrb-|-LRB- IP|IP|NNP -RRB-|-rrb-|-RRB- buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN HEPES-KOH|hepes-koh|NN -LSB-|-lsb-|-LRB- pH|ph|NN 7.5|7.5|CD -RSB-|-rsb-|-RRB- ,|,|, 150|150|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 0.1|0.1|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN ,|,|, 0.1|0.1|CD %|%|NN sodium|sodium|NN dodecyl|dodecyl|NN sulfate|sulfate|NN -LSB-|-lsb-|-LRB- SDS|sds|NN -RSB-|-rsb-|-RRB- and|and|CC PMSF|pmsf|NN -LSB-|-lsb-|-LRB- final|final|JJ concentration|concentration|NN 1|1|CD mM|mm|NN -RSB-|-rsb-|-RRB- -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC the|the|DT lysate|lysate|NN passed|pass|VBN through|through|IN a|a|DT French|french|JJ pressure|pressure|NN cell|cell|NN twice|twice|RB .|.|. 2|2|CD ml|ml|NN aliquots|aliquot|NNS were|be|VBD removed|remove|VBN and|and|CC the|the|DT DNA|dna|NN sheared|shear|VBD to|to|TO an|a|DT average|average|JJ size|size|NN of|of|IN ~|~|NN 200|200|CD bp|bp|NN using|use|VBG a|a|DT Bioruptor|bioruptor|NN -LRB-|-lrb-|-LRB- Diagenode|diagenode|NN -RRB-|-rrb-|-RRB- with|with|IN 30|30|CD cycles|cycle|NNS of|of|IN 30|30|CD sec|sec|NN on/off|on/off|JJ at|at|IN high|high|JJ setting|setting|NN .|.|. Insoluble|insoluble|JJ cellular|cellular|JJ matter|matter|NN was|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN for|for|IN 10|10|CD min|min|NN at|at|IN 4degree|4degree|CD C|c|NN ,|,|, and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD split|split|VBN into|into|IN two|two|CD 800|800|CD microl|microl|NN aliquots|aliquot|NNS .|.|. The|the|DT remaining|remain|VBG 400|400|CD microl|microl|NN was|be|VBD kept|keep|VBN to|to|TO check|check|VB the|the|DT size|size|NN of|of|IN the|the|DT DNA|dna|NN fragments|fragment|NNS .|.|. <br>|<br>|JJ <br>|<br>|NN Each|each|DT 800|800|CD microl|microl|NN aliquot|aliquot|NN was|be|VBD incubated|incubate|VBN with|with|IN 20|20|CD microl|microl|NN Protein|protein|NN A/G|a/g|NN UltraLink|UltraLink|NNP Resin|Resin|NNP -LRB-|-lrb-|-LRB- Pierce|Pierce|NNP -RRB-|-rrb-|-RRB- on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN for|for|IN 45|45|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN to|to|TO get|get|VB rid|rid|JJ of|of|IN complexes|complex|NNS binding|bind|VBG to|to|TO the|the|DT resin|resin|NN non-specifically|non-specifically|RB .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD then|then|RB removed|remove|VBN and|and|CC incubated|incubate|VBN with|with|IN either|either|CC no|no|DT antibody|antibody|NN -LRB-|-lrb-|-LRB- mdegree|mdegree|NN Ck-IP|ck-ip|NN -RRB-|-rrb-|-RRB- ,|,|, FLAG|flag|NN mouse|mouse|NN mondegree|mondegree|NN Clonal|clonal|JJ antibody|antibody|NN -LRB-|-lrb-|-LRB- Sigma-Aldrich|sigma-aldrich|NN -RRB-|-rrb-|-RRB- or|or|CC RNAP|rnap|NN Beta|beta|NN subunit|subunit|NN mouse|mouse|NN mondegree|mondegree|NN Clonal|clonal|JJ -LRB-|-lrb-|-LRB- Nedegree|nedegree|JJ Clone|clone|NN -RRB-|-rrb-|-RRB- and|and|CC 30|30|CD microl|microl|NN Protein|protein|NN A/G|a/g|NN UltraLink|UltraLink|NNP Resin|Resin|NNP ,|,|, pre-incubated|pre-incubated|JJ with|with|IN 1mg/ml|1mg/ml|JJ bovine|bovine|JJ serum|serum|NN albumin|albumin|NN -LRB-|-lrb-|-LRB- BSA|bsa|NN -RRB-|-rrb-|-RRB- in|in|IN TBS|tbs|NN ,|,|, on|on|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN at|at|IN 4degree|4degree|CD C|c|NN overnight|overnight|JJ -LRB-|-lrb-|-LRB- FLAG|flag|NN antibody|antibody|NN -RRB-|-rrb-|-RRB- or|or|CC at|at|IN room|room|NN temperature|temperature|NN for|for|IN 90|90|CD min|min|NN -LRB-|-lrb-|-LRB- RNAP|rnap|NN Beta|beta|NN subunit|subunit|NN antibody|antibody|NN -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS were|be|VBD washed|wash|VBN once|once|RB with|with|IN IP|IP|NNP buffer|buffer|NN ,|,|, twice|twice|RB with|with|IN IP|IP|NNP buffer|buffer|NN +|+|CC 500|500|CD mM|mm|NN NaCl|nacl|NN ,|,|, once|once|RB with|with|IN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|tris|NN -LSB-|-lsb-|-LRB- pH|ph|NN 8.0|8.0|CD -RSB-|-rsb-|-RRB- ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.5|0.5|CD %|%|NN Nonidet|Nonidet|NNP P-40|P-40|NNP and|and|CC 0.5|0.5|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN -RRB-|-rrb-|-RRB- and|and|CC once|once|RB with|with|IN TE|te|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.5|7.5|CD -RRB-|-rrb-|-RRB- .|.|. Immunoprecipitated|immunoprecipitate|VBN complexes|complex|NNS were|be|VBD eluted|elute|VBN in|in|IN 100|100|CD microl|microl|NN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|tris|NN -LSB-|-lsb-|-LRB- pH|ph|NN 7.5|7.5|CD -RSB-|-rsb-|-RRB- ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN and|and|CC 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- at|at|IN 65degree|65degree|CD C|c|NN for|for|IN 20|20|CD min|min|NN .|.|.
Numer|Numer|NNP of|of|IN reads|read|VBZ per|per|IN gene|gene|NN were|be|VBD counted|count|VBN using|use|VBG Bioconductor|Bioconductor|NNP Rsubread|Rsubread|NNP package|package|NN v1|v1|NN .12.6|.12.6|CD
nupC|nupc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
nupC|nupc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
nupC|nupc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r3|r3|NN
nupC|nupc|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
NusA|nusa|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 56226|56226|CD -RRB-|-rrb-|-RRB-
NusA|nusa|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 61392|61392|CD -RRB-|-rrb-|-RRB-
NusA|nusa|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 64131|64131|CD -RRB-|-rrb-|-RRB-
NusA|nusa|NN ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS
NusG|nusg|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 70568|70568|CD -RRB-|-rrb-|-RRB-
NusG|nusg|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN HA3|ha3|NN :|:|: :|:|: nusG|nusg|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 62261|62261|CD -RRB-|-rrb-|-RRB-
NusG|nusg|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN HA3|ha3|NN :|:|: :|:|: nusG|nusg|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 62263|62263|CD -RRB-|-rrb-|-RRB-
NusG|nusg|NN ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS
NusG|nusg|NN ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN HA3|ha3|NN :|:|: :|:|: nusG|nusg|NN cells|cell|NNS
∆|∆|CD nusG|nusg|NN UvsW|uvsw|NN _|_|CD replicate1|replicate1|NN
∆|∆|CD nusG|nusg|NN UvsW|uvsw|NN _|_|CD replicate2|replicate2|NN
∆|∆|CD nusG|nusg|NN UvsW|uvsw|NN _|_|CD replicate3|replicate3|NN
NZ502|nz502|NN _|_|CD 12|12|CD %|%|NN Glu|glu|NN
NZ502|nz502|NN _|_|CD 5|5|CD %|%|NN Glu|glu|NN
O103|o103|NN no.|no.|NN 1|1|CD -LRB-|-lrb-|-LRB- strain|strain|NN 10828|10828|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O103|o103|NN no.|no.|NN 1|1|CD -LRB-|-lrb-|-LRB- strain|strain|NN 10828|10828|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O103|o103|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11117|11117|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O103|o103|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11117|11117|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O103|o103|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11711|11711|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O103|o103|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11711|11711|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O103|o103|NN no.|no.|NN 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11845|11845|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O103|o103|NN no.|no.|NN 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11845|11845|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O103|o103|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 12009|12009|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O103|o103|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 12009|12009|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O103|o103|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN PMK5|pmk5|NN -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O103|o103|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN PMK5|pmk5|NN -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O111|o111|NN no.|no.|NN 1|1|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11109|11109|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O111|o111|NN no.|no.|NN 1|1|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11109|11109|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O111|o111|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11128|11128|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O111|o111|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11128|11128|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O111|o111|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11619|11619|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O111|o111|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11619|11619|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O111|o111|NN no.|no.|RB 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11788|11788|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O111|o111|NN no.|no.|NN 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11788|11788|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O111|o111|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 13369|13369|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O111|o111|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 13369|13369|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O111|o111|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN ED71|ed71|NN -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O111|o111|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN ED71|ed71|NN -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN _|_|CD CL|cl|NN MC|MC|NNP fraction|fraction|NN vs|vs|CC control|control|NN
O157|o157|NN :|:|: H7|h7|NN cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN in|in|IN Luria|Luria|NNP broth|broth|NN with|with|IN or|or|CC without|without|IN 0.8|0.8|CD %|%|NN bile|bile|NN salts|salt|NNS .|.|.
O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN in|in|IN LB|LB|NNP
O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN sdhA|sdha|NN in|in|IN LB|LB|NNP
O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN sdhA|sdha|NN in|in|IN LB|lb|NN with|with|IN FA|fa|NN
O157|o157|NN :|:|: H7|h7|NN strain|strain|NN EDL933|edl933|NN ,|,|, 100|100|CD mcg/ml|mcg/ml|NN bicyclomycin|bicyclomycin|NN 20|20|CD min|min|NN ,|,|, exponential|exponential|JJ phase|phase|NN
O157|o157|NN :|:|: H7|h7|NN strain|strain|NN EDL933|edl933|NN ,|,|, control|control|NN sample|sample|NN ,|,|, exponential|exponential|JJ phase|phase|NN
O157|o157|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 980938|980938|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 980938|980938|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 980706|980706|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 980706|980706|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN no.|no.|NN 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 990281|990281|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 990281|990281|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 980551|980551|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 980551|980551|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN 990570|990570|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN 990570|990570|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN no.|no.|NN 7|7|CD -LRB-|-lrb-|-LRB- strain|strain|NN 981456|981456|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 7|7|CD -LRB-|-lrb-|-LRB- strain|strain|NN 981456|981456|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN no.|no.|NN 8|8|CD -LRB-|-lrb-|-LRB- strain|strain|NN 982243|982243|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 8|8|CD -LRB-|-lrb-|-LRB- strain|strain|NN 982243|982243|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN no.|no.|NN 9|9|CD -LRB-|-lrb-|-LRB- strain|strain|NN 981795|981795|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O157|o157|NN no.|no.|NN 9|9|CD -LRB-|-lrb-|-LRB- strain|strain|NN 981795|981795|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O157|o157|NN strain|strain|NN Sakai|Sakai|NNP
O26|o26|NN no.|no.|NN 1|1|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11044|11044|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 1|1|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11044|11044|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O26|o26|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11368|11368|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 2|2|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11368|11368|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O26|o26|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11656|11656|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 3|3|CD -LRB-|-lrb-|-LRB- strain|strain|NN 11656|11656|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O26|o26|NN no.|no.|NN 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 12719|12719|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 4|4|CD -LRB-|-lrb-|-LRB- strain|strain|NN 12719|12719|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O26|o26|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 12929|12929|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 5|5|CD -LRB-|-lrb-|-LRB- strain|strain|NN 12929|12929|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O26|o26|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN 13065|13065|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 6|6|CD -LRB-|-lrb-|-LRB- strain|strain|NN 13065|13065|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O26|o26|NN no.|no.|NN 7|7|CD -LRB-|-lrb-|-LRB- strain|strain|NN 13247|13247|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 7|7|CD -LRB-|-lrb-|-LRB- strain|strain|NN 13247|13247|CD -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O26|o26|NN no.|no.|NN 8|8|CD -LRB-|-lrb-|-LRB- strain|strain|NN ED411|ed411|NN -RRB-|-rrb-|-RRB- replicate|replicate|VBP 1|1|CD
O26|o26|NN no.|no.|NN 8|8|CD -LRB-|-lrb-|-LRB- strain|strain|NN ED411|ed411|NN -RRB-|-rrb-|-RRB- replicate|replicate|VBP 2|2|CD
O500|o500|CD _|_|SYM 1|1|CD
O500|o500|CD _|_|NN 2|2|CD
O55|o55|NN :|:|: H6|h6|NN ICC219|icc219|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H6|h6|NN ICC219|icc219|NN replicate|replicate|VBP 2|2|CD
O55|o55|NN :|:|: H6|h6|NN ICC221|icc221|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H6|h6|NN ICC221|icc221|NN replicate|replicate|VBP 2|2|CD
O55|o55|NN :|:|: H6|h6|NN ICC222|icc222|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H6|h6|NN ICC222|icc222|NN replicate|replicate|VBP 2|2|CD
O55|o55|NN :|:|: H7|h7|NN st58|st58|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H7|h7|NN st58|st58|NN replicate|replicate|VBP 2|2|CD
O55|o55|NN :|:|: H7|h7|NN st957|st957|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H7|h7|NN st957|st957|NN replicate|replicate|VBP 2|2|CD
O55|o55|NN :|:|: H7|h7|NN TB182A|tb182a|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H7|h7|NN TB182A|tb182a|NN replicate|replicate|VBP 2|2|CD
O55|o55|NN :|:|: H7|h7|NN WC211|wc211|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H7|h7|NN WC211|wc211|NN replicate|replicate|VBP 2|2|CD
O55|o55|NN :|:|: H7|h7|NN WC416|wc416|NN replicate|replicate|VBP 1|1|CD
O55|o55|NN :|:|: H7|h7|NN WC416|wc416|NN replicate|replicate|VBP 2|2|CD
OD|od|NN :|:|: 0.1|0.1|CD
OD|od|NN :|:|: 0.1|0.1|CD
OD|od|NN :|:|: 0.3|0.3|CD
OD|od|NN :|:|: 0.3|0.3|CD
OD|od|NN :|:|: 0.4|0.4|CD
OD|od|NN :|:|: 0.4|0.4|CD
OD|od|NN :|:|: 0.5|0.5|CD
OD|od|NN :|:|: 0.6|0.6|CD
OD|od|NN :|:|: 0.6|0.6|CD
od|od|NN :|:|: 0.7|0.7|CD
od|od|NN :|:|: 0.8|0.8|CD
OD|od|NN :|:|: 1.0|1.0|CD
OD|od|NN :|:|: 1.0|1.0|CD
OD|od|NN :|:|: 1.3|1.3|CD
OD|od|NN :|:|: 1.3|1.3|CD
OD|od|NN :|:|: 1.7|1.7|CD
OD|od|NN :|:|: 1.7|1.7|CD
OD|od|NN :|:|: 2.7|2.7|CD
OD|od|NN :|:|: 2.7|2.7|CD
OD|od|NN :|:|: 4.5|4.5|CD
OD|od|NN 4.5|4.5|CD
OD|od|NN :|:|: 4.5|4.5|CD
OD|od|NN :|:|: 4.7|4.7|CD
OD|od|NN :|:|: 4.7|4.7|CD
OD|od|NN :|:|: 4.8|4.8|CD
OD|od|NN :|:|: 4.8|4.8|CD
od600|od600|CD :|:|: 0.4|0.4|CD
OD600|od600|NN 15|15|CD units|unit|NNS of|of|IN cells|cell|NNS were|be|VBD harvested|harvest|VBN for|for|IN each|each|DT ChIP|chip|NN procedure|procedure|NN .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 4,000|4,000|CD rpm|rpm|NN for|for|IN 8|8|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN and|and|CC resuspended|resuspend|VBN in|in|IN 50|50|CD ml|ml|NN of|of|IN pre-warmed|pre-warmed|JJ PBS|PBS|NNP -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN -RRB-|-rrb-|-RRB- in|in|IN a|a|DT 250|250|CD ml|ml|NN flask|flask|NN .|.|. DNA-protein|dna-protein|JJ and|and|CC protein-protein|protein-protein|JJ interactions|interaction|NNS were|be|VBD cross-linked|cross-link|VBN by|by|IN adding|add|VBG 1,351|1,351|CD µl|µl|NN of|of|IN formaldehyde|formaldehyde|NN drop-wise|drop-wise|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD %|%|NN .|.|. Samples|sample|NNS were|be|VBD cross-linked|cross-link|VBN at|at|IN room|room|NN temperature|temperature|NN with|with|IN stirring|stir|VBG for|for|IN 30|30|CD min|min|NN .|.|. Glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.125|0.125|CD M|m|NN with|with|IN stirring|stir|VBG for|for|IN 5|5|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. Cells|cell|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 4,000|4,000|CD rpm|rpm|NN for|for|IN 8|8|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN and|and|CC the|the|DT supernatant|supernatant|JJ removed|remove|VBN .|.|. The|the|DT pellet|pellet|NN was|be|VBD re-suspended|re-suspended|JJ in|in|IN 0.6|0.6|CD ml|ml|NN of|of|IN lysis|lysis|NN buffer|buffer|NN containing|contain|VBG 50|50|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN and|and|CC incubated|incubate|VBN on|on|IN ice|ice|NN for|for|IN 10|10|CD min|min|NN .|.|. 1.4|1.4|CD ml|ml|NN of|of|IN IP|IP|NNP dilution|dilution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 20|20|CD mM|mm|NN Tris-HCl|tris-hcl|NN pH|ph|NN 8.1|8.1|CD ,|,|, 150|150|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 0.01|0.01|CD %|%|NN SDS|sds|NN ,|,|, Roche|Roche|NNP protease|protease|NN inhibitor|inhibitor|NN cocktail|cocktail|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC the|the|DT chromatin|chromatin|NN was|be|VBD sonicated|sonicate|VBN on|on|IN ice|ice|NN in|in|IN a|a|DT 5|5|CD ml|ml|NN tube|tube|NN to|to|TO reduce|reduce|VB the|the|DT DNA|dna|NN length|length|NN to|to|TO an|a|DT average|average|JJ size|size|NN of|of|IN approximately|approximately|RB 500|500|CD bp|bp|NN using|use|VBG the|the|DT Sanyo/MES|Sanyo/MES|NNP Soniprep|Soniprep|NNP sonicator|sonicator|NN -LRB-|-lrb-|-LRB- 8|8|CD bursts|burst|NNS at|at|IN an|a|DT amplitude|amplitude|NN 10|10|CD microns|micron|NNS for|for|IN 30|30|CD seconds|seconds|NNS ,|,|, with|with|IN 1|1|CD minute|minute|NN cooling|cooling|NN between|between|IN bursts|burst|NNS -RRB-|-rrb-|-RRB- .|.|. This|this|DT was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT 2|2|CD ml|ml|NN microfuge|microfuge|NN tube|tube|NN and|and|CC spun|spin|VBD at|at|IN 13,200|13,200|CD rpm|rpm|NN for|for|IN 10|10|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Supernatant|supernatant|NN was|be|VBD removed|remove|VBN and|and|CC 1|1|CD ml|ml|NN dilution|dilution|NN buffer|buffer|NN added.The|added.the|NN chromatin|chromatin|NN material|material|NN was|be|VBD precleared|preclear|VBN by|by|IN adding|add|VBG 50|50|CD µl|µl|NN of|of|IN normal|normal|JJ rabbit|rabbit|NN immunoglobulin|immunoglobulin|NN G|g|NN -LRB-|-lrb-|-LRB- IgG|igg|NN ,|,|, 1|1|CD mg/ml|mg/ml|NN ,|,|, Millipore|Millipore|NNP -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS were|be|VBD incubated|incubate|VBN for|for|IN 1|1|CD h|h|NN at|at|IN 4|4|CD °C|°c|NN on|on|IN a|a|DT rotating|rotate|VBG wheel|wheel|NN .|.|. 100|100|CD µl|µl|NN of|of|IN homogenous|homogenous|JJ protein|protein|NN G-agarose|g-agarose|NN -LRB-|-lrb-|-LRB- Roche|Roche|NNP -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT precleared|precleared|JJ chromatin|chromatin|NN and|and|CC the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN for|for|IN 3-5|3-5|CD h|h|NN at|at|IN 4|4|CD °C|°c|NN on|on|IN a|a|DT rotating|rotate|VBG wheel|wheel|NN .|.|. Samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 4,000|4,000|CD rpm|rpm|NN for|for|IN 2|2|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN and|and|CC this|this|DT supernatant|supernatant|NN was|be|VBD used|use|VBN to|to|TO set|set|VB up|up|RP immunoprecipitation|immunoprecipitation|NN reactions|reaction|NNS .|.|. 200|200|CD µl|µl|NN chromatin|chromatin|NN was|be|VBD removed|remove|VBN and|and|CC used|use|VBN as|as|IN an|a|DT input|input|NN sample|sample|NN .|.|. Experimental|experimental|JJ immunoprecipitation|immunoprecipitation|NN were|be|VBD set|set|VBN up|up|RP using|use|VBG 1,350|1,350|CD µl|µl|NN chromatin|chromatin|NN and|and|CC 3.3|3.3|CD µg/µl|µg/µl|NN of|of|IN anti-FLAG|anti-flag|JJ antibody|antibody|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- .|.|. Mock|mock|JJ immunoprecipitation|immunoprecipitation|NN 1,350|1,350|CD µl|µl|NN chromatin|chromatin|NN and|and|CC 10|10|CD µg|µg|NN of|of|IN normal|normal|JJ mouse|mouse|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Millipore|millipore|NN -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS were|be|VBD incubated|incubate|VBN overnight|overnight|JJ on|on|IN a|a|DT rotating|rotate|VBG wheel|wheel|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 13,000|13,000|CD rpm|rpm|NN for|for|IN 5|5|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD transferred|transfer|VBN to|to|TO 2|2|CD ml|ml|NN microfuge|microfuge|NN tubes|tube|NNS .|.|. 50|50|CD µl|µl|NN of|of|IN protein|protein|NN G-agarose|g-agarose|NN was|be|VBD added|add|VBN to|to|TO each|each|DT sample|sample|NN and|and|CC incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN for|for|IN 3|3|CD h|h|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 7,500|7,500|CD rpm|rpm|NN for|for|IN 2|2|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN to|to|TO pellet|pellet|VB the|the|DT protein|protein|NN G-agarose|g-agarose|NN beads|bead|NNS .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD removed|remove|VBN and|and|CC the|the|DT protein|protein|NN G-agarose|g-agarose|NN beads|bead|NNS were|be|VBD carefully|carefully|RB washed|wash|VBN .|.|. 91|91|CD For|for|IN each|each|DT wash|wash|NN ,|,|, the|the|DT wash|wash|NN buffer|buffer|NN was|be|VBD added|add|VBN ;|;|: the|the|DT samples|sample|NNS were|be|VBD vortexed|vortex|VBN briefly|briefly|NN and|and|CC were|be|VBD centrifuged|centrifuge|VBN at|at|IN 7,500|7,500|CD rpm|rpm|NN for|for|IN 2|2|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD left|leave|VBN to|to|TO stand|stand|VB on|on|IN ice|ice|NN for|for|IN 1|1|CD min|min|NN before|before|IN removing|remove|VBG the|the|DT supernatant|supernatant|NN .|.|. The|the|DT washes|wash|NNS were|be|VBD carried|carry|VBN out|out|RP in|in|IN the|the|DT following|following|JJ sequence|sequence|NN :|:|: The|the|DT beads|bead|NNS were|be|VBD washed|wash|VBN twice|twice|RB with|with|IN 750|750|CD µl|µl|NN of|of|IN cold|cold|JJ IP|IP|NNP wash|wash|NN buffer|buffer|NN 1|1|CD containing|contain|VBG 20|20|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.1|8.1|CD -RRB-|-rrb-|-RRB- ,|,|, 50|50|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2mM|2mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 0.1|0.1|CD %|%|NN SDS|sds|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD transferred|transfer|VBN to|to|TO a|a|DT 1.5|1.5|CD ml|ml|NN microfuge|microfuge|NN tube|tube|NN after|after|IN the|the|DT first|first|JJ wash|wash|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD washed|wash|VBN once|once|RB with|with|IN 750|750|CD µl|µl|NN of|of|IN cold|cold|JJ IP|IP|NNP wash|wash|NN buffer|buffer|NN 2|2|CD containing|contain|VBG 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.1|8.1|CD -RRB-|-rrb-|-RRB- ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN NP-40|np-40|NN ,|,|, 1|1|CD %|%|NN deoxycholic|deoxycholic|JJ acid|acid|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD washed|wash|VBN twice|twice|RB with|with|IN 750|750|CD µl|µl|NN of|of|IN ice-cold|ice-cold|JJ TE|TE|NNP buffer|buffer|NN containing|contain|VBG 10|10|CD mM|mm|NN Tris|Tris|NNP base|base|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8|8|CD -RRB-|-rrb-|-RRB- and|and|CC 1|1|CD mM|mm|NN EDTA|edta|NN .|.|. DNA-protein-antibody|dna-protein-antibody|JJ complexes|complex|NNS were|be|VBD eluted|elute|VBN from|from|IN the|the|DT protein|protein|NN G-agarose|g-agarose|NN beads|bead|NNS by|by|IN adding|add|VBG 225|225|CD µl|µl|NN of|of|IN IP|IP|NNP elution|elution|NN buffer|buffer|NN containing|contain|VBG 100|100|CD mM|mm|NN NaHCO3|nahco3|NN and|and|CC 1|1|CD %|%|NN SDS|sds|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN IP|IP|NNP elution|elution|NN buffer|buffer|NN ,|,|, briefly|briefly|NN vortexed|vortex|VBD and|and|CC centrifuged|centrifuge|VBD at|at|IN 7,500|7,500|CD rpm|rpm|NN for|for|IN 2|2|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD collected|collect|VBN in|in|IN fresh|fresh|JJ 1.5|1.5|CD ml|ml|NN microfuge|microfuge|NN tubes|tube|NNS .|.|. The|the|DT bead|bead|NN pellets|pellet|NNS in|in|IN the|the|DT original|original|JJ tubes|tube|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 225|225|CD µl|µl|NN of|of|IN IP|IP|NNP elution|elution|NN buffer|buffer|NN again|again|RB and|and|CC briefly|briefly|RB vortexed|vortex|VBN and|and|CC centrifuged|centrifuge|VBN at|at|IN 7,500|7,500|CD rpm|rpm|NN for|for|IN 2|2|CD min|min|NN .|.|. IP|IP|NNP and|and|CC input|input|NN samples|sample|NNS were|be|VBD thawed|thaw|VBN on|on|IN ice|ice|NN .|.|. 0.1|0.1|CD µl|µl|NN of|of|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 10|10|CD mg/ml|mg/ml|NN ,|,|, ICN|ICN|NNP Biochemicals|Biochemicals|NNPS -RRB-|-rrb-|-RRB- and|and|CC 16|16|CD µl|µl|NN of|of|IN 5|5|CD M|m|NN NaCl|nacl|NN -LRB-|-lrb-|-LRB- to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.3|0.3|CD M|m|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT input|input|NN sample|sample|NN .|.|. Similarly|similarly|RB ,|,|, 0.2|0.2|CD µl|µl|NN of|of|IN RNase|rnase|NN A|a|NN and|and|CC 27|27|CD µl|µl|NN of|of|IN 5|5|CD M|m|NN NaCl|nacl|NN -LRB-|-lrb-|-LRB- to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.3|0.3|CD M|m|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO each|each|DT IP|IP|NNP sample|sample|NN .|.|. All|all|DT samples|sample|NNS including|include|VBG the|the|DT input|input|NN DNA|dna|NN were|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 6|6|CD h|h|NN to|to|TO reverse|reverse|VB cross-links|cross-link|NNS .|.|. 9|9|CD µl|µl|NN of|of|IN Proteinase|Proteinase|NNP K|K|NNP -LRB-|-lrb-|-LRB- 10|10|CD mg/ml|mg/ml|NN ,|,|, GibcoBRL|gibcobrl|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO each|each|DT sample|sample|NN and|and|CC incubated|incubate|VBN overnight|overnight|JJ at|at|IN 45|45|CD °C|°c|NN .|.|. 2|2|CD µl|µl|NN of|of|IN yeast|yeast|NN tRNA|trna|NN -LRB-|-lrb-|-LRB- 5mg/ml|5mg/ml|NN ,|,|, Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO each|each|DT sample|sample|NN followed|follow|VBN by|by|IN 250|250|CD µl|µl|NN of|of|IN phenol|phenol|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8|8|CD ,|,|, Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC 250|250|CD µl|µl|NN of|of|IN chloroform|chloroform|NN .|.|. Samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 13,000|13,000|CD rpm|rpm|NN for|for|IN 5|5|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. The|the|DT aqueous|aqueous|JJ layer|layer|NN was|be|VBD collected|collect|VBN in|in|IN fresh|fresh|JJ 1.5|1.5|CD ml|ml|NN centrifuge|centrifuge|NN tubes|tube|NNS and|and|CC 500|500|CD µl|µl|NN of|of|IN chloroform|chloroform|NN was|be|VBD added|add|VBN .|.|. The|the|DT samples|sample|NNS were|be|VBD vortexed|vortex|VBN and|and|CC centrifuged|centrifuge|VBN at|at|IN 13,000|13,000|CD rpm|rpm|NN for|for|IN 5|5|CD min|min|NN and|and|CC room|room|NN temperature|temperature|NN .|.|. The|the|DT aqueous|aqueous|JJ layer|layer|NN was|be|VBD transferred|transfer|VBN to|to|TO a|a|DT 2|2|CD ml|ml|NN microfuge|microfuge|NN tube|tube|NN .|.|. 5|5|CD µg|µg|NN of|of|IN glycogen|glycogen|NN -LRB-|-lrb-|-LRB- 5|5|CD mg/ml|mg/ml|NN ,|,|, Roche|Roche|NNP -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD µl|µl|NN of|of|IN tRNA|trna|NN -LRB-|-lrb-|-LRB- 5|5|CD mg/ml|mg/ml|NN ,|,|, Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- and|and|CC 50|50|CD µl|µl|NN of|of|IN 3|3|CD M|m|NN NaAc|naac|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO each|each|DT sample|sample|NN and|and|CC mixed|mixed|JJ well|well|RB .|.|. The|the|DT DNA|dna|NN was|be|VBD precipitated|precipitate|VBN with|with|IN 1,375|1,375|CD µl|µl|NN of|of|IN 95|95|CD %|%|NN ethanol|ethanol|NN and|and|CC incubated|incubate|VBN at|at|IN -80|-80|CD °C|°c|NN for|for|IN 1|1|CD h|h|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 13,000|13,000|CD rpm|rpm|NN for|for|IN 20|20|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT DNA|dna|NN pellets|pellet|NNS were|be|VBD washed|wash|VBN with|with|IN 500|500|CD µl|µl|NN of|of|IN ice-cold|ice-cold|JJ 70|70|CD %|%|NN ethanol|ethanol|NN and|and|CC centrifuged|centrifuge|VBN at|at|IN 13,000|13,000|CD rpm|rpm|NN for|for|IN 5|5|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD removed|remove|VBN and|and|CC the|the|DT samples|sample|NNS were|be|VBD air-dried|air-dried|JJ for|for|IN 10-15|10-15|CD min|min|NN .|.|. DNA|dna|NN pellets|pellet|NNS of|of|IN IP|IP|NNP samples|sample|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 50|50|CD µl|µl|NN nuclease-free|nuclease-free|JJ H2O|h2o|NN .|.|. Input|input|NN DNA|dna|NN samples|sample|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 100|100|CD µl|µl|NN of|of|IN nuclease-free|nuclease-free|JJ H2O|h2o|NN .|.|. Samples|sample|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN for|for|IN 1|1|CD h.|h.|NN
OD|od|NN :|:|: OD|od|NN 0.1|0.1|CD
of|of|IN -LRB-|-lrb-|-LRB- F|f|NN _|_|CD r-B|r-b|NN _|_|NN r|r|NN -RRB-|-rrb-|-RRB- /|/|: -LRB-|-lrb-|-LRB- F|f|NN _|_|CD g-B|g-b|NN _|_|CD g|g|NN -RRB-|-rrb-|-RRB- ,|,|, where|where|WRB F|f|NN _|_|NN r|r|NN ,|,|, B|b|NN _|_|NN r|r|NN ,|,|, F|f|NN _|_|CD g|g|NN and|and|CC B|b|NN _|_|CD g|g|NN represent|represent|VBP the|the|DT median|median|JJ Cy5|cy5|NN -LRB-|-lrb-|-LRB- red|red|NN -RRB-|-rrb-|-RRB-
Omega17|omega17|NN _|_|NN 1|1|CD
Omega17|omega17|NN _|_|NN 2|2|CD
Omega76|omega76|NN _|_|NN 1|1|CD
Omega76|omega76|NN _|_|NN 2|2|CD
OmpFrecode|ompfrecode|NN _|_|CD f.wig|f.wig|NN :|:|: NC|nc|NN _|_|SYM 000913.2|000913.2|CD
OmpFrecode|ompfrecode|NN _|_|CD r.wig|r.wig|NN :|:|: NC|nc|NN _|_|SYM 000913.2|000913.2|CD
ompR|ompr|NN _|_|NN 1|1|CD
ompR|ompr|NN _|_|NN 2|2|CD
OmpR|ompr|NN _|_|CD ChIPSeq|chipseq|NN
ompR|ompr|NN mutant|mutant|JJ rep|rep|NN 1|1|CD
ompR|ompr|NN mutant|mutant|JJ rep|rep|NN 2|2|CD
OmpR|ompr|NN NaCl|nacl|NN 1|1|CD
OmpR|ompr|NN NaCl|nacl|NN 2|2|CD
∆|∆|CD ompR|ompr|NN pH|ph|NN 5.6|5.6|CD A|a|DT
∆|∆|CD ompR|ompr|NN pH|ph|NN 5.6|5.6|CD B|b|NN
∆|∆|CD ompR|ompr|NN pH|ph|NN 5.6|5.6|CD C|c|NN
∆|∆|CD ompR|ompr|NN pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN A|a|NN
∆|∆|CD ompR|ompr|NN pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN B|b|NN
One|one|CD cell|cell|NN pellet|pellet|NN from|from|IN each|each|DT condition|condition|NN and|and|CC sampling|sampling|NN time|time|NN was|be|VBD thawed|thaw|VBN on|on|IN ice|ice|NN ;|;|: total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN by|by|IN RNAsnap|rnasnap|NN ™|™|NN -LRB-|-lrb-|-LRB- Stead|stead|NN et|et|FW al.|al.|FW ,|,|, 2012|2012|CD ,|,|, Nucleic|Nucleic|NNP Acids|Acids|NNP Res|Res|NNP -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN contamination|contamination|NN was|be|VBD removed|remove|VBN by|by|IN two|two|CD treatments|treatment|NNS with|with|IN Turbo-DNase|turbo-dnase|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ;|;|: Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|. Ribosomal|ribosomal|JJ RNA|rna|NN depletion|depletion|NN was|be|VBD performed|perform|VBN with|with|IN the|the|DT Ribo-Zero|Ribo-Zero|NNP ™|™|NN rRNA|rrna|NN removal|removal|NN kit|kit|NN for|for|IN Gram-negative|gram-negative|JJ bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- and|and|CC concentrated|concentrate|VBD using|use|VBG RNA|rna|NN Clean|clean|JJ and|and|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS -LRB-|-lrb-|-LRB- Zymo|Zymo|NNP Research|Research|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
One|one|CD conditions|condition|NNS :|:|: 1|1|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- hydrogen|hydrogen|NN peroxide|peroxide|NN -LRB-|-lrb-|-LRB- H2O2|h2o2|NN -RRB-|-rrb-|-RRB- ,|,|, 37|37|CD Ceilsus|Ceilsus|NNP degree|degree|NN
One|one|CD conditions|condition|NNS :|:|: 5|5|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- isooctane|isooctane|NN ,|,|, 37|37|CD Ceilsus|ceilsus|NN degree|degree|NN ,|,|, 250rpm|250rpm|JJ
One|one|CD hundred|hundred|CD µl|µl|NN tris-EDTA|tris-edta|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-Cl|tris-cl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, ph|ph|NN 8.0|8.0|CD ;|;|: Promega|Promega|NNP ;|;|: Madison|Madison|NNP ,|,|, WI|WI|NNP -RRB-|-rrb-|-RRB- containing|contain|VBG lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- 3|3|CD mg/ml|mg/ml|NN ;|;|: Sigma-Aldrich|Sigma-Aldrich|NNP ;|;|: St.|St.|NNP Louis|Louis|NNP ,|,|, MO|MO|NNP -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO each|each|DT cell|cell|NN pellet|pellet|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD thoroughly|thoroughly|RB mixed|mixed|JJ and|and|CC incubated|incubate|VBN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 10|10|CD min|min|NN .|.|. Buffer|buffer|NN RLT|rlt|NN -LRB-|-lrb-|-LRB- 350|350|CD µl|µl|NN -RRB-|-rrb-|-RRB- was|be|VBD combined|combine|VBN with|with|IN the|the|DT tris-EDTA/lysozyme|tris-edta/lysozyme|NN cell|cell|NN suspension|suspension|NN to|to|TO further|further|JJ lyse|lyse|NN cells|cell|NNS .|.|. The|the|DT total|total|JJ volume|volume|NN was|be|VBD combined|combine|VBN with|with|IN 250|250|CD µl|µl|NN of|of|IN 200|200|CD proof|proof|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- Aaper|Aaper|NNP Alcohol|Alcohol|NNP ;|;|: Shelbyville|Shelbyville|NNP ,|,|, KY|ky|NN -RRB-|-rrb-|-RRB- to|to|TO solubilize|solubilize|VB the|the|DT cell|cell|NN lysate|lysate|NN ,|,|, and|and|CC the|the|DT entire|entire|JJ sample|sample|NN was|be|VBD transferred|transfer|VBN to|to|TO the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Spin|Spin|NNP Column|Column|NNP in|in|IN a|a|DT collection|collection|NN tube|tube|NN and|and|CC centrifuged|centrifuge|VBN at|at|IN 8000|8000|CD x|x|CC g|g|NN for|for|IN 15|15|CD sec|sec|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. The|the|DT silica-based|silica-based|JJ membrane|membrane|NN efficiently|efficiently|RB binds|bind|VBZ up|up|RP to|to|TO 100|100|CD µg|µg|NN of|of|IN RNA|rna|NN longer|longer|RBR than|than|IN 200|200|CD bases|basis|NNS .|.|. The|the|DT collection|collection|NN tube|tube|NN and|and|CC eluate|eluate|NN were|be|VBD discarded|discard|VBN ,|,|, and|and|CC the|the|DT spin|spin|NN column|column|NN was|be|VBD placed|place|VBN in|in|IN a|a|DT new|new|JJ collection|collection|NN tube|tube|NN .|.|. Buffer|buffer|NN RW1|rw1|NN -LRB-|-lrb-|-LRB- 700|700|CD µl|µl|NN -RRB-|-rrb-|-RRB- was|be|VBD applied|apply|VBN to|to|TO the|the|DT column|column|NN ,|,|, centrifuged|centrifuge|VBN ,|,|, and|and|CC flow-through|flow-through|JJ was|be|VBD discarded|discard|VBN as|as|IN described|describe|VBN previously|previously|RB .|.|. Twice|twice|RB ,|,|, 500|500|CD µl|µl|NN of|of|IN buffer|buffer|NN RPE|rpe|NN was|be|VBD applied|apply|VBN to|to|TO the|the|DT spin|spin|NN column|column|NN allowing|allow|VBG 5|5|CD min|min|NN prior|prior|RB to|to|TO centrifugation|centrifugation|NN at|at|IN 8000|8000|CD x|x|CC g|g|NN for|for|IN 15|15|CD sec|sec|NN .|.|. The|the|DT spin|spin|NN column|column|NN was|be|VBD placed|place|VBN in|in|IN a|a|DT 1.5|1.5|CD ml|ml|NN collection|collection|NN tube|tube|NN that|that|WDT was|be|VBD used|use|VBN for|for|IN long-term|long-term|JJ storage|storage|NN .|.|. In|in|IN order|order|NN to|to|TO elute|elute|VB RNA|rna|NN from|from|IN the|the|DT spin|spin|NN column|column|NN ,|,|, 30|30|CD µl|µl|NN RNase-free|rnase-free|NN water|water|NN was|be|VBD applied|apply|VBN directly|directly|RB to|to|TO the|the|DT membrane|membrane|NN and|and|CC centrifuged|centrifuge|VBN at|at|IN 8000|8000|CD x|x|CC g|g|NN for|for|IN 15|15|CD sec|sec|NN .|.|. The|the|DT RNA|rna|NN eluate|eluate|NN was|be|VBD stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN until|until|IN evaluated|evaluate|VBN for|for|IN quantity|quantity|NN ,|,|, quality|quality|NN ,|,|, and|and|CC purity|purity|NN .|.|.
One|one|CD set|set|NN of|of|IN fermentations|fermentation|NNS were|be|VBD exposed|expose|VBN to|to|TO 5|5|CD mM|mm|NN IPTG|iptg|NN and|and|CC one|one|CD set|set|NN was|be|VBD not|not|RB exposed|expose|VBN to|to|TO IPTG|IPTG|NNP .|.|. Samples|sample|NNS were|be|VBD taken|take|VBN 0|0|CD ,|,|, 1|1|CD ,|,|, and|and|CC 4|4|CD hours|hour|NNS post-synchronization|post-synchronization|JJ -LRB-|-lrb-|-LRB- Time|time|NN S0|s0|NN ,|,|, S1|s1|NN ,|,|, and|and|CC S4|s4|NN -RRB-|-rrb-|-RRB- .|.|.
One|one|CD volume|volume|NN of|of|IN bacterial|bacterial|JJ culture|culture|NN was|be|VBD added|add|VBN to|to|TO two|two|CD volumes|volume|NNS of|of|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. All|all|DT samples|sample|NNS were|be|VBD on-column|on-column|JJ treated|treat|VBN with|with|IN DNase|dnase|NN I.|i.|NN
Only|only|RB ideal|ideal|JJ correspondence|correspondence|NN of|of|IN sequence|sequence|NN reads|read|VBZ to|to|TO the|the|DT genome|genome|NN in|in|IN both|both|DT cases|case|NNS was|be|VBD permitted|permit|VBN .|.|. The|the|DT profiles|profile|NNS obtained|obtain|VBN for|for|IN experimental|experimental|JJ and|and|CC control|control|JJ samples|sample|NNS were|be|VBD normalized|normalize|VBN by|by|IN the|the|DT scaling|scaling|NN method|method|NN initially|initially|RB offered|offer|VBN by|by|IN Affymetrix|Affymetrix|NNP for|for|IN microarray|microarray|NN data|data|NN analysis|analysis|NN and|and|CC later|later|RB implemented|implement|VBD in|in|IN several|several|JJ other|other|JJ approaches|approach|NNS .|.|. This|this|DT method|method|NN assumes|assume|VBZ unaffected|unaffected|JJ protein|protein|NN occupancy|occupancy|NN at|at|IN most|most|JJS genomic|genomic|JJ positions|position|NNS and|and|CC quantifies|quantify|VBZ the|the|DT scaling|scaling|NN factor|factor|NN on|on|IN the|the|DT basis|basis|NN of|of|IN corrected|correct|VBN mean|mean|NN values|value|NNS obtained|obtain|VBN after|after|IN removal|removal|NN of|of|IN 2|2|CD %|%|NN signals|signal|NNS with|with|IN highest|highest|JJS and|and|CC lowest|lowest|JJS intensities|intensity|NNS from|from|IN both|both|DT control|control|NN and|and|CC experimental|experimental|JJ sets|set|NNS .|.|.
optA1|opta1|NN _|_|NN 0|0|CD _|_|NN Hx|hx|NN Rep1|rep1|NN
optA1|opta1|NN _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep2|rep2|JJ
optA1|opta1|NN _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep3|rep3|JJ
optA1|opta1|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 0|0|CD _|_|NN Hx|hx|NN Rep1|rep1|NN
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 180|180|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 180|180|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 180|180|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 240|240|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 240|240|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 240|240|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 300|300|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 300|300|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 300|300|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 360|360|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 360|360|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 360|360|CD -LRB-|-lrb-|-LRB- High|high|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 360|360|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 360|360|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|CD gpt|gpt|NN _|_|NN 360|360|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
optA1|opta1|NN _|_|SYM gpt|gpt|FW _|_|FW 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
optA1|opta1|NN gpt|gpt|NN strain|strain|NN with|with|IN hypoxanthine|hypoxanthine|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 120|120|CD min|min|NN at|at|IN high|high|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 120|120|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 15|15|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 180|180|CD min|min|NN at|at|IN high|high|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 240|240|CD min|min|NN at|at|IN high|high|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 300|300|CD min|min|NN at|at|IN high|high|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 30|30|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 360|360|CD min|min|NN at|at|IN high|high|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 360|360|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 45|45|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN gpt|gpt|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 60|60|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN strain|strain|NN with|with|IN hypoxanthine|hypoxanthine|NN
optA1|opta1|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 120|120|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 15|15|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 30|30|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 45|45|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
optA1|opta1|NN strain|strain|NN w/o|w/o|NN hypoxanthine|hypoxanthine|NN 60|60|CD min|min|NN at|at|IN low|low|JJ dilution|dilution|NN protocol|protocol|NN
ORF1|orf1|NN _|_|NN 1|1|CD
ORF1|orf1|NN _|_|NN 1|1|CD _|_|CD IPTG|iptg|NN
ORF1|orf1|NN _|_|NN 2|2|CD
ORF1|orf1|NN _|_|NN 2|2|CD _|_|CD IPTG|iptg|NN
Original|original|JJ prototroph|prototroph|NN DH1|dh1|NN cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN
Original|original|JJ prototroph|prototroph|NN DH1|dh1|NN cells|cell|NNS at|at|IN log|log|NN phase|phase|NN in|in|IN monoculture|monoculture|NN ,|,|, a|a|DT technical|technical|JJ replicate|replicate|VBP
originate|originate|VB during|during|IN array|array|NN printing|printing|NN ,|,|, as|as|RB well|well|RB as|as|IN during|during|IN the|the|DT collection|collection|NN and|and|CC processing|processing|NN of|of|IN samples|sample|NNS ,|,|,
origin|origin|NN of|of|IN isolation|isolation|NN :|:|: patient|patient|NN with|with|IN hemolytic|hemolytic|JJ uremic|uremic|JJ syndrome|syndrome|NN -LRB-|-lrb-|-LRB- HUS|hus|NN -RRB-|-rrb-|-RRB-
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU11|osu11|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU11|osu11|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OSU11|osu11|NN ,|,|, nurishment|nurishment|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
OSU11|osu11|NN ,|,|, nurishment|nurishment|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
OSU11|osu11|NN ,|,|, nurishment|nurishment|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
OSU11|osu11|NN ,|,|, starved|starve|VBN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
OSU11|osu11|NN ,|,|, starved|starve|VBN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
OSU11|osu11|NN ,|,|, starved|starve|VBN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisA|osu12-hisa|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisB|osu12-hisb|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisC|osu12-hisc|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisC|osu12-hisc|NN ,|,|, nurishment|nurishment|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
OSU12-hisC|osu12-hisc|NN ,|,|, nurishment|nurishment|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
OSU12-hisC|osu12-hisc|NN ,|,|, nurishment|nurishment|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
OSU12-hisC|osu12-hisc|NN ,|,|, starved|starve|VBN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
OSU12-hisC|osu12-hisc|NN ,|,|, starved|starve|VBN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
OSU12-hisC|osu12-hisc|NN ,|,|, starved|starve|VBN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisD|osu12-hisd|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisF|osu12-hisf|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisG|osu12-hisg|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, >|>|JJR 10|10|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 10|10|CD min|min|NN ,|,|, rep|rep|NN 3|3|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 1|1|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 2|2|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN depleted|deplete|VBN ,|,|, 2|2|CD hrs|hr|NNS ,|,|, rep|rep|NN 3|3|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 1|1|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 2|2|CD
OSU12-hisI|osu12-hisi|NN ,|,|, histidine|histidine|NN supplied|supply|VBD ,|,|, 1|1|CD mM|mm|NN ,|,|, rep|rep|NN 3|3|CD
OTHER|other|NN
other|other|JJ extracted|extract|VBN using|use|VBG alkalyne|alkalyne|JJ lysis|lysis|NN preparation|preparation|NN .|.|. Plasmid|plasmid|NN DNA|dna|NN was|be|VBD clean|clean|JJ and|and|CC concentrated|concentrate|VBD using|use|VBG Zymo|Zymo|NNP Clean|Clean|NNP &|&|CC Concentrated|Concentrated|NNP -5|-5|CD kit|kit|NN
outbreak|outbreak|NN :|:|: 2011|2011|CD outbreak|outbreak|NN centered|center|VBN in|in|IN Northern|Northern|NNP Germany|Germany|NNP
overexpression|overexpression|NN :|:|: -|-|:
overexpression|overexpression|NN :|:|: BglJ|bglj|NN
overexpression|overexpression|NN :|:|: LeuO|leuo|NN
overexpression|overexpression|NN of|of|IN arT|art|NN -LRB-|-lrb-|-LRB- pCA24N|pca24n|NN _|_|CD arT|art|NN -RRB-|-rrb-|-RRB-
overexpression|overexpression|NN of|of|IN dosP|dosp|NN -LRB-|-lrb-|-LRB- pCA24N|pca24n|NN _|_|CD dosP|dosp|NN -RRB-|-rrb-|-RRB-
overexpression|overexpression|NN of|of|IN empty|empty|JJ vector|vector|NN -LRB-|-lrb-|-LRB- pCA24N|pca24n|NN -RRB-|-rrb-|-RRB-
Overnight|overnight|JJ bacterial|bacterial|JJ culture|culture|NN in|in|IN BHI|BHI|NNP broth|broth|NN .|.|.
overnight|overnight|JJ bacterial|bacterial|JJ culture|culture|NN in|in|IN Luria|Luria|NNP Broth|Broth|NNP at|at|IN 37C|37c|NN with|with|IN shaking|shake|VBG
overnight|overnight|JJ colony|colony|NN growth|growth|NN
Overnight|Overnight|NNP culture|culture|NN
Overnight|overnight|JJ culture|culture|NN in|in|IN LB|lb|NN medium|medium|NN was|be|VBD innoculated|innoculate|VBN from|from|IN a|a|DT single|single|JJ colony|colony|NN .|.|. The|the|DT overnight|overnight|JJ culture|culture|NN was|be|VBD diluted|dilute|VBN 1/200|1/200|CD into|into|IN MOPS|mop|NNS minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- Neidhardt|Neidhardt|NNP ,|,|, J.|J.|NNP Bacteriol.|Bacteriol.|NNP ,|,|, 1974|1974|CD -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN with|with|IN shaking|shake|VBG at|at|IN 37|37|CD C|c|NN until|until|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD or|or|CC OD600|od600|NN =|=|JJ 0.3|0.3|CD .|.|. Total|total|JJ culture|culture|NN volume|volume|NN 10|10|CD ml|ml|NN .|.|.
Overnight|overnight|JJ culture|culture|NN of|of|IN E.|e.|FW coli|coli|FW BW25113|bw25113|NN in|in|IN LB|lb|NN was|be|VBD diluted|dilute|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN with|with|IN supplements|supplement|NNS to|to|TO OD600|od600|NN =|=|JJ 0.02|0.02|CD and|and|CC was|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD Ceilsus|ceilsus|NN degree|degree|NN with|with|IN shaking|shake|VBG at|at|IN 250rpm|250rpm|NN until|until|IN its|its|PRP$ OD600|od600|NN reached|reach|VBD 0.1|0.1|CD .|.|.
Overnight|overnight|JJ culture|culture|NN of|of|IN E.|e.|FW coli|coli|FW in|in|IN LB|lb|NN was|be|VBD diluted|dilute|VBN in|in|IN LB|lb|NN supplemented|supplement|VBN with|with|IN 0.8|0.8|CD %|%|NN glucose|glucose|NN to|to|TO OD600|od600|NN =|=|JJ 0.02|0.02|CD and|and|CC was|be|VBD continuously|continuously|RB incubated|incubate|VBN at|at|IN 30|30|CD degree|degree|NN celcius|celcius|NNS with|with|IN shaking|shake|VBG until|until|IN its|its|PRP$ OD600|od600|NN reached|reach|VBD 1.0|1.0|CD
Overnight|overnight|JJ culture|culture|NN of|of|IN E.|e.|FW coli|coli|FW W3110|w3110|NN in|in|IN LB|lb|NN was|be|VBD diluted|dilute|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN with|with|IN supplements|supplement|NNS to|to|TO OD600|od600|NN =|=|JJ 0.01|0.01|CD and|and|CC was|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD Ceilsus|ceilsus|NN degree|degree|NN witouth|witouth|NN shaking|shake|VBG until|until|IN its|its|PRP$ OD600|od600|NN reached|reach|VBD 0.1|0.1|CD .|.|.
Overnight|Overnight|NNP cultures|culture|NNS from|from|IN isolated|isolate|VBN colonies|colony|NNS were|be|VBD diluted|dilute|VBN in|in|IN fresh|fresh|JJ medium|medium|NN to|to|TO an|a|DT initial|initial|JJ OD600|od600|NN ~|~|NN 0.03|0.03|CD and|and|CC grown|grow|VBN to|to|TO exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.3|0.3|CD -RRB-|-rrb-|-RRB- at|at|IN 37ºC|37ºc|NN ,|,|, with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- medium|medium|NN supplemented|supplement|VBN with|with|IN thymine|thymine|NN -LRB-|-lrb-|-LRB- 50|50|CD mg|mg|NN ml-1|ml-1|NN -RRB-|-rrb-|-RRB- .|.|. When|when|WRB required|require|VBN ,|,|, antibiotics|antibiotic|NNS were|be|VBD present|present|JJ at|at|IN the|the|DT following|follow|VBG concentrations|concentration|NNS :|:|: kanamycin|kanamycin|NN ,|,|, 50|50|CD mg|mg|NN ml-1|ml-1|NN ;|;|: tetracycline|tetracycline|NN ,|,|, 20|20|CD mg|mg|NN ml-1|ml-1|NN ;|;|: streptomycin/spectinomycin|streptomycin/spectinomycin|NNP 20|20|CD µg|µg|NN ml-1|ml-1|NN .|.|.
Overnight|Overnight|NNP cultures|culture|NNS in|in|IN M9|m9|NN glucose|glucose|NN were|be|VBD inoculated|inoculate|VBN into|into|IN 100|100|CD mL|ml|NN fresh|fresh|JJ M9|m9|NN glucose|glucose|NN to|to|TO a|a|DT final|final|JJ OD600|od600|NN of|of|IN 0.02|0.02|CD .|.|. The|the|DT flasks|flask|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN the|the|DT early|early|JJ exponential|exponential|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.3|0.3|CD -RRB-|-rrb-|-RRB- ,|,|, mid-exponential|mid-exponential|JJ -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.8|0.8|CD -RRB-|-rrb-|-RRB- ,|,|, transition|transition|NN to|to|TO stationary|stationary|JJ -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 1.6|1.6|CD -RRB-|-rrb-|-RRB- ,|,|, stationary|stationary|JJ -LRB-|-lrb-|-LRB- 16|16|CD hrs|hr|NNS ,|,|, OD600|od600|NN ~|~|NN 2|2|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC late|late|JJ stationary|stationary|JJ -LRB-|-lrb-|-LRB- 48|48|CD hrs|hr|NNS ,|,|, OD600|od600|NN ~|~|NN 1.6|1.6|CD -RRB-|-rrb-|-RRB- phases|phase|NNS of|of|IN growth|growth|NN .|.|.
Overnight|Overnight|NNP cultures|culture|NNS of|of|IN bacteria|bacterium|NNS were|be|VBD diluted|dilute|VBN 1:100|1:100|CD in|in|IN fresh|fresh|JJ LB|lb|NN broth|broth|NN and|and|CC grown|grow|VBN to|to|TO logarithmic|logarithmic|JJ phase|phase|NN at|at|IN an|a|DT OD600|od600|NN of|of|IN about|about|IN 0.8|0.8|CD .|.|.
Overnight|Overnight|NNP cultures|culture|NNS of|of|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN were|be|VBD diluted|dilute|VBN 1:625|1:625|CD into|into|IN 50|50|CD ml|ml|NN of|of|IN LB|lb|NN broth|broth|NN -LRB-|-lrb-|-LRB- Roth|Roth|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN .|.|.
Overnight|Overnight|NNP cultures|culture|NNS of|of|IN ESBL7|esbl7|NN from|from|IN the|the|DT original|original|JJ isolate|isolate|NN ,|,|, or|or|CC isolates|isolate|NNS pre-exposed|pre-expose|VBN 20|20|CD times|time|NNS to|to|TO CORM-2|corm-2|NN or|or|CC vehicle|vehicle|NN ,|,|, were|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB MS-medium|ms-medium|NN ,|,|, -LRB-|-lrb-|-LRB- OD620|od620|NN -RRB-|-rrb-|-RRB- of|of|IN 0.1|0.1|CD ,|,|, followed|follow|VBN by|by|IN exposure|exposure|NN to|to|TO CORM-2|corm-2|NN -LRB-|-lrb-|-LRB- 250|250|CD µM|µm|NN -RRB-|-rrb-|-RRB- or|or|CC vehicle|vehicle|NN for|for|IN 30|30|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN .|.|.
Overnight|Overnight|NNP cultures|culture|NNS of|of|IN strain|strain|NN JM83|jm83|NN were|be|VBD diluted|dilute|VBN 1/100|1/100|CD in|in|IN LB|lb|NN medium|medium|NN and|and|CC grown|grow|VBN in|in|IN microtiter|microtiter|NN plates|plate|NNS .|.|. To|to|TO study|study|VB the|the|DT effects|effect|NNS of|of|IN trimethoprim|trimethoprim|NN ,|,|, cells|cell|NNS grown|grow|VBN without|without|IN antibiotics|antibiotic|NNS were|be|VBD compared|compare|VBN to|to|TO cells|cell|NNS grown|grow|VBN with|with|IN 0.5|0.5|CD μg/ml|μg/ml|NN trimethoprim|trimethoprim|NN .|.|.
Overnight|Overnight|NNP cultures|culture|NNS of|of|IN the|the|DT dnaB-Ts|dnab-ts|JJ single|single|JJ mutant|mutant|NN -LRB-|-lrb-|-LRB- strain|strain|NN 2429|2429|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT dnaB-Ts|dnab-ts|JJ ΔahpC|δahpc|NN double|double|JJ mutant|mutant|JJ -LRB-|-lrb-|-LRB- strain|strain|NN 3780|3780|CD -RRB-|-rrb-|-RRB- were|be|VBD diluted|dilute|VBN 100-fold|100-fold|RB into|into|IN fresh|fresh|JJ SB|sb|NN medium|medium|NN -LRB-|-lrb-|-LRB- 3.2|3.2|CD %|%|NN peptone|peptone|NN ,|,|, 2|2|CD %|%|NN yeast|yeast|NN extract|extract|NN and|and|CC 1|1|CD %|%|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC they|they|PRP were|be|VBD then|then|RB grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN to|to|TO early-log|early-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.15|0.15|CD -RRB-|-rrb-|-RRB- .|.|. Next|next|JJ these|these|DT log-phase|log-phase|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN 20-fold|20-fold|RB into|into|IN 200|200|CD ml|ml|NN pre-warmed|pre-warmed|JJ ,|,|, fresh|fresh|JJ SB|sb|NN medium|medium|NN ,|,|, and|and|CC they|they|PRP were|be|VBD grown|grow|VBN at|at|IN 30|30|CD °C|°c|NN for|for|IN another|another|DT 60|60|CD min|min|NN .|.|.
overnight|overnight|JJ culture|culture|NN subcultured|subculture|VBN in|in|IN either|either|DT of|of|IN the|the|DT SCFA|scfa|NN mixes|mix|VBZ -LRB-|-lrb-|-LRB- or|or|CC the|the|DT sodium|sodium|NN chloride|chloride|NN controls|control|NNS -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN ,|,|, static|static|JJ with|with|IN 5|5|CD %|%|NN CO2|co2|NN to|to|TO OD600|od600|NN of|of|IN 1|1|CD
Overnight|overnight|NN cultures|culture|NNS were|be|VBD inoculated|inoculate|VBN 1:100|1:100|CD into|into|IN 20|20|CD ml|ml|NN of|of|IN EZ|ez|NN Rich|rich|JJ Defined|defined|JJ Medium|medium|NN -LRB-|-lrb-|-LRB- Neidhardt|Neidhardt|NNP et|et|FW al.|al.|FW ,|,|, 1974|1974|CD -RRB-|-rrb-|-RRB- in|in|IN 125|125|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flasks|flask|NNS and|and|CC grown|grow|VBN at|at|IN 37oC|37oc|NN and|and|CC 250|250|CD rpm|rpm|NN in|in|IN a|a|DT reciprocating|reciprocate|VBG water|water|NN bath|bath|NN .|.|.
Overnight|Overnight|NNP cultures|culture|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN fresh|fresh|JJ medium|medium|NN and|and|CC TMP|tmp|NN was|be|VBD added|add|VBN when|when|WRB the|the|DT optical|optical|JJ density|density|NN -LRB-|-lrb-|-LRB- O.D.|o.d.|NN 600|600|CD nm|nm|NN -RRB-|-rrb-|-RRB- of|of|IN the|the|DT culture|culture|NN reached|reach|VBD 0.3-0.4|0.3-0.4|CD .|.|.
overnight|overnight|JJ in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- broth|broth|NN with|with|IN continuous|continuous|JJ agitation|agitation|NN
overnight|overnight|JJ in|in|IN Lurie-Bertani|Lurie-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- broth|broth|NN with|with|IN continuous|continuous|JJ agitation|agitation|NN
oxic/anoxic|oxic/anoxic|JJ :|:|: anoxic|anoxic|JJ -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB-
oxic/anoxic|oxic/anoxic|NN :|:|: oxic|oxic|JJ
Oxidative|oxidative|JJ stress|stress|NN 200|200|CD ug/ml|ug/ml|NN of|of|IN 30|30|CD %|%|NN pre-warmed|pre-warmed|JJ hydrogen|hydrogen|NN peroxide|peroxide|NN -LRB-|-lrb-|-LRB- Fluka|fluka|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO 150|150|CD ml|ml|NN constantly|constantly|RB stirred|stir|VBD -LRB-|-lrb-|-LRB- 330|330|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- cultures|culture|NNS kept|keep|VBD in|in|IN 1000|1000|CD ml|ml|NN flasks|flask|NNS .|.|. Cold|Cold|NNP stress|stress|NN Cultures|culture|NNS were|be|VBD transferred|transfer|VBN from|from|IN 37oC|37oc|NN into|into|IN an|a|DT ice|ice|NN cold|cold|JJ water|water|NN bath|bath|NN in|in|IN order|order|NN to|to|TO lower|lower|VB the|the|DT temperature|temperature|NN ,|,|, while|while|IN stirring|stir|VBG ,|,|, to|to|TO 16oC|16oc|NN in|in|IN less|less|JJR than|than|IN 2|2|CD min|min|NN ,|,|, heat|heat|NN stress|stress|NN Cultures|culture|NNS were|be|VBD transferred|transfer|VBN from|from|IN 37oC|37oc|NN to|to|TO a|a|DT 50oC|50oc|NN water|water|NN bath|bath|NN .|.|. While|while|IN stirring|stir|VBG ,|,|, the|the|DT temperature|temperature|NN of|of|IN each|each|DT culture|culture|NN was|be|VBD raised|raise|VBN to|to|TO 45oC|45oc|NN in|in|IN less|less|JJR than|than|IN 2|2|CD min|min|NN .|.|. The|the|DT constantly|constantly|RB stirring|stir|VBG -LRB-|-lrb-|-LRB- 330rpm|330rpm|NN -RRB-|-rrb-|-RRB- cultures|culture|NNS were|be|VBD then|then|RB transferred|transfer|VBN to|to|TO a|a|DT 45oC|45oc|NN water|water|NN bath|bath|NN to|to|TO maintain|maintain|VB this|this|DT temperature|temperature|NN glucose|glucose|NN lactose|lactose|NN shift|shift|NN Carbon|Carbon|NNP source|source|NN concentrations|concentration|NNS of|of|IN 0.15|0.15|CD %|%|NN lactose|lactose|NN and|and|CC 0.05|0.05|CD %|%|NN glucose|glucose|NN were|be|VBD used|use|VBN -LRB-|-lrb-|-LRB- 150|150|CD ml|ml|NN culture|culture|NN in|in|IN 1000|1000|CD ml|ml|NN flasks|flask|NNS ,|,|, 330|330|CD rpm|rpm|NN stirring|stir|VBG -RRB-|-rrb-|-RRB- .|.|.
Oxidative|oxidative|JJ stress|stress|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN #|#|# 1|1|CD
Oxidative|oxidative|JJ stress|stress|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN #|#|# 2|2|CD
Oxidative|oxidative|JJ stress|stress|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN #|#|# 3|3|CD
Oxidative|oxidative|JJ stress|stress|NN in|in|IN E.|e.|FW coli|coli|FW O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- #|#|# 1|1|CD
Oxidative|oxidative|JJ stress|stress|NN in|in|IN E.|e.|FW coli|coli|FW O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- #|#|# 2|2|CD
Oxidative|oxidative|JJ stress|stress|NN in|in|IN E.|e.|FW coli|coli|FW O157|o157|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- #|#|# 3|3|CD
Oxo|Oxo|NNP _|_|NNP IN|in|IN _|_|CD 120mkM|120mkm|NN _|_|NN 3|3|CD
Oxo|Oxo|NNP _|_|NNP IN|in|IN _|_|SYM Mu|mu|FW _|_|FW 120mkM|120mkm|NN _|_|NN 1|1|CD
Oxo|Oxo|NNP _|_|NNP IN|in|IN _|_|SYM Mu|mu|FW _|_|FW 120mkM|120mkm|NN _|_|NN 2|2|CD
Oxo|Oxo|NNP _|_|NNP IP|IP|NNP _|_|SYM 120mkM|120mkm|NN _|_|NN 3|3|CD
Oxo|Oxo|NNP _|_|NNP IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 120mkM|120mkm|NN _|_|NN 1|1|CD
Oxo|Oxo|NNP _|_|NNP IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 120mkM|120mkm|NN _|_|NN 2|2|CD
Oxolinic|oxolinic|JJ acid|acid|NN Rep|Rep|NNP 1|1|CD +|+|CC A-IP|a-ip|JJ
Oxolinic|oxolinic|JJ acid|acid|NN Rep|Rep|NNP 1|1|CD +|+|CC A+IP|A+IP|NNP
Oxolinic|oxolinic|JJ acid|acid|NN Rep|Rep|NNP 2|2|CD +|+|CC A-IP|a-ip|JJ
Oxolinic|oxolinic|JJ acid|acid|NN Rep|Rep|NNP 2|2|CD +|+|CC A+IP|A+IP|NNP
Oxolinic|oxolinic|JJ acid|acid|NN Rep|Rep|NNP 3|3|CD +|+|CC A-IP|a-ip|JJ
Oxolinic|oxolinic|JJ acid|acid|NN Rep|Rep|NNP 3|3|CD +|+|CC A+IP|A+IP|NNP
oxygen|oxygen|NN condition|condition|NN :|:|: aerobic|aerobic|JJ
oxygen|oxygen|NN condition|condition|NN :|:|: anaerobic|anaerobic|JJ
oxygen|oxygen|NN _|_|CD down|down|IN _|_|CD 0|0|CD min|min|NN
oxygen|oxygen|NN _|_|CD down|down|IN _|_|CD 12|12|CD min|min|NN
oxygen|oxygen|NN _|_|CD down|down|IN _|_|CD 20|20|CD min|min|NN
oxygen|oxygen|NN _|_|CD down|down|IN _|_|CD 28|28|CD min|min|NN
oxygen|oxygen|NN _|_|CD down|down|IN _|_|CD 44|44|CD min|min|NN
oxygen|oxygen|NN _|_|CD down|down|IN _|_|CD 4|4|CD min|min|NN
oxygen|oxygen|NN _|_|CD down|down|IN _|_|CD 8|8|CD min|min|NN
oxygen|oxygen|NN down|down|IN shift|shift|NN ,|,|, 0|0|CD min|min|NN
oxygen|oxygen|NN down|down|IN shift|shift|NN ,|,|, 12|12|CD min|min|NN
oxygen|oxygen|NN down|down|IN shift|shift|NN ,|,|, 20|20|CD min|min|NN
oxygen|oxygen|NN down|down|IN shift|shift|NN ,|,|, 28|28|CD min|min|NN
oxygen|oxygen|NN down|down|IN shift|shift|NN ,|,|, 44|44|CD min|min|NN
oxygen|oxygen|NN down|down|IN shift|shift|NN ,|,|, 4|4|CD min|min|NN
oxygen|oxygen|NN down|down|IN shift|shift|NN ,|,|, 8|8|CD min|min|NN
oxygen|oxygen|NN regime|regime|NN :|:|: daily|daily|JJ shift|shift|NN between|between|IN shaking|shake|VBG and|and|CC static|static|JJ -LRB-|-lrb-|-LRB- no|no|DT shaking|shake|VBG -RRB-|-rrb-|-RRB- conditions|condition|NNS
oxygen|oxygen|NN regime|regime|NN :|:|: transfers|transfer|NNS in|in|IN constant|constant|JJ static|static|JJ conditions|condition|NNS
oxygen|oxygen|NN regime|regime|NN :|:|: transfers|transfer|NNS under|under|IN constant|constant|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 200rpm|200rpm|NN -RRB-|-rrb-|-RRB-
oxygen|oxygen|NN _|_|CD Up|up|IN _|_|CD 0|0|CD min|min|NN
oxygen|oxygen|NN _|_|CD Up|up|IN _|_|CD 12|12|CD min|min|NN
oxygen|oxygen|NN _|_|CD Up|up|IN _|_|CD 20|20|CD min|min|NN
oxygen|oxygen|NN _|_|CD Up|up|IN _|_|CD 28|28|CD min|min|NN
oxygen|oxygen|NN _|_|CD Up|up|IN _|_|CD 44|44|CD min|min|NN
oxygen|oxygen|NN _|_|CD Up|up|IN _|_|CD 4|4|CD min|min|NN
oxygen|oxygen|NN _|_|CD Up|up|IN _|_|CD 8|8|CD min|min|NN
oxygen|oxygen|NN up|up|IN shift|shift|NN ,|,|, 0|0|CD min|min|NN
oxygen|oxygen|NN up|up|IN shift|shift|NN ,|,|, 12|12|CD min|min|NN
oxygen|oxygen|NN up|up|IN shift|shift|NN ,|,|, 20|20|CD min|min|NN
oxygen|oxygen|NN up|up|IN shift|shift|NN ,|,|, 28|28|CD min|min|NN
oxygen|oxygen|NN up|up|IN shift|shift|NN ,|,|, 44|44|CD min|min|NN
oxygen|oxygen|NN up|up|IN shift|shift|NN ,|,|, 4|4|CD min|min|NN
oxygen|oxygen|NN up|up|IN shift|shift|NN ,|,|, 8|8|CD min|min|NN
oxyR-8myc-tagged|oxyr-8myc-tagged|JJ _|_|NN PQ|pq|NN treated|treat|VBN
OxyR|oxyr|NN PQ|pq|NN 1|1|CD
OxyR|oxyr|NN PQ|pq|NN 2|2|CD
P2-08|p2-08|NN
P2-08|p2-08|NN _|_|CD R1|r1|NN
P2-08|p2-08|NN _|_|CD R2|r2|NN
P2-08|p2-08|NN _|_|CD R3|r3|NN
P2-51|p2-51|NN
P2-51|p2-51|NN _|_|CD R1|r1|NN
P2-51|p2-51|NN _|_|CD R2|r2|NN
P2-51|p2-51|NN _|_|CD R3|r3|NN
P2-58|p2-58|NN
P2-58|p2-58|NN _|_|CD R1|r1|NN
P2-58|p2-58|NN _|_|CD R2|r2|NN
P2-58|p2-58|NN _|_|CD R3|r3|NN
P2-66|p2-66|NN
P2-66|p2-66|NN _|_|CD R1|r1|NN
P2-66|p2-66|NN _|_|CD R2|r2|NN
P2-66|p2-66|NN _|_|CD R3|r3|NN
P2-77|p2-77|NN
P2-77|p2-77|NN _|_|CD R1|r1|NN
P2-77|p2-77|NN _|_|CD R2|r2|NN
P2-77|p2-77|NN _|_|CD R3|r3|NN
P4XB2|p4xb2|NN Mutant|mutant|JJ -LRB-|-lrb-|-LRB- 1992|1992|CD -RRB-|-rrb-|-RRB- in|in|IN Arginine|arginine|NN
P4XB2|p4xb2|NN Mutant|mutant|JJ -LRB-|-lrb-|-LRB- 1993|1993|CD -RRB-|-rrb-|-RRB- in|in|IN Arginine|arginine|NN
P4XB2|p4xb2|NN Mutant|mutant|JJ -LRB-|-lrb-|-LRB- 1994|1994|CD -RRB-|-rrb-|-RRB- in|in|IN Arginine|arginine|NN
P4X|p4x|NN Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- 1753|1753|CD -RRB-|-rrb-|-RRB- Reference|Reference|NNP
P4X|P4X|NNP Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- 1754|1754|CD -RRB-|-rrb-|-RRB- in|in|IN Arginine|arginine|NN
P4X|p4x|NN Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- 1765|1765|CD -RRB-|-rrb-|-RRB- Reference|Reference|NNP
P4X|P4X|NNP Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- 1766|1766|CD -RRB-|-rrb-|-RRB- in|in|IN Arginine|arginine|NN
P4X|p4x|NN Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- 1989|1989|CD -RRB-|-rrb-|-RRB- Reference|Reference|NNP
P4X|P4X|NNP Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- 1990|1990|CD -RRB-|-rrb-|-RRB- in|in|IN Arginine|arginine|NN
P500|p500|CD _|_|NN 1|1|CD
PA20|pa20|NN cultures|culture|NNS
PA20|pa20|NN cultures|culture|NNS for|for|IN RNA-seq|rna-seq|NN were|be|VBD grown|grow|VBN on|on|IN T-agar|t-agar|JJ with|with|IN and|and|CC without|without|IN added|add|VBN Sulfamethoxazole|Sulfamethoxazole|NNP -|-|: Trimethoprim|Trimethoprim|NNP at|at|IN designated|designate|VBN levels|level|NNS for|for|IN the|the|DT indicated|indicated|JJ times|time|NNS and|and|CC temperatures|temperature|NNS .|.|. Working|work|VBG stocks|stock|NNS were|be|VBD tested|test|VBN and|and|CC maintained|maintain|VBN using|use|VBG LB|lb|NN -LRB-|-lrb-|-LRB- Miller|Miller|NNP formulation|formulation|NN -RRB-|-rrb-|-RRB- or|or|CC LB|lb|NN agar|agar|NN .|.|. Plasmid|plasmid|NN pSE380|pse380|NN derivatives|derivative|NNS were|be|VBD induced|induce|VBN by|by|IN IPTG|iptg|NN .|.|.
Paired-end|paired-end|NN reads|read|VBZ mapped|map|VBN to|to|TO MG1655|mg1655|NN genome|genome|NN using|use|VBG bowtie2|bowtie2|NN with|with|IN default|default|NN settings|setting|NNS .|.|. Any|any|DT adapter|adapter|NN sequences|sequence|NNS were|be|VBD removed|remove|VBN prior|prior|RB to|to|TO mapping|mapping|NN .|.|.
paired|paired|JJ end|end|NN sequencing|sequencing|NN with|with|IN Illumina|Illumina|NNP HiSeq|HiSeq|NNP 2500|2500|CD Sequencer|Sequencer|NNP
Paired-end|paired-end|NN ,|,|, strand-specific|strand-specific|JJ RNAseq|rnaseq|NN libraries|library|NNS were|be|VBD generated|generate|VBN using|use|VBG the|the|DT dUTP|dutp|NN method|method|NN -LCB-|-lcb-|-LRB- Levin|Levin|NNP JZ|JZ|NNP et|et|FW al.|al.|FW 2010|2010|CD ,|,|, Nat|Nat|NNP Methods|method|NNS -RCB-|-rcb-|-RRB- with|with|IN the|the|DT following|follow|VBG modifications|modification|NNS .|.|. rRNA|rrna|NN was|be|VBD removed|remove|VBN with|with|IN Epicentre|Epicentre|NNP 's|'s|POS Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN .|.|. Subtracted|subtract|VBN RNA|rna|NN was|be|VBD fragmented|fragmented|JJ for|for|IN 3|3|CD min|min|NN using|use|VBG Ambion|Ambion|NNP 's|'s|POS RNA|rna|NN Fragmentation|fragmentation|NN Reagents|reagent|NNS .|.|. cDNA|cdna|NN was|be|VBD generated|generate|VBN using|use|VBG Invitrogen|Invitrogen|NNP 's|'s|POS SuperScript|SuperScript|NNP III|III|NNP First-Strand|First-Strand|NNP Synthesis|synthesis|NN protocol|protocol|NN with|with|IN random|random|JJ hexamer|hexamer|NN priming|priming|NN .|.|.
Pale|Pale|NNP _|_|SYM 1|1|CD
Pale|Pale|NNP _|_|SYM 3|3|CD
Paraquat|paraquat|NN was|be|VBD added|add|VBN to|to|TO growing|grow|VBG cultures|culture|NNS at|at|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 250|250|CD ?|?|. M.|M.|NNP Samples|Samples|NNP -LRB-|-lrb-|-LRB- 1.4|1.4|CD ml|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD taken|take|VBN every|every|DT 2|2|CD minutes|minute|NNS following|follow|VBG paraquat|paraquat|NN treatment|treatment|NN for|for|IN the|the|DT length|length|NN of|of|IN the|the|DT time|time|NN course|course|NN ,|,|, and|and|CC flash-frozen|flash-frozen|JJ by|by|IN immersion|immersion|NN of|of|IN the|the|DT tubes|tube|NNS in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN for|for|IN 1|1|CD minute|minute|NN at|at|IN 13,000|13,000|CD rpm|rpm|NN ,|,|,
parental|parental|JJ _|_|NN temperature|temperature|NN _|_|CD Up|up|IN _|_|CD 0|0|CD min|min|NN
parental|parental|JJ _|_|NN temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 16|16|CD min|min|NN
parental|parental|JJ _|_|NN temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 44|44|CD min|min|NN
parental|parental|JJ temperature|temperature|NN up|up|IN shift|shift|NN 0|0|CD min|min|NN
parental|parental|JJ temperature|temperature|NN up|up|IN shift|shift|NN 16|16|CD min|min|NN
parental|parental|JJ temperature|temperature|NN up|up|IN shift|shift|NN 44|44|CD min|min|NN
Parent|Parent|NNP LB|LB|NNP rep1|rep1|NN
Parent|Parent|NNP LB|LB|NNP rep2|rep2|NN
Parent|Parent|NNP M9|M9|NNP rep1|rep1|NN
Parent|Parent|NNP M9|M9|NNP rep2|rep2|NN
parent|parent|NN strain|strain|NN :|:|: BW27785|bw27785|NN
Parent|Parent|NNP strain|strain|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN
Parent|Parent|NNP strain|strain|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN as|as|IN adaptive|adaptive|JJ evolved|evolve|VBD E.|e.|FW coli|coli|FW W3110|w3110|NN strain|strain|NN to|to|TO M9|m9|NN synthetic|synthetic|JJ medium|medium|NN without|without|IN ethanol|ethanol|NN stress|stress|NN
passage|passage|NN :|:|: 4|4|CD
Pause|pause|NN sites|site|NNS in|in|IN E.|e.|FW coli|coli|FW wild-type|wild-type|JJ strain|strain|NN identified|identify|VBN by|by|IN RNET-seq|rnet-seq|NN
Pause|pause|NN sites|site|NNS in|in|IN E.|e.|FW coli|coli|FW ΔgreAB|δgreab|NN strain|strain|NN identified|identify|VBN by|by|IN RNET-seq|rnet-seq|NN
PC|pc|NN 1|1|CD
PC|pc|NN 2|2|CD
PC|pc|NN 3|3|CD
pCA24N-hns|pca24n-hn|NNS biofilm|biofilm|NN
pCA24N-hnsK57N|pca24n-hnsk57n|NN biofilm|biofilm|NN
PCA|pca|NN analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT top|top|JJ 500|500|CD genes|gene|NNS with|with|IN the|the|DT most|most|RBS variations|variation|NNS .|.|.
PCK|pck|NN _|_|CD glucose-minimal|glucose-minimal|JJ medium|medium|NN _|_|NN early|early|JJ log|log|NN phase|phase|NN
PCK|pck|NN _|_|CD LB-GlC|lb-glc|JJ medium|medium|NN _|_|NN D|d|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN
PCK|pck|NN over|over|IN
pControl|pcontrol|NN _|_|CD exponential|exponential|JJ growth|growth|NN phase|phase|NN _|_|NN 1|1|CD ml|ml|NN cell|cell|NN pellet|pellet|NN
pControl|pcontrol|NN _|_|CD stationary|stationary|JJ growth|growth|NN phase|phase|NN _|_|NN 1|1|CD ml|ml|NN cell|cell|NN pellet|pellet|NN
pControl|pcontrol|NN _|_|CD transition|transition|NN growth|growth|NN phase|phase|NN _|_|NN 1|1|CD ml|ml|NN cell|cell|NN pellet|pellet|NN
Peak|peak|JJ calling|calling|NN was|be|VBD done|do|VBN using|use|VBG SPAT|spat|NN
Peak-calls|peak-call|NNS were|be|VBD done|do|VBN using|use|VBG GPS|gps|NN within|within|IN the|the|DT GEMS|gem|NNS software|software|NN package|package|NN -LRB-|-lrb-|-LRB- v2|v2|NN .3|.3|NN -RRB-|-rrb-|-RRB- adapted|adapt|VBD for|for|IN ChIP-exo|ChIP-exo|NNP data|datum|NNS
Peak|peak|JJ detection|detection|NN and|and|CC count|count|NN of|of|IN coverage|coverage|NN were|be|VBD done|do|VBN using|use|VBG SEQMONK|SEQMONK|NNP version|version|NN 0.21.0|0.21.0|CD by|by|IN Fasteris|Fasteris|NNP SA|SA|NNP
Peaks|Peaks|NNPS on|on|IN opposing|oppose|VBG strands|strand|NNS were|be|VBD paired|pair|VBN with|with|IN Genetrack|genetrack|NN -LRB-|-lrb-|-LRB- u|u|NN =|=|JJ 0|0|CD ,|,|, d|d|NN =|=|JJ 80|80|CD ,|,|, b|b|NN =|=|JJ 2|2|CD ,|,|, m|m|NN =|=|JJ mode|mode|NN -RRB-|-rrb-|-RRB-
peaks|peak|NNS were|be|VBD called|call|VBN using|use|VBG MACS2|macs2|NN with|with|IN default|default|NN parameters|parameter|NNS
Peaks|Peaks|NNPS were|be|VBD called|call|VBN with|with|IN GeneTrack|genetrack|NN 1.0.3|1.0.3|CD -LRB-|-lrb-|-LRB- s|s|NN =|=|JJ 5|5|CD ,|,|, e|e|SYM =|=|JJ 10|10|CD -RRB-|-rrb-|-RRB-
Peconic|Peconic|NNP LLC|LLC|NNP performed|perform|VBD data|datum|NNS processing|processing|NN
PEN205|pen205|NN
PEN205|pen205|NN strain|strain|NN first|first|JJ repetition|repetition|NN
PEN205|pen205|NN strain|strain|NN second|second|JJ repetition|repetition|NN
PEN205|pen205|NN strain|strain|NN third|third|JJ repetition|repetition|NN
PF2-04|pf2-04|NN
PF2-04|pf2-04|NN _|_|CD R1|r1|NN
PF2-04|pf2-04|NN _|_|CD R2|r2|NN
PF2-04|pf2-04|NN _|_|CD R3|r3|NN
PF2-08|pf2-08|NN
PF2-08|pf2-08|NN _|_|CD R1|r1|NN
PF2-08|pf2-08|NN _|_|CD R2|r2|NN
PF2-08|pf2-08|NN _|_|CD R3|r3|NN
PF2-12|pf2-12|NN
PF2-12|pf2-12|NN _|_|CD R1|r1|NN
PF2-12|pf2-12|NN _|_|CD R2|r2|NN
PF2-12|pf2-12|NN _|_|CD R3|r3|NN
pFlag-only|pflag-only|NN control|control|NN
pgi-ala-1|pgi-ala-1|NN
pgi-ala-2|pgi-ala-2|NN
pgi|pgi|NN mutantin|mutantin|NN Ala|ala|NN media|media|NNS
pgi|pgi|NN mutantin|mutantin|NN Gln|gln|NN media|media|NNS
pGIT1|pgit1|NN
pGIT1|pgit1|NN .1|.1|CD
pGIT1|pgit1|NN .1|.1|NN +|+|CC NO2|no2|NN
pGIT1|pgit1|NN .2|.2|NN
pGIT1|pgit1|NN .2|.2|NN +|+|CC NO2|no2|NN
pGIT1|pgit1|NN .3|.3|NN
pGIT1|pgit1|NN .3|.3|NN +|+|CC NO2|no2|NN
pGIT1|pgit1|NN .4|.4|CD
pGIT1|pgit1|NN .4|.4|NN +|+|CC NO2|no2|NN
pGIT1|pgit1|NN +|+|CC NO2|no2|NN
pGIT8|pgit8|NN
pGIT8|pgit8|NN .1|.1|NN +|+|CC NO2|no2|NN
pGIT8|pgit8|NN .2|.2|NN +|+|CC NO2|no2|NN
pGIT8|pgit8|NN .3|.3|NN +|+|CC NO2|no2|NN
pGIT8|pgit8|NN .4|.4|NN +|+|CC NO2|no2|NN
pGIT8|pgit8|NN +|+|CC NO2|no2|NN
PGRP-1|pgrp-1|NN ,|,|, biological|biological|JJ rep1|rep1|NN
PGRP-2|pgrp-2|NN ,|,|, biological|biological|JJ rep2|rep2|NN
PGRP-3|pgrp-3|NN ,|,|, biological|biological|JJ rep3|rep3|NN
pH|ph|NN =|=|JJ 5.3|5.3|CD
ph|ph|NN :|:|: 5.6|5.6|CD
pH|ph|NN =|=|JJ 5.7|5.7|CD
ph|ph|NN :|:|: 7.2|7.2|CD
phage|phage|NN DNA|dna|NN
phage|phage|NN :|:|: Lambda|Lambda|NNP
phase|phase|NN :|:|: early|early|JJ stationary|stationary|JJ phase|phase|NN
phase|phase|NN :|:|: logarithmic|logarithmic|JJ phase|phase|NN
phase|phase|NN :|:|: log|log|NN phase|phase|NN
phase|phase|NN of|of|IN growth|growth|NN :|:|: 15|15|CD min|min|NN post|post|NN stationary|stationary|JJ
phase|phase|NN of|of|IN growth|growth|NN :|:|: 180|180|CD min|min|NN post|post|NN stationary|stationary|JJ
phase|phase|NN of|of|IN growth|growth|NN :|:|: 30|30|CD min|min|NN post|post|NN stationary|stationary|JJ
phase|phase|NN of|of|IN growth|growth|NN :|:|: Late|late|JJ log|log|NN phase|phase|NN OD|od|NN 1.6|1.6|CD
phase|phase|NN of|of|IN growth|growth|NN :|:|: Log|log|VB phase|phase|NN OD|od|NN 0.1|0.1|CD
phase|phase|NN of|of|IN growth|growth|NN :|:|: Log|log|VB phase|phase|NN OD|od|NN 0.2|0.2|CD
phase|phase|NN of|of|IN growth|growth|NN :|:|: Log|log|VB phase|phase|NN OD|od|NN 0.3|0.3|CD
phase|phase|NN of|of|IN growth|growth|NN :|:|: Log|log|VB phase|phase|NN OD|od|NN 0.4|0.4|CD
phase|phase|NN of|of|IN growth|growth|NN :|:|: Log|log|VB phase|phase|NN OD|od|NN 0.8|0.8|CD
phase|phase|NN of|of|IN growth|growth|NN :|:|: Log|log|VB phase|phase|NN OD|od|NN 1.4|1.4|CD
pHDB3|phdb3|NN _|_|NN 1|1|CD
pHDB3|phdb3|NN _|_|NN 2|2|CD
pHDB3|phdb3|NN _|_|CD 3|3|CD
phenotype|phenotype|NN :|:|: 0.6|0.6|CD %|%|NN n-butanol|n-butanol|NN tolerance|tolerance|NN
phenotype|phenotype|NN :|:|: 2|2|CD %|%|NN n-butanol|n-butanol|NN tolerance|tolerance|NN
phenotype|phenotype|NN :|:|: Blue|Blue|NNP colony-color|colony-color|NN -LRB-|-lrb-|-LRB- prion-containing|prion-containing|JJ -RRB-|-rrb-|-RRB-
phenotype|phenotype|NN :|:|: lacking|lack|VBG FNR|fnr|NN protein|protein|NN
phenotype|phenotype|NN :|:|: normal|normal|JJ
phenotype|phenotype|NN :|:|: Pale|Pale|NNP colony-color|colony-color|NN -LRB-|-lrb-|-LRB- prion-lacking|prion-lacking|NN -RRB-|-rrb-|-RRB-
phenotype|phenotype|NN :|:|: small|small|JJ improvement|improvement|NN in|in|IN methyl|methyl|NN ketone|ketone|NN production|production|NN
Phenylalanine|Phenylalanine|NNP addition|addition|NN
phoA|phoa|NN _|_|NN 0|0|CD min|min|NN
phoA|phoa|NN _|_|CD 10|10|CD min|min|NN
phoA|phoa|NN _|_|CD 15|15|CD min|min|NN
phoA|phoa|NN _|_|NN 1|1|CD min|min|NN
phoA|phoa|NN _|_|NN 2|2|CD min|min|NN
phoA|phoa|NN _|_|CD 4|4|CD min|min|NN
phoA|phoa|NN _|_|CD 6|6|CD min|min|NN
phoA|phoa|NN _|_|CD 8|8|CD min|min|NN
PhoB|phob|NN _|_|CD ChIP|chip|NN ,|,|, rep1|rep1|NN
PhoB|phob|NN _|_|CD ChIP|chip|NN ,|,|, rep2|rep2|NN
PhoB|phob|NN _|_|CD ChIP|chip|NN ,|,|, rep3|rep3|NN
PhoB|phob|NN knock-out|knock-out|JJ strain|strain|NN ,|,|, rep1|rep1|NN
PhoB|phob|NN knock-out|knock-out|JJ strain|strain|NN ,|,|, rep2|rep2|NN
phoU|phou|NN _|_|NN 1|1|CD
phoU|phou|NN _|_|NN 2|2|CD
phoU|phou|NN _|_|CD 3|3|CD
phoU|phou|NN gene|gene|NN mutant|mutant|JJ
phoU|phou|NN gene|gene|NN mutant|mutant|NN ;|;|: minimal|minimal|JJ medium|medium|NN
Physiological|physiological|JJ perturbations|perturbation|NNS were|be|VBD carried|carry|VBN out|out|RP under|under|IN a|a|DT controlled|controlled|JJ environment|environment|NN in|in|IN the|the|DT context|context|NN of|of|IN bioreactor|bioreactor|NN -LRB-|-lrb-|-LRB- Bioflo|bioflo|NN 110|110|CD ,|,|, New|New|NNP Brunswick|Brunswick|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- growth|growth|NN .|.|. Thermoelectric|Thermoelectric|NNP sensors|sensor|NNS and|and|CC heaters|heater|NNS were|be|VBD used|use|VBN to|to|TO shift|shift|VB temperature|temperature|NN profiles|profile|NNS between|between|IN 250|250|CD C|c|NN and|and|CC 370|370|CD C|c|NN ,|,|, and|and|CC polarographic|polarographic|JJ dissolved|dissolve|VBN oxygen|oxygen|NN sensors|sensor|NNS -LRB-|-lrb-|-LRB- Mettler|Mettler|NNP Toledo|Toledo|NNP -RRB-|-rrb-|-RRB- and|and|CC nitrogen|nitrogen|NN gas|gas|NN was|be|VBD used|use|VBN to|to|TO rapidly|rapidly|RB change|change|VB oxygen|oxygen|NN saturation|saturation|NN between|between|IN anaerobic|anaerobic|JJ -LRB-|-lrb-|-LRB- 0|0|CD %|%|NN dissolved|dissolve|VBN oxygen|oxygen|NN -RRB-|-rrb-|-RRB- and|and|CC aerobic|aerobic|JJ -LRB-|-lrb-|-LRB- 16-21|16-21|CD %|%|NN dissolved|dissolve|VBN oxygen|oxygen|NN -RRB-|-rrb-|-RRB- condition|condition|NN .|.|.
P|p|NN is|be|VBZ defined|define|VBN by|by|IN the|the|DT pair|pair|NN of|of|IN integers|integer|NNS -LRB-|-lrb-|-LRB- X|x|NN ,|,|, Y|y|NN -RRB-|-rrb-|-RRB- .|.|. Log|log|VB ratios|ratio|NNS were|be|VBD defined|define|VBN as|as|IN the|the|DT base|base|NN 10|10|CD logarithm|logarithm|NN
Pixel|Pixel|NNP intensities|intensity|NNS were|be|VBD extracted|extract|VBN using|use|VBG the|the|DT ``|``|`` Feature|Feature|NNP Extraction|Extraction|NNP ''|''|'' software|software|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Palo|Palo|NNP Alto|Alto|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. No|no|DT normalization|normalization|NN step|step|NN was|be|VBD performed|perform|VBN and|and|CC the|the|DT retained|retain|VBN intensity|intensity|NN value|value|NN for|for|IN each|each|DT probe|probe|NN was|be|VBD the|the|DT ratio|ratio|NN between|between|IN the|the|DT spot|spot|NN 's|'s|POS median|median|JJ intensity|intensity|NN signals|signal|NNS and|and|CC the|the|DT median|median|NN of|of|IN background|background|NN signals|signal|NNS .|.|.
planktonic|planktonic|JJ cells|cell|NNS
Planktonic|planktonic|JJ cultures|culture|NNS of|of|IN E.|e.|FW coli|coli|FW were|be|VBD harvested|harvest|VBN and|and|CC resuspended|resuspend|VBN in|in|IN RNAlater|rnalater|NN and|and|CC kept|keep|VBD in|in|IN 4C|4c|NN fridge|fridge|NN overnight|overnight|JJ .|.|. Suspended|suspend|VBN cells|cell|NNS were|be|VBD removed|remove|VBN from|from|IN petri|petri|JJ dishes|dish|NNS and|and|CC biofilms|biofilm|NNS were|be|VBD washed|wash|VBN three|three|CD times|time|NNS with|with|IN fresh|fresh|JJ 10|10|CD %|%|NN LB|lb|NN before|before|IN being|be|VBG craped|crap|VBN from|from|IN the|the|DT bottom|bottom|JJ surface|surface|NN of|of|IN petri|petri|NN dishes|dish|NNS .|.|. Biofilms|biofilm|NNS were|be|VBD also|also|RB re-suspeded|re-suspeded|JJ into|into|IN RNAlater|rnalater|NN and|and|CC kept|keep|VBD at|at|IN 4C|4c|NN overnight|overnight|JJ .|.|. Both|both|DT planktonic|planktonic|JJ and|and|CC biofilm|biofilm|NN samples|sample|NNS were|be|VBD homogenized|homogenize|VBN for|for|IN 2|2|CD min|min|NN on|on|IN ice|ice|NN with|with|IN an|a|DT Omni|Omni|NNP TH|th|NN homogenizer|homogenizer|NN .|.|. Cells|cell|NNS were|be|VBD then|then|RB aliquoted|aliquote|VBN into|into|IN vials|vial|NNS containing|contain|VBG around|around|IN 2x10|2x10|JJ ^|^|NN 8|8|CD cells|cell|NNS .|.|. Cells|cell|NNS in|in|IN each|each|DT vial|vial|NN were|be|VBD then|then|RB re-suspended|re-suspended|JJ in|in|IN nuclease-free|nuclease-free|JJ phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN ,|,|, incubated|incubate|VBN with|with|IN anti-E|anti-e|JJ .|.|. coli|coli|NN antibody|antibody|NN and|and|CC microbeads|microbead|NNS ,|,|, followed|follow|VBN by|by|IN separation|separation|NN on|on|IN a|a|DT MACS|macs|NN separator|separator|NN -LRB-|-lrb-|-LRB- Miltenyi|Miltenyi|NNP ,|,|, Auburn|Auburn|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD degree|degree|NN C.|c.|NN Sorted|sort|VBN cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ into|into|IN RNAlater|rnalater|NN .|.|.
plasmid|plasmid|NN cured|cure|VBD rep1|rep1|NN
plasmid|plasmid|NN cured|cure|VBD rep2|rep2|NN
Plasmid|plasmid|NN DNA|dna|NN ,|,|, after|after|IN n-butanol|n-butanol|NN selection|selection|NN
Plasmid|plasmid|NN DNA|dna|NN ,|,|, BWG|BWG|NNP post|post|NN conjugation|conjugation|NN
Plasmid|plasmid|NN DNA|dna|NN ,|,|, BWY|BWY|NNP post|post|NN conjugation|conjugation|NN
Plasmid|plasmid|NN DNA|dna|NN ,|,|, donor|donor|NN ,|,|, XL1-Blue|xl1-blue|JJ
Plasmid|plasmid|NN DNA|dna|NN ,|,|, post|post|NN conjugation|conjugation|NN
plasmid|plasmid|NN :|:|: Donor|Donor|NNP Library|Library|NNP
plasmid|plasmid|NN :|:|: empty|empty|JJ vector|vector|NN
plasmid|plasmid|NN :|:|: G181D|g181d|NN NusA|nusa|NN
plasmid|plasmid|NN :|:|: G324D|g324d|NN Rho|rho|NN mutant|mutant|JJ
plasmid|plasmid|NN :|:|: Initial|initial|JJ Recipient|Recipient|NNP Library|Library|NNP -LRB-|-lrb-|-LRB- BWG|BWG|NNP -RRB-|-rrb-|-RRB-
plasmid|plasmid|NN :|:|: Initial|initial|JJ Recipient|Recipient|NNP Library|Library|NNP -LRB-|-lrb-|-LRB- BWY|BWY|NNP -RRB-|-rrb-|-RRB-
plasmid|plasmid|NN :|:|: N340S|n340s|NN Rho|rho|NN mutant|mutant|JJ
plasmid|plasmid|NN :|:|: None|none|NN
plasmid|plasmid|NN :|:|: pBAD|pbad|NN
plasmid|plasmid|NN :|:|: pBAD30-empty|pbad30-empty|NN
plasmid|plasmid|NN :|:|: pBAD30-MazF|pbad30-mazf|NN
plasmid|plasmid|NN :|:|: pBADsigma32I54N|pbadsigma32i54n|NN
plasmid|plasmid|NN :|:|: pBADsigma32wt|pbadsigma32wt|NN
plasmid|plasmid|NN :|:|: pBAD-tosR|pbad-tosr|NN
plasmid|plasmid|NN :|:|: pControl|pcontrol|NN
plasmid|plasmid|NN :|:|: PD864|pd864|NN
plasmid|plasmid|NN :|:|: pKEDR13|pkedr13|NN
plasmid|plasmid|NN :|:|: pKESK22|pkesk22|NN
plasmid|plasmid|NN :|:|: pKETS1|pkets1|NN
plasmid|plasmid|NN :|:|: pLCenvZM|plcenvzm|NN ,|,|, pPCB|ppcb|NN -LRB-|-lrb-|-LRB- mutation|mutation|NN -RRB-|-rrb-|-RRB-
Plasmid|plasmid|NN pLCenvZ|plcenvz|NN or|or|CC pLCenvZM|plcenvzm|NN was|be|VBD co-transformed|co-transform|VBN with|with|IN pPCB|ppcb|NN into|into|IN the|the|DT competent|competent|JJ cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW JW3367|jw3367|NN and|and|CC spread|spread|NN on|on|IN LB|LB|NNP agar|agar|NN plates|plate|NNS containing|contain|VBG Ampicillin|ampicillin|NN -LRB-|-lrb-|-LRB- 50|50|CD ng/μl|ng/μl|NN -RRB-|-rrb-|-RRB- and|and|CC Chloramphenicol|chloramphenicol|NN -LRB-|-lrb-|-LRB- 170|170|CD ng/μl|ng/μl|NN -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN overnight|overnight|JJ .|.|. A|a|DT single|single|JJ colony|colony|NN was|be|VBD diluted|dilute|VBN in|in|IN 2.5|2.5|CD ml|ml|NN LB|lb|NN medium|medium|NN containing|contain|VBG Ampicillin|ampicillin|NN -LRB-|-lrb-|-LRB- 50|50|CD ng/μl|ng/μl|NN -RRB-|-rrb-|-RRB- and|and|CC Chloramphenicol|chloramphenicol|NN -LRB-|-lrb-|-LRB- 170|170|CD ng/μl|ng/μl|NN -RRB-|-rrb-|-RRB- and|and|CC was|be|VBD shaken|shake|VBN at|at|IN 250|250|CD rpm|rpm|NN and|and|CC 37|37|CD °C|°c|NN overnight|overnight|JJ .|.|.
plasmid|plasmid|NN :|:|: pLCenvZ|plcenvz|NN ,|,|, pPCB|ppcb|NN -LRB-|-lrb-|-LRB- wild|wild|JJ type|type|NN -RRB-|-rrb-|-RRB-
plasmid|plasmid|NN :|:|: pLPLσ|plplσ|NN
plasmid|plasmid|NN :|:|: PLYS|plys|NN
plasmid|plasmid|NN :|:|: pMicL|pmicl|NN
plasmid|plasmid|NN :|:|: pMicL-S|pmicl-s|NN
Plasmid|plasmid|NN pool|pool|NN
plasmid|plasmid|NN :|:|: pPROEx-CAT|pproex-cat|NN
plasmid|plasmid|NN :|:|: PSB1C3|psb1c3|NN
plasmid|plasmid|NN :|:|: R258C|r258c|NN NusA|nusa|NN
plasmid|plasmid|NN :|:|: R258C|r258c|NN NuSA|nusa|NN
plasmid|plasmid|NN source|source|NN :|:|: Initial|initial|JJ Recipient|Recipient|NNP Library|Library|NNP
plasmid|plasmid|NN source|source|NN :|:|: Post|Post|NNP Selection|selection|NN Library|Library|NNP
plasmid|plasmid|NN :|:|: wild|wild|JJ type|type|NN NusA|nusa|NN
plasmid|plasmid|NN :|:|: WT|WT|NNP Rho|rho|NN
platform|platform|NN _|_|CD id|id|NN design|design|NN :|:|: EcFS|ecfs|NN _|_|NN 1|1|CD
platform|platform|NN _|_|CD id|id|NN design|design|NN :|:|: EcFS|ecfs|NN _|_|NN 2|2|CD
platform|platform|NN _|_|CD id|id|NN _|_|CD id|id|NN design|design|NN :|:|: EcFS|ecfs|NN _|_|NN 1|1|CD
platform|platform|NN _|_|CD id|id|NN _|_|CD id|id|NN design|design|NN :|:|: EcFS|ecfs|NN _|_|NN 2|2|CD
platform|platform|NN _|_|CD id|id|NN _|_|CD id|id|NN design|design|NN :|:|: EcFS|ecfs|NN _|_|NN 3|3|CD
pLCV1|plcv1|NN _|_|NN 1|1|CD
pLCV1|plcv1|NN _|_|NN 2|2|CD
pLCV1|plcv1|NN _|_|CD 3|3|CD
pLPLσ|plplσ|NN _|_|CD exponential|exponential|JJ growth|growth|NN phase|phase|NN _|_|NN 1|1|CD ml|ml|NN cell|cell|NN pellet|pellet|NN
pLPLσ|plplσ|NN _|_|CD stationary|stationary|JJ growth|growth|NN phase|phase|NN _|_|NN 1|1|CD ml|ml|NN cell|cell|NN pellet|pellet|NN
pLPLσ|plplσ|NN _|_|CD transition|transition|NN growth|growth|NN phase|phase|NN _|_|NN 1|1|CD ml|ml|NN cell|cell|NN pellet|pellet|NN
plus|plus|CC Symbioflor|symbioflor|JJ
∆|∆|CD pnp|pnp|NN _|_|CD RNA-Seq|rna-seq|NN
Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Pnp|Pnp|NNP -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Pnp|Pnp|NNP -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Pnp|Pnp|NNP -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Pnp|Pnp|NNP -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Pnp|Pnp|NNP -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1.5|1.5|CD '|'|'' post|post|JJ rif|rif|NN
Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3|3|CD '|'|'' post|post|JJ rif|rif|NN
Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6|6|CD '|'|'' post|post|JJ rif|rif|NN
Poly|poly|NN
Polyclonal|polyclonal|JJ antibody|antibody|NN for|for|IN NusG|nusg|NN -LRB-|-lrb-|-LRB- raised|raise|VBN for|for|IN this|this|DT study|study|NN -RRB-|-rrb-|-RRB-
Polyclonal|polyclonal|JJ antibody|antibody|NN for|for|IN Rho|rho|NN -LRB-|-lrb-|-LRB- gift|gift|NN from|from|IN Jeff|Jeff|NNP Roberts|Roberts|NNP -RRB-|-rrb-|-RRB-
polyphosphate|polyphosphate|NN kinase|kinase|NN 1|1|CD -LRB-|-lrb-|-LRB- PPK1|ppk1|NN -RRB-|-rrb-|-RRB- mutant|mutant|JJ
Polysomes|polysome|NNS were|be|VBD digested|digest|VBN with|with|IN MNase|mnase|NN ,|,|, monosomes|monosome|NNS were|be|VBD purified|purify|VBN by|by|IN sucrose|sucrose|NN gradient|gradient|NN ultracentrifugation|ultracentrifugation|NN ,|,|, and|and|CC the|the|DT resulting|result|VBG mRNA|mrna|NN fragments|fragment|NNS were|be|VBD extracted|extract|VBN with|with|IN phenol|phenol|NN chloroform|chloroform|NN and|and|CC gel-purified|gel-purified|JJ .|.|.
pooled|pool|VBD reference|reference|NN RNA|rna|NN
pooled|pool|VBD RNA|rna|NN from|from|IN all|all|DT conditions|condition|NNS including|include|VBG the|the|DT control|control|NN ,|,|, reference|reference|NN
pool|pool|NN of|of|IN aliquots|aliquot|NNS from|from|IN all|all|DT samples|sample|NNS
Pool|Pool|NNP of|of|IN eight|eight|CD independent|independent|JJ cultures|culture|NNS
population|population|NN :|:|: 1|1|CD
population|population|NN :|:|: 2|2|CD
population|population|NN :|:|: 3|3|CD
population|population|NN :|:|: 4|4|CD
population|population|NN :|:|: 5|5|CD
population|population|NN :|:|: 6|6|CD
population|population|NN :|:|: 7|7|CD
population|population|NN :|:|: A2|a2|NN
population|population|NN :|:|: A4|a4|NN
population|population|NN :|:|: G2|g2|NN
population|population|NN :|:|: G3|g3|NN
population|population|NN :|:|: G5|g5|NN
population|population|NN :|:|: G6|g6|NN
Post-processing|post-processing|NN of|of|IN the|the|DT sequencing|sequencing|NN reads|read|VBZ from|from|IN RNA-seq|rna-seq|NN experiments|experiment|NNS for|for|IN each|each|DT sample|sample|NN was|be|VBD performed|perform|VBN using|use|VBG HudsonAlpha|HudsonAlpha|NNP 's|'s|POS unique|unique|JJ in-house|in-house|JJ RNA-seq|rna-seq|NN data|data|NN analysis|analysis|NN pipeline|pipeline|NN .|.|. Briefly|briefly|RB ,|,|, quality|quality|NN control|control|NN checks|check|NNS on|on|IN raw|raw|JJ sequence|sequence|NN data|datum|NNS for|for|IN each|each|DT sample|sample|NN were|be|VBD performed|perform|VBN using|use|VBG FastQC|fastqc|NN -LRB-|-lrb-|-LRB- Babraham|babraham|NN Bioinformatics|bioinformatic|NNS ,|,|, Cambridge|Cambridge|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- .|.|. Data-analysis|data-analysis|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT CLC|clc|NN Genomics|genomic|NNS Workbench|Workbench|NNP -LRB-|-lrb-|-LRB- Version|Version|NNP 7.5.1|7.5.1|CD ,|,|, CLC|clc|NN Bio|bio|NN ,|,|, Aarhus|Aarhus|NNP ,|,|, Denmark|Denmark|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT reference|reference|NN genome|genome|NN Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- DH10B|dh10b|NN -RRB-|-rrb-|-RRB- sequence|sequence|NN was|be|VBD downloaded|download|VBN from|from|IN the|the|DT UCSC|UCSC|NNP genome|genome|NN browser|browser|NN .|.|. For|for|IN read|read|VBN mapping|mapping|NN ,|,|, the|the|DT following|follow|VBG parameters|parameter|NNS were|be|VBD used|use|VBN :|:|: mismatch|mismatch|NN cost|cost|NN =|=|JJ 2|2|CD ,|,|, insertion|insertion|NN and|and|CC deletion|deletion|NN cost|cost|NN =|=|JJ 3|3|CD ,|,|, length|length|NN fraction|fraction|NN :|:|: 0.8|0.8|CD ,|,|, similarity|similarity|NN fraction|fraction|NN =|=|JJ 0.8|0.8|CD ,|,|, global|global|JJ alignment|alignment|NN =|=|JJ no|no|DT ,|,|, auto-detect|auto-detect|JJ paired|paired|JJ distances|distance|NNS =|=|JJ yes|yes|UH .|.|. Samples|sample|NNS were|be|VBD grouped|group|VBN and|and|CC differential|differential|JJ expression|expression|NN of|of|IN genes|gene|NNS was|be|VBD calculated|calculate|VBN on|on|IN the|the|DT basis|basis|NN of|of|IN fold|fold|JJ changes|change|NNS -LRB-|-lrb-|-LRB- using|use|VBG the|the|DT default|default|NN cut-off|cut-off|JJ ≥|≥|NN ±|±|NN 2.0|2.0|CD -RRB-|-rrb-|-RRB- observed|observe|VBN in|in|IN comparisons|comparison|NNS between|between|IN defined|define|VBN conditions|condition|NNS .|.|.
postscript|postscript|NN -LRB-|-lrb-|-LRB- file|file|NN =\|=\|CD
PPC|PPC|NNP _|_|SYM glucose-minimal|glucose-minimal|JJ medium|medium|NN _|_|NN early|early|JJ log|log|NN phase|phase|NN
PPC|PPC|NNP _|_|SYM LB-GlC|lb-glc|JJ medium|medium|NN _|_|NN D|d|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN
PPK1-PPX|ppk1-ppx|NN double|double|JJ mutant|mutant|JJ
ppk|ppk|NN KO|KO|NNP LB|LB|NNP rep1|rep1|NN
ppk|ppk|NN KO|KO|NNP LB|LB|NNP rep2|rep2|NN
ppk|ppk|NN KO|ko|NN M9|m9|NN rep1|rep1|NN
ppk|ppk|NN KO|ko|NN M9|m9|NN rep2|rep2|NN
∆|∆|CD ppk|ppk|NN parent|parent|NN Sample|sample|NN 24|24|CD
∆|∆|CD ppk|ppk|NN parent|parent|NN Sample|sample|NN 43|43|CD
∆|∆|CD ppk|ppk|NN parent|parent|NN Sample|sample|NN 5|5|CD
ppk|ppk|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 25|25|CD
ppk|ppk|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 44|44|CD
ppk|ppk|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 6|6|CD
ppk|ppk|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 26|26|CD
ppk|ppk|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 45|45|CD
ppk|ppk|NN suppressor|suppressor|NN 2-1|2-1|CD Sample|sample|NN 7|7|CD
ppk|ppk|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 27|27|CD
ppk|ppk|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 46|46|CD
ppk|ppk|NN suppressor|suppressor|NN 3-1|3-1|CD Sample|sample|NN 8|8|CD
ppsA|ppsa|NN mutant|mutant|JJ 15|15|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 15|15|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|NN 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|NN 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|NN 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|NN 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|NN 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|NN 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|NN 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|NN 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|NN 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|NN 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|NN 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|NN 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 30|30|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 30|30|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 5|5|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 5|5|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
ppsA|ppsa|NN mutant|mutant|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
ppsA|ppsa|NN mutant|mutant|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
preprocessed|preprocessed|JJ RNA-Seq|rna-seq|NN reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN Escherichia|escherichia|FW coli|coli|FW strain|strain|NN K12|k12|NN sub-strain|sub-strain|JJ MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN accession|accession|NN no|no|DT .|.|. U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- by|by|IN BWA|BWA|NNP toolkit|toolkit|NN version|version|NN 0.5.9-r16|0.5.9-r16|NN with|with|IN the|the|DT following|follow|VBG options|option|NNS :|:|: bwa|bwa|NN aln|aln|NN -|-|: q|q|NN 20|20|CD
print|print|NN tip|tip|NN ,|,|, and|and|CC subtracting|subtract|VBG the|the|DT resulting|result|VBG average|average|NN from|from|IN all|all|DT the|the|DT individual|individual|JJ log|log|NN ratios|ratio|NNS
Prior|prior|RB to|to|TO total|total|JJ RNA|rna|NN extraction|extraction|NN harvested|harvest|VBN bacterial|bacterial|JJ cells|cell|NNS were|be|VBD stored|store|VBN at|at|IN -80.0|-80.0|CD °C|°c|NN in|in|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN RNAlater|rnalater|NN .|.|.
Probabilistic|Probabilistic|NNP expression|expression|NN counting|counting|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT RNA-Seq|rna-seq|NN by|by|IN Expectation-Maximization|expectation-maximization|NN -LRB-|-lrb-|-LRB- RSEM|rsem|NN -RRB-|-rrb-|-RRB- version|version|NN 1.2.4|1.2.4|CD -LRB-|-lrb-|-LRB- Li|Li|NNP and|and|CC Dewey|Dewey|NNP ,|,|, 2011|2011|CD -RRB-|-rrb-|-RRB-
Probe|Probe|NNP signal|signal|NN intensities|intensity|NNS were|be|VBD preprocessed|preprocess|VBN using|use|VBG robust|robust|JJ multichip|multichip|NN averaging|averaging|NN -LRB-|-lrb-|-LRB- RMA|rma|NN -RRB-|-rrb-|-RRB- in|in|IN the|the|DT program|program|NN ArrayStar|arraystar|NN -LRB-|-lrb-|-LRB- DNASTAR|dnastar|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC the|the|DT resulting|result|VBG gene|gene|NN expression|expression|NN signals|signal|NNS were|be|VBD quantile-normalized|quantile-normalize|VBN across|across|IN all|all|DT samples|sample|NNS using|use|VBG the|the|DT normalize.quantiles|normalize.quantiles|JJ function|function|NN in|in|IN the|the|DT Bioconductor|Bioconductor|NNP package|package|NN for|for|IN R.|R.|NNP
Procedures|procedure|NNS to|to|TO calculate|calculate|VB the|the|DT value|value|NN of|of|IN log2|log2|NN ratio|ratio|NN :|:|:
product|product|NN :|:|: Butanol|Butanol|NNP
Progesterone|progesterone|NN Treatment|treatment|NN
Proline|proline|NN addition|addition|NN
Promega|Promega|NNP RNase-free|RNase-free|NNP DNase|dnase|NN
Protein|protein|NN DNA|dna|NN interactions|interaction|NNS were|be|VBD crosslinked|crosslink|VBN for|for|IN 10|10|CD min|min|NN at|at|IN 22.5|22.5|CD C|c|NN with|with|IN 1|1|CD %|%|NN formaldehyde|formaldehyde|NN and|and|CC quenched|quench|VBN using|use|VBG glycine|glycine|NN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.5|0.5|CD M|m|NN
protein|protein|NN :|:|: GST|gst|NN expressed|express|VBN in|in|IN E.|e.|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- from|from|IN pGEX-4T-3|pgex-4t-3|NN
protocol|protocol|NN :|:|: late|late|JJ log|log|NN phase|phase|NN ,|,|, LB|lb|NN
protocol|protocol|NN :|:|: late|late|JJ log|log|NN phase|phase|NN ,|,|, LB|lb|NN ,|,|, 30|30|CD min|min|NN after|after|IN butanol|butanol|NN treatment|treatment|NN
protocol|protocol|NN :|:|: M9|m9|NN
protocol|protocol|NN :|:|: M9|m9|NN supplemented|supplement|VBN with|with|IN 0.6|0.6|CD M|m|NN NaCl|nacl|NN
protocol|protocol|NN :|:|: small|small|JJ RNA|rna|NN DicF|dicf|NN
protocol|protocol|NN :|:|: vector|vector|NN control|control|NN
pseudoalignment|pseudoalignment|NN and|and|CC quantitation|quantitation|NN with|with|IN kallisto|kallisto|FW v0|v0|FW .42.5|.42.5|CD with|with|IN parameters|parameter|NNS --|--|: single|single|JJ -|-|: l|l|NN 450|450|CD -|-|: s|s|NNS 250|250|CD
Ptac|ptac|NN :|:|: :|:|: fnr|fnr|SYM -|-|: A|a|NN -|-|: 16|16|CD µM|µm|NN IPTG|iptg|NN
Ptac|ptac|NN :|:|: :|:|: fnr|fnr|SYM -|-|: A|a|NN -|-|: 4|4|CD µM|µm|NN IPTG|iptg|NN
Ptac|ptac|NN :|:|: :|:|: fnr|fnr|SYM -|-|: A|a|NN -|-|: 8|8|CD µM|µm|NN IPTG|iptg|NN
Ptac|ptac|NN :|:|: :|:|: fnr|fnr|SYM -|-|: B|b|NN -|-|: 16|16|CD µM|µm|NN IPTG|iptg|NN
Ptac|ptac|NN :|:|: :|:|: fnr|fnr|SYM -|-|: B|b|NN -|-|: 4|4|CD µM|µm|NN IPTG|iptg|NN
Ptac|ptac|NN :|:|: :|:|: fnr|fnr|SYM -|-|: B|b|NN -|-|: 8|8|CD µM|µm|NN IPTG|iptg|NN
Ptac|ptac|NN :|:|: :|:|: fnr|fnr|SYM -|-|: C|c|NN -|-|: 16|16|CD µM|µm|NN IPTG|iptg|NN
ptsN|ptsn|NN mutant|mutant|NN replicate|replicate|VBP 1|1|CD
ptsN|ptsn|NN mutant|mutant|NN replicate|replicate|VBP 2|2|CD
Pure|pure|JJ culture|culture|NN in|in|IN LB|LB|NNP
purification|purification|NN :|:|: Protein|protein|NN purified|purify|VBN using|use|VBG GSH-sepharose|gsh-sepharose|JJ 4b|4b|NN -LRB-|-lrb-|-LRB- GE|GE|NNP Life|Life|NNP Sciences|Sciences|NNP -RRB-|-rrb-|-RRB-
Purified|purify|VBN total|total|JJ RNA|rna|NN was|be|VBD depleted|deplete|VBN of|of|IN rRNA|rrna|NN using|use|VBG a|a|DT Ribo-Zero|ribo-zero|NN -LRB-|-lrb-|-LRB- Bacteria|bacterium|NNS -RRB-|-rrb-|-RRB- rRNA|rrna|NN Removal|removal|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|. cDNA|cdna|NN libraries|library|NNS were|be|VBD constructed|construct|VBN and|and|CC sequenced|sequence|VBN on|on|IN an|a|DT Illumina|Illumina|NNP NextSeq|NextSeq|NNP 500|500|CD sequencer|sequencer|NN at|at|IN the|the|DT Harvard|Harvard|NNP Biopolymers|Biopolymers|NNP Facility|Facility|NNP .|.|.
PurR|purr|NN _|_|CD Adenine|Adenine|NNP _|_|SYM 1|1|CD
PurR|purr|NN _|_|CD Adenine|Adenine|NNP _|_|NN 2|2|CD
PurR|purr|NN _|_|CD glucose|glucose|NN _|_|NN 1|1|CD
PurR|purr|NN _|_|CD glucose|glucose|NN _|_|NN 2|2|CD
putP|putp|NN KO|ko|NN rep1|rep1|NN
putP|putp|NN KO|ko|NN rep2|rep2|NN
putP|putp|NN KO|ko|NN rep3|rep3|NN
pyrC|pyrc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
pyrC|pyrc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
pyrC|pyrc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
pyrC|pyrc|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
qC|qc|NN :|:|: We|we|PRP checked|check|VBD the|the|DT quality|quality|NN of|of|IN the|the|DT raw|raw|JJ reads|read|VBZ data|datum|NNS for|for|IN each|each|DT sample|sample|NN using|use|VBG FastQC|fastqc|NN -LRB-|-lrb-|-LRB- version|version|NN 0.11.3|0.11.3|CD -RRB-|-rrb-|-RRB- to|to|TO identify|identify|VB features|feature|NNS of|of|IN the|the|DT data|datum|NNS that|that|WDT may|may|MD indicate|indicate|VB quality|quality|NN problems|problem|NNS -LRB-|-lrb-|-LRB- e.g.|e.g.|FW low|low|JJ quality|quality|NN scores|score|NNS ,|,|, over-represented|over-represented|JJ sequences|sequence|NNS ,|,|, inappropriate|inappropriate|JJ GC|gc|NN content|content|NN ,|,|, etc.|etc.|FW -RRB-|-rrb-|-RRB- .|.|.
Qiagen|Qiagen|NNP Genomic|genomic|JJ Tip|tip|NN 500/G|500/g|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT Genomic|genomic|JJ DNA|dna|NN Buffer|buffer|NN set|set|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB-
Qiagen|qiagen|NN RNA|rna|NN extraction|extraction|NN kit|kit|NN
Qiagen|Qiagen|NNP Rneasy|Rneasy|NNP column|column|NN
Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Midikit|Midikit|NNP
Qiagen|Qiagen|NNP Rneasy|Rneasy|NNP mini|minus|NNS kit|kit|NN
Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN
Quality|quality|JJ and|and|CC adapter|adapter|NN trimming|trim|VBG was|be|VBD performed|perform|VBN with|with|IN the|the|DT CLC|clc|NN Genomics|genomic|NNS Workbench|workbench|JJ 9.0|9.0|CD software|software|NN package|package|NN using|use|VBG the|the|DT `|`|`` Trim|Trim|NNP Sequences|sequence|NNS '|'|POS tool|tool|NN with|with|IN standard|standard|JJ parameters|parameter|NNS .|.|.
Quality|Quality|NNP control|control|NN and|and|CC microarray|microarray|NN data|data|NN analysis|analysis|NN of|of|IN all|all|DT 60|60|CD chips|chip|NNS was|be|VBD done|do|VBN using|use|VBG R/Bioconductor|r/bioconductor|NN -LRB-|-lrb-|-LRB- http://www.bioconductor.org/|http://www.bioconductor.org/|NN -RRB-|-rrb-|-RRB- .|.|. Signal|signal|NN intensity|intensity|NN files|file|NNS -LRB-|-lrb-|-LRB- CEL|cel|NN files|file|NNS -RRB-|-rrb-|-RRB- of|of|IN all|all|DT 60|60|CD chips|chip|NNS were|be|VBD summarized|summarize|VBN using|use|VBG RMA|rma|NN -LRB-|-lrb-|-LRB- robust|robust|JJ multi|multus|NNS array|array|NN average|average|NN -RRB-|-rrb-|-RRB- as|as|IN processing|processing|NN algorithm|algorithm|NN and|and|CC quantile|quantile|NN normalization|normalization|NN .|.|. A|a|DT modified|modify|VBN t-test|t-test|NN using|use|VBG limma|limma|NN was|be|VBD performed|perform|VBN for|for|IN comparison|comparison|NN of|of|IN experimental|experimental|JJ conditions|condition|NNS .|.|. See|see|VB also|also|RB additional|additional|JJ files|file|NNS containing|contain|VBG only|only|RB E.coli|e.coli|JJ K-12|k-12|NN MG1655|mg1655|NN probes|probe|NNS with|with|IN P-values|p-value|NNS and|and|CC ratio|ratio|NN .|.|.
Quality|Quality|NNP control|control|NN processing|processing|NN of|of|IN sequence|sequence|NN data|datum|NNS was|be|VBD performed|perform|VBN using|use|VBG Galaxy|galaxy|NN -LRB-|-lrb-|-LRB- https://galaxyproject.org|https://galaxyproject.org|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT FASTX|fastx|NN tools|tool|NNS in|in|IN Galaxy|galaxy|NN -LRB-|-lrb-|-LRB- http://hannonlab.cshl.edu/fastx_toolkit|http://hannonlab.cshl.edu/fastx_toolkit|NN -RRB-|-rrb-|-RRB- were|be|VBD used|use|VBN for|for|IN filtering|filter|VBG by|by|IN quality|quality|NN -LRB-|-lrb-|-LRB- 80|80|CD %|%|NN of|of|IN sequence|sequence|NN >|>|JJR quality|quality|NN score|score|NN of|of|IN 20|20|CD -RRB-|-rrb-|-RRB- ,|,|, then|then|RB reads|read|VBZ were|be|VBD trimmed|trim|VBN at|at|IN both|both|DT 5|5|CD '|'|'' and|and|CC 3|3|CD '|'|'' ends|end|VBZ using|use|VBG a|a|DT window|window|NN and|and|CC step|step|NN size|size|NN of|of|IN 1|1|CD with|with|IN quality|quality|NN score|score|NN >|>|JJR 20|20|CD .|.|.
Quality|Quality|NNP trimming|trim|VBG of|of|IN 3|3|CD '|'|'' end|end|NN at|at|IN Read|Read|NNP Segment|Segment|NNP Quality|Quality|NNP Control|Control|NNP Indicator|Indicator|NNP .|.|.
Quality|Quality|NNP trimming|trim|VBG using|use|VBG FASTX-toolkit|fastx-toolkit|NN ,|,|, version|version|NN 0.0.13.2|0.0.13.2|CD ,|,|, parameters|parameter|NNS -|-|: v|v|LS -|-|: t|t|NN 20|20|CD -|-|: l|l|NN 10|10|CD
Quantification|quantification|NN of|of|IN gene|gene|NN expression|expression|NN and|and|CC analysis|analysis|NN of|of|IN gene|gene|NN differential|differential|JJ expression|expression|NN were|be|VBD performed|perform|VBN using|use|VBG Fragment|fragment|NN Per|per|IN Kilo|Kilo|NNP bases|basis|NNS per|per|IN Million|Million|NNP reads|read|VBZ -LRB-|-lrb-|-LRB- FPKM|fpkm|NN -RRB-|-rrb-|-RRB- value|value|NN based|base|VBN rsem|rsem|NN software|software|NN version|version|NN 1.2.4|1.2.4|CD and|and|CC edgeR|edger|NN version|version|NN 3.4.2|3.4.2|CD -LRB-|-lrb-|-LRB- Bioconductor|bioconductor|NN -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB
Quantification|quantification|NN of|of|IN the|the|DT scans|scan|NNS were|be|VBD performed|perform|VBN with|with|IN ImaGene|imagene|NN -LRB-|-lrb-|-LRB- Version|version|NN 6.0.1|6.0.1|CD ;|;|: BioDiscovery|BioDiscovery|NNP ;|;|: El|El|NNP Segundo|Segundo|NNP ,|,|, CA|CA|NNP ;|;|: www.biodiscovery.com|www.biodiscovery.com|NNP -RRB-|-rrb-|-RRB- ;|;|: with|with|IN the|the|DT results|result|NNS presented|present|VBN in|in|IN the|the|DT associated|associate|VBN text|text|NN files|file|NNS .|.|. The|the|DT normalized|normalize|VBN data|datum|NNS VALUE|value|NN was|be|VBD generated|generate|VBN using|use|VBG LOWESS|LOWESS|NNP normalization|normalization|NN with|with|IN rank|rank|NN invariant|invariant|JJ selection|selection|NN ,|,|, as|as|IN implemented|implement|VBN in|in|IN lcDNA|lcdna|NN -LRB-|-lrb-|-LRB- receptor.seas.ucla.edu/lcDNA|receptor.seas.ucla.edu/lcdna|NN ;|;|: Hyduke|Hyduke|NNP DR|dr|NN ,|,|, Rohlin|Rohlin|NNP L|L|NNP ,|,|, Kao|Kao|NNP KC|KC|NNP ,|,|, Liao|Liao|NNP JC|JC|NNP .|.|. 2003|2003|CD A|a|DT software|software|NN package|package|NN for|for|IN cDNA|cdna|NN microarray|microarray|NN data|datum|NNS normalization|normalization|NN and|and|CC assessing|assess|VBG confidence|confidence|NN intervals|interval|NNS .|.|. OMICS|omics|NN 7|7|CD -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- :|:|: 227-234|227-234|CD .|.|. -RRB-|-rrb-|-RRB-
Quantification|quantification|NN of|of|IN the|the|DT scans|scan|NNS were|be|VBD performed|perform|VBN with|with|IN ImaGene|imagene|NN -LRB-|-lrb-|-LRB- Version|version|NN 6.0.1|6.0.1|CD ;|;|: BioDiscovery|BioDiscovery|NNP ;|;|: El|El|NNP Segundo|Segundo|NNP ,|,|, CA|CA|NNP ;|;|: www.biodiscovery.com|www.biodiscovery.com|NNP -RRB-|-rrb-|-RRB- ;|;|: with|with|IN the|the|DT results|result|NNS presented|present|VBN in|in|IN the|the|DT associated|associate|VBN text|text|NN files|file|NNS .|.|. The|the|DT normalized|normalize|VBN data|datum|NNS VALUE|value|NN was|be|VBD generated|generate|VBN using|use|VBG LOWESS|LOWESS|NNP normalization|normalization|NN with|with|IN rank|rank|NN invariant|invariant|JJ selection|selection|NN ,|,|, as|as|IN implemented|implement|VBN in|in|IN lcDNA|lcdna|NN -LRB-|-lrb-|-LRB- receptor.seas.ucla.edu/lcDNA|receptor.seas.ucla.edu/lcdna|NN ;|;|: Hyduke|Hyduke|NNP DR|dr|NN ,|,|, Rohlin|Rohlin|NNP L|L|NNP ,|,|, Kao|Kao|NNP KC|KC|NNP ,|,|, Liao|Liao|NNP JC|JC|NNP .|.|. 2003|2003|CD A|a|DT software|software|NN package|package|NN for|for|IN cDNA|cdna|NN microarray|microarray|NN data|datum|NNS normalization|normalization|NN and|and|CC assessing|assess|VBG confidence|confidence|NN intervals|interval|NNS .|.|. OMICS|omics|NN 7|7|CD -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- :|:|: 227-234|227-234|CD .|.|. -RRB-|-rrb-|-RRB-
R11|r11|NN DH10BGFP|dh10bgfp|NN _|_|CD pLys|ply|VBZ _|_|SYM 1|1|CD
R16|r16|NN MG1655GFP|mg1655gfp|NN _|_|CD pLys|ply|VBZ _|_|SYM M1|m1|NN _|_|NN 1|1|CD
R19|r19|NN MG1655GFP|mg1655gfp|NN _|_|CD Lux|lux|FW _|_|FW 1|1|CD
R26|r26|NN MG1655GFP|mg1655gfp|NN _|_|CD Lux|lux|FW _|_|FW 1|1|CD
R27|r27|NN MG1655GFP|mg1655gfp|NN _|_|CD pD864|pd864|NN _|_|CD LacZ|lacz|NN _|_|NN 1|1|CD
R29|r29|NN DH10BGFP|dh10bgfp|NN _|_|CD None|none|NN _|_|NN 1|1|CD
R2|r2|NN DH10BGFP|dh10bgfp|NN _|_|CD pLys|ply|VBZ _|_|SYM M1|m1|NN _|_|NN 1|1|CD
R3|r3|NN DH10BGFP|dh10bgfp|NN _|_|CD pSB1C3|psb1c3|NN _|_|NN 1|1|CD
R6|r6|NN DH10BGFP|dh10bgfp|NN _|_|CD pD864|pd864|NN _|_|CD LacZ|lacz|NN _|_|NN 1|1|CD
ration|ration|NN of|of|IN median|median|NN -LRB-|-lrb-|-LRB- 635/532|635/532|CD -RRB-|-rrb-|-RRB-
Ratio|Ratio|NNP of|of|IN median|median|JJ
ratio|ratio|NN set|set|VBN to|to|TO missing|miss|VBG where|where|WRB SNR|snr|NN -LRB-|-lrb-|-LRB- feature|feature|NN mean|mean|NN -|-|: backround|backround|NN mean|mean|VB /|/|: background|background|NN SD|sd|NN -RRB-|-rrb-|-RRB- less|less|JJR than|than|IN 2|2|CD in|in|IN both|both|CC channels|channel|NNS ;|;|:
Raw|raw|NN CEL|cel|NN files|file|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG robust|robust|JJ multi-array|multi-array|JJ average|average|NN for|for|IN normalization|normalization|NN and|and|CC calculation|calculation|NN of|of|IN probe|probe|NN intensities|intensity|NNS .|.|. The|the|DT processed|process|VBN probe|probe|NN signals|signal|NNS derived|derive|VBN from|from|IN each|each|DT microarray|microarray|NN were|be|VBD averaged|average|VBN for|for|IN both|both|CC the|the|DT wild|wild|JJ type|type|NN and|and|CC deletion|deletion|NN mutant|mutant|JJ strains|strain|NNS .|.|. This|this|DT was|be|VBD done|do|VBN using|use|VBG the|the|DT GCRMA|GCRMA|NNP package|package|NN -LRB-|-lrb-|-LRB- version|version|NN 2.13|2.13|CD -RRB-|-rrb-|-RRB- from|from|IN Bioconductor|Bioconductor|NNP in|in|IN R.|R.|NNP
Raw|raw|NN counts|count|NNS of|of|IN mapped|map|VBN reads|read|VBZ per|per|IN reference|reference|NN base|base|NN pair|pair|NN were|be|VBD then|then|RB calculated|calculate|VBN using|use|VBG SAMtools|samtool|NNS software|software|NN -LRB-|-lrb-|-LRB- with|with|IN parameter|parameter|NN --|--|: d|d|NN set|set|VBN to|to|TO 10|10|CD ^|^|CD 6|6|CD -RRB-|-rrb-|-RRB- .|.|.
Raw|raw|NN counts|count|NNS were|be|VBD derived|derive|VBN for|for|IN each|each|DT gene|gene|NN based|base|VBN on|on|IN the|the|DT respective|respective|JJ annotations|annotation|NNS available|available|JJ from|from|IN UCSC|UCSC|NNP genome|genome|NN browser|browser|NN -LRB-|-lrb-|-LRB- http://genome.ucsc.edu|http://genome.ucsc.edu|NN -RRB-|-rrb-|-RRB- for|for|IN the|the|DT chosen|choose|VBN reference|reference|NN sequence|sequence|NN applying|apply|VBG HTseq-count|htseq-count|JJ v.|v.|CC 0.6.1|0.6.1|CD in|in|IN the|the|DT intersection-nonempty|intersection-nonempty|JJ mode|mode|NN .|.|.
Raw|raw|NN data|datum|NNS -LRB-|-lrb-|-LRB- .|.|. pair|pair|NN files|file|NNS -RRB-|-rrb-|-RRB- was|be|VBD analyzed|analyze|VBN using|use|VBG Matlab|Matlab|NNP -LRB-|-lrb-|-LRB- The|the|DT MathWorks|MathWorks|NNPS ,|,|, Natick|Natick|NNP ,|,|, MA|MA|NNP -RRB-|-rrb-|-RRB- .|.|. For|for|IN each|each|DT probe|probe|NN ,|,|, the|the|DT average|average|JJ intensity|intensity|NN of|of|IN three|three|CD replicates|replicate|VBZ were|be|VBD calculated|calculate|VBN after|after|IN the|the|DT elimination|elimination|NN of|of|IN outliers|outlier|NNS based|base|VBN on|on|IN a|a|DT standard|standard|JJ deviation|deviation|NN test|test|NN .|.|. The|the|DT average|average|NN of|of|IN control|control|NN -LRB-|-lrb-|-LRB- Nonsense|nonsense|NN -RRB-|-rrb-|-RRB- probes|probe|NNS was|be|VBD subtracted|subtract|VBN from|from|IN all|all|DT averages|average|NNS to|to|TO obtain|obtain|VB background-corrected|background-corrected|JJ results|result|NNS .|.|.
Raw|raw|NN data|datum|NNS were|be|VBD created|create|VBN by|by|IN analyzing|analyze|VBG 16-bit|16-bit|JJ tiff|tiff|NN files|file|NNS with|with|IN the|the|DT Scan|scan|VB Array|Array|NNP Express|Express|NNP imaging|imaging|NN software|software|NN -LRB-|-lrb-|-LRB- microarray|microarray|NN analysis|analysis|NN system|system|NN ,|,|, version|version|NN 3.0.0.0016|3.0.0.0016|CD ,|,|, PerkinElmer|PerkinElmer|NNP ,|,|, Massachusetts|Massachusetts|NNP ,|,|, USA|USA|NNP ;|;|: adaptive|adaptive|JJ treshold|treshold|NN method|method|NN ,|,|, total|total|JJ normalization|normalization|NN method|method|NN -RRB-|-rrb-|-RRB- .|.|.
Raw|raw|NN data|datum|NNS were|be|VBD normalized|normalize|VBN and|and|CC log2|log2|NN transformed|transform|VBN with|with|IN the|the|DT Acuity|acuity|NN 4.0|4.0|CD software|software|NN package|package|NN ,|,|, and|and|CC data|datum|NNS with|with|IN low|low|JJ fluorescence|fluorescence|NN intensities|intensity|NNS were|be|VBD eliminated|eliminate|VBN .|.|. Genes|gene|NNS were|be|VBD considered|consider|VBN to|to|TO be|be|VB differentially|differentially|RB expressed|express|VBN if|if|IN the|the|DT absolute|absolute|JJ values|value|NNS of|of|IN log2|log2|NN mean|mean|NN expression|expression|NN ratios|ratio|NNS were|be|VBD ≥|≥|CD 1|1|CD .|.|.
Raw|raw|NN data|datum|NNS were|be|VBD normalized|normalize|VBN -LRB-|-lrb-|-LRB- quantile|quantile|JJ method|method|NN -RRB-|-rrb-|-RRB- ,|,|, merged|merged|JJ and|and|CC filtered|filter|VBN by|by|IN Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- .|.|. For|for|IN the|the|DT sibiling|sibiling|NN probes|probe|NNS -LRB-|-lrb-|-LRB- multiple|multiple|JJ probes|probe|NNS to|to|TO one|one|CD gene|gene|NN -RRB-|-rrb-|-RRB- ,|,|, we|we|PRP used|use|VBD the|the|DT median|median|JJ indensity|indensity|NN for|for|IN representation|representation|NN .|.|.
Raw|raw|NN data|datum|NNS were|be|VBD quality|quality|JJ filtered|filter|VBN on|on|IN the|the|DT Galaxy|Galaxy|NNP server|server|NN -LRB-|-lrb-|-LRB- Filter|Filter|NNP by|by|IN Quality|Quality|NNP tool|tool|NN ,|,|, Q|Q|NNP ≥|≥|SYM 20|20|CD -RRB-|-rrb-|-RRB- providing|provide|VBG 99|99|CD %|%|NN probability|probability|NN of|of|IN correct|correct|JJ sequencing|sequencing|NN for|for|IN all|all|DT nucleotides|nucleotide|NNS in|in|IN each|each|DT read|read|NN .|.|. As|as|IN a|a|DT result|result|NN ,|,|, the|the|DT sets|set|NNS contain|contain|VBP 31,656,551|31,656,551|CD and|and|CC 45,396,252|45,396,252|CD sequences|sequence|NNS in|in|IN the|the|DT control|control|NN and|and|CC immunoprecipitated|immunoprecipitate|VBN samples|sample|NNS of|of|IN the|the|DT first|first|JJ experiment|experiment|NN ,|,|, and|and|CC ,|,|, respectively|respectively|RB ,|,|, 7,493,528|7,493,528|CD and|and|CC 8,214,737|8,214,737|CD reads|read|VBZ for|for|IN the|the|DT second|second|JJ experiment|experiment|NN .|.|.
Raw|raw|NN .|.|. fastq|fastq|NN files|file|NNS were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC000913|nc000913|NN .2|.2|NN -RRB-|-rrb-|-RRB- using|use|VBG BWA|bwa|NN -LRB-|-lrb-|-LRB- version|version|NN 0.7|0.7|CD -RRB-|-rrb-|-RRB- .|.|. Mapped|map|VBN reads|read|VBZ were|be|VBD then|then|RB converted|convert|VBN to|to|TO read|read|VB count|count|NN per|per|IN gene|gene|NN using|use|VBG bedtools|bedtool|NNS -LRB-|-lrb-|-LRB- version|version|NN 2|2|CD -RRB-|-rrb-|-RRB- .|.|. In|in|IN the|the|DT case|case|NN of|of|IN Ion|ion|NN torrent|torrent|NN data|datum|NNS .|.|. bam|bam|NN files|file|NNS were|be|VBD converted|convert|VBN using|use|VBG BWA|BWA|NNP .|.|.
Raw|raw|NN fluorescence|fluorescence|NN intensity|intensity|NN data|datum|NNS were|be|VBD normalized|normalize|VBN in|in|IN R|r|NN -LRB-|-lrb-|-LRB- http://cran.r-project.org/|http://cran.r-project.org/|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Limma|limma|NN -LRB-|-lrb-|-LRB- Bioconductor|bioconductor|NN -RRB-|-rrb-|-RRB- package|package|NN
Raw|raw|NN Microarray|Microarray|NNP data|datum|NNS evaluation|evaluation|NN including|include|VBG preprocessing|preprocessing|NN ,|,|, normalization|normalization|NN ,|,|, grouping|group|VBG the|the|DT differentially|differentially|RB expressed|express|VBN genes|gene|NNS and|and|CC statistical|statistical|JJ analyses|analysis|NNS with|with|IN Moderated|moderate|VBN T-test|t-test|NN and|and|CC Bonferroni|Bonferroni|NNP FWER|FWER|NNP was|be|VBD carried|carry|VBN out|out|RP with|with|IN GeneSpring|genespring|NN 13.0|13.0|CD Software|Software|NNP .|.|.
Raw|raw|NN microarray|microarray|NN intensity|intensity|NN data|datum|NNS were|be|VBD normalized|normalize|VBN per|per|IN chip|chip|NN to|to|TO the|the|DT same|same|JJ mean|mean|NN value|value|NN ,|,|, which|which|WDT is|be|VBZ recommended|recommend|VBN by|by|IN the|the|DT manufacturer|manufacturer|NN .|.|.
Raw|raw|NN ,|,|, not|not|RB normalised|normalised|JJ
Raw|raw|NN probe|probe|NN intensities|intensity|NNS -LRB-|-lrb-|-LRB- .|.|. pair|pair|NN files|file|NNS three|three|CD replicates|replicate|VBZ for|for|IN each|each|DT growth|growth|NN condition|condition|NN with|with|IN respectively|respectively|RB 0|0|CD ,|,|, 5.0|5.0|CD ,|,|, 6.5|6.5|CD and|and|CC 8.5|8.5|CD µM|µm|NN of|of|IN AgNO3|agno3|NN in|in|IN the|the|DT medium|medium|NN -RRB-|-rrb-|-RRB- was|be|VBD processed|process|VBN and|and|CC analyzed|analyze|VBN with|with|IN R|r|NN computing|computing|NN environment|environment|NN using|use|VBG the|the|DT affy|affy|NN and|and|CC limma|limma|NN package|package|NN of|of|IN Bioconductor|Bioconductor|NNP .|.|. Raw|raw|NN data|datum|NNS were|be|VBD submitted|submit|VBN to|to|TO a|a|DT RMA-base|rma-base|NN background|background|NN correction|correction|NN -LSB-|-lsb-|-LRB- Irizarry|Irizarry|NNP et|et|FW al|al|FW ,|,|, 2003|2003|CD ,|,|, Biostatistics|biostatistic|NNS 4|4|CD -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- :|:|: 249-264|249-264|CD -RSB-|-rsb-|-RRB- .|.|. After|after|IN background|background|NN correction|correction|NN ,|,|, intra-replicate|intra-replicate|JJ quantil|quantil|NN normalization|normalization|NN was|be|VBD performed|perform|VBN for|for|IN each|each|DT growth|growth|NN condition|condition|NN .|.|. A|a|DT set|set|NN of|of|IN probes|probe|NNS in|in|IN the|the|DT background|background|NN for|for|IN which|which|WDT the|the|DT ranks|rank|NNS were|be|VBD roughly|roughly|RB invariant|invariant|JJ across|across|IN all|all|PDT the|the|DT twelve|twelve|CD arrays|array|NNS was|be|VBD selected|select|VBN .|.|. The|the|DT median|median|JJ value|value|NN of|of|IN the|the|DT invariant|invariant|JJ probeset|probeset|NN intensities|intensity|NNS on|on|IN each|each|DT array|array|NN was|be|VBD used|use|VBN as|as|IN a|a|DT scaling|scaling|NN factor|factor|NN for|for|IN normalization|normalization|NN between|between|IN growth|growth|NN conditions|condition|NNS .|.|.
Raw|raw|NN probe|probe|NN intensities|intensity|NNS were|be|VBD normalized|normalize|VBN across|across|IN all|all|DT samples|sample|NNS using|use|VBG the|the|DT Robust|Robust|NNP Multichip|Multichip|NNP Average|Average|NNP -LRB-|-lrb-|-LRB- RMA|RMA|NNP -RRB-|-rrb-|-RRB- algorithm|algorithm|NN in|in|IN the|the|DT NimbleScan|NimbleScan|NNP software|software|NN package|package|NN -LRB-|-lrb-|-LRB- version|version|NN 2.5|2.5|CD -RRB-|-rrb-|-RRB- .|.|.
Raw|raw|NN probe|probe|NN intensities|intensity|NNS were|be|VBD normalized|normalize|VBN across|across|IN samples|sample|NNS using|use|VBG RMA|rma|NN analysis|analysis|NN implemented|implement|VBD in|in|IN the|the|DT NimbleScan|NimbleScan|NNP software|software|NN package|package|NN -LRB-|-lrb-|-LRB- v.|v.|CC 2.4|2.4|CD -RRB-|-rrb-|-RRB- .|.|.
Raw|raw|NN read|read|VBD counts|count|NNS of|of|IN transcripts|transcript|NNS were|be|VBD obtained|obtain|VBN by|by|IN aligning|align|VBG samples|sample|NNS 1-14|1-14|CD to|to|TO the|the|DT reference|reference|NN genome|genome|NN and|and|CC counting|count|VBG mapped|map|VBN reads|read|VBZ per|per|IN feature|feature|NN using|use|VBG Rockhopper|Rockhopper|NNP v2|v2|NN .0.3|.0.3|CD .|.|.
Raw|raw|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW w3110|w3110|NN MuSGS|musgs|NN genome|genome|NN -LRB-|-lrb-|-LRB- containing|contain|VBG a|a|DT strong|strong|JJ gyrase|gyrase|NN binding|binding|NN site|site|NN from|from|IN bacteriophage|bacteriophage|NN Mu|mu|NN -RRB-|-rrb-|-RRB- with|with|IN BWA|bwa|NN MEM|mem|NN -LRB-|-lrb-|-LRB- default|default|NN settings|setting|NNS -RRB-|-rrb-|-RRB-
Raw|raw|NN reads|read|VBZ were|be|VBD trimmed|trim|VBN by|by|IN two|two|CD nt|nt|NNS from|from|IN the|the|DT 5|5|CD '|'|'' end|end|NN -LRB-|-lrb-|-LRB- to|to|TO remove|remove|VB any|any|DT non-templated|non-templated|JJ nts|nt|NNS added|add|VBN by|by|IN reverse|reverse|JJ transcriptase|transcriptase|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC were|be|VBD then|then|RB mapped|map|VBN using|use|VBG the|the|DT Burrows-Wheeler|Burrows-Wheeler|NNP Aligner|Aligner|NNP to|to|TO the|the|DT Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- NCBI|ncbi|NN accession|accession|NN NC|nc|NN _|_|SYM 000913|000913|CD -RRB-|-rrb-|-RRB- .|.|.
Raw|raw|NN sequence|sequence|NN data|datum|NNS obtained|obtain|VBN in|in|IN the|the|DT fastq|fastq|NN format|format|NN were|be|VBD aligned|align|VBN to|to|TO the|the|DT genome|genome|NN of|of|IN E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913.2|000913.2|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Burrows-Wheeler|Burrows-Wheeler|NNP matching|match|VBG program|program|NN BWA|bwa|NN .|.|. Reads|read|NNS mapping|map|VBG uniquely|uniquely|RB to|to|TO the|the|DT genome|genome|NN were|be|VBD selected|select|VBN .|.|.
Raw|raw|NN sequence|sequence|NN data|datum|NNS obtained|obtain|VBN in|in|IN the|the|DT fastq|fastq|NN format|format|NN were|be|VBD aligned|align|VBN to|to|TO the|the|DT genome|genome|NN of|of|IN E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913.2|000913.2|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Burrows-Wheeler|Burrows-Wheeler|NNP matching|match|VBG program|program|NN BWA|bwa|NN .|.|. Reads|read|NNS mapping|map|VBG uniquely|uniquely|RB to|to|TO the|the|DT genome|genome|NN were|be|VBD selected|select|VBN .|.|. Files|file|NNS were|be|VBD coverted|covert|VBN to|to|TO .|.|. bam|bam|NN format|format|NN using|use|VBG samtools|samtool|NNS .|.|. The|the|DT MACS|macs|NN 2.1.0|2.1.0|CD software|software|NN was|be|VBD used|use|VBN to|to|TO call|call|VB peaks|peak|NNS .|.|. Peaks|peak|NNS overlapping|overlap|VBG in|in|IN both|both|CC replicates|replicate|VBZ were|be|VBD selected|select|VBN for|for|IN further|further|JJ analysis|analysis|NN .|.|.
Raw|raw|NN sequence|sequence|NN data|datum|NNS obtained|obtain|VBN in|in|IN the|the|DT fastq|fastq|NN format|format|NN were|be|VBD aligned|align|VBN to|to|TO the|the|DT genome|genome|NN of|of|IN E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913.2|000913.2|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Burrows-Wheeler|Burrows-Wheeler|NNP matching|match|VBG program|program|NN BWA|bwa|NN .|.|. Reads|read|NNS mapping|map|VBG uniquely|uniquely|RB to|to|TO the|the|DT genome|genome|NN were|be|VBD selected|select|VBN .|.|. Files|file|NNS were|be|VBD coverted|covert|VBN to|to|TO .|.|. bam|bam|NN format|format|NN using|use|VBG samtools|samtool|NNS .|.|. The|the|DT MACS|macs|NN 2.1.0|2.1.0|CD software|software|NN was|be|VBD used|use|VBN to|to|TO call|call|VB peaks|peak|NNS .|.|. Peaks|peak|NNS overlapping|overlap|VBG in|in|IN both|both|CC replicates|replicate|VBZ were|be|VBD selected|select|VBN for|for|IN further|further|JJ analysis|analysis|NN .|.|.
Raw|raw|NN sequence|sequence|NN data|datum|NNS obtained|obtain|VBN in|in|IN the|the|DT fastq|fastq|NN format|format|NN were|be|VBD aligned|align|VBN to|to|TO the|the|DT genome|genome|NN of|of|IN E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN using|use|VBG the|the|DT Burrows-Wheeler|Burrows-Wheeler|NNP matching|match|VBG program|program|NN BWA|bwa|NN .|.|. Reads|read|NNS mapping|map|VBG uniquely|uniquely|RB to|to|TO the|the|DT genome|genome|NN were|be|VBD selected|select|VBN and|and|CC the|the|DT number|number|NN of|of|IN reads|read|VBZ mapping|map|VBG to|to|TO each|each|DT gene|gene|NN was|be|VBD computed|compute|VBN using|use|VBG custom|custom|NN scripts|script|NNS .|.|.
Raw|raw|NN sequencing|sequencing|NN reads|read|VBZ -LRB-|-lrb-|-LRB- FASTQ|fastq|NN -RRB-|-rrb-|-RRB- were|be|VBD processed|process|VBN by|by|IN Xpression|xpression|NN and|and|CC only|only|RB the|the|DT uniquely|uniquely|RB mapped|map|VBN reads|read|VBZ were|be|VBD subjected|subject|VBN to|to|TO further|further|JJ analysis|analysis|NN .|.|.
Raw|raw|NN signal|signal|NN data|datum|NNS were|be|VBD extracted|extract|VBN from|from|IN the|the|DT TIFF|tiff|NN image|image|NN with|with|IN Agilent|Agilent|NNP Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- V10|V10|NNP .7.1.1|.7.1.1|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT data|data|NN analysis|analysis|NN is|be|VBZ done|do|VBN using|use|VBG a|a|DT microarray|microarray|NN specialized|specialized|JJ analysis|analysis|NN software|software|NN ,|,|, Genespring|Genespring|NNP GX|GX|NNP .|.|. In|in|IN this|this|DT experiment|experiment|NN ,|,|, the|the|DT microarray|microarray|NN type|type|NN used|use|VBN is|be|VBZ a|a|DT slide|slide|NN having|have|VBG 8|8|CD arrays|array|NNS with|with|IN 60|60|CD thousand|thousand|CD features|feature|NNS per|per|IN array|array|NN .|.|. The|the|DT exact|exact|JJ number|number|NN of|of|IN features|feature|NNS in|in|IN the|the|DT each|each|DT array|array|NN ,|,|, inclusive|inclusive|NN of|of|IN control|control|NN probes|probe|NNS ,|,|, is|be|VBZ 10,751|10,751|CD features|feature|NNS .|.|. The|the|DT microarray|microarray|NN has|have|VBZ a|a|DT specific|specific|JJ Agilent|Agilent|NNP identifier|identifier|NN called|call|VBD an|a|DT AMADID|amadid|NN which|which|WDT is|be|VBZ used|use|VBN to|to|TO identify|identify|VB what|what|WP kind|kind|NN of|of|IN array|array|NN is|be|VBZ being|be|VBG used|use|VBN ;|;|: in|in|IN this|this|DT experiment|experiment|NN the|the|DT AMADID|AMADID|NNP used|use|VBN is|be|VBZ the|the|DT design|design|NN ID|id|NN 020097|020097|CD .|.|.
Read|Read|NNP alignment|alignment|NN was|be|VBD performed|perform|VBN with|with|IN BWA|bwa|NN -LRB-|-lrb-|-LRB- version|version|NN 0.6.2|0.6.2|CD -RRB-|-rrb-|-RRB- with|with|IN default|default|NN parameter|parameter|NN .|.|.
Read|Read|NNP counting|count|VBG using|use|VBG bedtools|bedtool|NNS ,|,|, version|version|NN 2.17.0|2.17.0|CD ,|,|, parameter|parameter|NN :|:|: -|-|: s|s|NNS ,|,|, the|the|DT middle|middle|JJ nucleotide|nucleotide|NN of|of|IN each|each|DT read|read|NN was|be|VBD taken|take|VBN
Read|Read|NNP counts|count|VBZ for|for|IN each|each|DT host|host|NN and|and|CC circuit|circuit|NN gene|gene|NN was|be|VBD carried|carry|VBN out|out|RP using|use|VBG the|the|DT htseq-count|htseq-count|JJ command|command|NN of|of|IN the|the|DT HTSeq|htseq|NN toolkit|toolkit|NN with|with|IN user-defined|user-defined|JJ GFF|gff|NN annotations|annotation|NNS of|of|IN the|the|DT reference|reference|NN sequences|sequence|NNS and|and|CC the|the|DT options|option|NNS '|'|POS -|-|: s|s|NNS reverse|reverse|JJ -|-|: a|a|DT 10|10|CD -|-|: m|m|NN union|union|NN '|'|'' .|.|.
Read|Read|NNP counts|count|VBZ per|per|IN gene|gene|NN determined|determine|VBN using|use|VBG HTseq|htseq|NN count|count|NN before|before|IN normalized|normalize|VBN using|use|VBG DESeq2|deseq2|NN
Read|read|VBP counts|count|NNS were|be|VBD normalized|normalize|VBN by|by|IN million|million|CD mapped|map|VBD reads|read|VBZ for|for|IN each|each|DT nucleotide|nucleotide|NN
Read|Read|NNP count|count|NN was|be|VBD calculated|calculate|VBN for|for|IN each|each|DT genomic|genomic|JJ position|position|NN from|from|IN sequence|sequence|NN alignment|alignment|NN ,|,|, and|and|CC 95|95|CD %|%|NN strongest|strongest|JJS intensity|intensity|NN was|be|VBD used|use|VBN as|as|IN background|background|NN intensity|intensity|NN .|.|.
Read|Read|NNP coverage|coverage|NN maps|map|NNS and|and|CC RPKM|RPKM|NNP data|datum|NNS was|be|VBD subsequently|subsequently|RB generated|generate|VBN by|by|IN Geneious|Geneious|NNP .|.|.
Read|Read|NNP mapping|mapping|NN using|use|VBG segemehl|segemehl|NN version|version|NN 0.13|0.13|CD -LRB-|-lrb-|-LRB- TRAPL|trapl|NN -RRB-|-rrb-|-RRB-
Read|read|VB mapping|mapping|NN using|use|VBG segemehl|segemehl|NN -LRB-|-lrb-|-LRB- via|via|IN READemption|reademption|NN -RRB-|-rrb-|-RRB-
Read-mapping|read-mapping|NN was|be|VBD done|do|VBN with|with|IN soap2|soap2|NN .21|.21|CD .|.|. Mapping|mapping|NN towards|towards|IN genes|gene|NNS was|be|VBD done|do|VBN by|by|IN the|the|DT following|follow|VBG parameters|parameter|NNS -|-|: m|m|NN 0|0|CD -|-|: x|x|CC 1000|1000|CD -|-|: s|s|NNS 28|28|CD -|-|: l|l|NN 32|32|CD -|-|: v|v|LS 5|5|LS -|-|: r|r|NN 2|2|CD -|-|: p|p|NN 3|3|CD
reads|read|VBZ aligned|align|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN Mg1655|mg1655|NN using|use|VBG BWA|BWA|NNP ,|,|, with|with|IN quality|quality|NN threshold|threshold|NN of|of|IN 20|20|CD
Reads|read|VBZ aligning|align|VBG to|to|TO each|each|DT protein-encoding|protein-encoding|JJ gene|gene|NN family|family|NN with|with|IN strand-specific|strand-specific|JJ mapping|mapping|NN quality|quality|NN above|above|IN 23|23|CD were|be|VBD counted|count|VBN using|use|VBG HTSeq-count|htseq-count|JJ
Reads|read|VBZ longer|longer|JJR than|than|IN 25|25|CD nt|nt|NNS and|and|CC ≤|≤|NN 2|2|CD N|n|NN -LRB-|-lrb-|-LRB- ambiguous|ambiguous|JJ nucleotides|nucleotide|NNS -RRB-|-rrb-|-RRB- were|be|VBD preserved|preserve|VBN .|.|.
Reads|read|VBZ mapped|map|VBN to|to|TO more|more|JJR than|than|IN one|one|CD locus|locus|NN were|be|VBD discarded|discard|VBN .|.|. The|the|DT mapped|map|VBN position|position|NN obtained|obtain|VBN from|from|IN the|the|DT SAM|SAM|NNP output|output|NN file|file|NN from|from|IN BWA|bwa|NN lists|list|NNS was|be|VBD taken|take|VBN and|and|CC the|the|DT position|position|NN was|be|VBD extended|extend|VBN to|to|TO 280|280|CD bp|bp|NN which|which|WDT is|be|VBZ the|the|DT average|average|JJ length|length|NN of|of|IN DNA|dna|NN fragments|fragment|NNS submitted|submit|VBN for|for|IN sequencing|sequencing|NN .|.|.
Reads|read|VBZ mapped|map|VBN to|to|TO reference|reference|NN using|use|VBG BWA|bwa|NN versiopn|versiopn|NN 0.7.4|0.7.4|CD with|with|IN default|default|NN settings|setting|NNS
Reads|read|VBZ per|per|IN kilobase|kilobase|NN of|of|IN exon|exon|NN model|model|NN per|per|IN million|million|CD mapped|map|VBD reads|read|VBZ -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN as|as|IN a|a|DT normalized|normalize|VBN metric|metric|JJ to|to|TO present|present|VB the|the|DT gene|gene|NN expression|expression|NN levels|level|NNS .|.|. -LRB-|-lrb-|-LRB- Nature|Nature|NNP methods|method|NNS 2008|2008|CD ,|,|, 5|5|CD :|:|: 621-628|621-628|CD -RRB-|-rrb-|-RRB-
Reads|read|VBZ Per|per|IN Kilobase|kilobase|NN of|of|IN exon|exon|NN per|per|IN Megabase|megabase|NN of|of|IN library|library|NN size|size|NN -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN using|use|VBG a|a|DT protocol|protocol|NN from|from|IN Chepelev|Chepelev|NNP et|et|FW al.|al.|FW ,|,|, Nucleic|Nucleic|NNP Acids|Acids|NNP Research|Research|NNP ,|,|, 2009|2009|CD .|.|.
Reads|read|VBZ Per|per|IN Kilobase|kilobase|NN of|of|IN exon|exon|NN per|per|IN Megabase|megabase|NN of|of|IN library|library|NN size|size|NN -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN using|use|VBG a|a|DT protocol|protocol|NN from|from|IN Chepelev|Chepelev|NNP et|et|FW al.|al.|FW ,|,|, Nucleic|Nucleic|NNP Acids|Acids|NNP Research|Research|NNP ,|,|, 2009|2009|CD .|.|. In|in|IN short|short|RB ,|,|, exons|exon|NNS from|from|IN all|all|DT isoforms|isoform|NNS of|of|IN a|a|DT gene|gene|NN were|be|VBD merged|merge|VBN to|to|TO create|create|VB one|one|CD meta-transcript|meta-transcript|JJ .|.|. The|the|DT number|number|NN of|of|IN reads|read|VBZ falling|fall|VBG in|in|IN the|the|DT exons|exon|NNS of|of|IN this|this|DT meta-transcript|meta-transcript|JJ were|be|VBD counted|count|VBN and|and|CC normalized|normalize|VBN by|by|IN the|the|DT size|size|NN of|of|IN the|the|DT meta-transcript|meta-transcript|JJ and|and|CC by|by|IN the|the|DT size|size|NN of|of|IN the|the|DT library|library|NN .|.|. For|for|IN the|the|DT S.|S.|NNP pneumoniae|pneumoniae|FW samples|sample|NNS this|this|DT was|be|VBD done|do|VBN internally|internally|RB by|by|IN Rockhopper|Rockhopper|NNP version|version|NN 1.21|1.21|CD after|after|IN aligning|align|VBG reads|read|VBZ .|.|.
Reads|read|VBZ Per|per|IN Kilobase|kilobase|NN of|of|IN exon|exon|NN per|per|IN Megabase|megabase|NN of|of|IN library|library|NN size|size|NN -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN using|use|VBG cufflinks|cufflink|NNS v.|v.|CC 1.3.0|1.3.0|CD
Reads|read|VBZ per|per|IN kilobase|kilobase|NN of|of|IN gene|gene|NN per|per|IN million|million|CD mapped|map|VBN sequence|sequence|NN reads|read|VBZ -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN for|for|IN normalization|normalization|NN .|.|.
Reads|Reads|NNPS were|be|VBD adapter|adapter|NN removed|remove|VBN and|and|CC trimmed|trim|VBN to|to|TO 40Bp|40bp|NN using|use|VBG trimmomatic|trimmomatic|JJ 0.32|0.32|CD with|with|IN parameters|parameter|NNS ILLUMINACLIP|ILLUMINACLIP|NNP :|:|: /|/|: Trimmomatic-0.32|trimmomatic-0.32|NN /|/|: adapters/TruSeq3-PE|adapters/truseq3-pe|JJ -2|-2|CD .|.|. fa|fa|NN :|:|: 2:30:10|2:30:10|CD HEADCROP|headcrop|NN :|:|: 8|8|CD CROP|crop|NN :|:|: 40|40|CD SLIDINGWINDOW|SLIDINGWINDOW|NNP :|:|: 6:5|6:5|CD MINLEN|MINLEN|NNP :|:|: 40|40|CD
Reads|read|NNS were|be|VBD aligned|align|VBN to|to|TO E.coli|e.coli|VB rRNA|rrna|NN and|and|CC tRNA|trna|NN using|use|VBG Bowtie|Bowtie|NNP v.|v.|CC 0.12.0|0.12.0|CD allowing|allow|VBG for|for|IN one|one|CD mismatch|mismatch|NN and|and|CC reads|read|VBZ aligning|align|VBG to|to|TO more|more|JJR than|than|IN one|one|CD position|position|NN in|in|IN the|the|DT genome|genome|NN were|be|VBD randomly|randomly|RB assigned|assign|VBN to|to|TO one|one|CD of|of|IN those|those|DT positions|position|NNS
Reads|Reads|NNPS were|be|VBD aligned|align|VBN to|to|TO GenBank|genbank|NN ID|id|NN U00096|u00096|NN .2|.2|NN
Reads|read|NNS were|be|VBD aligned|align|VBN to|to|TO the|the|DT MG1655|mg1655|NN genome|genome|NN with|with|IN Bowtie|Bowtie|NNP .|.|.
Reads|Reads|NNPS were|be|VBD aligned|align|VBN using|use|VBG MG15655|mg15655|NN as|as|IN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC000913|nc000913|NN .2|.2|NN -RRB-|-rrb-|-RRB- using|use|VBG Bowtie2|bowtie2|NN tool|tool|NN .|.|.
Reads|Reads|NNPS were|be|VBD end-to-end|end-to-end|JJ aligned|align|VBN ,|,|, with|with|IN no|no|DT mismatches|mismatch|NNS allowed|allow|VBN ,|,|, to|to|TO the|the|DT respective|respective|JJ draft|draft|NN genomes|genome|NNS using|use|VBG Bowtie2|bowtie2|NN with|with|IN default|default|NN settings|setting|NNS
reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- NC000913|nc000913|NN .3|.3|NN -RRB-|-rrb-|-RRB- genome|genome|NN using|use|VBG Novoalign|novoalign|JJ version|version|NN 2.07|2.07|CD -LRB-|-lrb-|-LRB- www.novocraft.com|www.novocraft.com|NN -RRB-|-rrb-|-RRB- -|-|: Example|example|NN :|:|: -LRB-|-lrb-|-LRB- novoalign|novoalign|JJ -|-|: f|f|FW DL4900|dl4900|FW _|_|SYM clip|clip|VB _|_|SYM clp.fasta|clp.fasta|SYM -|-|: d|d|NN NC000913|nc000913|NN .3|.3|NN .|.|. nix|nix|SYM -|-|: r|r|NN Random|Random|NNP >|>|JJR DL4900.novo|dl4900.novo|NN -RRB-|-rrb-|-RRB-
Reads|read|NNS were|be|VBD mapped|map|VBN to|to|TO the|the|DT NC|NC|NNP _|_|SYM 000913.2|000913.2|CD reference|reference|NN genome|genome|NN using|use|VBG the|the|DT default|default|NN settings|setting|NNS in|in|IN bowtie2|bowtie2|NN -LRB-|-lrb-|-LRB- Langmead|langmead|NN and|and|CC Salzberg|Salzberg|NNP ,|,|, 2012|2012|CD -RRB-|-rrb-|-RRB- .|.|. Datasets|dataset|NNS were|be|VBD quantified|quantify|VBN using|use|VBG cuffdiff|cuffdiff|NN in|in|IN the|the|DT cufflinks|cufflink|NNS package|package|NN to|to|TO generate|generate|VB FPKM|fpkm|NN -LRB-|-lrb-|-LRB- Framents|Framents|NNP Per|per|IN Kilobase|Kilobase|NNP per|per|IN Million|Million|NNP reads|read|VBZ mapped|map|VBN -RRB-|-rrb-|-RRB- values|value|NNS for|for|IN all|all|DT genes|gene|NNS -LRB-|-lrb-|-LRB- Trapnell|Trapnell|NNP et|et|FW al.|al.|FW ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- .|.|.
Reads|Reads|NNPS were|be|VBD mapped|map|VBN using|use|VBG BWA|BWA|NNP 0.7.5|0.7.5|CD a|a|DT
Reads|read|NNS were|be|VBD trimmed|trim|VBN and|and|CC adaptors|adaptor|NNS removed|remove|VBN using|use|VBG the|the|DT fastx|fastx|NN _|_|NN toolkit|toolkit|NN .|.|.
Reads|Reads|NNPS were|be|VBD trimmed|trim|VBN for|for|IN quality|quality|NN using|use|VBG Trimmomatic-0.32|trimmomatic-0.32|NN with|with|IN a|a|DT cutoff|cutoff|JJ quality|quality|NN score|score|NN of|of|IN 20|20|CD
Read|read|VBP using|use|VBG bedtools|bedtool|NNS ,|,|, version|version|NN 2.17.0|2.17.0|CD ,|,|, parameter|parameter|NN :|:|: -|-|: s|s|NNS ,|,|, for|for|IN samples|sample|NNS 1-5|1-5|CD the|the|DT middle|middle|NN nucleotide|nucleotide|NN of|of|IN each|each|DT read|read|NN was|be|VBD taken|take|VBN ,|,|, for|for|IN samples|sample|NNS 6-9|6-9|CD the|the|DT first|first|JJ nucleotide|nucleotide|NN was|be|VBD taken|take|VBN and|and|CC the|the|DT read|read|NN count|count|NN was|be|VBD assigned|assign|VBN to|to|TO the|the|DT nucleotide|nucleotide|NN 5|5|CD '|'|'' of|of|IN the|the|DT first|first|JJ nucleotide|nucleotide|NN see|see|VB -LCB-|-lcb-|-LRB- Kertesz|Kertesz|NNP ,|,|, 2010|2010|CD -RCB-|-rcb-|-RRB- for|for|IN details|detail|NNS
recA730|reca730|NN _|_|CD vs|vs|CC _|_|CD recA730|reca730|NN ,|,|, dcd|dcd|NN
recA730|reca730|NN _|_|CD vs|vs|CC _|_|CD recA730|reca730|NN ,|,|, ndk|ndk|NN
recA|reca|NN deletion|deletion|NN 0.05|0.05|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
recA|reca|NN deletion|deletion|NN 0|0|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
recA|reca|NN deletion|deletion|NN 1.0|1.0|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
recA|reca|NN _|_|NN D|d|NN _|_|CD N0000|n0000|NN _|_|CD r1|r1|NN
recA|reca|NN _|_|NN D|d|NN _|_|CD N0000|n0000|NN _|_|CD r2|r2|NN
recA|reca|NN _|_|NN D|d|NN _|_|CD N0050|n0050|NN _|_|CD r1|r1|NN
recA|reca|NN _|_|NN D|d|NN _|_|CD N0050|n0050|NN _|_|CD r2|r2|NN
recA|reca|NN _|_|NN D|d|NN _|_|CD N1000|n1000|NN _|_|CD r1|r1|NN
recA|reca|NN _|_|NN D|d|NN _|_|CD N1000|n1000|NN _|_|CD r2|r2|NN
recA|reca|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|NNP r1|r1|NN
recA|reca|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r2|r2|FW
recA|reca|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
recA|reca|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP 0|0|CD ,|,|, no|no|DT IPTG|iptg|NN
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP 1|1|CD h|h|NN ,|,|, 5|5|CD mM|mm|NN IPTG|iptg|NN
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP 1|1|CD h|h|NN ,|,|, no|no|DT IPTG|iptg|NN
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP 4|4|CD h|h|NN ,|,|, no|no|DT IPTG|iptg|NN
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S0|S0|NNP ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 1|1|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S0|S0|NNP ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 2|2|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S0|S0|NNP ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 3|3|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S1|s1|NN ,|,|, IPTG|iptg|NN ,|,|, 1|1|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S1|s1|NN ,|,|, IPTG|iptg|NN ,|,|, 2|2|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S1|s1|NN ,|,|, IPTG|iptg|NN ,|,|, 3|3|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S1|s1|NN ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 1|1|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S1|s1|NN ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 2|2|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S1|s1|NN ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 3|3|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S4|S4|NNP ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 1|1|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S4|S4|NNP ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 2|2|CD
Recombinant|recombinant|JJ ,|,|, high|high|JJ cell|cell|NN density|density|NN ,|,|, Time|Time|NNP S4|S4|NNP ,|,|, no|no|DT IPTG|iptg|NN ,|,|, 3|3|CD
Reduced|reduce|VBN genome|genome|NN strain|strain|NN MDS42|mds42|NN ,|,|, 100|100|CD mcg/ml|mcg/ml|NN bicyclomycin|bicyclomycin|NN 20|20|CD min|min|NN ,|,|, exponential|exponential|JJ phase|phase|NN
Reduced|reduce|VBN genome|genome|NN strain|strain|NN MDS42|mds42|NN ,|,|, control|control|NN sample|sample|NN ,|,|, exponential|exponential|JJ phase|phase|NN
Reduced|reduce|VBN genome|genome|NN strain|strain|NN MDS42|mds42|NN ,|,|, deletion|deletion|NN of|of|IN nusA|nusa|NN gene|gene|NN ,|,|, OD600|od600|NN =|=|JJ 0.3|0.3|CD
Reduced|reduce|VBN genome|genome|NN strain|strain|NN MDS42|mds42|NN ,|,|, deletion|deletion|NN of|of|IN nusG|nusg|NN gene|gene|NN ,|,|, OD600|od600|NN =|=|JJ 0.3|0.3|CD ,|,|, overnight|overnight|JJ culture|culture|NN
referece|referece|NN :|:|: The|the|DT three|three|CD genomes|genome|NNS contributing|contribute|VBG to|to|TO the|the|DT ORFs|orf|NNS on|on|IN the|the|DT microarray|microarray|NN .|.|.
reference|reference|NN 0|0|CD '|'|'' ,|,|, min|min|NN +.2|+.2|CD %|%|NN glu|glu|NN ,|,|, 25|25|CD ug|ug|NN RNA|rna|NN
Reference|Reference|NNP Design|Design|NNP timecourse|timecourse|NN c|c|NN _|_|CD t10|t10|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t10|t10|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t1|t1|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t11|t11|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t11|t11|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t1|t1|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t2|t2|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t2|t2|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t3|t3|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t3|t3|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t4|t4|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t4|t4|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t5|t5|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t5|t5|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t6|t6|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t6|t6|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t7|t7|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t7|t7|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t8|t8|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t8|t8|NN .2|.2|NN
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t9|t9|NN .1|.1|CD
Reference|Reference|NNP Design|design|NN timecourse|timecourse|NN c|c|NN _|_|CD t9|t9|NN .2|.2|NN
reference|reference|NN DNA|dna|NN
Reference|Reference|NNP DNA|DNA|NNP genomic|genomic|JJ DNA|dna|NN
reference|reference|NN :|:|: E.|e.|FW coli|coli|FW TOP10|top10|NN containing|contain|VBG pBAD18|pbad18|NN vector|vector|NN with|with|IN no|no|DT arabinose|arabinose|NN added|add|VBD
Reference|Reference|NNP files|file|VBZ for|for|IN the|the|DT genome|genome|NN sequence|sequence|NN being|be|VBG queried|query|VBN ,|,|, Escherichia|escherichia|FW coli|coli|FW BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 012971|012971|CD -RRB-|-rrb-|-RRB- were|be|VBD uploaded|upload|VBN .|.|.
reference|reference|NN genome|genome|NN :|:|: U00096|u00096|NN .2|.2|NN
Reference|Reference|NNP genome|genome|NN used|use|VBN :|:|: Escherichia|escherichia|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN ,|,|, version|version|NN :|:|: iGenome|iGenome|NNP
Reference|Reference|NNP genomic|genomic|JJ DNA|dna|NN
Reference|Reference|NNP Genomic|genomic|JJ DNA|dna|NN
REference|reference|NN genomic|genomic|JJ DNA|dna|NN
reference|reference|NN :|:|: Input|input|NN DNA|dna|NN
reference|reference|NN :|:|: input|input|NN Genomic|genomic|JJ DNA|dna|NN control|control|NN
Reference|Reference|NNP Pool|Pool|NNP
References|References|NNPS
References|References|NNPS :|:|:
reference|reference|NN sample|sample|NN harvested|harvest|VBN immediately|immediately|RB prior|prior|RB to|to|TO glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
Reformat|reformat|VB Illumina|Illumina|NNP files|file|NNS to|to|TO Sanger|Sanger|NNP format|format|NN ,|,|, FASTQ|FASTQ|NNP Groomer|Groomer|NNP
REL606|REL606|NNP ,|,|, exponential|exponential|JJ phase|phase|NN ,|,|, LB|lb|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 168|168|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 168|168|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 24|24|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 24|24|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 336|336|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 336|336|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 3|3|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 3|3|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 48|48|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 48|48|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 4|4|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 4|4|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|SYM 5|5|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|SYM 5|5|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 6|6|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 6|6|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 8|8|CD hr|hr|NN
REL606|rel606|NN _|_|CD glucose-limited|glucose-limited|JJ minimal|minimal|JJ medium|medium|NN _|_|NN 8|8|CD hr|hr|NN _|_|NN rRNA|rrna|NN not|not|RB depleted|deplete|VBN
REL606|rel606|NN ,|,|, stationary|stationary|JJ phase|phase|NN ,|,|, LB|lb|NN
relE|rele|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r1|r1|NN
relE|rele|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r2|r2|NN
relE|rele|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r3|r3|NN
relE|rele|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
Remaining|remain|VBG linker-1|linker-1|NN reads|read|VBZ -LRB-|-lrb-|-LRB- CTGTAGGCACCATCAAT|ctgtaggcaccatcaat|NN -RRB-|-rrb-|-RRB- were|be|VBD removed|remove|VBN from|from|IN fastq|fastq|NN files|file|NNS using|use|VBG fastx|fastx|NN _|_|NN clipper|clipper|NN
Removal|removal|NN of|of|IN PCR|pcr|NN duplicates|duplicate|VBZ based|base|VBN on|on|IN the|the|DT 20|20|CD first|first|JJ bp|bp|NN of|of|IN the|the|DT read|read|NN containing|contain|VBG a|a|DT 6|6|CD nt|nt|NN random|random|JJ tag|tag|NN -LRB-|-lrb-|-LRB- home|home|NN made|make|VBN script|script|NN -RRB-|-rrb-|-RRB- .|.|.
Removal|removal|NN of|of|IN un-informative|un-informative|JJ events|event|NNS -LRB-|-lrb-|-LRB- uncuts|uncut|NNS ,|,|, loops|loop|NNS etc|etc|FW -RRB-|-rrb-|-RRB- as|as|IN described|describe|VBN in|in|IN Cournac|Cournac|NNP et|et|FW al.|al.|FW .|.|. BMC|BMC|NNP 2012|2012|CD .|.|.
Remove|remove|VBP non-protein|non-protein|JJ coding|code|VBG counts|count|NNS
replicate|replicate|VBP :|:|: 1|1|CD
Replicate|replicate|VB 1|1|LS -|-|: timepoint|timepoint|NN 1|1|CD -LRB-|-lrb-|-LRB- 4.5|4.5|CD h|h|NN -RRB-|-rrb-|-RRB-
Replicate|replicate|VB 1|1|LS -|-|: timepoint|timepoint|NN 1|1|CD -LRB-|-lrb-|-LRB- 4.5|4.5|CD h|h|NN -RRB-|-rrb-|-RRB- -|-|: dye|dye|VB swap|swap|NN
Replicate|replicate|VB 1|1|LS -|-|: timepoint|timepoint|NN 2|2|CD -LRB-|-lrb-|-LRB- 6h|6h|NN -RRB-|-rrb-|-RRB-
Replicate|replicate|VB 1|1|LS -|-|: timepoint|timepoint|NN 2|2|CD -LRB-|-lrb-|-LRB- 6h|6h|NN -RRB-|-rrb-|-RRB- -|-|: dye|dye|VB swap|swap|NN
Replicate|replicate|VB 1|1|LS -|-|: timepoint|timepoint|NN 3|3|CD -LRB-|-lrb-|-LRB- 9h|9h|NN -RRB-|-rrb-|-RRB-
Replicate|replicate|VB 1|1|LS -|-|: timepoint|timepoint|NN 3|3|CD -LRB-|-lrb-|-LRB- 9h|9h|NN -RRB-|-rrb-|-RRB- -|-|: dye|dye|VB swap|swap|NN
replicate|replicate|VBP :|:|: 2|2|CD
Replicate|replicate|VB 2|2|LS -|-|: timepoint|timepoint|NN 1|1|CD -LRB-|-lrb-|-LRB- 4.5|4.5|CD h|h|NN -RRB-|-rrb-|-RRB-
Replicate|replicate|VB 2|2|LS -|-|: timepoint|timepoint|NN 1|1|CD -LRB-|-lrb-|-LRB- 4.5|4.5|CD h|h|NN -RRB-|-rrb-|-RRB- -|-|: dye|dye|VB swap|swap|NN
Replicate|replicate|VB 2|2|LS -|-|: timepoint|timepoint|NN 2|2|CD -LRB-|-lrb-|-LRB- 6h|6h|NN -RRB-|-rrb-|-RRB-
Replicate|replicate|VB 2|2|LS -|-|: timepoint|timepoint|NN 2|2|CD -LRB-|-lrb-|-LRB- 6h|6h|NN -RRB-|-rrb-|-RRB- -|-|: dye|dye|VB swap|swap|NN
Replicate|replicate|VB 2|2|LS -|-|: timepoint|timepoint|NN 3|3|CD -LRB-|-lrb-|-LRB- 9h|9h|NN -RRB-|-rrb-|-RRB-
Replicate|replicate|VB 2|2|LS -|-|: timepoint|timepoint|NN 3|3|CD -LRB-|-lrb-|-LRB- 9h|9h|NN -RRB-|-rrb-|-RRB- -|-|: dye|dye|VB swap|swap|NN
replicate|replicate|VBP :|:|: 3|3|CD
replicate|replicate|VB :|:|: 4|4|CD
replicates|replicate|VBZ :|:|: ORF1|orf1|NN replicate|replicate|VB 1|1|CD /|/|: induced|induce|VBN
replicates|replicate|VBZ :|:|: ORF1|orf1|NN replicate|replicate|VB 1|1|CD /|/|: not|not|RB induced|induce|VBN
replicates|replicate|VBZ :|:|: ORF1|orf1|NN replicate|replicate|VB 2|2|CD /|/|: induced|induce|VBN
replicates|replicate|VBZ :|:|: ORF1|orf1|NN replicate|replicate|VB 2|2|CD /|/|: not|not|RB induced|induce|VBN
replicates|replicate|VBZ :|:|: Svi3-3|svi3-3|NN replicate|replicate|VB 1|1|CD /|/|: induced|induce|VBN
replicates|replicate|VBZ :|:|: Svi3-3|svi3-3|NN replicate|replicate|VB 1|1|CD /|/|: not|not|RB induced|induce|VBN
replicates|replicate|VBZ :|:|: Svi3-3|svi3-3|NN replicate|replicate|VB 2|2|CD /|/|: induced|induce|VBN
replicates|replicate|VBZ :|:|: Svi3-3|svi3-3|NN replicate|replicate|VB 2|2|CD /|/|: not|not|RB induced|induce|VBN
replicates|replicate|VBZ :|:|: WT|WT|NNP replicate|replicate|VB 1|1|CD /|/|: induced|induce|VBN
replicates|replicate|VBZ :|:|: WT|WT|NNP replicate|replicate|VB 2|2|CD /|/|: induced|induce|VBN
reporter|reporter|NN :|:|: CRE|cre|NN multi-hit|multi-hit|JJ
reporter|reporter|NN :|:|: CRE|cre|NN single-hit|single-hit|JJ
reporter|reporter|NN :|:|: IFNB|ifnb|NN multi-hit|multi-hit|JJ
reporter|reporter|NN :|:|: IFNB|ifnb|NN single-hit|single-hit|JJ
Require|require|VB peaks|peak|NNS to|to|TO be|be|VB present|present|JJ in|in|IN at|at|IN least|least|JJS 2|2|CD replicates|replicate|VBZ and|and|CC conform|conform|VB to|to|TO a|a|DT peak|peak|JJ shape|shape|NN by|by|IN visual|visual|JJ inspection|inspection|NN
Respiratory|respiratory|JJ defecient|defecient|JJ E.|e.|FW coli|coli|FW mutant|mutant|NN -LRB-|-lrb-|-LRB- ECOM4|ecom4|NN -RRB-|-rrb-|-RRB- ,|,|, M9|m9|NN media|media|NNS with|with|IN 4|4|CD g/L|g/l|NN glucose|glucose|NN ,|,|, aerobic|aerobic|JJ ,|,|, log|log|NN phase|phase|NN
Resulting|result|VBG mRNA|mrna|NN was|be|VBD reverse-transcribed|reverse-transcribed|JJ to|to|TO cDNA|cdna|NN libraries|library|NNS via|via|IN SuperScript|SuperScript|NNP III|III|NNP First|First|NNP Strand|Strand|NNP reverse|reverse|VB transcription|transcription|NN kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP ,|,|, 18080051|18080051|CD -RRB-|-rrb-|-RRB- as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. The|the|DT cDNA|cdna|NN libraries|library|NNS were|be|VBD multiplexed|multiplex|VBN to|to|TO distinguish|distinguish|VB replicates|replicate|VBZ from|from|IN one|one|CD another|another|DT ,|,|, barcoded|barcode|VBN for|for|IN sequencing|sequencing|NN ,|,|, and|and|CC then|then|RB amplified|amplify|VBN with|with|IN random|random|JJ hexamers|hexamer|NNS for|for|IN 15|15|CD PCR|pcr|NN cycles|cycle|NNS .|.|. Transcripts|transcript|NNS were|be|VBD sequenced|sequence|VBN for|for|IN 50|50|CD bases|basis|NNS in|in|IN single-end|single-end|JJ fashion|fashion|NN within|within|IN one|one|CD lane|lane|NN of|of|IN an|a|DT Illumina|Illumina|NNP Hiseq|Hiseq|NNP 2000|2000|CD flow|flow|NN cell|cell|NN .|.|. This|this|DT yielded|yield|VBD roughly|roughly|RB 30|30|CD million|million|CD reads|read|VBZ per|per|IN sample|sample|NN .|.|.
Resulting|Resulting|NNP read|read|VBD count|count|NN matrix|matrix|NN was|be|VBD used|use|VBN as|as|IN input|input|NN for|for|IN the|the|DT differntial|differntial|JJ expression|expression|NN analysis|analysis|NN in|in|IN edgeR|edger|NN -LRB-|-lrb-|-LRB- version|version|NN 3.12.1|3.12.1|CD -RRB-|-rrb-|-RRB- .|.|.
Resulting|Resulting|NNP reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT published|publish|VBN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT software|software|NN package|package|NN SOAP|soap|NN -LRB-|-lrb-|-LRB- Li|Li|NNP et|et|FW al|al|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- ,|,|, allowing|allow|VBG no|no|RB more|more|JJR than|than|IN two|two|CD mismatches|mismatch|NNS -LRB-|-lrb-|-LRB- Supplemental|Supplemental|NNP File|File|NNP -RRB-|-rrb-|-RRB- .|.|. Reads|read|VBZ aligning|align|VBG to|to|TO repeated|repeated|JJ elements|element|NNS in|in|IN the|the|DT genome|genome|NN -LRB-|-lrb-|-LRB- e.g.|e.g.|FW rRNA|rrna|NN -RRB-|-rrb-|-RRB- were|be|VBD removed|remove|VBN from|from|IN analysis|analysis|NN .|.|. For|for|IN reads|read|VBZ that|that|IN had|have|VBD no|no|DT mapping|mapping|NN locations|location|NNS for|for|IN the|the|DT first|first|JJ 36|36|CD bp|bp|NN ,|,|, the|the|DT 3-30|3-30|CD bp|bp|NN subsequences|subsequence|NNS were|be|VBD used|use|VBN in|in|IN the|the|DT subsequent|subsequent|JJ mapping|mapping|NN to|to|TO the|the|DT reference|reference|NN genome|genome|NN .|.|. Reads|read|NNS that|that|WDT had|have|VBD unique|unique|JJ mapping|mapping|NN locations|location|NNS and|and|CC did|do|VBD not|not|RB match|match|VB annotated|annotated|JJ rRNA|rrna|NN genes|gene|NNS were|be|VBD used|use|VBN for|for|IN further|further|JJ analysis|analysis|NN .|.|. For|for|IN each|each|DT gene|gene|NN ,|,|, the|the|DT tag|tag|NN density|density|NN was|be|VBD estimated|estimate|VBN as|as|IN the|the|DT number|number|NN of|of|IN aligned|align|VBN sequencing|sequencing|NN tags|tag|NNS divided|divide|VBN by|by|IN gene|gene|NN size|size|NN in|in|IN kb|kb|NN .|.|. Per-gene|per-gene|JJ tag|tag|NN density|density|NN was|be|VBD normalized|normalize|VBN using|use|VBG quantile|quantile|JJ normalization|normalization|NN -LRB-|-lrb-|-LRB- Supplemental|Supplemental|NNP Files|Files|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT tag|tag|NN density|density|NN data|datum|NNS were|be|VBD analyzed|analyze|VBN for|for|IN statistically|statistically|RB significant|significant|JJ differential|differential|JJ expression|expression|NN using|use|VBG BaySeq|BaySeq|NNP -LRB-|-lrb-|-LRB- Hardcastle|Hardcastle|NNP &|&|CC Kelly|Kelly|NNP ,|,|, 2010|2010|CD -RRB-|-rrb-|-RRB- with|with|IN a|a|DT FDR|FDR|NNP of|of|IN 0.01|0.01|CD ,|,|, and|and|CC genes|gene|NNS were|be|VBD organized|organize|VBN into|into|IN operons|operon|NNS using|use|VBG data|datum|NNS from|from|IN EcoCyc|EcoCyc|NNP -LRB-|-lrb-|-LRB- Keseler|Keseler|NNP et|et|FW al|al|FW ,|,|, 2011|2011|CD -RRB-|-rrb-|-RRB- .|.|.
Resulting|Resulting|NNP SAM|SAM|NNP files|file|NNS were|be|VBD processed|process|VBN with|with|IN custom|custom|NN script|script|NN -LRB-|-lrb-|-LRB- SAM_to_coverage_and_N5E_N3E.py|sam_to_coverage_and_n5e_n3e.py|NN ,|,|, github|github|NN :|:|: https://github.com/sutormin94/Gyrase_Topo-seq|https://github.com/sutormin94/gyrase_topo-seq|NN -RRB-|-rrb-|-RRB- ,|,|, giving|give|VBG coverage|coverage|NN depth|depth|NN of|of|IN the|the|DT genome|genome|NN and|and|CC N3E|n3e|NN values|value|NNS -LRB-|-lrb-|-LRB- number|number|NN of|of|IN DNA|dna|NN fragments|fragment|NNS 3|3|CD '|'|'' -|-|: ends|end|NNS -RRB-|-rrb-|-RRB- for|for|IN every|every|DT position|position|NN
re-suspended|re-suspended|JJ in|in|IN 200|200|CD ul|ul|NN Trizol|trizol|NN and|and|CC combined|combine|VBN for|for|IN a|a|DT total|total|JJ volume|volume|NN of|of|IN 1|1|CD ml|ml|NN ,|,|, then|then|RB promptly|promptly|RB
RF2|rf2|NN *|*|SYM _|_|SYM exp1|exp1|NN _|_|NN mRNA|mrna|NN
RF2|rf2|NN *|*|SYM _|_|SYM exp1|exp1|FW _|_|FW ribosome|ribosome|NN
RF2|rf2|NN *|*|SYM _|_|SYM exp3|exp3|FW _|_|FW mRNA|mrna|NN
RF2|rf2|NN *|*|SYM _|_|SYM exp3|exp3|FW _|_|FW ribosome|ribosome|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|SYM exp2|exp2|FW _|_|FW repA|repa|NN _|_|NN mRNA|mrna|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|SYM exp2|exp2|FW _|_|FW repA|repa|NN _|_|NN ribosome|ribosome|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|CD exp2|exp2|NN _|_|CD repB|repb|NN _|_|NN mRNA|mrna|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|CD exp2|exp2|NN _|_|CD repB|repb|NN _|_|NN ribosome|ribosome|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|CD exp3|exp3|NN _|_|NN mRNA|mrna|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|CD exp3|exp3|NN _|_|NN ribosome|ribosome|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|SYM exp4|exp4|FW _|_|FW repA|repa|NN _|_|NN mRNA|mrna|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|SYM exp4|exp4|FW _|_|FW repA|repa|NN _|_|NN ribosome|ribosome|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|CD exp4|exp4|NN _|_|CD repB|repb|NN _|_|NN mRNA|mrna|NN
RF2|rf2|NN *|*|SYM ∆|∆|SYM RF3|rf3|NN _|_|CD exp4|exp4|NN _|_|CD repB|repb|NN _|_|NN ribosome|ribosome|NN
∆|∆|CD RF3|rf3|NN _|_|CD exp1|exp1|NN _|_|NN mRNA|mrna|NN
∆|∆|CD RF3|rf3|NN _|_|CD exp1|exp1|NN _|_|NN ribosome|ribosome|NN
∆|∆|CD RF3|rf3|NN _|_|CD exp3|exp3|NN _|_|NN mRNA|mrna|NN
∆|∆|CD RF3|rf3|NN _|_|CD exp3|exp3|NN _|_|NN ribosome|ribosome|NN
∆|∆|CD RF3|rf3|NN _|_|NN minimal|minimal|JJ _|_|NN mRNA|mrna|NN
∆|∆|CD RF3|rf3|NN _|_|NN minimal|minimal|JJ _|_|NN ribosome|ribosome|NN
rfbA|rfba|NN KO|ko|NN rep1|rep1|NN
rfbA|rfba|NN KO|ko|NN rep2|rep2|NN
rfbA|rfba|NN KO|ko|NN rep3|rep3|NN
RhIB|rhib|NN wild|wild|JJ type|type|NN
RhlBP238L|rhlbp238l|NN mutant|mutant|JJ
RhlBP238L|rhlbp238l|NN vs|vs|CC flag|flag|NN only|only|RB 1|1|CD
RhlBP238L|rhlbp238l|NN vs|vs|CC flag|flag|NN only|only|RB 2|2|CD
RhlBP238L|rhlbp238l|NN vs|vs|CC flag|flag|NN only|only|RB 3|3|CD
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1.5|1.5|CD '|'|'' post|post|JJ rif|rif|NN
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3|3|CD '|'|'' post|post|JJ rif|rif|NN
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3|3|CD '|'|'' post|post|JJ rif|rif|NN
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6|6|CD '|'|'' post|post|JJ rif|rif|NN
RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD Mid|Mid|NNP Log|Log|NNP 6|6|CD '|'|'' post|post|JJ rif|rif|NN
RhlBwt|rhlbwt|NN vs|vs|CC flag|flag|NN only|only|RB 1|1|CD
RhlBwt|rhlbwt|NN vs|vs|CC flag|flag|NN only|only|RB 2|2|CD
RhlBwt|rhlbwt|NN vs|vs|CC flag|flag|NN only|only|RB 3|3|CD
Rho|rho|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 3421602|3421602|CD -RRB-|-rrb-|-RRB-
Rho|rho|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 70261|70261|CD -RRB-|-rrb-|-RRB-
Rho|rho|NN ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS
Rhodococcus|rhodococcus|NN jostii|jostii|NN RHA1|rha1|NN
∆|∆|CD rho|rho|NN UvsW|uvsw|NN _|_|CD replicate1|replicate1|NN
∆|∆|CD rho|rho|NN UvsW|uvsw|NN _|_|CD replicate2|replicate2|NN
∆|∆|CD rho|rho|NN UvsW|uvsw|NN _|_|CD replicate3|replicate3|NN
Ribosomal|ribosomal|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- rRNA|rrna|NN -RRB-|-rrb-|-RRB- was|be|VBD removed|remove|VBN using|use|VBG Ribo-Zero|Ribo-Zero|NNP ™|™|NNP Gold|Gold|NNP -LRB-|-lrb-|-LRB- Yeast|yeast|NN -RRB-|-rrb-|-RRB- kit|kit|NN -LRB-|-lrb-|-LRB- Epicenter|epicenter|NN ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP -RRB-|-rrb-|-RRB- using|use|VBG manufacturer|manufacturer|NN 's|'s|POS recommended|recommend|VBN protocol|protocol|NN .|.|. Immediately|immediately|RB after|after|IN the|the|DT rRNA|rrna|NN removal|removal|NN the|the|DT RNA|rna|NN was|be|VBD fragmented|fragmented|JJ and|and|CC primed|prime|VBN for|for|IN the|the|DT first|first|JJ strand|strand|NN synthesis|synthesis|NN using|use|VBG the|the|DT NEBnext|NEBnext|NNP First|First|NNP Strand|Strand|NNP synthesis|synthesis|NN module|module|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP BioLabs|BioLabs|NNP Inc.|Inc.|NNP ,|,|, Ipswich|Ipswich|NNP ,|,|, MA|MA|NNP -RRB-|-rrb-|-RRB- .|.|. Directional|directional|JJ second|second|JJ strand|strand|NN synthesis|synthesis|NN was|be|VBD performed|perform|VBN using|use|VBG NEBNExt|NEBNExt|NNP Ultra|Ultra|NNP Directional|Directional|NNP second|second|JJ strand|strand|NN synthesis|synthesis|NN kit|kit|NN .|.|. Following|follow|VBG this|this|DT the|the|DT samples|sample|NNS were|be|VBD taken|take|VBN into|into|IN standard|standard|JJ library|library|NN preparation|preparation|NN protocol|protocol|NN using|use|VBG NEBNext|nebnext|NN ®|®|NN DNA|dna|NN Library|Library|NNP Prep|Prep|NNP Master|Master|NNP Mix|Mix|NNP Set|set|VB for|for|IN Illumina|Illumina|NNP ®|®|SYM with|with|IN slight|slight|JJ modifications|modification|NNS .|.|. Briefly|briefly|RB ,|,|, end-repair|end-repair|NN was|be|VBD done|do|VBN followed|follow|VBN by|by|IN polyA|polya|NN addition|addition|NN and|and|CC adapter|adapter|NN ligation|ligation|NN .|.|. Post-ligated|post-ligated|JJ materials|material|NNS were|be|VBD individually|individually|RB barcoded|barcode|VBN with|with|IN primers|primer|NNS and|and|CC amplified|amplify|VBN through|through|IN 12|12|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN .|.|. Final|final|JJ library|library|NN quantity|quantity|NN was|be|VBD assessed|assess|VBN by|by|IN Quant-iT|quant-it|NN ™|™|CD PicoGreen|PicoGreen|NNP ®|®|CD dsDNA|dsDNA|NNP Assay|assay|NN Kit|kit|NN and|and|CC the|the|DT library|library|NN quality|quality|NN was|be|VBD estimated|estimate|VBN on|on|IN LabChip|LabChip|NNP ®|®|NNP GX|GX|NNP -LRB-|-lrb-|-LRB- Caliper|Caliper|NNP ,|,|, PerkinElmer|PerkinElmer|NNP ,|,|, Waltham|Waltham|NNP ,|,|, MA|MA|NNP -RRB-|-rrb-|-RRB- .|.|. Accurate|accurate|JJ quantification|quantification|NN of|of|IN the|the|DT final|final|JJ libraries|library|NNS for|for|IN sequencing|sequencing|NN applications|application|NNS was|be|VBD determined|determine|VBN using|use|VBG the|the|DT qPCR-based|qpcr-based|JJ KAPA|KAPA|NNP Biosystems|Biosystems|NNP Library|Library|NNP Quantification|Quantification|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Kapa|Kapa|NNP Biosystems|Biosystems|NNP ,|,|, Inc.|Inc.|NNP ,|,|, Woburn|Woburn|NNP ,|,|, MA|MA|NNP -RRB-|-rrb-|-RRB- .|.|. Each|each|DT library|library|NN was|be|VBD diluted|dilute|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 12.5|12.5|CD nM|nm|NN and|and|CC pooled|pooled|JJ equimolar|equimolar|JJ prior|prior|JJ to|to|TO clustering|clustering|NN .|.|. Paired-End|paired-end|NN -LRB-|-lrb-|-LRB- PE|pe|NN -RRB-|-rrb-|-RRB- sequencing|sequencing|NN was|be|VBD performed|perform|VBN on|on|IN an|a|DT Illumina|Illumina|NNP HiSeq2500|hiseq2500|NN sequencer|sequencer|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- .|.|.
Ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD first|first|JJ removed|remove|VBN using|use|VBG the|the|DT Ribozero|Ribozero|NNP rRNA|rrna|NN Removal|removal|NN Meta-Bacteria|Meta-Bacteria|NNP kit|kit|NN .|.|. Enriched|enriched|JJ mRNAs|mrna|NNS were|be|VBD then|then|RB converted|convert|VBN into|into|IN indexed|index|VBN libraries|library|NNS using|use|VBG the|the|DT into|into|IN ScriptSeqTM|scriptseqtm|NN v2|v2|NN RNA-Seq|rna-seq|NN Library|Library|NNP Preparation|Preparation|NNP Kit|kit|NN
Ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD removed|remove|VBN from|from|IN 1|1|CD μg|μg|NN of|of|IN total|total|JJ RNA|rna|NN using|use|VBG Ribozero|Ribozero|NNP rRNA|rrna|NN Removal|removal|NN Meta-Bacteria|Meta-Bacteria|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP Biotechnologies|Biotechnologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC the|the|DT mRNA-enriched|mrna-enriched|JJ fraction|fraction|NN was|be|VBD converted|convert|VBN to|to|TO indexed|index|VBN RNA-seq|rna-seq|NN libraries|library|NNS with|with|IN the|the|DT ScriptSeq|ScriptSeq|NNP ™|™|CD v2|v2|NN RNA-Seq|rna-seq|NN Library|Library|NNP Preparation|Preparation|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP Biotechnologies|Biotechnologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
Ribosome|Ribosome|NNP profiling|profile|VBG 10|10|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS _|_|VBP 1|1|CD
Ribosome|Ribosome|NNP profiling|profile|VBG 10|10|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS _|_|VBP 2|2|CD
Ribosome|Ribosome|NNP profiling|profile|VBG 15|15|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|ribosome|NN profiling|profiling|NN 2|2|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG 30|30|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG 3|3|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG 4|4|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG 5|5|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG 6|6|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD cspABEG|cspabeg|NN cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG at|at|IN 37|37|CD °C|°c|NN in|in|IN ∆|∆|CD cspABCEG|cspabceg|NN cells|cell|NNS
Ribosome|Ribosome|NNP profiling|profile|VBG at|at|IN 37|37|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS _|_|VBP 1|1|CD
Ribosome|Ribosome|NNP profiling|profile|VBG at|at|IN 37|37|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS _|_|VBP 2|2|CD
ribosome|ribosome|NN profiling|profiling|NN in|in|IN rich|rich|JJ defined|define|VBN media|media|NNS
ribosome|ribosome|NN profiling|profile|VBG MicL|micl|NN t0|t0|NN
ribosome|ribosome|NN profiling|profile|VBG MicL|micl|NN t20|t20|NN
Ribosome|ribosome|NN protected|protect|VBD and|and|CC total|total|JJ mRNA|mrna|NN fragments|fragment|NNS were|be|VBD size|size|NN selected|select|VBN via|via|IN gel|gel|NN purification|purification|NN .|.|. Fragments|fragment|NNS were|be|VBD ligated|ligate|VBN to|to|TO 5|5|CD '|'|'' adenylated|adenylate|VBN DNA|dna|NN oligo|oligo|JJ .|.|. After|after|IN reverse|reverse|JJ transcription|transcription|NN ,|,|, the|the|DT single|single|JJ stranded|stranded|JJ DNA|dna|NN was|be|VBD circularized|circularize|VBN ,|,|, and|and|CC PCR|pcr|NN amplified|amplify|VBD -LSB-|-lsb-|-LRB- Oh|oh|UH et|et|FW al|al|FW ,|,|, .|.|. Cell|cell|NN 147|147|CD ,|,|, 1295|1295|CD -LRB-|-lrb-|-LRB- 2011|2011|CD -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- .|.|. More|more|JJR details|detail|NNS at|at|IN MS|ms|NN Guo|Guo|NNP ,|,|, TB|tb|NN Updegrove|Updegrove|NNP ,|,|, et|et|FW al|al|FW ,|,|, Genes|gene|NNS Dev|dev|NN .|.|. -LRB-|-lrb-|-LRB- 2014|2014|CD -RRB-|-rrb-|-RRB- .|.|.
Ribosome|Ribosome|NNP protected|protect|VBD mRNA|mrna|NN fragments|fragment|NNS were|be|VBD size|size|NN selected|select|VBN via|via|IN gel|gel|NN purification|purification|NN ,|,|, and|and|CC ligated|ligate|VBN to|to|TO 5|5|CD '|'|'' adenylated|adenylate|VBN DNA|dna|NN oligo|oligo|JJ .|.|. After|after|IN reverse|reverse|JJ transcription|transcription|NN ,|,|, the|the|DT single|single|JJ stranded|stranded|JJ DNA|dna|NN was|be|VBD circularized|circularize|VBN ,|,|, and|and|CC PCR|pcr|NN amplified|amplify|VBD -LSB-|-lsb-|-LRB- Oh|oh|UH et|et|FW al|al|FW ,|,|, .|.|. Cell|cell|NN 147|147|CD ,|,|, 1295|1295|CD -LRB-|-lrb-|-LRB- 2011|2011|CD -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- .|.|. More|more|RBR at|at|IN G.W.|G.W.|NNP Li|Li|NNP ,|,|, D.|D.|NNP Burkhardt|Burkhardt|NNP ,|,|, C.A.|C.A.|NNP Gross|Gross|NNP ,|,|, J.|J.|NNP S.|S.|NNP Weissman|Weissman|NNP -LRB-|-lrb-|-LRB- Cell|cell|NN -RRB-|-rrb-|-RRB- .|.|.
Ribosome|Ribosome|NNP protected|protect|VBD mRNA|mrna|NN fragments|fragment|NNS were|be|VBD size|size|NN selected|select|VBN via|via|IN gel|gel|NN purification|purification|NN ,|,|, and|and|CC ligated|ligate|VBN to|to|TO 5|5|CD '|'|'' adenylated|adenylate|VBN DNA|dna|NN oligo|oligo|JJ .|.|. After|after|IN reverse|reverse|JJ transcription|transcription|NN ,|,|, the|the|DT single|single|JJ stranded|stranded|JJ DNA|dna|NN was|be|VBD circularized|circularize|VBN ,|,|, and|and|CC PCR|pcr|NN amplified|amplify|VBD -LSB-|-lsb-|-LRB- Oh|oh|UH et|et|FW al|al|FW ,|,|, .|.|. Cell|cell|NN 147|147|CD ,|,|, 1295|1295|CD -LRB-|-lrb-|-LRB- 2011|2011|CD -RRB-|-rrb-|-RRB- -RSB-|-rsb-|-RRB- .|.|. More|more|RBR at|at|IN G.W.|G.W.|NNP Li|Li|NNP ,|,|, E.|E.|NNP Oh|oh|UH ,|,|, and|and|CC J.S.|J.S.|NNP Weissman|Weissman|NNP ,|,|, Nature|Nature|NNP -LRB-|-lrb-|-LRB- in|in|IN press|press|NN -RRB-|-rrb-|-RRB-
ribosome-protected|ribosome-protected|JJ :|:|: No|no|DT
ribosome-protected|ribosome-protected|JJ :|:|: Yes|yes|UH
ribozero|ribozero|NN :|:|: No|no|DT
ribozero|ribozero|NN :|:|: Yes|yes|UH
Rifampicine|Rifampicine|NNP Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 1|1|LS -|-|: A-IP|a-ip|NN
Rifampicine|Rifampicine|NNP Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 1|1|CD +|+|CC A-IP|a-ip|JJ
Rifampicine|Rifampicine|NNP Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 1|1|CD +|+|CC A+IP|A+IP|NNP
Rifampicine|Rifampicine|NNP Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 2|2|CD +|+|CC A-IP|a-ip|JJ
Rifampicine|Rifampicine|NNP Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 2|2|CD +|+|CC A+IP|A+IP|NNP
Rifampicine|Rifampicine|NNP Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 3|3|CD +|+|CC A-IP|a-ip|JJ
Rifampicine|Rifampicine|NNP Ciprofloxacin|Ciprofloxacin|NNP Rep|Rep|NNP 3|3|CD +|+|CC A+IP|A+IP|NNP
RifCfx|RifCfx|NNP _|_|NNP IN|in|IN _|_|CD Mu|mu|NN _|_|NN 122mkM|122mkm|NN _|_|CD 10mkM|10mkm|NN _|_|NN 1|1|CD
RifCfx|rifcfx|NN _|_|CD IN|in|IN _|_|CD Mu|mu|NN _|_|NN 122mkM|122mkm|NN _|_|CD 10mkM|10mkm|NN _|_|NN 2|2|CD
RifCfx|rifcfx|NN _|_|CD IN|in|IN _|_|CD Mu|mu|NN _|_|NN 122mkM|122mkm|NN _|_|CD 10mkM|10mkm|NN _|_|NN 3|3|CD
RifCfx|rifcfx|NN _|_|CD IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 122mkM|122mkm|NN _|_|CD 10mkM|10mkm|NN _|_|NN 1|1|CD
RifCfx|rifcfx|NN _|_|CD IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 122mkM|122mkm|NN _|_|CD 10mkM|10mkm|NN _|_|NN 2|2|CD
RifCfx|rifcfx|NN _|_|CD IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 122mkM|122mkm|NN _|_|CD 10mkM|10mkm|NN _|_|NN 3|3|CD
Rif|rif|NN _|_|CD IN|in|IN _|_|CD Mu|mu|NN _|_|CD 122mkM|122mkm|NN _|_|NN 1|1|CD
rimI|rimi|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r1|r1|FW
rimI|rimi|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
rimI|rimi|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
rimI|rimi|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
rip|rip|VBP antibody|antibody|NN :|:|: Monoclonal|monoclonal|JJ ANTI-FLAG|anti-flag|NN ^|^|NN =|=|JJ AE|ae|NN M2|m2|NN antibody|antibody|NN produced|produce|VBN in|in|IN mouse|mouse|NN ,|,|, Sigma|Sigma|NNP ,|,|, F1804-200UG|f1804-200ug|NN ,|,|, SLBG5673V|slbg5673v|NN
riplot|riplot|NN -LRB-|-lrb-|-LRB- LogData|LogData|NNP ,|,|, onScreen|onscreen|NN =|=|JJ FALSE|false|NN -RRB-|-rrb-|-RRB-
riplot|riplot|NN -LRB-|-lrb-|-LRB- NormalData|NormalData|NNP ,|,|, onScreen|onscreen|NN =|=|JJ FALSE|false|NN -RRB-|-rrb-|-RRB-
RIP-Seq|rip-seq|JJ
RMA|rma|NN normalization|normalization|NN was|be|VBD performed|perform|VBN on|on|IN CELL|cell|NN files|files|NNS using|use|VBG the|the|DT Partek|Partek|NNP Genomic|genomic|JJ Suite|suite|NN 6.5|6.5|CD .|.|. Additional|additional|JJ statistical|statistical|JJ analysis|analysis|NN was|be|VBD carried|carry|VBN out|out|RP using|use|VBG the|the|DT Spotfire|Spotfire|NNP software|software|NN package|package|NN -LRB-|-lrb-|-LRB- Somerville|Somerville|NNP ,|,|, MA|MA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC custom|custom|NN Matlab|Matlab|NNP -LRB-|-lrb-|-LRB- R2010B|r2010b|NN -RRB-|-rrb-|-RRB- routines|routine|NNS .|.|.
RMA|rma|NN normalized|normalize|VBD probe|probe|NN data|datum|NNS was|be|VBD uploaded|upload|VBN into|into|IN the|the|DT Mochiview|Mochiview|NNP visualization|visualization|NN software|software|NN where|where|WRB data|datum|NNS cooresponding|coorespond|VBG to|to|TO the|the|DT plus|plus|NN and|and|CC minus|minus|CC strands|strand|NNS were|be|VBD subtracted|subtract|VBN to|to|TO get|get|VB a|a|DT strand-specific|strand-specific|JJ probe|probe|NN intesenity|intesenity|NN per|per|IN base|base|NN as|as|IN reported|report|VBN in|in|IN the|the|DT processed|process|VBN data|datum|NNS files|file|NNS .|.|.
RMA|rma|NN with|with|IN quartile|quartile|JJ normalization|normalization|NN according|accord|VBG to|to|TO method|method|NN of|of|IN Irizarry|Irizarry|NNP et|et|FW al|al|FW ,|,|, 2003|2003|CD .|.|. The|the|DT raw|raw|JJ .|.|. cel|cel|NN files|file|NNS were|be|VBD processed|process|VBN in|in|IN RMA|RMA|NNP using|use|VBG Bioconductor|Bioconductor|NNP R|R|NNP package|package|NN :|:|: affy|affy|VB Version|Version|NNP :|:|: 1.8.1|1.8.1|CD Date|date|NN :|:|: 2005-09-03|2005-09-03|CD ,|,|, with|with|IN the|the|DT option|option|NN Filter.genes|filter.genes|NNS containing|contain|VBG a|a|DT subset|subset|NN of|of|IN probesets|probeset|NNS corresponding|correspond|VBG to|to|TO MG1655|mg1655|NN genes|gene|NNS and|and|CC intergenic|intergenic|JJ regions|region|NNS listed|list|VBN in|in|IN the|the|DT matrix|matrix|NN data|datum|NNS .|.|. Replicates|replicate|VBZ were|be|VBD averaged|average|VBN for|for|IN ratio|ratio|NN calculations|calculation|NNS .|.|.
RNA|rna|NN _|_|NN 1|1|CD
RNA|rna|NN _|_|NN 2|2|CD
RNA|rna|NN degradation|degradation|NN was|be|VBD stopped|stop|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNAprotect|rnaprotect|NN reagent|reagent|NN
RNAeasy|rnaeasy|NN
RNAEasy|rnaeasy|NN with|with|IN RNAProtect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB-
RNA|rna|NN extracted|extract|VBN according|accord|VBG to|to|TO QiAgen|QiAgen|NNP RNeasy|RNeasy|NNP MiniKit|MiniKit|NNP protocol|protocol|NN for|for|IN bacterial|bacterial|JJ samples|sample|NNS
RNA|rna|NN extracted|extract|VBN by|by|IN hot|hot|JJ phenol|phenol|NN choloroform|choloroform|NN folled|foll|VBN by|by|IN Qiagen|Qiagen|NNP RNA|rna|NN Midi|midi|NN column|column|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN BW25113|bw25113|NN wild|wild|JJ type|type|NN after|after|IN 24h|24h|NN of|of|IN growth|growth|NN in|in|IN LBglu|lbglu|NN with|with|IN glass|glass|NN wool|wool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN BW25113|bw25113|NN ymgB|ymgb|NN mutant|mutant|NN after|after|IN 24h|24h|NN of|of|IN growth|growth|NN in|in|IN LBglu|lbglu|NN with|with|IN glass|glass|NN wool|wool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN tnaA|tnaa|NN mutant|mutant|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN and|and|CC 100|100|CD uM|um|NN indole|indole|NN at|at|IN 37ºC|37ºc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN tnaA|tnaa|NN mutant|mutant|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN and|and|CC DMF|dmf|NN at|at|IN 30ºC|30ºC|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN tnaA|tnaa|NN mutant|mutant|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN and|and|CC DMF|dmf|NN at|at|IN 37ºC|37ºc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN tnaA|tnaa|NN mutant|mutant|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN and|and|CC with|with|IN 100|100|CD uM|um|NN indole|indole|NN at|at|IN 30ºC|30ºC|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN w/t|w/t|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN at|at|IN 30ºC|30ºC|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN hha|hha|NN mutant|mutant|NN after|after|IN 15|15|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|LB|NNP glu|glu|NN with|with|IN glasswool|glasswool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN hha|hha|NN mutant|mutant|NN after|after|IN 24|24|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|LB|NNP glu|glu|NN with|with|IN glasswool|glasswool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN hha|hha|NN mutant|mutant|NN after|after|IN 4|4|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|LB|NNP glu|glu|NN with|with|IN glasswool|glasswool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN hha|hha|NN mutant|mutant|NN after|after|IN 4|4|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN sdiA|sdia|NN mutant|mutant|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN at|at|IN 30ºC|30ºc|NN with|with|IN 1|1|CD mM|mm|NN indole|indole|NN presence|presence|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN sdiA|sdia|NN mutant|mutant|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN at|at|IN 30ºC|30ºc|NN with|with|IN DMF|dmf|NN presence|presence|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN after|after|IN 15|15|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|LB|NNP glu|glu|NN with|with|IN glasswool|glasswool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN after|after|IN 24|24|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|LB|NNP glu|glu|NN with|with|IN glasswool|glasswool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN after|after|IN 4|4|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|LB|NNP glu|glu|NN with|with|IN glasswool|glasswool|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN wild|wild|JJ type|type|NN after|after|IN 4|4|CD hours|hour|NNS of|of|IN growth|growth|NN at|at|IN 37C|37c|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN EHEC|ehec|NN wild|wild|JJ type|type|NN after|after|IN 7h|7h|NN of|of|IN growth|growth|NN in|in|IN LB|lb|NN and|and|CC 0.1|0.1|CD %|%|NN DMF|dmf|NN with|with|IN glass|glass|NN wool|wool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN EHEC|ehec|NN wild|wild|JJ type|type|NN after|after|IN 7h|7h|NN of|of|IN growth|growth|NN in|in|IN LB|lb|NN and|and|CC 1000|1000|CD micro|micro|JJ M|m|NN 7-hydroxyindole|7-hydroxyindole|NN with|with|IN glass|glass|NN wool|wool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN EHEC|ehec|NN wild|wild|JJ type|type|NN after|after|IN 7h|7h|NN of|of|IN growth|growth|NN in|in|IN LB|lb|NN and|and|CC 250|250|CD micro|micro|JJ M|m|NN isatin|isatin|NN with|with|IN glass|glass|NN wool|wool|NN
RNA|rna|NN extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN K-12|k-12|NN sdiA-no|sdia-no|JJ SdiA|sdia|NN 1|1|CD after|after|IN 12h|12h|NN of|of|IN growth|growth|NN in|in|IN LB|lb|NN +|+|CC 1|1|CD mMIPTG|mmiptg|NN and|and|CC 30|30|CD microM|microm|NN Cm|cm|NN with|with|IN glass|glass|NN wool|wool|NN at|at|IN 30oC|30oC|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN K-12|k-12|NN sdiA-SdiA1E11|sdia-sdia1e11|NN after|after|IN 12h|12h|NN of|of|IN growth|growth|NN in|in|IN LB|lb|NN +|+|CC 1|1|CD mMIPTG|mmiptg|NN and|and|CC 30|30|CD microM|microm|NN Cm|cm|NN with|with|IN glass|glass|NN wool|wool|NN at|at|IN 30oC|30oC|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN biofilm|biofilm|NN cells|cell|NNS of|of|IN K-12|k-12|NN sdiA-WTSdiA|sdia-wtsdia|NN after|after|IN 12h|12h|NN of|of|IN growth|growth|NN in|in|IN LB|lb|NN +|+|CC 1|1|CD mMIPTG|mmiptg|NN and|and|CC 30|30|CD microM|microm|NN Cm|cm|NN with|with|IN glass|glass|NN wool|wool|NN at|at|IN 30oC|30oC|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN BW25113|bw25113|NN at|at|IN OD|od|NN 1.0|1.0|CD after|after|IN contacting|contact|VBG for|for|IN 10|10|CD min|min|NN with|with|IN 2|2|CD mM|mm|NN H2O2|h2o2|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN BW25113|bw25113|NN at|at|IN OD|od|NN 1.0|1.0|CD after|after|IN contacting|contact|VBG for|for|IN 10|10|CD min|min|NN with|with|IN water|water|NN -LRB-|-lrb-|-LRB- negative|negative|JJ control|control|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN BW25113|bw25113|NN ychH|ychh|NN at|at|IN OD|od|NN 1.0|1.0|CD after|after|IN contacting|contact|VBG for|for|IN 10|10|CD min|min|NN with|with|IN 2|2|CD mM|mm|NN H2O2|h2o2|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN BW25113|bw25113|NN ychH|ychh|NN at|at|IN OD|od|NN 1.0|1.0|CD after|after|IN contacting|contact|VBG for|for|IN 10|10|CD min|min|NN with|with|IN water|water|NN -LRB-|-lrb-|-LRB- negative|negative|JJ control|control|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN BW25113|bw25113|NN ygiW|ygiw|NN at|at|IN OD|od|NN 1.0|1.0|CD after|after|IN contacting|contact|VBG for|for|IN 10|10|CD min|min|NN with|with|IN 2|2|CD mM|mm|NN H2O2|h2o2|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN BW25113|bw25113|NN ygiW|ygiw|NN at|at|IN OD|od|NN 1.0|1.0|CD after|after|IN contacting|contact|VBG for|for|IN 10|10|CD min|min|NN with|with|IN water|water|NN -LRB-|-lrb-|-LRB- negative|negative|JJ control|control|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN TG1/pBS|tg1/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- /|/|: pMMB277|pmmb277|NN after|after|IN contacting|contact|VBG for|for|IN 2|2|CD h|h|NN with|with|IN cis-DCE|cis-dce|NN -LRB-|-lrb-|-LRB- 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB- in|in|IN Tris-HNO3|tris-hno3|NN buffer|buffer|NN with|with|IN succinate|succinate|NN -LRB-|-lrb-|-LRB- 5|5|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mM|mm|NN -RRB-|-rrb-|-RRB- at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN TG1/pBS|tg1/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: TOM-Green/pMMB277-IsoILR|tom-green/pmmb277-isoilr|NN 1-GSHI|1-gshi|NN after|after|IN contacting|contact|VBG for|for|IN 2|2|CD h|h|NN with|with|IN cis-DCE|cis-dce|NN -LRB-|-lrb-|-LRB- 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB- in|in|IN Tris-HNO3|tris-hno3|NN buffer|buffer|NN with|with|IN succinate|succinate|NN -LRB-|-lrb-|-LRB- 5|5|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mM|mm|NN -RRB-|-rrb-|-RRB- at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN TG1|tg1|NN /|/|: pMMB206-TOM-Green/pBS|pmmb206-tom-green/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- after|after|IN contacting|contact|VBG for|for|IN 2|2|CD h|h|NN with|with|IN cis-DCE|cis-dce|NN -LRB-|-lrb-|-LRB- 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB- in|in|IN Tris-HNO3|tris-hno3|NN buffer|buffer|NN with|with|IN succinate|succinate|NN -LRB-|-lrb-|-LRB- 5|5|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mM|mm|NN -RRB-|-rrb-|-RRB- at|at|IN 37oC|37oc|NN .|.|.
RNA|rna|NN extracted|extract|VBN from|from|IN cells|cell|NNS of|of|IN TG1/pMMB206-TOM-Green/pBS|tg1/pmmb206-tom-green/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: EchA|echa|NN F108L/I219L/C248I|f108l/i219l/c248i|NN after|after|IN contacting|contact|VBG for|for|IN 2|2|CD h|h|NN with|with|IN cis-DCE|cis-dce|NN -LRB-|-lrb-|-LRB- 1|1|CD mM|mm|NN -RRB-|-rrb-|-RRB- in|in|IN Tris-HNO3|tris-hno3|NN buffer|buffer|NN with|with|IN succinate|succinate|NN -LRB-|-lrb-|-LRB- 5|5|CD mM|mm|NN -RRB-|-rrb-|-RRB- ,|,|, IPTG|iptg|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mM|mm|NN -RRB-|-rrb-|-RRB- at|at|IN 37oC|37oc|NN
rna|rna|NN extracted|extract|VBN from|from|IN e.|e.|FW coli|coli|FW o157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN cells|cell|NNS grown|grow|VBN -LRB-|-lrb-|-LRB- 7|7|CD hrs|hr|NNS incubation|incubation|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37ºC|37ºc|NN
rna|rna|NN extracted|extract|VBN from|from|IN e.|e.|FW coli|coli|FW o157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN cells|cell|NNS grown|grow|VBN -LRB-|-lrb-|-LRB- 7|7|CD hrs|hr|NNS incubation|incubation|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37ºC|37ºc|NN with|with|IN 0.05|0.05|CD mg/ml|mg/ml|NN Phloretin|phloretin|NN
RNA|rna|NN extracted|extract|VBN from|from|IN e.|e.|FW coli|coli|FW o157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN cells|cell|NNS grown|grow|VBN -LRB-|-lrb-|-LRB- 7|7|CD hrs|hr|NNS incubation|incubation|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37ºC|37ºc|NN with|with|IN 0.1|0.1|CD mg/ml|mg/ml|NN of|of|IN IAAld|iaald|JJ
rna|rna|NN extracted|extract|VBN from|from|IN e.|e.|FW coli|coli|FW o157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN cells|cell|NNS grown|grow|VBN -LRB-|-lrb-|-LRB- 7|7|CD hrs|hr|NNS incubation|incubation|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37ºC|37ºc|NN with|with|IN 0.5|0.5|CD %|%|NN honey|honey|NN
RNA|rna|NN extracted|extract|VBN from|from|IN e.|e.|FW coli|coli|FW o157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN cells|cell|NNS grown|grow|VBN -LRB-|-lrb-|-LRB- 7|7|CD hrs|hr|NNS incubation|incubation|NN -RRB-|-rrb-|-RRB- in|in|IN LB|lb|NN at|at|IN 37ºC|37ºc|NN with|with|IN DMSO|dmso|NN
RNA|rna|NN extracted|extract|VBN from|from|IN free|free|JJ living|living|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN luxS|luxs|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- when|when|WRB growth|growth|NN to|to|TO OD600|od600|NN 0.5|0.5|CD at|at|IN 30ºC|30ºC|NNP in|in|IN LB|LB|NNP ,|,|, 100|100|CD uM|um|NN AI2|ai2|NN was|be|VBD added|add|VBN in|in|IN and|and|CC 3-h|3-h|JJ further|further|JJ incubation|incubation|NN was|be|VBD applied|apply|VBN -RRB-|-rrb-|-RRB-
RNA|rna|NN extracted|extract|VBN from|from|IN free|free|JJ living|living|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN luxS|luxs|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- when|when|WRB growth|growth|NN to|to|TO OD600|od600|NN 0.5|0.5|CD at|at|IN 30ºC|30ºC|NNP in|in|IN LB|LB|NNP ,|,|, no|no|DT AI2|ai2|NN was|be|VBD added|add|VBN in|in|IN and|and|CC 3-h|3-h|JJ further|further|JJ incubation|incubation|NN was|be|VBD applied|apply|VBN -RRB-|-rrb-|-RRB-
RNA|rna|NN extracted|extract|VBN from|from|IN free|free|JJ living|living|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN luxS|luxs|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- when|when|WRB growth|growth|NN to|to|TO OD600|od600|NN 0.5|0.5|CD at|at|IN 37ºC|37ºc|NN in|in|IN LB|LB|NNP ,|,|, 100|100|CD uM|um|NN AI2|ai2|NN was|be|VBD added|add|VBN in|in|IN and|and|CC 3-h|3-h|JJ further|further|JJ incubation|incubation|NN was|be|VBD applied|apply|VBN -RRB-|-rrb-|-RRB-
RNA|rna|NN extracted|extract|VBN from|from|IN free|free|JJ living|living|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN luxS|luxs|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- when|when|WRB growth|growth|NN to|to|TO OD600|od600|NN 0.5|0.5|CD at|at|IN 37ºC|37ºc|NN in|in|IN LB|LB|NNP ,|,|, no|no|DT AI2|ai2|NN was|be|VBD added|add|VBN in|in|IN and|and|CC 3-h|3-h|JJ further|further|JJ incubation|incubation|NN was|be|VBD applied|apply|VBN -RRB-|-rrb-|-RRB-
RNA|rna|NN extracted|extract|VBN from|from|IN free|free|JJ living|living|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN sdiA|sdia|NN mutant|mutant|NN when|when|WRB growth|growth|NN to|to|TO OD600|od600|NN 4.0|4.0|CD at|at|IN 30ºC|30ºC|NNP in|in|IN LB|LB|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN free|free|JJ living|living|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN wild|wild|JJ type|type|NN when|when|WRB growth|growth|NN to|to|TO OD600|od600|NN 4.0|4.0|CD at|at|IN 30ºC|30ºC|NNP in|in|IN LB|LB|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN mqsR|mqsr|NN deleted|delete|VBN mutant|mutant|JJ after|after|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD of|of|IN growth|growth|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N|bw25113/pca24n|NN -LRB-|-lrb-|-LRB- empty|empty|JJ vector|vector|NN -RRB-|-rrb-|-RRB- after|after|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD of|of|IN growth|growth|NN ,|,|, then|then|RB 2|2|CD mM|mm|NN IPTG|iptg|NN for|for|IN 15|15|CD min|min|NN short|short|JJ time|time|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N|bw25113/pca24n|NN -LRB-|-lrb-|-LRB- empty|empty|JJ vector|vector|NN -RRB-|-rrb-|-RRB- after|after|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD of|of|IN growth|growth|NN with|with|IN 2|2|CD mM|mm|NN IPTG|iptg|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN after|after|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD of|of|IN growth|growth|NN ,|,|, then|then|RB 2|2|CD mM|mm|NN IPTG|iptg|NN for|for|IN 15|15|CD min|min|NN short|short|JJ time|time|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113/pCA24N-mqsR|bw25113/pca24n-mqsr|NN after|after|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD of|of|IN growth|growth|NN with|with|IN 2|2|CD mM|mm|NN IPTG|iptg|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN wild|wild|JJ type|type|NN after|after|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD of|of|IN growth|growth|NN in|in|IN LB|lb|NN at|at|IN 37oC|37oc|NN
RNA|rna|NN extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN BW25113|bw25113|NN w/t|w/t|NN after|after|IN 7|7|CD hours|hour|NNS of|of|IN growth|growth|NN in|in|IN LB|lb|NN with|with|IN glasswool|glasswool|NN at|at|IN 30ºC|30ºC|NNP
RNA|RNA|NNP extracted|extract|VBN from|from|IN suspension|suspension|NN cells|cell|NNS of|of|IN EHEC|ehec|NN wild|wild|JJ type|type|NN after|after|IN 7|7|CD h|h|NN of|of|IN growth|growth|NN in|in|IN LB|lb|NN and|and|CC 0.1|0.1|CD %|%|NN DMF|dmf|NN with|with|IN glass|glass|NN wool|wool|NN
RNA|rna|NN extraction|extraction|NN :|:|: A|a|DT hot-phenol|hot-phenol|NN procedure|procedure|NN was|be|VBD used|use|VBN to|to|TO extract|extract|VB total|total|JJ RNA|rna|NN .|.|. Cell|cell|NN pellets|pellet|NNS were|be|VBD lysed|lyse|VBN with|with|IN 500|500|CD μl|μl|NN TE|te|NN -LRB-|-lrb-|-LRB- pH8|ph8|NN .0|.0|CD -RRB-|-rrb-|-RRB- ,|,|, 50|50|CD μl|μl|NN 10|10|CD %|%|NN SDS|sds|NN and|and|CC lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- .|.|. Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN sequentially|sequentially|RB with|with|IN phenol/chloroform|phenol/chloroform|NN -LRB-|-lrb-|-LRB- preheated|preheated|JJ to|to|TO 640|640|CD C|c|NN -RRB-|-rrb-|-RRB- ,|,|, followed|follow|VBN by|by|IN chloroform/isoamyl|chloroform/isoamyl|JJ alcohol|alcohol|NN .|.|. RNA|rna|NN was|be|VBD precipitated|precipitate|VBN with|with|IN 1/10|1/10|CD volume|volume|NN of|of|IN 3M|3M|NNP NaOAc|naoac|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- and|and|CC 2|2|CD volumes|volume|NNS of|of|IN ethanol|ethanol|NN .|.|. After|after|IN incubating|incubate|VBG overnight|overnight|JJ at|at|IN --|--|: 200|200|CD C|c|NN ,|,|, samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RB and|and|CC pellets|pellet|NNS were|be|VBD washed|wash|VBN with|with|IN ice|ice|NN cold|cold|JJ 70|70|CD %|%|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- prepared|prepare|VBN with|with|IN DEPC|depc|NN -|-|: H2O|h2o|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD resuspended|resuspend|VBN in|in|IN water|water|NN ,|,|, DNase|dnase|NN treated|treat|VBN -LRB-|-lrb-|-LRB- RQ1|rq1|NN RNase-free|rnase-free|NN DNase|dnase|NN /|/|: Promega|Promega|NNP ,|,|, WI|WI|NNP -RRB-|-rrb-|-RRB- and|and|CC purified|purify|VBN using|use|VBG an|a|DT RNeasy|rneasy|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN extraction|extraction|NN Kit|kit|NN
RNA|rna|NN extractions|extraction|NNS were|be|VBD performed|perform|VBN using|use|VBG RiboPure|RiboPure|NNP ™|™|CD Bacteria|bacterium|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS recommendations|recommendation|NNS
RNA|rna|NN extraction|extraction|NN was|be|VBD performed|perform|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- instructions|instruction|NNS .|.|.
RNA|rna|NN extraction|extraction|NN was|be|VBD performed|perform|VBN using|use|VBG phenol|phenol|NN treatment|treatment|NN .|.|.
RNA|rna|NN extraction|extraction|NN was|be|VBD performed|perform|VBN using|use|VBG RiboPure-BacteriaTM|RiboPure-BacteriaTM|NNP Bacteria|bacterium|NNS kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|. DNase|dnase|NN I|i|CD treatment|treatment|NN was|be|VBD applied|apply|VBN to|to|TO eliminate|eliminate|VB genomic|genomic|JJ DNA|dna|NN contamination|contamination|NN as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS recommendations|recommendation|NNS .|.|.
RNA|rna|NN extraction|extraction|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN from|from|IN 1|1|CD %|%|NN isobutanol|isobutanol|NN treated|treat|VBN sample|sample|NN and|and|CC untreated|untreated|JJ sample|sample|NN were|be|VBD mixed|mix|VBN after|after|IN RNA|rna|NN purification|purification|NN
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW 0.5|0.5|CD hours|hour|NNS after|after|IN inoculation|inoculation|NN
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW 1.5|1.5|CD hours|hour|NNS after|after|IN inoculation|inoculation|NN
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW 2|2|CD hours|hour|NNS after|after|IN inoculation|inoculation|NN
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW 3.5|3.5|CD hours|hour|NNS after|after|IN inoculation|inoculation|NN
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW 3|3|CD hours|hour|NNS after|after|IN inoculation|inoculation|NN
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW 4|4|CD hours|hour|NNS after|after|IN inoculation|inoculation|NN
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW expressing|express|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP for|for|IN 0.5|0.5|CD hours|hour|NNS
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW expressing|express|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP for|for|IN 1.5|1.5|CD hours|hour|NNS
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW expressing|express|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP for|for|IN 1|1|CD hours|hour|NNS
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW expressing|express|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP for|for|IN 2|2|CD hours|hour|NNS
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW expressing|express|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP for|for|IN 3.5|3.5|CD hours|hour|NNS
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW expressing|express|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP for|for|IN 3|3|CD hours|hour|NNS
RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW expressing|express|VBG synthetic|synthetic|JJ protein|protein|NN DX|DX|NNP for|for|IN 4|4|CD hours|hour|NNS
RNA|rna|NN from|from|IN Escherichia|escherichia|FW coli|coli|FW
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN EDL933|edl933|NN pooled|pool|VBD reference|reference|NN
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK2000|frik2000|NN rep|rep|NN 1|1|CD
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK2000|frik2000|NN rep|rep|NN 2|2|CD
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK2000|frik2000|NN rep|rep|NN 3|3|CD
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK2000|frik2000|NN rep|rep|NN 4|4|CD
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK966|frik966|NN rep|rep|NN 1|1|CD
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK966|frik966|NN rep|rep|NN 2|2|CD
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK966|frik966|NN rep|rep|NN 3|3|CD
RNA|rna|NN from|from|IN late|late|JJ log|log|NN phase|phase|NN E|e|NN coli|coli|NN FRIK966|frik966|NN rep|rep|NN 4|4|CD
RNA|rna|NN isolation|isolation|NN was|be|VBD performed|perform|VBN using|use|VBG an|a|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Technologies|Technologies|NNPS ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. DNA|dna|NN decontamination|decontamination|NN treatment|treatment|NN was|be|VBD performed|perform|VBN using|use|VBG Turbo|Turbo|NNP DNase|dnase|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT quantity|quantity|NN and|and|CC purity|purity|NN of|of|IN the|the|DT purified|purify|VBN RNA|rna|NN samples|sample|NNS were|be|VBD determined|determine|VBN using|use|VBG a|a|DT spectrophotometer|spectrophotometer|NN Nanodrop-1000|nanodrop-1000|NN -LRB-|-lrb-|-LRB- Nanodrop|Nanodrop|NNP Technologies|Technologies|NNPS Inc.|Inc.|NNP ,|,|, Wilmington|Wilmington|NNP ,|,|, DE|de|NN ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- by|by|IN measuring|measure|VBG the|the|DT absorbance|absorbance|NN -LRB-|-lrb-|-LRB- A260|a260|NN ,|,|, 230|230|CD ,|,|, 280|280|CD -RRB-|-rrb-|-RRB- and|and|CC calculating|calculate|VBG absorbance|absorbance|NN ratios|ratio|NNS -LRB-|-lrb-|-LRB- A260/A230|a260/a230|NN and|and|CC A260/A280|a260/a280|NN -RRB-|-rrb-|-RRB- .|.|. All|all|DT samples|sample|NNS had|have|VBD A260/A230|a260/a230|NN and|and|CC A260/A280|a260/a280|NN ratios|ratio|NNS above|above|IN 1.9|1.9|CD .|.|. The|the|DT RNA|rna|NN integrity|integrity|NN was|be|VBD analysed|analyse|VBN using|use|VBG Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Palo|Palo|NNP Alto|Alto|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- in|in|IN conjunction|conjunction|NN with|with|IN RNA|rna|NN 6000|6000|CD Nano|Nano|NNP LabChip|LabChip|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. RNA|rna|NN integrity|integrity|NN number|number|NN -LRB-|-lrb-|-LRB- RIN|rin|NN -RRB-|-rrb-|-RRB- values|value|NNS were|be|VBD >|>|JJR 8.5|8.5|CD for|for|IN all|all|DT samples|sample|NNS .|.|.
RNA|rna|NN isolation|isolation|NN was|be|VBD performed|perform|VBN using|use|VBG an|a|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Technologies|Technologies|NNPS ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. DNA|dna|NN decontamination|decontamination|NN treatment|treatment|NN was|be|VBD performed|perform|VBN using|use|VBG Turbo|Turbo|NNP DNase|dnase|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT quantity|quantity|NN and|and|CC purity|purity|NN of|of|IN the|the|DT purified|purify|VBN RNA|rna|NN samples|sample|NNS were|be|VBD determined|determine|VBN using|use|VBG a|a|DT spectrophotometer|spectrophotometer|NN Nanodrop-1000|nanodrop-1000|NN -LRB-|-lrb-|-LRB- Nanodrop|Nanodrop|NNP Technologies|Technologies|NNPS Inc.|Inc.|NNP ,|,|, Wilmington|Wilmington|NNP ,|,|, DE|de|NN ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- by|by|IN measuring|measure|VBG the|the|DT absorbance|absorbance|NN -LRB-|-lrb-|-LRB- A260|a260|NN ,|,|, 230|230|CD ,|,|, 280|280|CD -RRB-|-rrb-|-RRB- and|and|CC calculating|calculate|VBG absorbance|absorbance|NN ratios|ratio|NNS -LRB-|-lrb-|-LRB- A260/A230|a260/a230|NN and|and|CC A260/A280|a260/a280|NN -RRB-|-rrb-|-RRB- .|.|. All|all|DT samples|sample|NNS had|have|VBD A260/A230|a260/a230|NN and|and|CC A260/A280|a260/a280|NN ratios|ratio|NNS above|above|IN 1.9|1.9|CD .|.|. The|the|DT RNA|rna|NN integrity|integrity|NN was|be|VBD analysed|analyse|VBN using|use|VBG Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Palo|Palo|NNP Alto|Alto|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- in|in|IN conjunction|conjunction|NN with|with|IN RNA|rna|NN 6000|6000|CD Nano|Nano|NNP LabChip|LabChip|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. RNA|rna|NN integrity|integrity|NN number|number|NN -LRB-|-lrb-|-LRB- RIN|rin|NN -RRB-|-rrb-|-RRB- values|value|NNS were|be|VBD >|>|JJR 9|9|CD for|for|IN all|all|DT samples|sample|NNS .|.|.
RNAlater|rnalater|NN was|be|VBD removed|remove|VBN from|from|IN cells|cell|NNS by|by|IN filtration|filtration|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN cells|cell|NNS using|use|VBG a|a|DT hot|hot|JJ SDS/phenol|sds/phenol|NN protocol|protocol|NN -LRB-|-lrb-|-LRB- http://www.genome.wisc.edu/pub/reprints/|http://www.genome.wisc.edu/pub/reprints/|NN -RRB-|-rrb-|-RRB- with|with|IN an|a|DT additional|additional|JJ 1-min|1-min|JJ bead-beating|bead-beating|NN .|.|. Chemical|Chemical|NNP extractions|extraction|NNS were|be|VBD performed|perform|VBN in|in|IN phase|phase|NN lock|lock|NN gels|gel|NNS -LRB-|-lrb-|-LRB- Fisher|Fisher|NNP Scientific|Scientific|NNP ,|,|, Pittsburgh|Pittsburgh|NNP ,|,|, PA|pa|NN -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN by|by|IN the|the|DT company|company|NN Vertis|Vertis|NNP Biotechnologie|Biotechnologie|NNP AG|AG|NNP in|in|IN Germany|Germany|NNP
RNA|rna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS
RNA|rna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS .|.|.
RNA|rna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN for|for|IN sequencing|sequencing|NN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS ;|;|: rRNAs|rrna|NNS were|be|VBD removed|remove|VBN by|by|IN Ribozero|ribozero|NN -LRB-|-lrb-|-LRB- gram|gram|NN negative|negative|JJ -RRB-|-rrb-|-RRB- ,|,|, libraries|library|NNS were|be|VBD prepared|prepare|VBN using|use|VBG TruSeq|TruSeq|NNP protocol|protocol|NN .|.|.
RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW CC72|cc72|NN 10|10|CD min|min|NN after|after|IN osmotic|osmotic|JJ stress|stress|NN
RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW CC72|cc72|NN 20|20|CD min|min|NN after|after|IN osmotic|osmotic|JJ stress|stress|NN
RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW CC72|cc72|NN 45|45|CD min|min|NN after|after|IN osmotic|osmotic|JJ stress|stress|NN
RNAP|rnap|NN beta|beta|NN subunit|subunit|NN ChIP|chip|NN DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW CC72|cc72|NN at|at|IN early-exponential|early-exponential|JJ phase|phase|NN
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN DdksA|ddksa|NN cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN MDS42|mds42|NN cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN MDS42|mds42|NN ΔnusA|δnusa|NN *|*|NN cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN MDS42|mds42|NN ΔnusG|δnusg|NN cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN MG1655|mg1655|NN cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN MG1655|mg1655|NN Δhns|δhns|NN cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN starved|starve|VBN DdksA|ddksa|NN cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN starved|starve|VBN wt|wt|JJ cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN from|from|IN wt|wt|JJ cells|cell|NNS
RNAP|rnap|NN ChIP|chip|NN DNA|dna|NN ,|,|, old|old|JJ protocol|protocol|NN
RNAP|rnap|NN _|_|CD DdksA|ddksa|NN _|_|CD SHX|SHX|NNP _|_|CD rep1|rep1|NN
RNAP|rnap|NN _|_|CD DdksA|ddksa|NN _|_|CD SHX|SHX|NNP _|_|CD rep2|rep2|NN
RNAP|rnap|NN _|_|CD DdksA|ddksa|NN _|_|NN untreated|untreated|JJ _|_|NN rep1|rep1|NN
RNAP|rnap|NN _|_|CD DdksA|ddksa|NN _|_|NN untreated|untreated|JJ _|_|NN rep2|rep2|NN
RNAP|rnap|NN old|old|JJ rep1|rep1|NN
RNAP|rnap|NN old|old|JJ rep2|rep2|NN
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 100040|100040|CD -RRB-|-rrb-|-RRB-
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN -RRB-|-rrb-|-RRB- ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 3427302|3427302|CD -RRB-|-rrb-|-RRB-
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 56706|56706|CD -RRB-|-rrb-|-RRB-
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 62215|62215|CD -RRB-|-rrb-|-RRB-
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 100ug/ml|100ug/ml|JJ rifampicin|rifampicin|NN -LRB-|-lrb-|-LRB- Dataset|dataset|NN 81586|81586|CD -RRB-|-rrb-|-RRB-
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN -RRB-|-rrb-|-RRB- ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 20ug/ml|20ug/ml|JJ bicyclomycin|bicyclomycin|NN -LRB-|-lrb-|-LRB- Dataset|dataset|NN 3428302|3428302|CD -RRB-|-rrb-|-RRB-
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 20ug/ml|20ug/ml|JJ bicyclomycin|bicyclomycin|NN -LRB-|-lrb-|-LRB- Dataset|dataset|NN 94828|94828|CD -RRB-|-rrb-|-RRB-
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 100ug/ml|100ug/ml|JJ rifampicin|rifampicin|NN
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 20ug/ml|20ug/ml|JJ bicyclomycin|bicyclomycin|NN
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN -RRB-|-rrb-|-RRB- ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 20ug/ml|20ug/ml|JJ bicyclomycin|bicyclomycin|NN
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN '|'|'' -RRB-|-rrb-|-RRB- ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS ,|,|, untreated|untreated|JJ
RNA|rna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Beta|beta|NN -RRB-|-rrb-|-RRB- ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS ,|,|, untreated|untreated|JJ
RNA|rna|NN produced|produce|VBN by|by|IN in|in|FW vitro|vitro|FW transcription|transcription|NN ,|,|, with|with|IN RNA|rna|NN polymerase|polymerase|NN E|e|NN σ70|σ70|NN ,|,|, of|of|IN 2|2|CD ug|ug|NN of|of|IN genomic|genomic|JJ DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN digested|digest|VBN with|with|IN EcoRI|ecori|NN
RNA|rna|NN produced|produce|VBN by|by|IN in|in|FW vitro|vitro|FW transcription|transcription|NN ,|,|, with|with|IN RNA|rna|NN polymerase|polymerase|NN E|e|NN σS|σs|NN ,|,|, of|of|IN 2|2|CD ug|ug|NN of|of|IN genomic|genomic|JJ DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN digested|digest|VBN with|with|IN EcoRI|ecori|NN
RNAP|rnap|NN _|_|CD wt|wt|JJ _|_|NN SHX|shx|NN _|_|CD rep1|rep1|NN
RNAP|rnap|NN _|_|CD wt|wt|JJ _|_|NN SHX|shx|NN _|_|CD rep2|rep2|NN
RNAP|rnap|NN _|_|CD wt|wt|JJ _|_|NN untreated|untreated|JJ _|_|NN rep1|rep1|NN
RNAP|rnap|NN _|_|CD wt|wt|JJ _|_|NN untreated|untreated|JJ _|_|NN rep2|rep2|NN
RNA|rna|NN quality|quality|NN was|be|VBD confirmed|confirm|VBN with|with|IN the|the|DT Bioanalyzer|Bioanalyzer|NNP system|system|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC sequencing|sequencing|NN -LRB-|-lrb-|-LRB- 50|50|CD cycles|cycle|NNS ,|,|, pooling|pool|VBG eight|eight|CD bar-coded|bar-coded|JJ samples|sample|NNS per|per|IN lane|lane|NN -RRB-|-rrb-|-RRB- was|be|VBD performed|perform|VBN on|on|IN the|the|DT Illumina|Illumina|NNP HiSeq|HiSeq|NNP platform|platform|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, San|San|NNP Diego|Diego|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- at|at|IN the|the|DT Research|Research|NNP Technology|Technology|NNP Support|support|NN Facility|facility|NN -LRB-|-lrb-|-LRB- RTSF|rtsf|NN -RRB-|-rrb-|-RRB- at|at|IN Michigan|Michigan|NNP State|State|NNP University|University|NNP .|.|.
RNA|rna|NN samples|sample|NNS were|be|VBD extracted|extract|VBN via|via|IN Invitrogen|Invitrogen|NNP RNAeasy|RNAeasy|NNP Kit|kit|NN and|and|CC treated|treat|VBN with|with|IN DNaseI|dnasei|NN to|to|TO remove|remove|VB all|all|DT DNA|dna|NN
RNA-Seq|rna-seq|NN
RNA-seq|rna-seq|NN 37C|37c|NN LB|lb|NN rep1|rep1|NN
RNA-seq|rna-seq|NN 37C|37c|NN LB|lb|NN rep2|rep2|NN
RNA-seq|rna-seq|NN data|datum|NNS were|be|VBD mapped|map|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN Sakai|Sakai|NNP genome|genome|NN using|use|VBG the|the|DT Subjunc|subjunc|NN aligner|aligner|NN program|program|NN from|from|IN the|the|DT Subread|Subread|NNP package|package|NN -LRB-|-lrb-|-LRB- v1|v1|NN .4.6|.4.6|CD -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- http://bioinf.wehi.edu.au/subread/|http://bioinf.wehi.edu.au/subread/|NN -RRB-|-rrb-|-RRB- .|.|.
RNAseq|rnaseq|NN _|_|CD delAr1delAr2|delar1delar2|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD delAr1delAr2|delar1delar2|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD delAr1delAr2|delar1delar2|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD
RNAseq|rnaseq|NN _|_|CD delAr1|delar1|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD delAr1|delar1|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD delAr1|delar1|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD
RNAseq|rnaseq|NN _|_|CD delAr2|delar2|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD delAr2|delar2|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD delAr2|delar2|NN _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD delta-crp|delta-crp|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD
RNA-seq|rna-seq|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN by|by|IN Vertis|Vertis|NNP AG|AG|NNP -LRB-|-lrb-|-LRB- Freising-Weihenstephan|Freising-Weihenstephan|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. Briefly|briefly|RB ,|,|, RNA|rna|NN was|be|VBD polyadenylated|polyadenylated|JJ with|with|IN poly|poly|NN -LRB-|-lrb-|-LRB- A|a|NN -RRB-|-rrb-|-RRB- polymerase|polymerase|NN ,|,|, 5|5|CD '|'|'' -|-|: triphosphates|triphosphate|NNS were|be|VBD removed|remove|VBN with|with|IN tobacco|tobacco|NN acid|acid|NN pyrophosphatase|pyrophosphatase|NN followed|follow|VBN by|by|IN ligation|ligation|NN of|of|IN a|a|DT 5|5|CD '|'|'' -|-|: adapter|adapter|NN .|.|. First-strand|first-strand|JJ cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD performed|perform|VBN with|with|IN the|the|DT use|use|NN of|of|IN an|a|DT oligo|oligo|JJ -LRB-|-lrb-|-LRB- dT|dt|NN -RRB-|-rrb-|-RRB- barcoded|barcoded|JJ adapter|adapter|NN primer|primer|NN and|and|CC the|the|DT M-MVL|m-mvl|NN reverse|reverse|JJ transcriptase|transcriptase|NN .|.|. The|the|DT resulting|result|VBG cDNA|cdna|NN was|be|VBD PCR-amplified|pcr-amplified|JJ with|with|IN a|a|DT high|high|JJ fidelity|fidelity|NN DNA|dna|NN polymerase|polymerase|NN .|.|. cDNA|cdna|NN was|be|VBD purified|purify|VBN with|with|IN the|the|DT Agencourt|Agencourt|NNP AMPure|AMPure|NNP XP|xp|NN kit|kit|NN -LRB-|-lrb-|-LRB- Beckman|Beckman|NNP Coulter|Coulter|NNP Genomics|Genomics|NNPS -RRB-|-rrb-|-RRB- .|.|.
RNA-Seq|rna-seq|NN of|of|IN E.|e.|FW coli|coli|FW were|be|VBD done|do|VBN using|use|VBG blind|blind|JJ and|and|CC fit-only|fit-only|JJ parameter|parameter|NN in|in|IN DE-Seq|de-seq|NN pakage|pakage|NN
RNA-seq|rna-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN stationary|stationary|JJ phase|phase|NN 30|30|CD °C|°c|NN -LRB-|-lrb-|-LRB- 30h|30h|NN -RRB-|-rrb-|-RRB-
RNA-seq|rna-seq|NN of|of|IN E.|e.|FW coli|coli|FW wt|wt|JJ cells|cell|NNS in|in|IN stationary|stationary|JJ phase|phase|NN 30|30|CD °C|°c|NN -LRB-|-lrb-|-LRB- 30h|30h|NN -RRB-|-rrb-|-RRB- -|-|: Replicate|replicate|VB 1|1|CD
RNA-seq|rna-seq|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT CFT073|cft073|NN genome|genome|NN using|use|VBG bowtie|bowtie|NN -LRB-|-lrb-|-LRB- version|version|NN 0.12.8|0.12.8|CD -RRB-|-rrb-|-RRB-
RNA-seq|rna-seq|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT W3110|w3110|NN genome|genome|NN using|use|VBG CASAVA|CASAVA|NNP 1.8.2|1.8.2|CD
RNA-seq|rna-seq|NN reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN ID|id|NN U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- using|use|VBG short|short|JJ oligonucleotide|oligonucleotide|NN alignment|alignment|NN program|program|NN -LRB-|-lrb-|-LRB- SOAP|soap|NN -RRB-|-rrb-|-RRB-
RNA-Seq|rna-seq|NN reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN using|use|VBG EDGE-Pro|edge-pro|NN -LRB-|-lrb-|-LRB- Magoc|magoc|NN T|t|NN ,|,|, Wood|Wood|NNP D|D|NNP and|and|CC Salzberg|Salzberg|NNP SL|SL|NNP ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- with|with|IN default|default|NN parameters|parameter|NNS
RNA|rna|NN sequences|sequence|NNS from|from|IN each|each|DT of|of|IN the|the|DT two|two|CD differential|differential|JJ analyses|analysis|NNS were|be|VBD processed|process|VBN and|and|CC mapped|map|VBN to|to|TO the|the|DT corresponding|corresponding|JJ genomes|genome|NNS as|as|IN a|a|DT service|service|NN provided|provide|VBN by|by|IN vertis|vertis|NN Biotechnologie|Biotechnologie|NNP AG|AG|NNP ,|,|, Germany|Germany|NNP -LRB-|-lrb-|-LRB- www.vertis-biotech.com|www.vertis-biotech.com|NNP -RRB-|-rrb-|-RRB- .|.|. This|this|DT involved|involved|JJ trimming|trim|VBG adaptor|adaptor|NN sequence|sequence|NN and|and|CC masking|mask|VBG for|for|IN low-quality|low-quality|JJ sequence|sequence|NN .|.|.
RNA|rna|NN sequences|sequence|NNS were|be|VBD quality|quality|JJ assessed|assess|VBN and|and|CC trimmed|trim|VBN using|use|VBG FastQC|fastqc|NN version|version|NN 0.10.1|0.10.1|NN -LRB-|-lrb-|-LRB- www.bioinformatics.babraham.ac.uk/projects/fastqc/|www.bioinformatics.babraham.ac.uk/projects/fastqc/|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT identification|identification|NN of|of|IN differentially|differentially|RB expressed|express|VBN genes|gene|NNS was|be|VBD performed|perform|VBN using|use|VBG cufflinks|cufflink|NNS version|version|NN 2.0.2|2.0.2|CD to|to|TO analyse|analyse|VB the|the|DT trimmed|trimmed|RBR sequences|sequence|NNS as|as|IN a|a|DT time|time|NN course|course|NN .|.|. Briefly|briefly|RB ,|,|, trimmed|trim|VBD reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW MG1655|mg1655|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913|000913|CD 13-Feb-2011|13-feb-2011|NN -RRB-|-rrb-|-RRB- using|use|VBG Tophat|Tophat|NNP version|version|NN 2.0.7|2.0.7|CD .|.|. Aligned|align|VBN reads|read|VBZ were|be|VBD assembled|assemble|VBN for|for|IN differential|differential|JJ expression|expression|NN using|use|VBG cufflinks|cufflink|NNS version|version|NN and|and|CC merged|merge|VBD using|use|VBG cuffmerge|cuffmerge|NN with|with|IN an|a|DT `|`|`` assemblies|assembly|NNS '|'|POS file|file|NN containing|contain|VBG the|the|DT transcript.gtf|transcript.gtf|JJ output|output|NN files|file|NNS from|from|IN culfflinks|culfflink|NNS .|.|. Differential|differential|JJ expression|expression|NN analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT merged.gtf|merged.gtf|JJ output|output|NN file|file|NN from|from|IN cuffmerge|cuffmerge|NN .|.|.
RNA-Seq|rna-seq|NN was|be|VBD performed|perform|VBN by|by|IN the|the|DT DOE|DOE|NNP Joint|Joint|NNP Genome|Genome|NNP Institute|Institute|NNP using|use|VBG the|the|DT dUTP|dutp|NN method|method|NN .|.|. Briefly|briefly|RB ,|,|, ribosome-depleted|ribosome-depleted|JJ RNA|rna|NN was|be|VBD fragmented|fragmented|JJ in|in|IN a|a|DT buffered|buffer|VBN zinc|zinc|NN solution|solution|NN ,|,|, then|then|RB purified|purify|VBN using|use|VBG AMPure|ampure|NN SPRI|spri|NN beads|bead|NNS .|.|. First-strand|first-strand|JJ cDNAs|cdna|NNS were|be|VBD then|then|RB synthesized|synthesize|VBN from|from|IN the|the|DT fragmented|fragmented|JJ RNA|rna|NN using|use|VBG Superscript|Superscript|NNP II|II|NNP reverse|reverse|JJ transcriptase|transcriptase|NN ,|,|, followed|follow|VBN by|by|IN a|a|DT second|second|JJ bead|bead|NN purification|purification|NN .|.|. dUTP|dutp|NN was|be|VBD included|include|VBN in|in|IN the|the|DT second|second|JJ strand|strand|NN synthesis|synthesis|NN reaction|reaction|NN in|in|IN addition|addition|NN to|to|TO dTTP|dttp|NN to|to|TO chemically|chemically|RB mark|mark|VB the|the|DT second|second|JJ strand|strand|NN .|.|. Two|two|CD further|further|JJ bead|bead|NN purification|purification|NN steps|step|NNS using|use|VBG different|different|JJ ratios|ratio|NNS of|of|IN beads|bead|NNS to|to|TO cDNA|cdna|NN -LRB-|-lrb-|-LRB- 85/100|85/100|CD ,|,|, then|then|RB 140/100|140/100|CD -RRB-|-rrb-|-RRB- selected|select|VBN cDNAs|cdna|NNS in|in|IN a|a|DT range|range|NN between|between|IN 150-350|150-350|CD bp|bp|NN .|.|. cDNAs|cdna|NNS were|be|VBD then|then|RB A-tailed|a-tailed|JJ using|use|VBG Exo|Exo|NNP -|-|: Klenow|Klenow|NNP ,|,|, followed|follow|VBN by|by|IN ligation|ligation|NN of|of|IN sequencing|sequencing|NN adapter|adapter|NN oligos|oligo|NNS .|.|. Following|follow|VBG bead|bead|NN purification|purification|NN ,|,|, dUTP|dutp|NN was|be|VBD cleaved|cleave|VBN from|from|IN the|the|DT second|second|JJ strand|strand|NN using|use|VBG AmpErase|AmpErase|NNP Uracil|Uracil|NNP N-glycosylase|n-glycosylase|NN ,|,|, resulting|result|VBG in|in|IN adaptor|adaptor|NN ligated|ligate|VBD single|single|JJ stranded|strand|VBN cDNAs|cdna|NNS .|.|.
RNAseq|rnaseq|NN _|_|CD wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD wt|wt|JJ _|_|NN fructose|fructose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNAseq|rnaseq|NN _|_|CD wt|wt|JJ _|_|NN glucose|glucose|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 3|3|CD
RNAseq|rnaseq|NN _|_|CD wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 1|1|CD
RNAseq|rnaseq|NN _|_|CD wt|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD NH4Cl|nh4cl|NN _|_|CD O2|o2|CD _|_|NN 2|2|CD
RNA-size|rna-size|NN selection|selection|NN and|and|CC generation|generation|NN of|of|IN the|the|DT cDNA|cdna|NN libraries|library|NNS was|be|VBD performed|perform|VBN as|as|IN described|describe|VBN -LCB-|-lcb-|-LRB- Ingolia|Ingolia|NNP ,|,|, 2009|2009|CD -RCB-|-rcb-|-RRB-
RNAsnap|rnasnap|NN
RNAsnap|rnasnap|NN followed|follow|VBN by|by|IN purification|purification|NN through|through|IN Zymo|Zymo|NNP RNA|rna|NN clean|clean|JJ and|and|CC concentrator|concentrator|NN .|.|.
RNAsnap|rnasnap|NN followed|follow|VBN by|by|IN RiboZero|RiboZero|NNP rRNA|rrna|NN removal|removal|NN kit|kit|NN for|for|IN gram-negative|gram-negative|JJ bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB-
rna|rna|NN treatment|treatment|NN :|:|: no|no|DT RNA|rna|NN treatment|treatment|NN
rna|rna|NN treatment|treatment|NN :|:|: rRNA|rrna|NN depleted|deplete|VBD
rna|rna|NN treatment|treatment|NN :|:|: rRNA|rrna|NN depleted|deplete|VBN ;|;|: Terminal|terminal|JJ Exonuclease|exonuclease|NN
RNA|rna|NN was|be|VBD dephosphorylated|dephosphorylate|VBN ,|,|, ligated|ligate|VBN to|to|TO an|a|DT adaptor|adaptor|NN ,|,|, reverse|reverse|JJ transcribed|transcribe|VBN ,|,|, circularized|circularize|VBN then|then|RB amplified|amplify|VBN with|with|IN Illumina|Illumina|NNP adaptors|adaptor|NNS and|and|CC barcodes|barcode|NNS .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN and|and|CC purified|purify|VBN using|use|VBG a|a|DT Masterpure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN and|and|CC purified|purify|VBN using|use|VBG a|a|DT Masterpure|masterpure|NN RNA|rna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN each|each|DT sample|sample|NN using|use|VBG a|a|DT QIAGEN|QIAGEN|NNP RNA|rna|NN extraction|extraction|NN kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instruction|instruction|NN
RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN harvested|harvest|VBN cultures|culture|NNS using|use|VBG a|a|DT hot|hot|JJ lysis|lysis|NN buffer|buffer|NN and|and|CC acid|acid|NN phenol-based|phenol-based|JJ extraction|extraction|NN method|method|NN and|and|CC isopropanol|isopropanol|NN precipitation|precipitation|NN .|.|. Following|follow|VBG RNA|rna|NN extraction|extraction|NN ,|,|, Turbo|Turbo|NNP DNase|dnase|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO treat|treat|VB the|the|DT samples|sample|NNS as|as|IN per|per|IN manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Each|each|DT sample|sample|NN was|be|VBD split|split|VBN into|into|IN five|five|CD 20|20|CD μL|μl|NN aliquots|aliquot|NNS and|and|CC two|two|CD rounds|round|NNS of|of|IN DNase|dnase|NN treatment|treatment|NN were|be|VBD performed|perform|VBN on|on|IN each|each|DT aliquot|aliquot|NN .|.|. Following|follow|VBG DNase|dnase|NN treatment|treatment|NN ,|,|, RNA|rna|NN samples|sample|NNS were|be|VBD purified|purify|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- as|as|IN per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. For|for|IN each|each|DT sample|sample|NN ,|,|, the|the|DT DNase-treated|dnase-treated|JJ aliquots|aliquot|NNS were|be|VBD pooled|pool|VBN together|together|RB before|before|IN purification|purification|NN .|.|. RNA|rna|NN quality|quality|NN was|be|VBD measured|measure|VBN using|use|VBG the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- with|with|IN the|the|DT RNA|rna|NN 6000|6000|CD Nano|Nano|NNP Chip|Chip|NNP kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS while|while|IN RNA|rna|NN was|be|VBD quantified|quantify|VBN using|use|VBG the|the|DT Quant-iT|quant-it|JJ RNA|rna|NN Assay|assay|NN kit|kit|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC measured|measure|VBN on|on|IN a|a|DT Qubit|Qubit|NNP ®|®|NNP 2.0|2.0|CD fluorometer|fluorometer|NN .|.|. RNA|rna|NN was|be|VBD sequenced|sequence|VBN on|on|IN the|the|DT Illumina|Illumina|NNP HiSeq|HiSeq|NNP 2000|2000|CD platform|platform|NN at|at|IN BGI|BGI|NNP -LRB-|-lrb-|-LRB- Shenzen|Shenzen|NNP ,|,|, China|China|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN samples|sample|NNS using|use|VBG hot|hot|JJ phenol|phenol|NN .|.|. The|the|DT integrity|integrity|NN of|of|IN total|total|JJ RNA|rna|NN was|be|VBD determined|determine|VBN from|from|IN agarose|agarose|NN gels|gel|NNS .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN the|the|DT harvested|harvest|VBN cells|cell|NNS using|use|VBG Trizol|Trizol|NNP reagent|reagent|NN .|.|. Depending|depend|VBG upon|upon|IN the|the|DT concentration|concentration|NN of|of|IN total|total|JJ RNA|rna|NN ,|,|, sample|sample|NN were|be|VBD treated|treat|VBN with|with|IN Dnase|dnase|NN and|and|CC ribocleanup|ribocleanup|NN was|be|VBD given|give|VBN according|accord|VBG to|to|TO the|the|DT instruction|instruction|NN manual|manual|NN .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN two|two|CD biological|biological|JJ replicates|replicate|VBZ -LRB-|-lrb-|-LRB- 30|30|CD mL|ml|NN -RRB-|-rrb-|-RRB- of|of|IN each|each|DT bacterial|bacterial|JJ culture|culture|NN isolated|isolate|VBN at|at|IN each|each|DT time|time|NN point|point|NN .|.|. The|the|DT 30|30|CD mL|ml|NN culture|culture|NN was|be|VBD aliquoted|aliquote|VBN into|into|IN three|three|CD 15|15|CD mL|ml|NN tubes|tube|NNS containing|contain|VBG 5|5|CD mL|ml|NN of|of|IN ice-cold|ice-cold|JJ EtOH/Phenol|etoh/phenol|NN stop|stop|VB solution|solution|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN water-saturated|water-saturated|JJ phenol|phenol|NN pH|ph|NN 4.2|4.2|CD -LSB-|-lsb-|-LRB- Invitrogen|invitrogen|NN -RSB-|-rsb-|-RRB- in|in|IN 100|100|CD %|%|NN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 4,000|4,000|CD rpm|rpm|NN ,|,|, 5|5|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT pellet|pellet|NN suspended|suspend|VBN in|in|IN 800|800|CD µL|µl|NN TE|TE|NNP pH|ph|NN 8.0|8.0|CD supplemented|supplement|VBN with|with|IN 0.5|0.5|CD mg/mL|mg/ml|NN lysozyme|lysozyme|NN .|.|. SDS|sds|NN -LRB-|-lrb-|-LRB- 80|80|CD µL|µl|NN at|at|IN 10|10|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN ,|,|, samples|sample|NNS mixed|mix|VBN by|by|IN inversion|inversion|NN ,|,|, and|and|CC incubated|incubate|VBN -LRB-|-lrb-|-LRB- 65|65|CD °C|°c|NN ,|,|, 2|2|CD min|min|NN -RRB-|-rrb-|-RRB- ,|,|, before|before|IN the|the|DT addition|addition|NN of|of|IN 88|88|CD µL|µl|NN 1|1|CD M|m|NN NaOAc|naoac|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- .|.|. Each|each|DT sample|sample|NN was|be|VBD added|add|VBN to|to|TO an|a|DT equal|equal|JJ volume|volume|NN -LRB-|-lrb-|-LRB- 1mL|1ml|NN -RRB-|-rrb-|-RRB- of|of|IN water-saturated|water-saturated|JJ phenol|phenol|NN -LRB-|-lrb-|-LRB- pH|ph|NN 4.2|4.2|CD ,|,|, 65|65|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN -LRB-|-lrb-|-LRB- 65|65|CD °C|°c|NN ,|,|, 6|6|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT solution|solution|NN was|be|VBD separated|separate|VBN into|into|IN layers|layer|NNS by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 14,000|14,000|CD rpm|rpm|NN ,|,|, 10|10|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT upper|upper|JJ aqueous|aqueous|JJ RNA|rna|NN containing|contain|VBG layer|layer|NN removed|remove|VBD and|and|CC transferred|transfer|VBD into|into|IN a|a|DT fresh|fresh|JJ tube|tube|NN .|.|. RNA|rna|NN was|be|VBD cleaned|clean|VBN by|by|IN three|three|CD extractions|extraction|NNS with|with|IN phenol|phenol|NN :|:|: CHCl3|chcl3|NN :|:|: IAA|iaa|NN -LRB-|-lrb-|-LRB- 25:24:1|25:24:1|CD ,|,|, pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- before|before|IN being|be|VBG precipitated|precipitated|JJ -LRB-|-lrb-|-LRB- -80|-80|CD °C|°c|NN ,|,|, O/N|o/n|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT addition|addition|NN of|of|IN 1/10|1/10|CD volume|volume|NN of|of|IN 3M|3M|NNP NaOAc|naoac|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- and|and|CC 2|2|CD volumes|volume|NNS of|of|IN ice|ice|NN cold|cold|JJ 100|100|CD %|%|NN EtOH|etoh|NN .|.|. RNA|rna|NN was|be|VBD pelleted|pelleted|JJ -LRB-|-lrb-|-LRB- 14,000|14,000|CD rpm|rpm|NN ,|,|, 25|25|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT supernatant|supernatant|JJ removed|remove|VBN and|and|CC the|the|DT pellet|pellet|NN washed|wash|VBN with|with|IN 1|1|CD mL|ml|NN 75|75|CD %|%|NN cold|cold|JJ EtOH|etoh|NN -LRB-|-lrb-|-LRB- made|make|VBN with|with|IN DEPC-treated|depc-treated|JJ water|water|NN -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN two|two|CD biological|biological|JJ replicates|replicate|VBZ -LRB-|-lrb-|-LRB- 30|30|CD mL|ml|NN -RRB-|-rrb-|-RRB- of|of|IN each|each|DT bacterial|bacterial|JJ culture|culture|NN isolated|isolate|VBN at|at|IN each|each|DT time|time|NN point|point|NN .|.|. The|the|DT 30|30|CD mL|ml|NN culture|culture|NN was|be|VBD aliquoted|aliquote|VBN into|into|IN three|three|CD 15|15|CD mL|ml|NN tubes|tube|NNS containing|contain|VBG 5|5|CD mL|ml|NN of|of|IN ice-cold|ice-cold|JJ EtOH/Phenol|etoh/phenol|NN stop|stop|VB solution|solution|NN -LRB-|-lrb-|-LRB- 5|5|CD %|%|NN water-saturated|water-saturated|JJ phenol|phenol|NN pH|ph|NN 4.2|4.2|CD -LSB-|-lsb-|-LRB- Invitrogen|invitrogen|NN -RSB-|-rsb-|-RRB- in|in|IN 100|100|CD %|%|NN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 4,000|4,000|CD rpm|rpm|NN ,|,|, 5|5|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT pellet|pellet|NN suspended|suspend|VBN in|in|IN 800|800|CD µL|µl|NN TE|TE|NNP pH|ph|NN 8.0|8.0|CD supplemented|supplement|VBN with|with|IN 0.5|0.5|CD mg/mL|mg/ml|NN lysozyme|lysozyme|NN .|.|. SDS|sds|NN -LRB-|-lrb-|-LRB- 80|80|CD µL|µl|NN at|at|IN 10|10|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN ,|,|, samples|sample|NNS mixed|mix|VBN by|by|IN inversion|inversion|NN ,|,|, and|and|CC incubated|incubate|VBN -LRB-|-lrb-|-LRB- 65|65|CD °C|°c|NN ,|,|, 2|2|CD min|min|NN -RRB-|-rrb-|-RRB- ,|,|, before|before|IN the|the|DT addition|addition|NN of|of|IN 88|88|CD µL|µl|NN 1|1|CD M|m|NN NaOAc|naoac|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- .|.|. Each|each|DT sample|sample|NN was|be|VBD added|add|VBN to|to|TO an|a|DT equal|equal|JJ volume|volume|NN -LRB-|-lrb-|-LRB- 1mL|1ml|NN -RRB-|-rrb-|-RRB- of|of|IN water-saturated|water-saturated|JJ phenol|phenol|NN -LRB-|-lrb-|-LRB- pH|ph|NN 4.2|4.2|CD ,|,|, 65|65|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN -LRB-|-lrb-|-LRB- 65|65|CD °C|°c|NN ,|,|, 6|6|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT solution|solution|NN was|be|VBD separated|separate|VBN into|into|IN layers|layer|NNS by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 14,000|14,000|CD rpm|rpm|NN ,|,|, 10|10|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT upper|upper|JJ aqueous|aqueous|JJ RNA|rna|NN containing|contain|VBG layer|layer|NN removed|remove|VBD and|and|CC transferred|transfer|VBD into|into|IN a|a|DT fresh|fresh|JJ tube|tube|NN .|.|. RNA|rna|NN was|be|VBD cleaned|clean|VBN by|by|IN three|three|CD extractions|extraction|NNS with|with|IN phenol|phenol|NN :|:|: CHCl3|chcl3|NN :|:|: IAA|iaa|NN -LRB-|-lrb-|-LRB- 25:24:1|25:24:1|CD ,|,|, pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- before|before|IN being|be|VBG precipitated|precipitated|JJ -LRB-|-lrb-|-LRB- -80|-80|CD °C|°c|NN ,|,|, O/N|o/n|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT addition|addition|NN of|of|IN 1/10|1/10|CD volume|volume|NN of|of|IN 3M|3M|NNP NaOAc|naoac|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- and|and|CC 2|2|CD volumes|volume|NNS of|of|IN ice|ice|NN cold|cold|JJ 100|100|CD %|%|NN EtOH|etoh|NN .|.|. RNA|rna|NN was|be|VBD pelleted|pelleted|JJ -LRB-|-lrb-|-LRB- 14,000|14,000|CD rpm|rpm|NN ,|,|, 25|25|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT supernatant|supernatant|JJ removed|remove|VBN and|and|CC the|the|DT pellet|pellet|NN washed|wash|VBN with|with|IN 1|1|CD mL|ml|NN 75|75|CD %|%|NN cold|cold|JJ EtOH|etoh|NN -LRB-|-lrb-|-LRB- made|make|VBN with|with|IN DEPC-treated|depc-treated|JJ water|water|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD pelleted|pelleted|JJ -LRB-|-lrb-|-LRB- 14,000|14,000|CD rpm|rpm|NN ,|,|, 5|5|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC air|air|NN dried|dry|VBD before|before|IN suspension|suspension|NN in|in|IN 80|80|CD µL|µl|NN RNAse|rnase|NN free|free|JJ water|water|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- and|and|CC treatment|treatment|NN with|with|IN TURBO|TURBO|NNP DNAse|dnase|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Briefly|briefly|RB ,|,|, 0.1|0.1|CD V|v|NN of|of|IN 10|10|CD X|x|NN Turbo|Turbo|NNP DNAse|dnase|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT RNA|rna|NN solution|solution|NN .|.|. 1|1|CD µL|µl|NN of|of|IN TURBO|TURBO|NNP DNAse|dnase|NN was|be|VBD added|add|VBN to|to|TO the|the|DT solution|solution|NN ,|,|, which|which|WDT was|be|VBD then|then|RB incubated|incubate|VBN -LRB-|-lrb-|-LRB- 30|30|CD min|min|NN ,|,|, 37|37|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|. Following|follow|VBG incubation|incubation|NN ,|,|, 0.1|0.1|CD V|v|NN of|of|IN DNase|dnase|NN Inactivation|inactivation|NN Reagent|reagent|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC then|then|RB incubated|incubate|VBN -LRB-|-lrb-|-LRB- 5|5|CD min|min|NN ,|,|, RT|rt|NN -RRB-|-rrb-|-RRB- with|with|IN occasional|occasional|JJ mixing|mix|VBG .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN and|and|CC transferred|transfer|VBN into|into|IN a|a|DT fresh|fresh|JJ microfuge|microfuge|NN tube|tube|NN .|.|. RNA|rna|NN quality|quality|NN tested|test|VBN using|use|VBG the|the|DT the|the|DT Agilent|Agilent|NNP RNA|rna|NN 6000|6000|CD Nano|Nano|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC quality|quality|NN analysed|analyse|VBN using|use|VBG the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG an|a|DT RNeasy|rneasy|JJ kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC after|after|IN 1st|1st|JJ and|and|CC 2nd|2nd|JJ strand|strand|NN cDNA|cdna|NN synthesis|synthesis|NN ,|,|, linker|linker|NN ligation|ligation|NN and|and|CC size|size|NN selection|selection|NN subjected|subject|VBN to|to|TO shotgun|shotgun|NN sequencing|sequencing|NN using|use|VBG single|single|JJ read|read|NN 40bp|40bp|JJ read|read|NN length|length|NN runs|run|VBZ on|on|IN an|a|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP GAII|GAII|NNP .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG QIAGEN|QIAGEN|NNP RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNeasy|rneasy|NN minikit|minikit|NN Cat|cat|NN #|#|# 74106|74106|CD
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNAeasy|rnaeasy|NN columns|column|NNS -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS recommendations|recommendation|NNS .|.|. RNA|rna|NN was|be|VBD quantified|quantify|VBN using|use|VBG a|a|DT NanoDrop-1000|nanodrop-1000|NN spectrophotometer|spectrophotometer|NN and|and|CC quality|quality|NN was|be|VBD monitored|monitor|VBN with|with|IN the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNAeasy|rnaeasy|NN mini-Kit|mini-kit|NN Qiagen|Qiagen|NNP and|and|CC hybridizated|hybridizate|VBN on|on|IN Affymatrix|Affymatrix|NNP microarrays|microarray|NNS .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- 74104|74104|CD -RRB-|-rrb-|-RRB- and|and|CC mechanical|mechanical|JJ cell|cell|NN disruption|disruption|NN with|with|IN glass|glass|NN beads|bead|NNS but|but|CC without|without|IN enzymatic|enzymatic|JJ lysis|lysis|NN .|.|. This|this|DT was|be|VBD carried|carry|VBN out|out|RP in|in|IN the|the|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP kit|kit|NN lysis|lysis|NN RLT|rlt|NN buffer|buffer|NN with|with|IN beta-mercaptethanol|beta-mercaptethanol|NN ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS recommendations|recommendation|NNS .|.|. Mechanical|mechanical|JJ cell|cell|NN disruption|disruption|NN was|be|VBD completed|complete|VBN through|through|IN shaking|shake|VBG for|for|IN five|five|CD min|min|NN using|use|VBG a|a|DT Retsch|Retsch|NNP mill|mill|NN -LRB-|-lrb-|-LRB- Retsch|retsch|JJ MM200|mm200|NN -RRB-|-rrb-|-RRB- on|on|IN maximum|maximum|NN speed|speed|NN .|.|. RNA|rna|NN was|be|VBD subsequently|subsequently|RB cleaned|clean|VBN on-column|on-column|JJ with|with|IN an|a|DT additional|additional|JJ DNase|dnase|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP 79254|79254|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT quality|quality|NN of|of|IN extracted|extract|VBN RNA|rna|NN was|be|VBD determined|determine|VBN with|with|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD bioanalyzer|bioanalyzer|NN having|have|VBG used|use|VBN an|a|DT Agilent|agilent|JJ RNA|rna|NN 6000|6000|CD Nano|Nano|NNP Kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS recommendations|recommendation|NNS .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT SuperScript|SuperScript|NNP indirect|indirect|JJ cDNA|cdna|NN labeling|labeling|NN system|system|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO generate|generate|VB cDNA|cdna|NN .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG Trizol|Trizol|NNP and|and|CC chloroform|chloroform|NN in|in|IN conjunction|conjunction|NN with|with|IN Qiagen|Qiagen|NNP 's|'s|POS RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT A.|a.|NN Untergasser|Untergasser|NNP protocol|protocol|NN -LRB-|-lrb-|-LRB- http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|http://www.molbi.de/protocols/rna_prep_comb_trizol_v1_0.htm|NN -RRB-|-rrb-|-RRB- with|with|IN one|one|CD modification|modification|NN :|:|: Phase|phase|NN Lock|lock|NN Gel|gel|NN tubes|tube|NNS -LRB-|-lrb-|-LRB- Eppendorf|Eppendorf|NNP ,|,|, Westbury|Westbury|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- were|be|VBD used|use|VBN to|to|TO better|better|JJR separate|separate|JJ organic|organic|JJ and|and|CC aqueous|aqueous|JJ phases|phase|NNS after|after|IN the|the|DT addition|addition|NN of|of|IN chloroform|chloroform|NN .|.|. DNA|dna|NN was|be|VBD digested|digest|VBN with|with|IN Ambion|Ambion|NNP rDNAse|rDNAse|NNP I|I|NNP -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD further|further|JJ cleaned|clean|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN and|and|CC quality|quality|NN was|be|VBD assessed|assess|VBN by|by|IN the|the|DT RNA|rna|NN ScreenTape|screentape|NN Assay|assay|NN on|on|IN the|the|DT TapeStation|TapeStation|NNP 2200|2200|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS with|with|IN RIN|rin|NN values|value|NNS greater|greater|JJR than|than|IN 8.0|8.0|CD were|be|VBD treated|treat|VBN with|with|IN the|the|DT Ambion|Ambion|NNP MICROBExpress|MICROBExpress|NNPS Bacterial|bacterial|JJ mRNA|mrna|NN Enrichment|Enrichment|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- and|and|CC were|be|VBD used|use|VBN for|for|IN library|library|NN construction|construction|NN .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG Trizol|trizol|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB-
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG Trizol|Trizol|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- and|and|CC Direct-zol|direct-zol|NN RNA|rna|NN MiniPrep|MiniPrep|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Zymo|zymo|NN -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG TRIzol|trizol|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD treated|treat|VBN with|with|IN DNAse|dnase|NN I|i|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, Cat|Cat|NNP No.|No.|NNP 18068-015|18068-015|CD -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. Further|further|JJ precipitation|precipitation|NN of|of|IN RNA|rna|NN and|and|CC ribosomal|ribosomal|JJ RNA|rna|NN cleanup|cleanup|NN was|be|VBD achieved|achieve|VBN by|by|IN Ambion|Ambion|NNP MICROBExpress|MICROBExpress|NNPS bacterial|bacterial|JJ mRNA|mrna|NN purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- cat|cat|NN .|.|. no|no|DT .|.|. AM1905|am1905|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. The|the|DT RNA|rna|NN was|be|VBD finally|finally|RB suspended|suspend|VBN in|in|IN 10|10|CD μL|μl|NN RNAse|rnase|NN free|free|JJ water|water|NN .|.|.
RNA|rna|NN was|be|VBD fragmented|fragmented|JJ using|use|VBG the|the|DT NEBNext|nebnext|NN Magnesium|magnesium|NN RNA|rna|NN Fragmentation|fragmentation|NN Module|module|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- .|.|. Then|then|RB ,|,|, RNA|rna|NN was|be|VBD phosphorylated|phosphorylate|VBN using|use|VBG T4|t4|NN polynucleotide|polynucleotide|NN kinase|kinase|NN and|and|CC prepared|prepare|VBN using|use|VBG the|the|DT NEBNext|nebnext|NN Small|small|JJ RNA|rna|NN Library|Library|NNP Prep|Prep|NNP Set|set|VB for|for|IN Illumina|Illumina|NNP -LRB-|-lrb-|-LRB- Multiplex|Multiplex|NNP Compatible|Compatible|NNP -RRB-|-rrb-|-RRB- .|.|. DNA|dna|NN fragments|fragment|NNS greater|greater|JJR than|than|IN 100|100|CD bp|bp|NN were|be|VBD excised|excise|VBN from|from|IN a|a|DT 4|4|CD %|%|NN agarose|agarose|NN gel|gel|NN after|after|IN library|library|NN preparation|preparation|NN and|and|CC recovered|recover|VBD using|use|VBG the|the|DT Zymoclean|Zymoclean|NNP Gel|gel|NN DNA|dna|NN Recovery|recovery|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Zymo|Zymo|NNP Research|Research|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN following|follow|VBG cell|cell|NN lysis|lysis|NN and|and|CC phenol|phenol|NN :|:|: chloroform|chloroform|NN extraction|extraction|NN as|as|IN previously|previously|RB described|describe|VBN -LRB-|-lrb-|-LRB- Andrade|Andrade|NNP ,|,|, Pobre|Pobre|NNP et|et|FW al.|al.|FW 2012|2012|CD -RRB-|-rrb-|-RRB- .|.|. After|after|IN precipitation|precipitation|NN step|step|NN in|in|IN ethanol|ethanol|NN and|and|CC 300|300|CD mM|mm|NN sodium|sodium|NN acetate|acetate|NN ,|,|, RNA|rna|NN was|be|VBD resuspended|resuspend|VBN in|in|IN MilliQ-water|MilliQ-water|NNP .|.|. The|the|DT integrity|integrity|NN of|of|IN RNA|rna|NN samples|sample|NNS was|be|VBD evaluated|evaluate|VBN by|by|IN agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN .|.|. Turbo|Turbo|NNP DNase|dnase|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- treatment|treatment|NN was|be|VBD used|use|VBN to|to|TO remove|remove|VB contaminant|contaminant|NN DNA|dna|NN .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN late|late|JJ exponential|exponential|JJ cultures|culture|NNS ,|,|, or|or|CC from|from|IN late|late|JJ exponential|exponential|JJ cells|cell|NNS heat-shocked|heat-shock|VBN by|by|IN exposure|exposure|NN to|to|TO 50|50|CD °C|°c|NN for|for|IN 15|15|CD min|min|NN .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN samples|sample|NNS using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. Prior|prior|RB to|to|TO lysis|lysis|NN all|all|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN for|for|IN 30|30|CD min|min|NN on|on|IN ice|ice|NN in|in|IN RNA|rna|NN stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 0.1|0.1|CD %|%|NN SDS|sds|NN ,|,|, 1|1|CD %|%|NN Acidic|acidic|JJ phenol|phenol|NN ,|,|, 19|19|CD %|%|NN ethanol|ethanol|NN ,|,|, ice|ice|NN cold|cold|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT lysis|lysis|NN and|and|CC digestion|digestion|NN protocol|protocol|NN was|be|VBD followed|follow|VBN with|with|IN two|two|CD 50|50|CD μl|μl|NN ddH20|ddh20|NN elutions|elution|NNS .|.|. Each|each|DT sample|sample|NN was|be|VBD treated|treat|VBN with|with|IN 2|2|CD μl|μl|NN of|of|IN DNase|dnase|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD min|min|NN .|.|. Samples|sample|NNS were|be|VBD purified|purify|VBN and|and|CC concentrated|concentrate|VBN using|use|VBG Microcon|Microcon|NNP YM-30|ym-30|NN columns|column|NNS -LRB-|-lrb-|-LRB- Millipore|Millipore|NNP ,|,|, Billerica|Billerica|NNP ,|,|, MA|MA|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC the|the|DT quantity|quantity|NN and|and|CC purity|purity|NN were|be|VBD determined|determine|VBN using|use|VBG an|a|DT ND-1000|nd-1000|NN spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Nanodrop|Nanodrop|NNP ,|,|, Wilmington|Wilmington|NNP ,|,|, DE|de|NN -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS were|be|VBD determined|determine|VBN to|to|TO be|be|VB free|free|JJ of|of|IN contaminating|contaminate|VBG genomic|genomic|JJ DNA|dna|NN by|by|IN absence|absence|NN of|of|IN a|a|DT band|band|NN on|on|IN a|a|DT DNA|dna|NN electrophoresis|electrophoresis|NN gel|gel|NN after|after|IN 30|30|CD rounds|round|NNS of|of|IN PCR|pcr|NN .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN the|the|DT culture|culture|NN by|by|IN using|use|VBG the|the|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini-prep|mini-prep|NN kit.cDNA|kit.cdna|NN was|be|VBD synthesized|synthesize|VBN using|use|VBG 5-10|5-10|CD µg/ml|µg/ml|NN of|of|IN RNA|rna|NN and|and|CC the|the|DT first|first|JJ strand|strand|NN cDNA|cdna|NN synthesis|synthesis|NN kit|kit|NN from|from|IN Invitrogen|Invitrogen|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP Bioservices|Bioservices|NNP India|India|NNP Pvt.|Pvt.|NNP Ltd.|Ltd.|NNP ,|,|, Bangalore|Bangalore|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN the|the|DT pellet|pellet|NN of|of|IN E.|e.|FW coli|coli|FW cells|cell|NNS using|use|VBG a|a|DT well-established|well-established|JJ ,|,|, published|publish|VBN protocol|protocol|NN -LRB-|-lrb-|-LRB- Kime|Kime|NNP et|et|FW al.|al.|FW 2008|2008|CD .|.|. In|in|IN RNA|rna|NN Turnover|turnover|NN in|in|IN Bacteria|bacterium|NNS ,|,|, Archaea|Archaea|NNP and|and|CC Organelles|Organelles|NNP ,|,|, Vol|Vol|NNP 447|447|CD -LRB-|-lrb-|-LRB- ed|ed|VBN .|.|. LE|LE|NNP Maquat|Maquat|NNP ,|,|, CM|cm|NN Arraiano|arraiano|NN -RRB-|-rrb-|-RRB- ,|,|, pp.|pp.|NN 215|215|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT cell|cell|NN pellet|pellet|NN of|of|IN S.|S.|NNP coelicolor|coelicolor|NN was|be|VBD resuspended|resuspend|VBN in|in|IN Kirby|Kirby|NNP mix|mix|NN -LRB-|-lrb-|-LRB- Kieser|Kieser|NNP et|et|FW al.|al.|FW 2000|2000|CD .|.|. Practical|Practical|NNP Streptomyces|Streptomyces|NNP Genetics|Genetics|NNP .|.|. The|the|DT John|John|NNP Innes|Innes|NNP Foundation|Foundation|NNP ,|,|, Norwich|Norwich|NNP .|.|. -RRB-|-rrb-|-RRB- ,|,|, 100|100|CD µL|µl|NN per|per|IN 1|1|CD O.D.|O.D.|NNP 600nm|600nm|NNP unit|unit|NN ,|,|, and|and|CC transferred|transfer|VBN to|to|TO Lysing|lyse|VBG Matrix|Matrix|NNP B|B|NNP tubes|tube|NNS containing|contain|VBG fine|fine|JJ silica|silica|NN beads|bead|NNS -LRB-|-lrb-|-LRB- MP|mp|NN Biomedical|biomedical|JJ -RRB-|-rrb-|-RRB- .|.|. Tubes|tube|NNS were|be|VBD then|then|RB placed|place|VBN in|in|IN a|a|DT high-speed|high-speed|JJ benchtop|benchtop|NN homogenizer|homogenizer|NN -LRB-|-lrb-|-LRB- Fastprep-24|fastprep-24|NN ,|,|, MP|mp|NN Biomedical|biomedical|NN ;|;|: set|set|VBN at|at|IN 6.5|6.5|CD M/s|m/s|NNS -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD lysed|lyse|VBN by|by|IN three|three|CD cycles|cycle|NNS of|of|IN homogenisation|homogenisation|NN for|for|IN 1|1|CD min|min|NN with|with|IN cooling|cooling|NN between|between|IN each|each|DT cycle|cycle|NN in|in|IN an|a|DT ice-water|ice-water|JJ bath|bath|NN for|for|IN 1|1|CD min|min|NN .|.|. The|the|DT lysates|lysate|NNS were|be|VBD extracted|extract|VBN using|use|VBG an|a|DT equal|equal|JJ volume|volume|NN of|of|IN acidic|acidic|JJ phenol|phenol|NN :|:|: chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN -LRB-|-lrb-|-LRB- 50|50|CD :|:|: 50|50|CD :|:|: 1|1|CD -RRB-|-rrb-|-RRB- and|and|CC then|then|RB chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN -LRB-|-lrb-|-LRB- 49|49|CD :|:|: 1|1|CD -RRB-|-rrb-|-RRB- .|.|. Nucleic|nucleic|JJ acid|acid|NN in|in|IN the|the|DT aqueous|aqueous|JJ phase|phase|NN was|be|VBD precipitated|precipitate|VBN by|by|IN adding|add|VBG NaCl|nacl|NN to|to|TO 150|150|CD mM|mm|NN and|and|CC 2.5|2.5|CD x|x|CC volumes|volume|NNS of|of|IN 100|100|CD %|%|NN -LSB-|-lsb-|-LRB- v/v|v/v|NN -RSB-|-rsb-|-RRB- ethanol|ethanol|NN ,|,|, chilling|chill|VBG at|at|IN -20|-20|CD °C|°c|NN for|for|IN 1|1|CD h|h|NN ,|,|, and|and|CC then|then|RB harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 13,000|13,000|CD x|x|CC g|g|NN for|for|IN 30|30|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT nucleic|nucleic|JJ acid|acid|NN pellet|pellet|NN was|be|VBD washed|wash|VBN twice|twice|RB with|with|IN 700|700|CD µL|µl|NN of|of|IN 70|70|CD %|%|NN -LSB-|-lsb-|-LRB- v/v|v/v|NN -RSB-|-rsb-|-RRB- ethanol|ethanol|NN ,|,|, air|air|NN dried|dry|VBD for|for|IN 5|5|CD min|min|NN and|and|CC resuspended|resuspend|VBN in|in|IN RNase-free|rnase-free|JJ water|water|NN .|.|. Contaminating|contaminate|VBG DNA|dna|NN was|be|VBD removed|remove|VBN from|from|IN both|both|DT E.|e.|FW coli|coli|FW and|and|CC S.|s.|FW coelicolor|coelicolor|FW by|by|IN incubating|incubate|VBG with|with|IN DNase|dnase|NN as|as|IN described|describe|VBN by|by|IN the|the|DT vendor|vendor|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- and|and|CC extracted|extract|VBN with|with|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN as|as|IN described|describe|VBN above|above|IN .|.|. The|the|DT concentration|concentration|NN and|and|CC integrity|integrity|NN of|of|IN RNA|rna|NN samples|sample|NNS were|be|VBD determined|determine|VBN using|use|VBG a|a|DT NanoDropTM|nanodroptm|NN 1000|1000|CD spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- and|and|CC agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN -LRB-|-lrb-|-LRB- Kime|Kime|NNP et|et|FW al.|al.|FW 2008|2008|CD -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB .|.|. Samples|sample|NNS were|be|VBD enriched|enrich|VBN for|for|IN mRNA|mrna|NN using|use|VBG MICROBExpress-Bacteria|microbexpress-bacteria|JJ beads|bead|NNS ,|,|, as|as|IN described|describe|VBN by|by|IN the|the|DT manufacturer|manufacturer|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG standard|standard|JJ Trizol|trizol|NN lysis|lysis|NN and|and|CC aqueous|aqueous|JJ extraction|extraction|NN ,|,|, followed|follow|VBN by|by|IN further|further|JJ purification|purification|NN using|use|VBG a|a|DT Qiagen|Qiagen|NNP RNAeasy|RNAeasy|NNP kit|kit|NN .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Protect|Protect|NNP Bacteria|bacterium|NNS Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- ,|,|, following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Trizol|Trizol|NNP reagent|reagent|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB-
RNA|rna|NN was|be|VBD obtained|obtain|VBN from|from|IN cells|cell|NNS pellets|pellet|NNS by|by|IN lysozyme|lysozyme|NN treatment|treatment|NN and|and|CC phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN ,|,|, analyzed|analyze|VBN by|by|IN agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN to|to|TO confirm|confirm|VB integrity|integrity|NN ,|,|, quantified|quantify|VBN using|use|VBG a|a|DT Nanodrop|Nanodrop|NNP spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN
RNA|rna|NN was|be|VBD obtained|obtain|VBN from|from|IN each|each|DT culture|culture|NN using|use|VBG Ambion|Ambion|NNP RiboPureTM-bacteria|RiboPureTM-bacteria|NNP RNA|rna|NN extraction|extraction|NN kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
RNA|rna|NN was|be|VBD obtained|obtain|VBN using|use|VBG the|the|DT RNAeasy|rnaeasy|NN MIDI|midi|NN RNA|rna|NN extraction|extraction|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- using|use|VBG lysis|lysis|NN buffer|buffer|NN containing|contain|VBG 0.1|0.1|CD %|%|NN beta-mercaptoethanol|beta-mercaptoethanol|NN .|.|. RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN lysates|lysate|NNS and|and|CC purified|purify|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS standard|standard|JJ protocol|protocol|NN and|and|CC subsequently|subsequently|RB stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|. RNA|rna|NN quality|quality|NN was|be|VBD assessed|assess|VBN with|with|IN electrophoresis|electrophoresis|NN using|use|VBG a|a|DT RNA|rna|NN bioanalyser|bioanalyser|NN 2100|2100|CD and|and|CC Lab|lab|NN RNAChip|rnachip|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- before|before|IN progression|progression|NN to|to|TO microarray|microarray|NN hybridization|hybridization|NN .|.|.
RNA|rna|NN was|be|VBD pelleted|pelleted|JJ -LRB-|-lrb-|-LRB- 14,000|14,000|CD rpm|rpm|NN ,|,|, 5|5|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC air|air|NN dried|dry|VBD before|before|IN suspension|suspension|NN in|in|IN 80|80|CD µL|µl|NN RNAse|rnase|NN free|free|JJ water|water|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- and|and|CC treatment|treatment|NN with|with|IN TURBO|TURBO|NNP DNAse|dnase|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Briefly|briefly|RB ,|,|, 0.1|0.1|CD V|v|NN of|of|IN 10|10|CD X|x|NN Turbo|Turbo|NNP DNAse|dnase|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT RNA|rna|NN solution|solution|NN .|.|. 1|1|CD µL|µl|NN of|of|IN TURBO|TURBO|NNP DNAse|dnase|NN was|be|VBD added|add|VBN to|to|TO the|the|DT solution|solution|NN ,|,|, which|which|WDT was|be|VBD then|then|RB incubated|incubate|VBN -LRB-|-lrb-|-LRB- 30|30|CD min|min|NN ,|,|, 37|37|CD °C|°c|NN -RRB-|-rrb-|-RRB- .|.|. Following|follow|VBG incubation|incubation|NN ,|,|, 0.1|0.1|CD V|v|NN of|of|IN DNase|dnase|NN Inactivation|inactivation|NN Reagent|reagent|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN and|and|CC then|then|RB incubated|incubate|VBN -LRB-|-lrb-|-LRB- 5|5|CD min|min|NN ,|,|, RT|rt|NN -RRB-|-rrb-|-RRB- with|with|IN occasional|occasional|JJ mixing|mix|VBG .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN and|and|CC transferred|transfer|VBN into|into|IN a|a|DT fresh|fresh|JJ microfuge|microfuge|NN tube|tube|NN .|.|. RNA|rna|NN quality|quality|NN tested|test|VBN using|use|VBG the|the|DT the|the|DT Agilent|Agilent|NNP RNA|rna|NN 6000|6000|CD Nano|Nano|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- and|and|CC quality|quality|NN analysed|analyse|VBN using|use|VBG the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD prepared|prepare|VBN using|use|VBG the|the|DT Trizol|Trizol|NNP Reagent|Reagent|NNP and|and|CC a|a|DT RiboPure|RiboPure|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. RNA|rna|NN integrity|integrity|NN was|be|VBD assessed|assess|VBN using|use|VBG an|a|DT Agilent|Agilent|NNP 2100|2100|CD bioanalyser|bioanalyser|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP ,|,|, Palo|Palo|NNP Alto|Alto|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD purified|purify|VBN by|by|IN a|a|DT standard|standard|JJ protocol|protocol|NN using|use|VBG Phenol|Phenol|NNP Chloroform|Chloroform|NNP .|.|. Ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD removed|remove|VBN using|use|VBG Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Gram-Negative|gram-negative|JJ Bacteria|bacterium|NNS -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|. Then|then|RB ,|,|, the|the|DT conventional|conventional|JJ Illumina|Illumina|NNP protocol|protocol|NN for|for|IN mRNA|mrna|NN Sequencing|sequencing|NN Sample|Sample|NNP Preparation|Preparation|NNP was|be|VBD applied|apply|VBN with|with|IN a|a|DT few|few|JJ modifications|modification|NNS -LRB-|-lrb-|-LRB- see|see|VB original|original|JJ paper|paper|NN -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD purified|purify|VBN from|from|IN 200|200|CD µL|µl|NN of|of|IN overnight|overnight|JJ culture|culture|NN by|by|IN pelleting|pelleting|NN and|and|CC resuspeding|resuspeding|NN in|in|IN 500|500|CD µL|µl|NN of|of|IN Trizol|trizol|NN at|at|IN 65|65|CD °C|°c|NN ,|,|, followed|follow|VBN by|by|IN purification|purification|NN on|on|IN a|a|DT column|column|NN -LRB-|-lrb-|-LRB- Direct-Zol|Direct-Zol|NNP ,|,|, Zymo|Zymo|NNP Research|Research|NNP -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS received|receive|VBD two|two|CD 30-minute|30-minute|JJ DNase|dnase|NN treatments|treatment|NNS using|use|VBG TURBO|TURBO|NNP DNA-free|dna-free|JJ -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturers|manufacturer|NNS instructions|instruction|NNS .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD then|then|RB purified|purify|VBN on|on|IN a|a|DT column|column|NN -LRB-|-lrb-|-LRB- RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ,|,|, Zymo|Zymo|NNP Research|Research|NNP -RRB-|-rrb-|-RRB- .|.|. Three|three|CD samples|sample|NNS were|be|VBD prepped|prep|VBN from|from|IN each|each|DT culture|culture|NN and|and|CC pooled|pool|VBD to|to|TO generate|generate|VB sufficient|sufficient|JJ RNA|rna|NN .|.|.
RNA|rna|NN was|be|VBD purified|purify|VBN from|from|IN lysates|lysate|NNS by|by|IN phenol/chloroform|phenol/chloroform|NN method|method|NN .|.|. rRNA|rrna|NN was|be|VBD first|first|JJ removed|remove|VBN using|use|VBG MICROBExpress|microbexpress|NN following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN ,|,|, except|except|IN RNA|rna|NN was|be|VBD collected|collect|VBN using|use|VBG Zymo|Zymo|NNP 's|'s|POS RNA|rna|NN columns|column|NNS .|.|. A|a|DT second|second|JJ rRNA|rrna|NN removal|removal|NN step|step|NN was|be|VBD performed|perform|VBN following|follow|VBG the|the|DT protocol|protocol|NN described|describe|VBN in|in|IN Affymetrix|Affymetrix|NNP Expression|expression|NN Handbook|handbook|NN ,|,|, substituting|substitute|VBG enzymes|enzyme|NNS MMLV|mmlv|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- ,|,|, RNase|rnase|NN H|h|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC DnaseI|dnasei|NN -LRB-|-lrb-|-LRB- Amplification|amplification|NN grade|grade|NN ,|,|, Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- .|.|.
RNA|rna|NN was|be|VBD purified|purify|VBN on|on|IN RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|SYM -5|-5|CD columns|column|NNS following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS ,|,|, and|and|CC eluted|elute|VBN in|in|IN 6|6|CD μl|μl|NN of|of|IN nuclease-free|nuclease-free|JJ water|water|NN .|.|. 6|6|CD μl|μl|NN of|of|IN 2X|2x|NN RNA|rna|NN Loading|load|VBG Dye|dye|NN -LRB-|-lrb-|-LRB- ThermoScientific|ThermoScientific|NNP ,|,|, cat|cat|NN .|.|. R0641|r0641|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO purified|purify|VBN RNA|rna|NN .|.|. Both|both|DT DMS|dms|NN treated|treat|VBN and|and|CC untreated|untreated|JJ samples|sample|NNS were|be|VBD heated|heat|VBN at|at|IN 95|95|CD °C|°c|NN for|for|IN 2|2|CD minutes|minute|NNS ,|,|, and|and|CC immediately|immediately|RB placed|place|VBN on|on|IN ice|ice|NN .|.|. Samples|sample|NNS were|be|VBD resolved|resolve|VBN on|on|IN a|a|DT 10|10|CD %|%|NN TBE-Urea|tbe-urea|NN polyacrylamide|polyacrylamide|NN gel|gel|NN ,|,|, and|and|CC a|a|DT gel|gel|NN slice|slice|NN ranging|range|VBG from|from|IN 50|50|CD nt|nt|NNS to|to|TO the|the|DT full-length|full-length|JJ product|product|NN was|be|VBD cut|cut|VBN .|.|. Gel|gel|NN slices|slice|NNS were|be|VBD crushed|crush|VBN by|by|IN centrifugation|centrifugation|NN through|through|IN a|a|DT punctured|punctured|JJ 0.5|0.5|CD ml|ml|NN tube|tube|NN ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 500|500|CD μl|μl|NN of|of|IN Diffusion|Diffusion|NNP buffer|buffer|NN -LSB-|-lsb-|-LRB- 500|500|CD mM|mm|NN Ammonium|ammonium|NN acetate|acetate|NN ;|;|: 0.05|0.05|CD %|%|NN SDS|sds|NN -RSB-|-rsb-|-RRB- supplemented|supplement|VBN with|with|IN 60|60|CD U|U|NNP SUPERase|SUPERase|NNP •|•|SYM In|in|IN ™|™|CD RNase|rnase|NN Inhibitor|inhibitor|NN ,|,|, then|then|RB rotated|rotate|VBD at|at|IN 4|4|CD °C|°c|NN for|for|IN 16|16|CD hours|hour|NNS to|to|TO allow|allow|VB passive|passive|JJ diffusion|diffusion|NN of|of|IN RNA|rna|NN fragments|fragment|NNS into|into|IN buffer|buffer|NN .|.|. RNA|rna|NN was|be|VBD precipitated|precipitate|VBN by|by|IN addition|addition|NN of|of|IN 1|1|CD ml|ml|NN Isopropanol|isopropanol|NN ,|,|, and|and|CC 2|2|CD μl|μl|NN Glycogen|glycogen|NN -LRB-|-lrb-|-LRB- 20|20|CD μg/μl|μg/μl|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC resuspended|resuspend|VBN in|in|IN 6|6|CD μl|μl|NN nuclease-free|nuclease-free|JJ water|water|NN .|.|.
RNA|rna|NN were|be|VBD isolated|isolate|VBN from|from|IN wild|wild|JJ type|type|NN and|and|CC mutants|mutant|NNS .|.|. Trizol|trizol|NN extraction|extraction|NN of|of|IN total|total|JJ RNA|rna|NN was|be|VBD performed|perform|VBN according|accord|VBG to|to|TO standard|standard|JJ affymetrix|affymetrix|NN labeling|labeling|NN protocols|protocol|NNS .|.|.
∆|∆|SYM rnb|rnb|FW _|_|FW RNA-Seq|rna-seq|NN
rnc|rnc|SYM -|-|: _|_|SYM time0|time0|CD
rnc|rnc|SYM -|-|: _|_|SYM time10|time10|CD
rnc|rnc|SYM -|-|: _|_|SYM time20|time20|CD
rnc|rnc|SYM -|-|: _|_|SYM time2|time2|CD .5|.5|CD
rnc|rnc|SYM -|-|: _|_|SYM time5|time5|CD
rnc|rnc|SYM -|-|: _|_|SYM time7|time7|CD .5|.5|CD
rne-3071|rne-3071|NN ts|t|NNS
RNeasy|rneasy|NN Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Austin|Austin|NNP ,|,|, TX|TX|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- with|with|IN on-column|on-column|JJ DNase|dnase|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- RNase-Free|rnase-free|JJ DNase|dnase|NN Set|set|VB ,|,|, Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- .|.|.
rne|rne|NN wild-type|wild-type|JJ
rng|rng|NN mutant|mutant|JJ
rng|rng|NN wild-type|wild-type|JJ
rnpB|rnpb|NN SPET-seq|spet-seq|NN -LRB-|-lrb-|-LRB- in|in|FW vitro|vitro|FW -RRB-|-rrb-|-RRB-
∆|∆|CD rnr|rnr|NN _|_|CD RNA-Seq|rna-seq|NN
Rockhopper|rockhopper|NN version|version|NN 1.20|1.20|CD -LRB-|-lrb-|-LRB- manuscript|manuscript|NN submitted|submit|VBN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN alignment|alignment|NN ,|,|, normalization|normalization|NN ,|,|, and|and|CC quantification|quantification|NN .|.|. Rockhopper|Rockhopper|NNP is|be|VBZ available|available|JJ for|for|IN download|download|NN from|from|IN http://cs.wellesley.edu/~btjaden/Rockhopper|http://cs.wellesley.edu/~btjaden/rockhopper|NN
Rodrigue|Rodrigue|NNP _|_|SYM 10-WT-Ni-3|10-wt-ni-3|NN
Rodrigue|Rodrigue|NNP _|_|SYM 1-WT-phiNi-1|1-wt-phini-1|NN
Rodrigue|Rodrigue|NNP _|_|SYM 2-WT-Ni-1|2-wt-ni-1|NN
Rodrigue|Rodrigue|NNP _|_|SYM 5-WT-Ni-2|5-wt-ni-2|NN
Rodrigue|Rodrigue|NNP _|_|SYM 6-WT-phiNi-2|6-wt-phini-2|JJ
Rodrigue|Rodrigue|NNP _|_|SYM 9-WT-phiNi-3|9-wt-phini-3|NN
Roemerine|roemerine|JJ _|_|NN 0|0|CD min|min|NN _|_|CD rep1|rep1|NN
Roemerine|roemerine|JJ _|_|NN 0|0|CD min|min|NN _|_|CD rep2|rep2|NN
Roemerine|roemerine|JJ _|_|NN 0|0|CD min|min|NN _|_|CD rep3|rep3|NN
Roemerine|roemerine|JJ _|_|NN 60|60|CD min|min|NN _|_|CD rep1|rep1|NN
Roemerine|roemerine|JJ _|_|NN 60|60|CD min|min|NN _|_|CD rep2|rep2|NN
Roemerine|roemerine|JJ _|_|NN 60|60|CD min|min|NN _|_|CD rep3|rep3|NN
-LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- -|-|: Roemerine|roemerine|NN treatment|treatment|NN ,|,|, 0|0|CD min|min|NN ,|,|, replicate|replicate|VB 1|1|CD
-LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- -|-|: Roemerine|roemerine|NN treatment|treatment|NN ,|,|, 0|0|CD min|min|NN ,|,|, replicate|replicate|VB 2|2|CD
-LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- -|-|: Roemerine|roemerine|NN treatment|treatment|NN ,|,|, 0|0|CD min|min|NN ,|,|, replicate|replicate|VB 3|3|CD
-LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- -|-|: Roemerine|roemerine|NN treatment|treatment|NN ,|,|, 60|60|CD min|min|NN ,|,|, replicate|replicate|VB 1|1|CD
-LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- -|-|: Roemerine|roemerine|NN treatment|treatment|NN ,|,|, 60|60|CD min|min|NN ,|,|, replicate|replicate|VB 2|2|CD
-LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- -|-|: Roemerine|roemerine|NN treatment|treatment|NN ,|,|, 60|60|CD min|min|NN ,|,|, replicate|replicate|VB 3|3|CD
RP437|rp437|NN persisters|persister|NNS treated|treat|VBN with|with|IN BF8|bf8|NN at|at|IN 5|5|CD µg/mL|µg/ml|NN for|for|IN 1|1|CD hour|hour|NN
RP437|rp437|NN was|be|VBD inoculated|inoculate|VBN in|in|IN 100|100|CD mL|ml|NN LB|lb|NN and|and|CC grown|grow|VBN for|for|IN 18|18|CD h|h|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN ,|,|, 37oC|37oc|NN -RRB-|-rrb-|-RRB- .|.|. Persister|persister|NN cells|cell|NNS were|be|VBD isolated|isolate|VBN by|by|IN lysing|lyse|VBG the|the|DT normal|normal|JJ cells|cell|NNS with|with|IN 5|5|CD µg/mL|µg/ml|NN Ofloxacin|ofloxacin|NN -LRB-|-lrb-|-LRB- 3.5|3.5|CD h|h|NN ,|,|, 200|200|CD rpm|rpm|NN ,|,|, 37oC|37oc|NN -RRB-|-rrb-|-RRB- ,|,|, followed|follow|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC washing|wash|VBG with|with|IN 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN .|.|.
RPMI|rpmi|NN 1A|1a|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD first|first|JJ duplicate|duplicate|VB
RPMI|rpmi|NN 1B|1b|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD second|second|JJ replicate|replicate|VBP
RPMI|rpmi|NN 2A|2a|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD ,|,|, first|first|RB replicate|replicate|VB
RPMI|rpmi|NN 2B|2b|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD second|second|JJ replicate|replicate|VBP
RpoB|rpob|NN ∆|∆|CD cra|cra|NN 1|1|CD
RpoB|rpob|NN ∆|∆|CD cra|cra|NN 2|2|CD
RpoB|rpob|NN ∆|∆|CD crp|crp|NN 1|1|CD
RpoB|rpob|NN ∆|∆|CD crp|crp|NN 2|2|CD
RpoB|rpob|NN with|with|IN DPD|dpd|NN 1|1|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN with|with|IN DPD|dpd|NN 2|2|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN with|with|IN DPD|dpd|NN and|and|CC rifampicin|rifampicin|NN 1|1|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN with|with|IN DPD|dpd|NN and|and|CC rifampicin|rifampicin|NN 2|2|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN with|with|IN Fe|Fe|NNP 1|1|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN with|with|IN Fe|Fe|NNP 2|2|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN with|with|IN Fe|Fe|NNP and|and|CC rifampicin|rifampicin|NN 1|1|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN with|with|IN Fe|Fe|NNP and|and|CC rifampicin|rifampicin|NN 2|2|CD -LRB-|-lrb-|-LRB- ChIP-exo|chip-exo|NN -RRB-|-rrb-|-RRB-
RpoB|rpob|NN WT|wt|NN 1|1|CD
RpoB|rpob|NN WT|wt|NN 2|2|CD
rpo|rpo|NN ,|,|, delfis|delfis|NN ,|,|, ME|me|NN
rpo|rpo|NN ,|,|, delhns|delhn|NNS ,|,|, ME|me|NN
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 0|0|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 10|10|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 15|15|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 15|15|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 20|20|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 2.5|2.5|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 30|30|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 5|5|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 5|5|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoE|rpoe|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 60|60|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoH|rpoh|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 0|0|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoH|rpoh|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 10|10|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoH|rpoh|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 20|20|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoH|rpoh|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 2.5|2.5|CD min|min|NN -RRB-|-rrb-|-RRB-
RpoH|rpoh|NN induced|induce|VBN -LRB-|-lrb-|-LRB- 5|5|CD min|min|NN -RRB-|-rrb-|-RRB-
rpoN|rpon|NN mutant|mutant|JJ grown|grow|VBN to|to|TO logarithmic|logarithmic|JJ phase|phase|NN
rpoN|rpon|NN mutant|mutant|JJ grown|grow|VBN to|to|TO transition|transition|NN phase|phase|NN
rpoS|rpos|NN _|_|CD 04|04|CD _|_|NN rep1|rep1|NN
rpoS|rpos|NN _|_|CD 04|04|CD _|_|NN rep2|rep2|NN
rpoS|rpos|NN _|_|CD 04|04|CD _|_|SYM TEX|TEX|NNP
rpoS|rpos|NN _|_|CD 15|15|CD min|min|NN _|_|CD rep1|rep1|NN
rpoS|rpos|NN _|_|CD 16|16|CD _|_|NN rep1|rep1|NN
rpoS|rpos|NN _|_|NN 180|180|CD min|min|NN _|_|CD rep1|rep1|NN
rpoS|rpos|NN _|_|CD 30|30|CD min|min|NN _|_|CD rep1|rep1|NN
rpoS|rpos|NN _|_|CD 30|30|CD min|min|NN _|_|CD rep2|rep2|NN
rpoS|rpos|NN _|_|CD 30|30|CD min|min|NN _|_|CD TEX|TEX|NNP
rpoS|rpos|NN _|_|CD EE|ee|NN _|_|NN 1|1|CD
rpoS|rpos|NN _|_|CD EE|ee|NN _|_|NN 2|2|CD
rpos|rpo|NNS level|level|NN :|:|: 0|0|CD %|%|NN
rpos|rpo|NNS level|level|NN :|:|: 100|100|CD %|%|NN
rpos|rpo|NNS level|level|NN :|:|: 26|26|CD %|%|NN
rpoS|rpos|NN _|_|NN LS|ls|NN _|_|NN 1|1|CD
rpoS|rpos|NN _|_|NN LS|ls|NN _|_|NN 2|2|CD
rpoS|rpos|NN _|_|CD ME|me|NN _|_|NN 1|1|CD
rpoS|rpos|NN _|_|CD ME|me|NN _|_|NN 2|2|CD
rpoS|rpos|NN mutant|mutant|JJ
rpoS|rpos|NN _|_|CD N|n|NN _|_|CD strv|strv|NN
rpoS|rpos|NN _|_|CD N|n|NN _|_|SYM strv|strv|FW _|_|FW TEX|tex|NN
rpoS|rpos|NN _|_|CD S|s|NN _|_|NN 1|1|CD
rpoS|rpos|NN _|_|CD S|s|NN _|_|NN 2|2|CD
rpoS|rpos|NN _|_|CD TS|ts|NN _|_|NN 1|1|CD
rpoS|rpos|NN _|_|CD TS|ts|NN _|_|NN 2|2|CD
rpo|rpo|NN ,|,|, wt|wt|JJ ,|,|, ME|me|JJ
rraA|rraa|NN deletion|deletion|NN ,|,|, OD600|od600|NN =|=|JJ 0.3|0.3|CD
rraA|rraa|NN deletion|deletion|NN ,|,|, OD600|od600|NN =|=|JJ 0.5|0.5|CD
rraA|rraa|NN deletion|deletion|NN ,|,|, OD600|od600|NN =|=|JJ 1.0|1.0|CD
rRNA|rrna|NN depleted|deplete|VBN RNA|rna|NN was|be|VBD then|then|RB primed|prime|VBN using|use|VBG random|random|JJ hexamers|hexamer|NNS and|and|CC reverse|reverse|VB transcribed|transcribe|VBN using|use|VBG SuperScript|SuperScript|NNP III|III|NNP -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
rRNA|rrna|NN depletion|depletion|NN ,|,|, fragmentation|fragmentation|NN ,|,|, reverse|reverse|JJ transcription|transcription|NN ,|,|, tagging|tagging|NN ,|,|, barcoding|barcoding|NN ,|,|, limited|limited|JJ cycle|cycle|NN PCR|pcr|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB-
rRNA|rrna|NN depletion|depletion|NN :|:|: Genomic|genomic|JJ DNA|dna|NN was|be|VBD removed|remove|VBN with|with|IN TURBO|TURBO|NNP DNAse|dnase|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC then|then|RB total|total|JJ RNA|rna|NN was|be|VBD run|run|VBN over|over|IN two|two|CD MEGAClear|megaclear|NN columns|column|NNS -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- to|to|TO deplete|deplete|VB tRNAs|trna|NNS and|and|CC 5S|5s|NN rRNA|rrna|NN .|.|. In|in|IN between|between|IN the|the|DT two|two|CD column|column|NN purifications|purification|NNS ,|,|, a|a|DT second|second|JJ DNAse|dnase|NN digestion|digestion|NN was|be|VBD performed|perform|VBN -LRB-|-lrb-|-LRB- Baseline-ZERO|baseline-zero|JJ Epicenter|epicenter|NN -RRB-|-rrb-|-RRB- .|.|. 16S|16s|NN and|and|CC 23S|23s|NN rRNA|rrna|NN were|be|VBD depleted|deplete|VBN using|use|VBG MICROBExpress|microbexpress|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- and|and|CC custom|custom|NN depletion|depletion|NN oligos|oligo|NNS -LRB-|-lrb-|-LRB- Rey|Rey|NNP et.al|et.al|NNP .|.|. 2010|2010|CD ;|;|: JBC|JBC|NNP -RRB-|-rrb-|-RRB- .|.|.
rRNA|rrna|NN reduction|reduction|NN with|with|IN EpiCentre|EpiCentre|NNP Ribo-Zero|Ribo-Zero|NNP Gram|Gram|NNP Negative|negative|JJ Ribosomal|ribosomal|JJ RNA|rna|NN reduction|reduction|NN kit|kit|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ug|ug|NN -RRB-|-rrb-|-RRB- &|&|CC TruSeq|TruSeq|NNP RNA|rna|NN Library|Library|NNP Prep|Prep|NNP
rRNA|rrna|NN was|be|VBD removed|remove|VBN from|from|IN total|total|JJ RNA|rna|NN by|by|IN using|use|VBG the|the|DT Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN removal|removal|NN kit|kit|NN .|.|. Reverse|reverse|JJ transcription|transcription|NN and|and|CC cDNA|cdna|NN amplification|amplification|NN were|be|VBD performed|perform|VBN with|with|IN the|the|DT SMART-Seq|smart-seq|NN v4|v4|NN Ultra|Ultra|NNP Low|Low|NNP Input|Input|NNP RNA|rna|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Clontech|clontech|NN -RRB-|-rrb-|-RRB- .|.|. Libraries|library|NNS were|be|VBD constructed|construct|VBN using|use|VBG the|the|DT Illumina|Illumina|NNP Nextera|Nextera|NNP XT|XT|NNP kit|kit|NN and|and|CC analyzed|analyze|VBN for|for|IN concentration|concentration|NN ,|,|, size|size|NN distribution|distribution|NN and|and|CC quantification|quantification|NN of|of|IN viable|viable|JJ sequencing|sequencing|NN templates|template|NNS via|via|IN qPCR|qpcr|NN .|.|.
R|r|NN scripts|script|NNS -LRB-|-lrb-|-LRB- Bioconductor|bioconductor|NN GenomicRanges|genomicrange|NNS -RRB-|-rrb-|-RRB- and|and|CC custom|custom|NN scripts|script|NNS were|be|VBD used|use|VBN to|to|TO calculate|calculate|VB RPKMs|rpkm|NNS .|.|. Fold-change|fold-change|NN was|be|VBD calculated|calculate|VBN as|as|IN ratio|ratio|NN of|of|IN RPKMs|rpkm|NNS after|after|IN TF|tf|NN induction|induction|NN to|to|TO control|control|VB experiment|experiment|NN .|.|.
rsd|rsd|NN _|_|CD EE|ee|NN _|_|NN 1|1|CD
rsd|rsd|NN _|_|CD EE|ee|NN _|_|NN 2|2|CD
rsd|rsd|NN _|_|NN LS|ls|NN _|_|NN 1|1|CD
rsd|rsd|NN _|_|NN LS|ls|NN _|_|NN 2|2|CD
rsd|rsd|NN _|_|CD ME|me|NN _|_|NN 1|1|CD
rsd|rsd|NN _|_|CD ME|me|NN _|_|NN 2|2|CD
rsd|rsd|NN _|_|CD S|s|NN _|_|NN 1|1|CD
rsd|rsd|NN _|_|CD S|s|NN _|_|NN 2|2|CD
rsdssrS|rsdssrs|NN _|_|CD EE|ee|NN _|_|NN 1|1|CD
rsdssrS|rsdssrs|NN _|_|CD EE|ee|NN _|_|NN 2|2|CD
rsdssrS|rsdssrs|NN _|_|NN LS|ls|NN _|_|NN 1|1|CD
rsdssrS|rsdssrs|NN _|_|NN LS|ls|NN _|_|NN 2|2|CD
rsdssrS|rsdssrs|NN _|_|CD ME|me|NN _|_|NN 1|1|CD
rsdssrS|rsdssrs|NN _|_|CD ME|me|NN _|_|NN 2|2|CD
rsdssrS|rsdssrs|NN _|_|CD S|s|NN _|_|NN 1|1|CD
rsdssrS|rsdssrs|NN _|_|CD S|s|NN _|_|NN 2|2|CD
rsdssrS|rsdssrs|NN _|_|CD TS|ts|NN _|_|NN 1|1|CD
rsdssrS|rsdssrs|NN _|_|CD TS|ts|NN _|_|NN 2|2|CD
rsd|rsd|NN _|_|CD TS|ts|NN _|_|NN 1|1|CD
rsd|rsd|NN _|_|CD TS|ts|NN _|_|NN 2|2|CD
R.|R.|NNP sphaeroides|sphaeroide|NNS was|be|VBD phototrophically|phototrophically|RB grown|grow|VBN to|to|TO mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- 100-150|100-150|CD kletts|klett|NNS -RRB-|-rrb-|-RRB- in|in|IN Sistrom|Sistrom|NNP 's|'s|POS minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- Sistrom|sistrom|NN ,|,|, W.|W.|NNP 1960|1960|CD .|.|. Journal|Journal|NNP of|of|IN General|General|NNP Microbiology|Microbiology|NNP .|.|. 22:778-785|22:778-785|NN -RRB-|-rrb-|-RRB- amended|amend|VBN with|with|IN 33.9|33.9|CD mM|mm|NN succinate|succinate|NN .|.|.
rstB|rstb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
rstB|rstb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
rstB|rstb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
rstB|rstb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
ruvA|ruva|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r1|r1|NN
ruvA|ruva|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r2|r2|NN
ruvA|ruva|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
ruvA|ruva|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
ruvC|ruvc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
ruvC|ruvc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
ruvC|ruvc|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
ruvC|ruvc|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
∆|∆|CD ryhB|ryhb|NN Aerobic|aerobic|JJ
∆|∆|CD ryhB|ryhb|NN Anaerobic|anaerobic|JJ
RyhB-minus_cDNA_Aerobic_WIG.txt|ryhb-minus_cdna_aerobic_wig.txt|NN
RyhB-minus_cDNA_Anaerobic_WIG.txt|ryhb-minus_cdna_anaerobic_wig.txt|NN
s70|s70|NN ChIP|chip|NN DNA|dna|NN from|from|IN DdksA|ddksa|NN cells|cell|NNS
s70|s70|NN ChIP|chip|NN DNA|dna|NN from|from|IN starved|starve|VBN DdksA|ddksa|NN cells|cell|NNS
s70|s70|NN ChIP|chip|NN DNA|dna|NN from|from|IN starved|starve|VBN wt|wt|JJ cells|cell|NNS
s70|s70|NN ChIP|chip|NN DNA|dna|NN from|from|IN wt|wt|JJ cells|cell|NNS
s70|s70|NN _|_|CD DdksA|ddksa|NN _|_|CD SHX|SHX|NNP _|_|CD rep1|rep1|NN
s70|s70|NN _|_|CD DdksA|ddksa|NN _|_|CD SHX|SHX|NNP _|_|CD rep2|rep2|NN
s70|s70|NN _|_|CD DdksA|ddksa|NN _|_|NN untreated|untreated|JJ _|_|NN rep1|rep1|NN
s70|s70|NN _|_|CD DdksA|ddksa|NN _|_|NN untreated|untreated|JJ _|_|NN rep2|rep2|NN
s70|s70|NN _|_|CD wt|wt|JJ _|_|NN SHX|shx|NN _|_|CD rep1|rep1|NN
s70|s70|NN _|_|CD wt|wt|JJ _|_|NN SHX|shx|NN _|_|CD rep2|rep2|NN
s70|s70|NN _|_|CD wt|wt|JJ _|_|NN untreated|untreated|JJ _|_|NN rep1|rep1|NN
s70|s70|NN _|_|CD wt|wt|JJ _|_|NN untreated|untreated|JJ _|_|NN rep2|rep2|NN
Sakai|Sakai|NNP grown|grow|VBN to|to|TO OD600|od600|NN =|=|JJ 1.8|1.8|CD in|in|IN DMEM-MOPS|dmem-mops|NN 0.4|0.4|CD %|%|NN glucose|glucose|NN at|at|IN a|a|DT 10:1|10:1|CD flask-to-media|flask-to-media|NN volume|volume|NN in|in|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN -LRB-|-lrb-|-LRB- 180|180|CD RPM|rpm|NN -RRB-|-rrb-|-RRB- .|.|.
Sakai|Sakai|NNP -LRB-|-lrb-|-LRB- O157|O157|NNP :|:|: H7|h7|NN -RRB-|-rrb-|-RRB-
same|same|JJ cultures|culture|NNS used|use|VBN for|for|IN the|the|DT viability|viability|NN assay|assay|NN .|.|. For|for|IN each|each|DT experimental|experimental|JJ condition|condition|NN ,|,|, 15|15|CD aliquots|aliquot|NNS of|of|IN
SAM|SAM|NNP files|file|VBZ thus|thus|RB obtained|obtain|VBN were|be|VBD converted|convert|VBN to|to|TO BAM|BAM|NNP files|file|NNS using|use|VBG samtools|samtool|NNS view|view|VBP command|command|NN
Sample|sample|NN
Sample|sample|NN 1|1|CD
sample|sample|NN :|:|: 1A|1a|NN
Sample|sample|NN 2|2|CD
sample|sample|NN :|:|: 23S|23s|NN
sample|sample|NN :|:|: 2A|2a|NN
sample|sample|NN :|:|: 32D|32d|NN
sample|sample|NN :|:|: 33D|33d|NN
sample|sample|NN :|:|: 35B|35b|NN
sample|sample|NN :|:|: 3A|3a|NN
sample|sample|NN :|:|: 4A|4a|NN
sample|sample|NN :|:|: 5A|5a|NN
sample|sample|NN :|:|: #|#|# 6|6|CD
sample|sample|NN :|:|: 6A|6a|NN
Sample|sample|NN 79|79|CD
sample|sample|NN :|:|: 9A|9a|NN
sample|sample|NN :|:|: Bio-1|bio-1|NN
sample|sample|NN :|:|: Bio-2|bio-2|NN
sample|sample|NN :|:|: Bio-3|bio-3|NN
sample|sample|NN :|:|: Bio-4|bio-4|NN
sample|sample|NN :|:|: Biopile|Biopile|NNP control|control|NN
sample|sample|NN :|:|: BZ-NT|bz-nt|JJ
Sample|sample|NN collection|collection|NN from|from|IN M9|m9|NN medium|medium|NN
sample|sample|NN :|:|: Composite|Composite|NNP A|A|NNP
sample|sample|NN :|:|: Composite|Composite|NNP B|B|NNP
sample|sample|NN id|id|NN :|:|: 1a|1a|NN
sample|sample|NN id|id|NN :|:|: 1b|1b|CD
sample|sample|NN id|id|NN :|:|: 1c|1c|NN
sample|sample|NN id|id|NN :|:|: 1d|1d|CD
sample|sample|NN id|id|NN :|:|: 2a|2a|NN
sample|sample|NN id|id|NN :|:|: 2b|2b|JJ
sample|sample|NN id|id|NN :|:|: 2c|2c|JJ
sample|sample|NN id|id|NN :|:|: 2d|2d|JJ
sample|sample|NN id|id|NN :|:|: 3a|3a|NN
sample|sample|NN id|id|NN :|:|: 3b|3b|CD
sample|sample|NN id|id|NN :|:|: 3c|3c|NN
sample|sample|NN id|id|NN :|:|: 3d|3d|JJ
sample|sample|NN id|id|NN :|:|: 4a|4a|NN
sample|sample|NN id|id|NN :|:|: 4b|4b|NN
sample|sample|NN id|id|NN :|:|: 4c|4c|NN
sample|sample|NN id|id|NN :|:|: 4d|4d|NN
sample|sample|NN id|id|NN :|:|: 5a|5a|NN
sample|sample|NN id|id|NN :|:|: 5b|5b|NN
sample|sample|NN id|id|NN :|:|: 5c|5c|NN
sample|sample|NN id|id|NN :|:|: 5d|5d|JJ
sample|sample|NN id|id|NN :|:|: 6a|6a|FW
sample|sample|NN id|id|NN :|:|: 6b|6b|JJ
sample|sample|NN id|id|NN :|:|: 6c|6c|JJ
sample|sample|NN id|id|NN :|:|: 6d|6d|JJ
sample|sample|NN id|id|NN :|:|: 7a|7a|NN
sample|sample|NN id|id|NN :|:|: 7b|7b|CD
sample|sample|NN id|id|NN :|:|: 7c|7c|CD
sample|sample|NN id|id|NN :|:|: 7d|7d|CD
sample|sample|NN :|:|: LC-1|lc-1|NN
sample|sample|NN :|:|: NC|nc|NN
sample|sample|NN :|:|: NF-NT|nf-nt|JJ
sample|sample|NN :|:|: Polygons|polygon|NNS
sample|sample|NN port|port|NN :|:|: PFR|pfr|NN P1|p1|NN
sample|sample|NN port|port|NN :|:|: PFR|pfr|NN P3|p3|NN
sample|sample|NN port|port|NN :|:|: PFR|pfr|NN P5|p5|NN
sample|sample|NN port|port|NN :|:|: STR|str|NN
Samples|sample|NNS -LRB-|-lrb-|-LRB- 200-ml|200-ml|JJ -RRB-|-rrb-|-RRB- of|of|IN the|the|DT above|above|JJ cultures|culture|NNS for|for|IN each|each|DT strain|strain|NN were|be|VBD split|split|VBN into|into|IN two|two|CD aliquots|aliquot|NNS -LRB-|-lrb-|-LRB- each|each|DT 100|100|CD ml|ml|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC the|the|DT aliquots|aliquot|NNS were|be|VBD then|then|RB incubated|incubate|VBN at|at|IN 30|30|CD °C|°c|NN or|or|CC 42|42|CD °C|°c|NN for|for|IN another|another|DT 60|60|CD min|min|NN .|.|.
Samples|sample|NNS -LRB-|-lrb-|-LRB- 30|30|CD ml|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD harvested|harvest|VBN directly|directly|RB into|into|IN cold|cold|JJ phenol|phenol|NN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- 187|187|CD µl|µl|NN phenol|phenol|NN ,|,|, 3.56|3.56|CD ml|ml|NN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- to|to|TO stabilize|stabilize|VB RNA|rna|NN ,|,|, and|and|CC total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN as|as|IN recommended|recommend|VBN by|by|IN suppliers|supplier|NNS .|.|. RNA|rna|NN was|be|VBD quantified|quantify|VBN using|use|VBG a|a|DT BioPhotometer|biophotometer|NN -LRB-|-lrb-|-LRB- Eppendorf|eppendorf|NN -RRB-|-rrb-|-RRB- .|.|.
Samples|sample|NNS 931|931|CD ,|,|, 933|933|CD ,|,|, 935|935|CD and|and|CC 937|937|CD were|be|VBD aligned|align|VBN with|with|IN bowtie|bowtie|NN -LRB-|-lrb-|-LRB- V|v|NN 1.1.2|1.1.2|CD -RRB-|-rrb-|-RRB- with|with|IN parameters|parameter|NNS --|--|: wrapper|wrapper|NN basic-0|basic-0|NN -|-|: q|q|SYM -|-|: m|m|NN 1|1|CD -|-|: l|l|NN 55|55|CD -|-|: k|k|NN 1|1|CD -5|-5|CD 3|3|CD -3|-3|CD 40|40|CD --|--|: best|best|JJS -|-|: S|s|NN -|-|: p|p|NN 24|24|CD ,|,|, and|and|CC samples|sample|NNS 1311|1311|CD ,|,|, 1314|1314|CD ,|,|, 1317|1317|CD and|and|CC 1320|1320|CD were|be|VBD aligned|align|VBN with|with|IN bowtie|bowtie|NN -LRB-|-lrb-|-LRB- V|v|NN 1.1.2|1.1.2|CD -RRB-|-rrb-|-RRB- with|with|IN paramters|paramter|NNS --|--|: wrapper|wrapper|NN basic-0|basic-0|NN -|-|: q|q|SYM -|-|: m|m|NN 1|1|CD -|-|: v|v|LS 2|2|CD --|--|: best|best|JJS -|-|: p|p|NN 24|24|CD -|-|: S|s|NN
Samples|sample|NNS for|for|IN microarray|microarray|NN analyses|analysis|NNS were|be|VBD taken|take|VBN before|before|IN ciprofloxacin|ciprofloxacin|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- t0|t0|NN -RRB-|-rrb-|-RRB- and|and|CC then|then|RB at|at|IN 1|1|CD hour|hour|NN post-treatment|post-treatment|JJ -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB- .|.|. Cell|cell|NN concentration|concentration|NN was|be|VBD adjusted|adjust|VBN to|to|TO 109|109|CD cells/ml|cells/ml|NNS and|and|CC cultures|culture|NNS were|be|VBD treated|treat|VBN with|with|IN ciprofloxacin|ciprofloxacin|NN in|in|IN Erlenmeyer|Erlenmeyer|NNP flasks|flask|NNS using|use|VBG 20|20|CD ml|ml|NN fresh|fresh|JJ LB|lb|NN .|.|. ~|~|NN 109|109|CD cells|cell|NNS were|be|VBD taken|take|VBN at|at|IN each|each|DT timepoint|timepoint|NN as|as|IN samples|sample|NNS for|for|IN RNA|rna|NN isolation|isolation|NN .|.|. In|in|IN order|order|NN to|to|TO stabilize|stabilize|VB RNA|rna|NN ,|,|, RNA|rna|NN Bacteria|bacterium|NNS Protect|protect|VB Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT samples|sample|NNS according|accord|VBG to|to|TO the|the|DT instructions|instruction|NNS of|of|IN the|the|DT manufacturer|manufacturer|NN and|and|CC then|then|RB samples|sample|NNS were|be|VBD stored|store|VBN overnight|overnight|RB at|at|IN -80|-80|CD °C|°c|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN by|by|IN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Sample|sample|VB concentration|concentration|NN was|be|VBD estimated|estimate|VBN using|use|VBG the|the|DT NanoDrop|NanoDrop|NNP 1000|1000|CD -LRB-|-lrb-|-LRB- Thermoscientific|thermoscientific|NN -RRB-|-rrb-|-RRB- spectrophotometer|spectrophotometer|NN .|.|.
Samples|sample|NNS for|for|IN microarray|microarray|NN analysis|analysis|NN were|be|VBD collected|collect|VBN as|as|IN described|describe|VBN earlier|earlier|JJR -LSB-|-lsb-|-LRB- 1|1|CD -RSB-|-rsb-|-RRB- ,|,|, -LRB-|-lrb-|-LRB- Samples|sample|NNS were|be|VBD shortly|shortly|RB mixed|mix|VBN by|by|IN vortexing|vortex|VBG ,|,|, divided|divide|VBN in|in|IN 0.5|0.5|CD mL|ml|NN aliquots|aliquot|NNS and|and|CC 1|1|CD .|.|. centrifuged|centrifuge|VBN for|for|IN 3|3|CD min|min|NN at|at|IN 16,100|16,100|CD ×|×|CD g|g|NN and|and|CC +4|+4|NN °C|°c|NN .|.|. The|the|DT pellets|pellet|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 250|250|CD µL|µl|NN of|of|IN RNALater|rnalater|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN until|until|IN analysis|analysis|NN .|.|. RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT total|total|JJ RNA|rna|NN kit|kit|NN -LRB-|-lrb-|-LRB- A&A|A&A|NNP Biotechnology|Biotechnology|NNP ,|,|, Poland|Poland|NNP -RRB-|-rrb-|-RRB- .|.|.
Samples|sample|NNS for|for|IN transcriptome|transcriptome|NN analysis|analysis|NN were|be|VBD taken|take|VBN from|from|IN exponentially|exponentially|RB growing|grow|VBG cells|cell|NNS .|.|. From|from|IN the|the|DT cells|cell|NNS treated|treat|VBN by|by|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- ,|,|, total|total|JJ RNA|rna|NN samples|sample|NNS were|be|VBD isolated|isolate|VBN using|use|VBG RNeasy|rneasy|JJ columns|column|NNS -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- in|in|IN accordance|accordance|NN with|with|IN manufacturer|manufacturer|NN 's|'s|POS instruction|instruction|NN .|.|.
Samples|sample|NNS of|of|IN ~|~|NN 7.2|7.2|CD ml|ml|NN bacterial|bacterial|JJ culture|culture|NN were|be|VBD mixed|mix|VBN with|with|IN 0.8|0.8|CD ml|ml|NN stop|stop|NN solution|solution|NN ,|,|, pelleted|pelleted|JJ and|and|CC total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. DNase|dnase|NN treatment|treatment|NN was|be|VBD done|do|VBN twice|twice|RB with|with|IN RQ1|rq1|NN DNase|dnase|NN -LRB-|-lrb-|-LRB- Promega|promega|NN -RRB-|-rrb-|-RRB- to|to|TO remove|remove|VB genomic|genomic|JJ DNA|dna|NN .|.|. cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD done|do|VBN according|accord|VBG to|to|TO the|the|DT GeneChip|GeneChip|NNP ®|®|NNP Expression|expression|NN Analysis|analysis|NN Technical|Technical|NNP Manual|Manual|NNP of|of|IN Affymetrix|Affymetrix|NNP using|use|VBG M-MLV|m-mlv|NN reverse|reverse|JJ transcriptase|transcriptase|NN -LRB-|-lrb-|-LRB- Promega|promega|NN -RRB-|-rrb-|-RRB- ,|,|, without|without|IN DTT|dtt|NN addition|addition|NN .|.|. 13|13|CD µl|µl|NN of|of|IN EB|EB|NNP buffer|buffer|NN were|be|VBD used|use|VBN for|for|IN elution|elution|NN of|of|IN cDNA|cdna|NN after|after|IN its|its|PRP$ clean-up|clean-up|JJ with|with|IN the|the|DT MiniElute|MiniElute|NNP CR|cr|NN purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. cDNA|cdna|NN fragmentation|fragmentation|NN was|be|VBD done|do|VBN in|in|IN a|a|DT 20-µl|20-µl|JJ reaction|reaction|NN containing|contain|VBG 3.5|3.5|CD µg|µg|NN cDNA|cdna|NN ,|,|, 2|2|CD µl|µl|NN 10x|10x|CD One|one|CD Phor-All|phor-all|NN buffer|buffer|NN ,|,|, 2|2|CD µl|µl|NN DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- diluted|dilute|VBN to|to|TO 0.2|0.2|CD U|U|NNP /|/|: µl|µl|NN ,|,|, Amersham|Amersham|NNP Pharmacia|Pharmacia|NNP Biotech|Biotech|NNP -RRB-|-rrb-|-RRB- in|in|IN nuclease-free|nuclease-free|JJ water|water|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 4|4|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN ,|,|, DNase|dnase|NN I|i|CD was|be|VBD heat|heat|NN inactivated|inactivate|VBN at|at|IN 98|98|CD °C|°c|NN for|for|IN 10|10|CD min|min|NN .|.|.
Samples|sample|NNS of|of|IN magnetic|magnetic|JJ field-treated|field-treated|JJ or|or|CC sham-treated|sham-treated|JJ cells|cell|NNS were|be|VBD withdrawn|withdraw|VBN as|as|IN fast|fast|JJ as|as|IN possible|possible|JJ from|from|IN the|the|DT bioreactor|bioreactor|NN -LRB-|-lrb-|-LRB- not|not|RB later|later|RB than|than|IN 3|3|CD min|min|NN -RRB-|-rrb-|-RRB- after|after|IN the|the|DT specified|specify|VBN treatement|treatement|NN period|period|NN .|.|. Samples|sample|NNS taken|take|VBN during|during|IN intermittent|intermittent|JJ exposure|exposure|NN were|be|VBD withdrawn|withdraw|VBN in|in|IN the|the|DT 4|4|CD min|min|NN exposure|exposure|NN break|break|NN .|.|. Unexposed|unexposed|JJ samples|sample|NNS were|be|VBD withdrawn|withdraw|VBN as|as|IN fast|fast|JJ as|as|IN possible|possible|JJ during|during|IN steady-state|steady-state|JJ conditions|condition|NNS in|in|IN the|the|DT chemostat|chemostat|NN .|.|. In|in|IN the|the|DT response|response|NN control|control|NN experiment|experiment|NN ,|,|, samples|sample|NNS were|be|VBD withdrawn|withdraw|VBN 10|10|CD min|min|NN after|after|IN addition|addition|NN of|of|IN 1|1|CD mM|mm|NN H2O2|h2o2|NN -LRB-|-lrb-|-LRB- treated|treated|JJ culture|culture|NN -RRB-|-rrb-|-RRB- or|or|CC the|the|DT equivalent|equivalent|JJ water|water|NN volume|volume|NN -LRB-|-lrb-|-LRB- reference|reference|NN culture|culture|NN -RRB-|-rrb-|-RRB- .|.|.
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09049|.09049|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09050|.09050|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09051|.09051|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09052|.09052|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09053|.09053|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09054|.09054|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09055|.09055|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09056|.09056|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09057|.09057|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09058|.09058|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09059|.09059|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09620|.09620|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09621|.09621|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09622|.09622|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09623|.09623|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09624|.09624|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 10-gut|10-gut|JJ bacteria|bacterium|NNS .|.|. Mouse|mouse|NN was|be|VBD fed|feed|VBN Harlan|Harlan|NNP Teklad|Teklad|NNP Diet|Diet|NNP TD|TD|NNP .09625|.09625|CD
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 8-gut|8-gut|JJ bacteria|bacterium|NNS
sample|sample|NN source|source|NN :|:|: Fecal|fecal|JJ pellet|pellet|NN from|from|IN a|a|DT mouse|mouse|NN -LRB-|-lrb-|-LRB- c57Bl6|c57bl6|NN -RRB-|-rrb-|-RRB- colonized|colonize|VBN with|with|IN 9-gut|9-gut|JJ bacteria|bacterium|NNS
Samples|sample|NNS were|be|VBD aligned|align|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW K|k|NN 12|12|CD MG1655|mg1655|NN reference|reference|NN sequence|sequence|NN -LRB-|-lrb-|-LRB- version|version|NN NC000913|nc000913|NN .2|.2|NN -RRB-|-rrb-|-RRB- ,|,|, using|use|VBG BWA|bwa|NN -LRB-|-lrb-|-LRB- version|version|NN 0.5|0.5|CD -RRB-|-rrb-|-RRB- WITH|with|IN -|-|: q|q|NN 30|30|CD parameter|parameter|NN for|for|IN trimming|trim|VBG of|of|IN reads|read|VBZ below|below|IN PHRED|PHRED|NNP quality|quality|NN score|score|NN of|of|IN 30|30|CD .|.|.
Samples|sample|NNS were|be|VBD background|background|NN corrected|correct|VBN using|use|VBG the|the|DT normexp|normexp|NN -LRB-|-lrb-|-LRB- -RRB-|-rrb-|-RRB- function|function|NN in|in|IN the|the|DT Limma|Limma|NNP package|package|NN in|in|IN R|r|NN .|.|. This|this|DT was|be|VBD followed|follow|VBN by|by|IN quantile|quantile|NN normalization|normalization|NN and|and|CC log2|log2|NN transformation|transformation|NN .|.|.
Samples|sample|NNS were|be|VBD diluted|dilute|VBN 1:1|1:1|CD in|in|IN RNA|rna|NN Protect|protect|VB -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- to|to|TO inhibit|inhibit|VB RNase|rnase|NN activity|activity|NN and|and|CC then|then|RB centrifuged|centrifuge|VBD -LRB-|-lrb-|-LRB- 5000|5000|CD x|x|CC g|g|NN ,|,|, 10|10|CD min|min|NN -RRB-|-rrb-|-RRB- .|.|. Pellets|pellet|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN TE/lysozyme|te/lysozyme|NN -LRB-|-lrb-|-LRB- 10|10|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN ,|,|, 0.5|0.5|CD %|%|NN SDS|sds|NN ,|,|, pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- with|with|IN added|add|VBN proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- 1.5|1.5|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNeasy|RNeasy|NNP kit|kit|NN according|accord|VBG to|to|TO manufacturer|manufacturer|NN instructions|instruction|NNS with|with|IN slight|slight|JJ modification|modification|NN .|.|. Before|before|IN centrifugation|centrifugation|NN ,|,|, β-mercaptoethanol|β-mercaptoethanol|NN was|be|VBD added|add|VBN to|to|TO RNeasy|RNeasy|NNP kit|kit|NN buffer|buffer|NN RLT|rlt|NN -LRB-|-lrb-|-LRB- 10|10|CD %|%|NN v/v|v/v|NN -RRB-|-rrb-|-RRB- .|.|. Additionally|additionally|RB ,|,|, during|during|IN the|the|DT wash|wash|NN step|step|NN RNase-free|rnase-free|JJ DNase|dnase|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- was|be|VBD diluted|dilute|VBN in|in|IN RNeasy|RNeasy|NNP kit|kit|NN buffer|buffer|NN RDD|rdd|NN -LRB-|-lrb-|-LRB- 310|310|CD Kunitz|Kunitz|NNP units/mL|units/ml|NN -RRB-|-rrb-|-RRB- ,|,|, added|add|VBD to|to|TO the|the|DT purification|purification|NN column|column|NN ,|,|, and|and|CC incubated|incubate|VBN for|for|IN 15|15|CD minutes|minute|NNS at|at|IN room|room|NN temperature|temperature|NN -LRB-|-lrb-|-LRB- RT|rt|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN isolation|isolation|NN ,|,|, spectrophotometric|spectrophotometric|JJ NanoDrop|NanoDrop|NNP -LRB-|-lrb-|-LRB- NanoDrop|NanoDrop|NNP 1000|1000|CD v3|v3|NN .8.1|.8.1|CD ;|;|: Thermo|Thermo|NNP Fisher|Fisher|NNP -RRB-|-rrb-|-RRB- curves|curve|NNS were|be|VBD obtained|obtain|VBN for|for|IN each|each|DT total|total|JJ RNA|rna|NN sample|sample|NN and|and|CC verified|verify|VBN for|for|IN purity|purity|NN ,|,|, as|as|IN defined|define|VBN by|by|IN absorbance|absorbance|NN ratios|ratio|NNS at|at|IN 260/280|260/280|CD nm|nm|NN and|and|CC 260/230|260/230|CD nm|nm|NN .|.|. Total|total|JJ RNA|rna|NN samples|sample|NNS were|be|VBD sent|send|VBN to|to|TO Oregon|Oregon|NNP State|State|NNP University|University|NNP 's|'s|POS Center|Center|NNP for|for|IN Genome|Genome|NNP Research|Research|NNP and|and|CC Biocomputing|Biocomputing|NNP .|.|. RNA|rna|NN integrity|integrity|NN -LRB-|-lrb-|-LRB- RIN|rin|NN -RRB-|-rrb-|-RRB- measurements|measurement|NNS were|be|VBD taken|take|VBN using|use|VBG an|a|DT Agilent|Agilent|NNP Bioanalyzer|Bioanalyzer|NNP ,|,|, resulting|result|VBG in|in|IN RIN|RIN|NNP scores|score|NNS of|of|IN 10|10|CD ,|,|, out|out|IN of|of|IN a|a|DT possible|possible|JJ 10|10|CD ,|,|, for|for|IN each|each|DT sample|sample|NN .|.|. Ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD depleted|deplete|VBN using|use|VBG the|the|DT RiboZero|RiboZero|NNP rRNA|rrna|NN removal|removal|NN kit|kit|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS ,|,|, Eugene|Eugene|NNP ,|,|, OR|or|NN -RRB-|-rrb-|-RRB- .|.|.
samples|sample|NNS were|be|VBD grown|grow|VBN aerobically|aerobically|RB in|in|IN rich|rich|JJ media|media|NNS
Samples|sample|NNS were|be|VBD grown|grow|VBN anaerobically|anaerobically|RB in|in|IN MOPS|mop|NNS minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN casamino|casamino|NN acids|acid|NNS using|use|VBG glucose|glucose|NN as|as|IN the|the|DT carbon|carbon|NN source|source|NN .|.|. 20mM|20mm|NN nitrate|nitrate|NN was|be|VBD added|add|VBN to|to|TO -LRB-|-lrb-|-LRB- +|+|CC NO|no|NN -RRB-|-rrb-|-RRB- cultures|culture|NNS for|for|IN inducing|induce|VBG nitrosative|nitrosative|JJ stress|stress|NN .|.|.
Samples|sample|NNS were|be|VBD grown|grow|VBN to|to|TO mid|mid|JJ exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD|od|NN approx|approx|RB 0.5|0.5|CD -RRB-|-rrb-|-RRB- .|.|. Cultures|culture|NNS were|be|VBD then|then|RB harvested|harvest|VBN with|with|IN rapid|rapid|JJ filtration|filtration|NN and|and|CC resuspended|resuspend|VBN in|in|IN RNALater|rnalater|NN to|to|TO stop|stop|VB RNA|rna|NN degradation|degradation|NN .|.|. The|the|DT Zymo|Zymo|NNP Quick-RNA|quick-rna|NN miniprep|miniprep|NN kit|kit|NN was|be|VBD used|use|VBN to|to|TO extract|extract|VB pure|pure|JJ RNA|rna|NN for|for|IN subsequent|subsequent|JJ analysis|analysis|NN
Samples|sample|NNS were|be|VBD grown|grow|VBN to|to|TO mid|mid|JJ exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD|od|NN approx|approx|RB 0.5|0.5|CD -RRB-|-rrb-|-RRB- .|.|. Cultures|culture|NNS were|be|VBD then|then|RB quickly|quickly|RB chilled|chill|VBN to|to|TO ≤|≤|VB 4|4|CD ºC|ºc|NN on|on|IN dry|dry|JJ ice/isopropanol|ice/isopropanol|NN bath|bath|NN ,|,|, harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 4470|4470|CD ×|×|CD g|g|NN -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD ºC|ºc|NN and|and|CC resuspended|resuspend|VBN in|in|IN RNALater|rnalater|NN to|to|TO stop|stop|VB RNA|rna|NN degradation|degradation|NN .|.|. The|the|DT Zymo|Zymo|NNP Quick-RNA|quick-rna|NN miniprep|miniprep|NN kit|kit|NN was|be|VBD used|use|VBN to|to|TO extract|extract|VB pure|pure|JJ RNA|rna|NN for|for|IN subsequent|subsequent|JJ analysis|analysis|NN
Samples|sample|NNS were|be|VBD mixed|mixed|JJ ,|,|, incubated|incubate|VBN on|on|IN ice|ice|NN for|for|IN 10|10|CD min|min|NN after|after|IN which|which|WDT cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 4150|4150|CD rpm|rpm|NN at|at|IN 4|4|CD ˚C|˚c|NN for|for|IN 10|10|CD min|min|NN .|.|. Cell|cell|NN pellets|pellet|NNS were|be|VBD snap|snap|JJ frozen|freeze|VBN in|in|IN an|a|DT ethanol/dry|ethanol/dry|NN ice|ice|NN slurry|slurry|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN until|until|IN total|total|JJ RNA|rna|NN could|could|MD be|be|VB extracted|extract|VBN .|.|.
Samples|sample|NNS were|be|VBD sent|send|VBN to|to|TO the|the|DT International|International|NNP Space|Space|NNP Station|Station|NNP at|at|IN 4C|4c|NN in|in|IN FPAs|fpa|NNS ,|,|, as|as|IN described|describe|VBN above|above|IN .|.|. Temperature|temperature|NN was|be|VBD increased|increase|VBN to|to|TO 37C|37c|NN and|and|CC 23|23|CD hours|hour|NNS later|later|RB ,|,|, the|the|DT experiment|experiment|NN was|be|VBD started|start|VBN by|by|IN introducing|introduce|VBG the|the|DT inoculum|inoculum|NN -LRB-|-lrb-|-LRB- E.|e.|FW coli|coli|FW ATCC|atcc|NN 4157|4157|CD -RRB-|-rrb-|-RRB- into|into|IN the|the|DT growth|growth|NN medium|medium|NN -LRB-|-lrb-|-LRB- Medium|medium|NN E|e|NN as|as|IN described|describe|VBN in|in|IN Vogel|Vogel|NNP &|&|CC Bonner|Bonner|NNP -LRB-|-lrb-|-LRB- 1956|1956|CD -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN 5|5|CD g/L|g/l|NN glucose|glucose|NN -RRB-|-rrb-|-RRB- ,|,|, yielding|yield|VBG 3.25|3.25|CD mL|ml|NN of|of|IN a|a|DT culture|culture|NN with|with|IN a|a|DT starting|start|VBG cell|cell|NN concentration|concentration|NN of|of|IN 1.22|1.22|CD e6|e6|NN cell/mL|cell/ml|NN .|.|.
Samples|sample|NNS were|be|VBD treated|treat|VBN with|with|IN Prokaryotic|Prokaryotic|NNP Target|target|NN Preparation|preparation|NN protocol|protocol|NN -LRB-|-lrb-|-LRB- GeneChip|genechip|NN Expression|expression|NN Analysis|analysis|NN Technical|Technical|NNP Manual|Manual|NNP -RRB-|-rrb-|-RRB- .|.|.
Samples|sample|NNS were|be|VBD treated|treat|VBN with|with|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN until|until|IN preparation|preparation|NN .|.|. rRNA|rrna|NN was|be|VBD removed|remove|VBN using|use|VBG RiboZero|RiboZero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, San|San|NNP Diego|Diego|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC sequencing|sequencing|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN with|with|IN TruSeq|truseq|NN ™|™|CD RNA|rna|NN Sample|sample|NN Preparation|preparation|NN Kitv2|kitv2|NN -LRB-|-lrb-|-LRB- Illumina|illumina|NN -RRB-|-rrb-|-RRB-
Samples|sample|NNS were|be|VBD used|use|VBN for|for|IN on-bead|on-bead|JJ enzymatic|enzymatic|JJ reactions|reaction|NNS of|of|IN the|the|DT ChIP-exo|ChIP-exo|NNP procedure|procedure|NN and|and|CC Illumina|Illumina|NNP Tru-seq|tru-seq|JJ sequencing|sequencing|NN libraries|library|NNS were|be|VBD construction|construction|NN as|as|IN described|describe|VBN in|in|IN Rhee|Rhee|NNP and|and|CC Pugh|Pugh|NNP ,|,|, 2012|2012|CD
sample|sample|NN type|type|NN :|:|: AT1|at1|NN digested|digest|VBD total|total|JJ RNA|rna|NN
sample|sample|NN type|type|NN :|:|: cDNA|cdna|NN produced|produce|VBN by|by|IN RT|rt|NN of|of|IN RNA|rna|NN deriving|derive|VBG from|from|IN vitro|vitro|FW transcription|transcription|NN ,|,|, with|with|IN RNA|rna|NN polymerase|polymerase|NN E|e|NN σ70|σ70|NN ,|,|, of|of|IN 2|2|CD ug|ug|NN of|of|IN genomic|genomic|JJ DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN digested|digest|VBN with|with|IN EcoRI|ecori|NN
sample|sample|NN type|type|NN :|:|: cDNA|cdna|NN produced|produce|VBN by|by|IN RT|rt|NN of|of|IN RNA|rna|NN deriving|derive|VBG from|from|IN vitro|vitro|FW transcription|transcription|NN ,|,|, with|with|IN RNA|rna|NN polymerase|polymerase|NN E|e|NN σS|σs|NN ,|,|, of|of|IN 2|2|CD ug|ug|NN of|of|IN genomic|genomic|JJ DNA|dna|NN from|from|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN digested|digest|VBN with|with|IN EcoRI|ecori|NN
sample|sample|NN type|type|NN :|:|: control|control|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 100|100|CD μg/ml|μg/ml|NN NA|na|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 10|10|CD μg/ml|μg/ml|NN NA|na|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS without|without|IN treatment|treatment|NN .|.|.
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEF|mazef|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 100|100|CD μg/ml|μg/ml|NN NA|na|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEF|mazef|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 10|10|CD μg/ml|μg/ml|NN NA|na|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEF|mazef|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS without|without|IN treatment|treatment|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEFlexA3|mazeflexa3|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 100|100|CD μg/ml|μg/ml|NN NA|na|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEFlexA3|mazeflexa3|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN 10|10|CD μg/ml|μg/ml|NN NA|na|NN
sample|sample|NN type|type|NN :|:|: E.|e.|FW coli|coli|FW strain|strain|NN MC4100relA|mc4100rela|NN +|+|CC ∆|∆|SYM mazEFlexA3|mazeflexa3|NN in|in|IN mid|mid|JJ log|log|NN phase|phase|NN incubated|incubate|VBN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS without|without|IN treatment|treatment|NN
sample|sample|NN type|type|NN :|:|: input|input|NN control|control|NN
sample|sample|NN type|type|NN :|:|: input|input|NN DNA|dna|NN
sample|sample|NN type|type|NN :|:|: mock|mock|JJ community|community|NN -LSB-|-lsb-|-LRB- artificial|artificial|JJ bacterial|bacterial|JJ DNA|dna|NN mix|mix|NN -RSB-|-rsb-|-RRB-
sample|sample|NN type|type|NN :|:|: no|no|DT RNA|rna|NN treatment|treatment|NN
sample|sample|NN type|type|NN :|:|: plasmid|plasmid|NN pool|pool|NN
sample|sample|NN type|type|NN :|:|: ribosome|ribosome|NN protected|protect|VBD
sample|sample|NN type|type|NN :|:|: test|test|NN
sample|sample|NN type|type|NN :|:|: V1|v1|NN digested|digest|VBD total|total|JJ RNA|rna|NN
sample|sample|NN :|:|: Vegetated|vegetated|JJ
Sampling|sample|VBG by|by|IN directly|directly|RB placing|place|VBG the|the|DT culture|culture|NN sample|sample|NN into|into|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- ,|,|, following|follow|VBG short|short|JJ centrifugation|centrifugation|NN the|the|DT pellet|pellet|NN was|be|VBD stored|store|VBN at|at|IN −|−|CD 70|70|CD °C|°c|NN .|.|.
SA|SA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl1|repl1|NN
SA|SA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl2|repl2|NN
SA|SA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl3|repl3|NN
SA|SA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl4|repl4|NN
SA|SA|NNP _|_|NNP TP1|tp1|NN _|_|CD repl5|repl5|NN
SA|SA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl1|repl1|NN
SA|SA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl2|repl2|NN
SA|SA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl3|repl3|NN
SA|SA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl4|repl4|NN
SA|SA|NNP _|_|SYM TP2|tp2|NN _|_|CD repl5|repl5|NN
SA|SA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl1|repl1|NN
SA|SA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl2|repl2|NN
SA|SA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl3|repl3|NN
SA|SA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl4|repl4|NN
SA|SA|NNP _|_|SYM TP3|tp3|NN _|_|CD repl5|repl5|NN
SA|SA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl1|repl1|NN
SA|SA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl2|repl2|NN
SA|SA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl3|repl3|NN
SA|SA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl4|repl4|NN
SA|SA|NNP _|_|SYM TP4|tp4|NN _|_|CD repl5|repl5|NN
Saturated|Saturated|NNP E.|E.|NNP coli|coli|NN cultures|culture|NNS were|be|VBD diluted|dilute|VBN in|in|IN LB|lb|NN to|to|TO an|a|DT OD.of|od.of|JJ 0.05|0.05|CD OD600|od600|NN ,|,|, grown|grow|VBN at|at|IN 37|37|CD degrees|degree|NNS Celsius|Celsius|NNP
Saturated|Saturated|NNP E.|E.|NNP coli|coli|NN cultures|culture|NNS were|be|VBD diluted|dilute|VBN in|in|IN LB|LB|NNP toan|toan|NN OD.of|od.of|NN 0.05|0.05|CD OD600|od600|NN ,|,|, grown|grow|VBN at|at|IN 37|37|CD degrees|degree|NNS Celsius|Celsius|NNP
SB10|sb10|NN _|_|NN 1|1|CD
SB10|sb10|NN _|_|NN 2|2|CD
SB10|sb10|NN _|_|CD 3|3|CD
SB1|sb1|NN _|_|NN 1|1|CD
SB11|sb11|NN _|_|NN 1|1|CD
SB11|sb11|NN _|_|NN 2|2|CD
SB11|sb11|NN _|_|CD 3|3|CD
SB1|sb1|NN _|_|NN 2|2|CD
SB12|sb12|NN _|_|NN 1|1|CD
SB12|sb12|NN _|_|NN 2|2|CD
SB12|sb12|NN _|_|CD 3|3|CD
SB1|sb1|NN _|_|CD 3|3|CD
SB13|sb13|NN _|_|NN 1|1|CD
SB13|sb13|NN _|_|NN 2|2|CD
SB13|sb13|NN _|_|CD 3|3|CD
SB14|sb14|NN _|_|NN 1|1|CD
SB14|sb14|NN _|_|NN 2|2|CD
SB14|sb14|NN _|_|CD 3|3|CD
SB15|sb15|NN _|_|NN 1|1|CD
SB15|sb15|NN _|_|NN 2|2|CD
SB15|sb15|NN _|_|CD 3|3|CD
SB16|sb16|NN _|_|NN 1|1|CD
SB16|sb16|NN _|_|NN 2|2|CD
SB16|sb16|NN _|_|CD 3|3|CD
SB17|sb17|NN _|_|NN 1|1|CD
SB17|sb17|NN _|_|NN 2|2|CD
SB17|sb17|NN _|_|CD 3|3|CD
SB18|sb18|NN _|_|NN 1|1|CD
SB18|sb18|NN _|_|NN 2|2|CD
SB18|sb18|NN _|_|CD 3|3|CD
SB1|sb1|NN genomic|genomic|JJ DNA|dna|NN
SB2|sb2|NN _|_|NN 1|1|CD
SB2|sb2|NN _|_|NN 2|2|CD
SB2|sb2|NN _|_|CD 3|3|CD
SB3|sb3|NN _|_|NN 1|1|CD
SB3|sb3|NN _|_|NN 2|2|CD
SB3|sb3|NN _|_|CD 3|3|CD
SB5|sb5|NN _|_|NN 1|1|CD
SB5|sb5|NN _|_|NN 2|2|CD
SB5|sb5|NN _|_|CD 3|3|CD
SB6|sb6|NN _|_|NN 1|1|CD
SB6|sb6|NN _|_|NN 2|2|CD
SB6|sb6|NN _|_|CD 3|3|CD
SB7|sb7|NN _|_|NN 1|1|CD
SB7|sb7|NN _|_|NN 2|2|CD
SB7|sb7|NN _|_|CD 3|3|CD
SB8|sb8|NN _|_|NN 1|1|CD
SB8|sb8|NN _|_|NN 2|2|CD
SB8|sb8|NN _|_|CD 3|3|CD
SB9|sb9|NN _|_|CD 1|1|CD
SB9|sb9|NN _|_|NN 2|2|CD
SB9|sb9|NN _|_|SYM 3|3|CD
sbcB|sbcb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
sbcB|sbcb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
sbcB|sbcb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
sbcB|sbcb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
Scale|Scale|NNP data|datum|NNS set|set|VBN to|to|TO 20|20|CD million|million|CD reads|read|VBZ
Scanned|scan|VBN arrays|array|NNS were|be|VBD analyzed|analyze|VBN with|with|IN Affymetrix|Affymetrix|NNP GCOS|GCOS|NNP 1.4|1.4|CD software|software|NN to|to|TO obtain|obtain|VB Detection|detection|NN calls|call|NNS and|and|CC Expression|expression|NN values|value|NNS based|base|VBN on|on|IN MAS|MAS|NNP 5.0|5.0|CD algorithms|algorithm|NNS .|.|. All|all|DT arrays|array|NNS were|be|VBD scaled|scale|VBN to|to|TO a|a|DT target|target|NN value|value|NN of|of|IN 500|500|CD .|.|.
Scanned|scan|VBD images|image|NNS were|be|VBD analyzed|analyze|VBN with|with|IN GenePix|GenePix|NNP Pro|pro|FW 3.0|3.0|CD software|software|NN -LRB-|-lrb-|-LRB- Axon|Axon|NNP Instruments|Instruments|NNP ,|,|, Union|Union|NNP City|City|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- to|to|TO obtain|obtain|VB gene|gene|NN expression|expression|NN ratios|ratio|NNS .|.|.
Scanned|scan|VBD images|image|NNS were|be|VBD analyzed|analyze|VBN with|with|IN GenePix|GenePix|NNP Pro|pro|FW 3.0|3.0|CD software|software|NN -LRB-|-lrb-|-LRB- Axon|Axon|NNP Instruments|Instruments|NNP ,|,|, Union|Union|NNP City|City|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- to|to|TO obtain|obtain|VB gene|gene|NN expression|expression|NN ratios|ratio|NNS .|.|. Logged|log|VBN gene|gene|NN expression|expression|NN ratios|ratio|NNS were|be|VBD normalized|normalize|VBN by|by|IN LOWESS|lowess|NN regression|regression|NN -LRB-|-lrb-|-LRB- Yang|Yang|NNP et|et|FW al.|al.|FW ,|,|, 2002|2002|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT GeneSpring|GeneSpring|NNP GX|GX|NNP 7.3|7.3|CD software|software|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
Scanned|scan|VBD spot|spot|NN signals|signal|NNS were|be|VBD normalized|normalize|VBN using|use|VBG internal|internal|JJ Protoarray|Protoarray|NNP control|control|NN proteins|protein|NNS and|and|CC Z|z|NN scores|score|NNS subsequently|subsequently|RB determined|determine|VBD based|base|VBN on|on|IN comparisons|comparison|NNS of|of|IN mean|mean|NN signals|signal|NNS for|for|IN each|each|DT spot|spot|NN pair|pair|NN to|to|TO the|the|DT mean|mean|NN spot|spot|NN intensity|intensity|NN for|for|IN the|the|DT array|array|NN .|.|. Z|z|NN scores|score|NNS greater|greater|JJR than|than|IN 3.0|3.0|CD were|be|VBD considered|consider|VBN significant|significant|JJ
Scatter|Scatter|NNP signal|signal|NN intensity|intensity|NN after|after|IN illumination|illumination|NN at|at|IN 150|150|CD ms|m|NNS exposure|exposure|NN without|without|IN normalization|normalization|NN ,|,|, without|without|IN transformation|transformation|NN .|.|. The|the|DT non-normalized|non-normalized|JJ signals|signal|NNS form|form|VBP the|the|DT basis|basis|NN of|of|IN conclusions|conclusion|NNS in|in|IN the|the|DT accompanying|accompany|VBG manuscript|manuscript|NN .|.|.
scraping|scrape|VBG bacteria|bacterium|NNS ,|,|, opening|open|VBG with|with|IN bead|bead|NN beating|beating|NN ,|,|, Trizol-based|trizol-based|JJ RNA|rna|NN isolation|isolation|NN ,|,|, rRNA|rrna|NN depletion|depletion|NN with|with|IN RiboZero|RiboZero|NNP ,|,|, DNA|DNA|NNP digest|digest|VB ,|,|, SoLiD|solid|JJ seq|seq|NN by|by|IN CeGaT|cegat|NN -LRB-|-lrb-|-LRB- Tübingen|tübingen|NN ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB-
ScriptSeq|scriptseq|NN v2|v2|NN Complete|complete|JJ Kit|kit|NN -LRB-|-lrb-|-LRB- EpiCentre|EpiCentre|NNP -RRB-|-rrb-|-RRB-
SD10|sd10|NN _|_|NN 1|1|CD
SD10|sd10|NN _|_|NN 2|2|CD
SD10|sd10|NN _|_|CD 3|3|CD
SD11|sd11|NN _|_|NN 1|1|CD
SD11|sd11|NN _|_|NN 2|2|CD
SD11|sd11|NN _|_|CD 3|3|CD
SD12|sd12|NN _|_|NN 1|1|CD
SD12|sd12|NN _|_|NN 2|2|CD
SD12|sd12|NN _|_|CD 3|3|CD
SD13|sd13|NN _|_|NN 1|1|CD
SD13|sd13|NN _|_|NN 2|2|CD
SD13|sd13|NN _|_|CD 3|3|CD
SD2|sd2|NN _|_|NN 1|1|CD
SD2|sd2|NN _|_|NN 2|2|CD
SD2|sd2|NN _|_|CD 3|3|CD
SD3|sd3|NN _|_|NN 1|1|CD
SD3|sd3|NN _|_|NN 2|2|CD
SD3|sd3|NN _|_|CD 3|3|CD
SD4|sd4|NN _|_|NN 1|1|CD
SD4|sd4|NN _|_|NN 2|2|CD
SD4|sd4|NN _|_|CD 3|3|CD
SD5|sd5|NN _|_|NN 1|1|CD
SD5|sd5|NN _|_|NN 2|2|CD
SD5|sd5|NN _|_|CD 3|3|CD
SD6|sd6|NN _|_|NN 1|1|CD
SD6|sd6|NN _|_|NN 2|2|CD
SD6|sd6|NN _|_|CD 3|3|CD
SD7|sd7|NN _|_|NN 1|1|CD
SD7|sd7|NN _|_|NN 2|2|CD
SD7|sd7|NN _|_|CD 3|3|CD
SD8|sd8|NN _|_|NN 1|1|CD
SD8|sd8|NN _|_|NN 2|2|CD
SD8|sd8|NN _|_|CD 3|3|CD
SD9|sd9|NN _|_|NN 1|1|CD
SD9|sd9|NN _|_|NN 2|2|CD
SD9|sd9|NN _|_|CD 3|3|CD
sdhA|sdha|NN _|_|CD FA|FA|NNP _|_|SYM I|I|PRP
sdhA|sdha|NN _|_|CD FA|FA|NNP _|_|NNP II|II|NNP
sdhA|sdhA|NNP _|_|NNP FA|FA|NNP _|_|VBD III|iii|CD
sdhA|sdha|NN _|_|CD LB|lb|NN _|_|NN I|I|PRP
sdhA|sdha|NN _|_|CD LB|lb|NN _|_|NN II|ii|CD
sdhA|sdha|NN _|_|CD LB|LB|NNP _|_|NNP III|III|NNP
sdhC|sdhC|NNP KO|KO|NNP rep1|rep1|NN
sdhC|sdhc|NN KO|ko|NN rep2|rep2|NN
sdhC|sdhc|NN KO|ko|NN rep3|rep3|NN
Second|second|JJ biological|biological|JJ repeat|repeat|NN 37|37|CD °C|°c|NN
Second|second|JJ biological|biological|JJ repeat|repeat|NN 50|50|CD °C|°c|NN
See|see|VB publication|publication|NN for|for|IN complete|complete|JJ protocol|protocol|NN .|.|. Briefly|briefly|RB ,|,|, samples|sample|NNS with|with|IN rRNA|rrna|NN subtraction|subtraction|NN with|with|IN treated|treat|VBN with|with|IN bacterial|bacterial|JJ Ribo-Zero|Ribo-Zero|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|. Next|next|RB ,|,|, RNA|rna|NN was|be|VBD fragmented|fragmented|JJ with|with|IN RNA|rna|NN fragmentation|fragmentation|NN reagents|reagent|NNS -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- .|.|. First|first|JJ strand|strand|NN cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD conducted|conduct|VBN using|use|VBG random|random|JJ primers|primer|NNS and|and|CC Superscript|Superscript|NNP III|III|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP -RRB-|-rrb-|-RRB- .|.|. To|to|TO enable|enable|VB strand|strand|NN specificity|specificity|NN ,|,|, second|second|JJ strand|strand|NN synthesis|synthesis|NN was|be|VBD conducted|conduct|VBN using|use|VBG dUTP|dutp|NN instead|instead|RB of|of|IN dTTP|dttp|NN with|with|IN RNase|rnase|NN H|h|NN ,|,|, E.|e.|FW coli|coli|FW DNA|dna|NN ligase|ligase|NN ,|,|, and|and|CC E.|e.|FW coli|coli|FW DNA|dna|NN polymerase|polymerase|NN .|.|. Ends|end|NNS were|be|VBD repaired|repair|VBN with|with|IN T4|t4|NN DNA|dna|NN polymerase|polymerase|NN ,|,|, Klenow|Klenow|NNP DNA|DNA|NNP polymerase|polymerase|NN ,|,|, and|and|CC T4|t4|NN PNK|pnk|NN .|.|. 3|3|CD '|'|'' ends|end|NNS were|be|VBD adenylated|adenylate|VBN with|with|IN the|the|DT Klenow|Klenow|NNP fragment|fragment|NN -LRB-|-lrb-|-LRB- 3|3|CD '|'|'' >|>|JJR 5|5|CD '|'|'' exo|exo|SYM -|-|: -RRB-|-rrb-|-RRB- .|.|. Y-shaped|y-shaped|JJ adapters|adapter|NNS were|be|VBD ligated|ligate|VBN and|and|CC 9-12|9-12|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN were|be|VBD conducted|conduct|VBN with|with|IN standard|standard|JJ Illumina|Illumina|NNP primers|primer|NNS with|with|IN multiplexing|multiplex|VBG indexes|index|NNS .|.|. Libraries|library|NNS were|be|VBD extracted|extract|VBN from|from|IN an|a|DT acrylamide|acrylamide|NN gel|gel|NN and|and|CC submitted|submit|VBN for|for|IN sequencing|sequencing|NN at|at|IN the|the|DT MIT|MIT|NNP BioMicro|BioMicro|NNP Center|Center|NNP using|use|VBG standard|standard|JJ Illumina|Illumina|NNP protocols|protocol|NNS .|.|.
See|see|VB the|the|DT paper|paper|NN Variation|variation|NN in|in|IN the|the|DT Genomic|genomic|JJ islands|island|NNS of|of|IN porcine|porcine|NN enteropathogenic|enteropathogenic|JJ Escherichia|escherichia|FW coli|coli|FW strains|strain|NNS of|of|IN serogroup|serogroup|NN O45|o45|NN revealed|reveal|VBN by|by|IN comparative|comparative|JJ genomic|genomic|JJ hybridization|hybridization|NN and|and|CC PCR|pcr|NN by|by|IN Bruant|Bruant|NNP and|and|CC Zhang|Zhang|NNP et|et|FW al.|al.|FW 2009|2009|CD
Separate|separate|JJ E.|e.|FW coli|coli|FW colonies|colony|NNS were|be|VBD picked|pick|VBN from|from|IN LB|LB|NNP agar|agar|NN plates|plate|NNS for|for|IN each|each|DT replicate|replicate|VBP .|.|. Overnight|overnight|JJ cultures|culture|NNS -LRB-|-lrb-|-LRB- 12-16|12-16|CD hrs|hr|NNS -RRB-|-rrb-|-RRB- were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN in|in|IN M9|m9|NN media|media|NNS supplemented|supplement|VBN with|with|IN 0.1|0.1|CD %|%|NN casamino|casamino|NN acids|acid|NNS ,|,|, 0.4|0.4|CD %|%|NN glycerol|glycerol|NN ,|,|, 0.4|0.4|CD %|%|NN glucose|glucose|NN ,|,|, 2|2|CD mM|mm|NN MgSO4|mgso4|NN ,|,|, and|and|CC 0.1|0.1|CD mM|mm|NN CaCl2|cacl2|NN .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD back|back|RB diluted|dilute|VBN into|into|IN fresh|fresh|JJ media|media|NNS and|and|CC grown|grow|VBN 3-4|3-4|CD hours|hour|NNS to|to|TO an|a|DT OD600|od600|NN of|of|IN ~|~|NN 0.35|0.35|CD at|at|IN 37|37|CD °C|°c|NN in|in|IN an|a|DT orbital|orbital|JJ shaker|shaker|NN at|at|IN 200|200|CD RPM|rpm|NN .|.|. Cultures|culture|NNS were|be|VBD centrifuged|centrifuge|VBN ,|,|, washed|wash|VBN ,|,|, and|and|CC back|back|RB diluted|dilute|VBN into|into|IN media|media|NNS lacking|lack|VBG glucose|glucose|NN .|.|. After|after|IN at|at|IN least|least|JJS 30|30|CD minutes|minute|NNS of|of|IN recovery|recovery|NN Para|para|NN was|be|VBD induced|induce|VBN by|by|IN adding|add|VBG arabinose|arabinose|NN to|to|TO 0.2|0.2|CD %|%|NN .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifuging|centrifuge|VBG 1|1|CD mL|ml|NN of|of|IN culture|culture|NN for|for|IN 1|1|CD minute|minute|NN at|at|IN maximum|maximum|JJ speed|speed|NN on|on|IN a|a|DT benchtop|benchtop|JJ centrifuge|centrifuge|NN .|.|. Pellets|pellet|NNS were|be|VBD immediately|immediately|RB flash|flash|VB frozen|freeze|VBN in|in|IN lN2|ln2|NN .|.|.
SeqA|seqa|NN ChIP|chip|NN DNA|dna|NN
SeqA|seqa|NN ChIP|chip|NN DNA|dna|NN ,|,|, new|new|JJ protocol|protocol|NN
SeqA|seqa|NN ChIP|chip|NN DNA|dna|NN ,|,|, old|old|JJ protocol|protocol|NN
SeqA|seqa|NN in|in|IN 0|0|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN 0|0|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN LB|lb|NN
SeqA|seqa|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN LB|lb|NN dam|dam|NN +|+|CC +|+|CC rep1|rep1|NN
SeqA|seqa|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN LB|lb|NN dam|dam|NN +|+|CC +|+|CC rep2|rep2|NN
SeqA|seqa|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN 15|15|CD min|min|NN dnaC2|dnac2|NN rep3|rep3|NN
SeqA|seqa|NN in|in|IN 16|16|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN 16|16|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN 17|17|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN 17|17|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN 35|35|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN 35|35|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN 50|50|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN 50|50|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN 5|5|CD min|min|NN dnaC2|dnac2|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN 5|5|CD min|min|NN dnaC2|dnac2|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN AB|AB|NNP acetate|acetate|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN AB|AB|NNP acetate|acetate|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN hisA|hisA|NNP GATC|GATC|NNP cluster|cluster|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN hisA|hisA|NNP GATC|GATC|NNP cluster|cluster|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN srlA|srla|NN GATC|gatc|NN cluster|cluster|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN srlA|srla|NN GATC|gatc|NN cluster|cluster|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN ter|ter|NN GATC|gatc|NN cluster|cluster|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN ter|ter|NN GATC|gatc|NN cluster|cluster|NN rep2|rep2|NN
SeqA|seqa|NN in|in|IN tnaA|tnaa|NN GATC|gatc|NN cluster|cluster|NN rep1|rep1|NN
SeqA|seqa|NN in|in|IN tnaA|tnaa|NN GATC|gatc|NN cluster|cluster|NN rep2|rep2|NN
SeqA|seqa|NN new|new|JJ deltaSeqA|deltaseqa|NN
SeqA|seqa|NN new|new|JJ rep1|rep1|NN
SeqA|seqa|NN new|new|JJ rep2|rep2|NN
SeqA|seqa|NN old|old|JJ deltaSeqA|deltaseqa|NN
SeqA|seqa|NN old|old|JJ rep1|rep1|NN
SeqA|seqa|NN old|old|JJ rep2|rep2|NN
Sequence|sequence|NN data|datum|NNS from|from|IN BGI|BGI|NNP had|have|VBD been|be|VBN filtered|filter|VBN to|to|TO remove|remove|VB reads|read|VBZ containing|contain|VBG ≥|≥|SYM 10|10|CD %|%|NN unreadable|unreadable|JJ bases|basis|NNS ,|,|, ≥|≥|SYM 20|20|CD %|%|NN low|low|JJ quality|quality|NN -LRB-|-lrb-|-LRB- ≤|≤|CD Q20|q20|NN -RRB-|-rrb-|-RRB- bases|basis|NNS ,|,|, adapter|adapter|NN contamination|contamination|NN or|or|CC duplicate|duplicate|VB read-pairs|read-pairs|JJ
Sequence|sequence|NN data|datum|NNS was|be|VBD processed|process|VBN by|by|IN conversion|conversion|NN of|of|IN the|the|DT sample|sample|NN alignment|alignment|NN -LRB-|-lrb-|-LRB- BAM|bam|NN -RRB-|-rrb-|-RRB- files|file|VBZ to|to|TO strand-specific|strand-specific|JJ base|base|NN count|count|NN -LRB-|-lrb-|-LRB- BigWIG|bigwig|NN -RRB-|-rrb-|-RRB- files|file|NNS .|.|. To|to|TO accomplish|accomplish|VB this|this|DT an|a|DT in-house|in-house|JJ script|script|NN was|be|VBD created|create|VBN to|to|TO extract|extract|VB strand-specific|strand-specific|JJ base|base|NN count|count|NN data|datum|NNS from|from|IN BAM|BAM|NNP files|file|NNS -LRB-|-lrb-|-LRB- outputs|output|NNS are|be|VBP positive|positive|JJ and|and|CC negative|negative|JJ strand|strand|NN BigWIG|bigwig|NN files|file|NNS -RRB-|-rrb-|-RRB- .|.|.
Sequence|sequence|NN data|datum|NNS was|be|VBD processed|process|VBN by|by|IN conversion|conversion|NN of|of|IN the|the|DT sample|sample|NN alignment|alignment|NN -LRB-|-lrb-|-LRB- BAM|bam|NN -RRB-|-rrb-|-RRB- files|file|VBZ to|to|TO strand-specific|strand-specific|JJ base|base|NN count|count|NN -LRB-|-lrb-|-LRB- WIG|wig|NN -RRB-|-rrb-|-RRB- files|file|NNS .|.|. To|to|TO accomplish|accomplish|VB this|this|DT an|a|DT in-house|in-house|JJ script|script|NN was|be|VBD created|create|VBN to|to|TO extract|extract|VB strand-specific|strand-specific|JJ base|base|NN count|count|NN data|datum|NNS from|from|IN BAM|BAM|NNP files|file|NNS -LRB-|-lrb-|-LRB- outputs|output|NNS are|be|VBP positive|positive|JJ and|and|CC negative|negative|JJ strand|strand|NN WIG|wig|NN files|file|NNS -RRB-|-rrb-|-RRB- .|.|. First|first|RB ,|,|, the|the|DT script|script|NN reads|read|VBZ in|in|IN the|the|DT paired-end|paired-end|JJ BAM|bam|NN file|file|NN and|and|CC counts|count|VBZ the|the|DT nucleotides|nucleotide|NNS spanning|span|VBG inserts|insert|NNS between|between|IN the|the|DT mated|mate|VBN 5|5|CD '|'|'' and|and|CC 3|3|CD '|'|'' reads|read|VBZ .|.|. Next|next|RB ,|,|, the|the|DT script|script|NN pulls|pull|VBZ in|in|IN the|the|DT orphan|orphan|JJ 5|5|CD '|'|'' and|and|CC 3|3|CD '|'|'' reads|read|VBZ from|from|IN the|the|DT respective|respective|JJ BAM|BAM|NNP files|file|NNS and|and|CC increments|increment|NNS the|the|DT base|base|NN counts|count|VBZ at|at|IN each|each|DT base|base|NN location|location|NN without|without|IN duplicating|duplicate|VBG the|the|DT reads|read|VBZ already|already|RB incremented|increment|VBN from|from|IN the|the|DT paired|paired|JJ ends|end|NNS .|.|.
Sequenced|sequence|VBD reads|read|VBZ were|be|VBD mapped|map|VBN onto|onto|IN NC|nc|NN _|_|CD 000913|000913|CD reference|reference|NN genome|genome|NN sequence|sequence|NN using|use|VBG bowtie|bowtie|NN v1|v1|NN .0.0|.0.0|CD with|with|IN parameters|parameter|NNS -|-|: X|x|NN 1000|1000|CD -|-|: n|n|NN 2|2|CD -3|-3|CD 3|3|LS -|-|: S|s|NN
Sequenced|sequence|VBN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN .|.|.
Sequenced|sequence|VBD reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN and|and|CC low-quality|low-quality|JJ sequence|sequence|NN using|use|VBG TrimGalore|trimgalore|NN version|version|NN 0.4.1|0.4.1|CD ,|,|, then|then|RB mapped|map|VBD to|to|TO mm8|mm8|VB whole|whole|JJ genome|genome|NN using|use|VBG bwa|bwa|NN mem|mem|NN version|version|NN 0.7.12|0.7.12|CD with|with|IN default|default|NN parameters|parameter|NNS
Sequenced|sequence|VBN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN ,|,|, and|and|CC masked|mask|VBN for|for|IN low-complexity|low-complexity|NN or|or|CC low-quality|low-quality|JJ sequence|sequence|NN ,|,|, then|then|RB mapped|map|VBD to|to|TO CP009273|CP009273|NNP .1|.1|CD whole|whole|JJ genome|genome|NN using|use|VBG bowtie2|bowtie2|NN
Sequenced|sequence|VBN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN ,|,|, and|and|CC masked|mask|VBN for|for|IN low-complexity|low-complexity|NN or|or|CC low-quality|low-quality|JJ sequence|sequence|NN ,|,|, then|then|RB mapped|map|VBD to|to|TO E.coli|e.coli|VB K2|k2|NN BW25113|bw25113|NN whole|whole|JJ genome|genome|NN using|use|VBG bowtie|bowtie|NN v0|v0|NN .12.2|.12.2|CD
Sequenced|sequence|VBN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN ,|,|, and|and|CC masked|mask|VBN for|for|IN low-complexity|low-complexity|NN or|or|CC low-quality|low-quality|JJ sequence|sequence|NN ,|,|, then|then|RB mapped|map|VBD to|to|TO Escherichia|escherichia|FW coli|coli|FW ATCC8739|atcc8739|NN genome|genome|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN CP000946|cp000946|NN .1|.1|NN -RRB-|-rrb-|-RRB- using|use|VBG Bowtie|Bowtie|NNP 2|2|CD -LRB-|-lrb-|-LRB- version|version|NN 2.2.5|2.2.5|CD -RRB-|-rrb-|-RRB-
Sequenced|sequence|VBN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN ,|,|, and|and|CC masked|mask|VBN for|for|IN low-complexity|low-complexity|NN or|or|CC low-quality|low-quality|JJ sequence|sequence|NN ,|,|, then|then|RB mapped|map|VBD to|to|TO Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN ,|,|, complete|complete|JJ genome|genome|NN using|use|VBG bowtie2|bowtie2|NN version|version|NN 2.0.5|2.0.5|CD with|with|IN default|default|NN parameters|parameter|NNS .|.|.
Sequenced|sequence|VBD reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN ,|,|, and|and|CC masked|mask|VBN for|for|IN low-complexity|low-complexity|NN or|or|CC low-quality|low-quality|JJ sequence|sequence|NN using|use|VBG FASTX-Toolkit|fastx-toolkit|NN version|version|NN 0.0.13|0.0.13|CD and|and|CC Perl|Perl|NNP version|version|NN 5.8.8|5.8.8|CD
Sequenced|sequence|VBN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN and|and|CC masked|mask|VBN for|for|IN low-complexity|low-complexity|JJ sequence|sequence|NN ,|,|, then|then|RB mapped|map|VBD to|to|TO E.coli|e.coli|VB W3110|w3110|NN whole|whole|JJ genome|genome|NN .|.|.
Sequenced|sequence|VBD reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequences|sequence|NNS using|use|VBG FastQC|fastqc|NN v0|v0|NN .11.2|.11.2|CD .|.|.
Sequenced|sequence|VBD reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN ,|,|, then|then|RB mapped|map|VBD to|to|TO E.|e.|FW coli|coli|FW K12|k12|NN genome|genome|NN using|use|VBG bowtie|bowtie|NN v0|v0|NN .12.7|.12.7|CD with|with|IN parameters|parameter|NNS bowtie|bowtie|VBP -|-|: t|t|NN -|-|: v|v|LS 3|3|LS -|-|: m|m|NN 1|1|CD --|--|: best|best|JJS -|-|: S|s|NN -|-|: p|p|NN 2|2|CD
Sequenced|sequence|VBN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN sequence|sequence|NN using|use|VBG Cutadapt|Cutadapt|NNP v.|v.|CC 1.8.3|1.8.3|CD ,|,|, then|then|RB mapped|map|VBD to|to|TO E.|e.|FW coli|coli|FW K12|k12|NN substr|substr|NN .|.|. W3110|w3110|CD whole|whole|JJ genome|genome|NN from|from|IN NCBI|ncbi|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN :|:|: AP009048|ap009048|NN .1|.1|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT RNA-seq|rna-seq|NN aligner|aligner|NN STAR|star|NN v.|v.|CC 2.4.2|2.4.2|CD a.|a.|IN
Sequenced|Sequenced|NNP reads|read|VBZ were|be|VBD trimmed|trim|VBN ,|,|, the|the|DT mapped|map|VBN to|to|TO the|the|DT Escherichia|escherichia|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- using|use|VBG SOAP|soap|NN .|.|.
Sequence|sequence|NN reads|read|VBZ for|for|IN cDNA|cdna|NN libraries|library|NNS were|be|VBD aligned|align|VBN onto|onto|IN E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN genome|genome|NN ,|,|, using|use|VBG Mosaik|mosaik|NN with|with|IN following|follow|VBG arguments|argument|NNS :|:|: hash|hash|VB size|size|NN =|=|JJ 10|10|CD ,|,|, mismatch|mismatch|NN =|=|JJ 0|0|CD .|.|. Only|only|RB reads|read|VBZ that|that|IN aligned|align|VBN to|to|TO the|the|DT unique|unique|JJ genomic|genomic|JJ location|location|NN were|be|VBD retained|retain|VBN .|.|.
Sequence|sequence|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT published|publish|VBN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .2|.2|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT software|software|NN packages|package|NNS SOAP|soap|NN -LRB-|-lrb-|-LRB- Li|Li|NNP et|et|FW al|al|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- and|and|CC ELAND|ELAND|NNP -LRB-|-lrb-|-LRB- within|within|IN the|the|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP Pipeline|Pipeline|NNP Software|Software|NNP -RRB-|-rrb-|-RRB- ,|,|, allowing|allow|VBG at|at|IN most|most|JJS two|two|CD mismatches|mismatch|NNS .|.|. Sequence|sequence|NN reads|read|VBZ with|with|IN sequences|sequence|NNS that|that|WDT did|do|VBD not|not|RB align|align|VB to|to|TO the|the|DT genome|genome|NN ,|,|, aligned|align|VBN to|to|TO multiple|multiple|JJ locations|location|NNS on|on|IN the|the|DT genome|genome|NN ,|,|, or|or|CC contained|contain|VBD more|more|JJR than|than|IN two|two|CD mismatches|mismatch|NNS were|be|VBD discarded|discard|VBN from|from|IN further|further|JJ analysis|analysis|NN -LRB-|-lrb-|-LRB- <|<|JJR 10|10|CD %|%|NN of|of|IN reads|read|VBZ -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Supplemental|Supplemental|NNP Files|Files|NNP -RRB-|-rrb-|-RRB- .|.|. For|for|IN visualization|visualization|NN the|the|DT raw|raw|JJ tag|tag|NN density|density|NN at|at|IN each|each|DT position|position|NN was|be|VBD calculated|calculate|VBN using|use|VBG QuEST|quest|NN -LRB-|-lrb-|-LRB- Valouev|Valouev|NNP et|et|FW al|al|FW ,|,|, 2008|2008|CD -RRB-|-rrb-|-RRB- and|and|CC normalized|normalize|VBD as|as|IN tag|tag|NN density|density|NN per|per|IN million|million|CD uniquely|uniquely|RB mapped|map|VBN reads|read|VBZ .|.|.
Sequence|sequence|NN reads|read|VBZ were|be|VBD obtained|obtain|VBN and|and|CC mapped|map|VBN to|to|TO the|the|DT W3110|w3110|NN genome|genome|NN -LRB-|-lrb-|-LRB- NCBI|ncbi|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP Pipeline|Pipeline|NNP .|.|. All|all|DT reads|read|VBZ mapping|mapping|NN with|with|IN two|two|CD or|or|CC fewer|fewer|JJR mismatches|mismatch|NNS were|be|VBD retained|retain|VBN .|.|. Repeated|repeated|JJ sequences|sequence|NNS were|be|VBD ignored|ignore|VBN -LRB-|-lrb-|-LRB- rRNA|rrna|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT counts|count|NNS in|in|IN each|each|DT sample|sample|NN was|be|VBD normalized|normalize|VBN by|by|IN ssrA|ssra|NN RNA|rna|NN and|and|CC then|then|RB converted|convert|VBD to|to|TO logarithmic|logarithmic|JJ values|value|NNS .|.|. A|a|DT value|value|NN of|of|IN 1|1|CD was|be|VBD added|add|VBN to|to|TO every|every|DT count|count|NN before|before|IN the|the|DT logarithmic|logarithmic|JJ conversion|conversion|NN to|to|TO avoid|avoid|VB an|a|DT undefined|undefined|JJ logarithm|logarithm|NN of|of|IN 0|0|CD .|.|. The|the|DT lifetime|lifetime|NN was|be|VBD determined|determine|VBN from|from|IN the|the|DT inverse|inverse|NN of|of|IN the|the|DT slope|slope|NN of|of|IN a|a|DT linear|linear|JJ fit|fit|NN to|to|TO the|the|DT logarithmic|logarithmic|JJ values|value|NNS .|.|.
Sequence|sequence|NN reads|read|VBZ were|be|VBD trimmed|trim|VBN for|for|IN adaptor|adaptor|NN reads|read|VBZ and|and|CC mapped|map|VBN to|to|TO E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN genome|genome|NN using|use|VBG CLC|clc|NN Genomics|genomic|NNS Workbench|workbench|JJ 6.0.1|6.0.1|CD
Sequences|sequence|NNS obtained|obtain|VBN from|from|IN the|the|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP were|be|VBD mapped|map|VBN to|to|TO both|both|DT strands|strand|NNS of|of|IN the|the|DT E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN genome|genome|NN using|use|VBG BLAT|BLAT|NNP allowing|allow|VBG no|no|DT gaps|gap|NNS and|and|CC up|up|RB to|to|TO two|two|CD mismatches|mismatch|NNS .|.|. Each|each|DT alignment|alignment|NN was|be|VBD extended|extend|VBN to|to|TO 200bp|200bp|VB the|the|DT approximate|approximate|JJ average|average|JJ length|length|NN of|of|IN DNA|dna|NN fragments|fragment|NNS on|on|IN the|the|DT 3|3|CD '|'|'' end|end|NN .|.|. Only|only|RB reads|read|VBZ which|which|WDT mapped|map|VBD to|to|TO a|a|DT single|single|JJ region|region|NN of|of|IN the|the|DT genome|genome|NN were|be|VBD considered|consider|VBN for|for|IN further|further|JJ analysis|analysis|NN .|.|. For|for|IN each|each|DT base|base|NN position|position|NN on|on|IN the|the|DT genome|genome|NN ,|,|, the|the|DT number|number|NN of|of|IN reads|read|VBZ that|that|IN mapped|map|VBN to|to|TO that|that|DT position|position|NN was|be|VBD calculated|calculate|VBN .|.|.
sequences|sequence|NNS were|be|VBD aligned|align|VBN to|to|TO the|the|DT parent|parent|NN E.|e.|FW coli|coli|FW strain|strain|NN genome|genome|NN template|template|NN and|and|CC transcript|transcript|NN levels|level|NNS were|be|VBD quantified|quantify|VBN for|for|IN triplicate|triplicate|NN groups|group|NNS of|of|IN each|each|DT primary|primary|JJ deletion|deletion|NN strain|strain|NN and|and|CC synthetic|synthetic|JJ rescue|rescue|NN -LRB-|-lrb-|-LRB- i.e.|i.e.|FW sup|sup|FW -RRB-|-rrb-|-RRB- strain|strain|NN using|use|VBG Rockhopper|Rockhopper|NNP -LRB-|-lrb-|-LRB- version|version|NN 2.0.3|2.0.3|CD -RRB-|-rrb-|-RRB-
Sequences|sequence|NNS were|be|VBD mapped|map|VBN to|to|TO NC|NC|NNP _|_|SYM 000913.2|000913.2|CD using|use|VBG bowtie2|bowtie2|NN v2|v2|NN .2.2|.2.2|CD with|with|IN parameters|parameter|NNS -|-|: N|n|NN 0|0|CD --|--|: sensitive|sensitive|JJ --|--|: minins|minin|NNS 130|130|CD --|--|: maxins|maxin|NNS 780|780|CD -|-|: q|q|NN --|--|: no-mixed|no-mixed|JJ --|--|: no-discordant|no-discordant|JJ --|--|: no-unal|no-unal|JJ
sequencing|sequencing|NN ||||SYM Immunoprecipitated|immunoprecipitate|VBN samples|sample|NNS and|and|CC the|the|DT sheared|sheared|JJ DNA|dna|NN following|follow|VBG the|the|DT Bioruptor|Bioruptor|NNP were|be|VBD de-crosslinked|de-crosslinked|JJ in|in|IN 0.5|0.5|CD x|x|CC elution|elution|NN buffer|buffer|NN containing|contain|VBG 0.8|0.8|CD mg/ml|mg/ml|NN Pronase|Pronase|NNP at|at|IN 42degree|42degree|CD C|c|NN for|for|IN 2|2|CD h|h|NN followed|follow|VBN by|by|IN 65degree|65degree|CD C|c|NN for|for|IN 6|6|CD h.|h.|NN DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG a|a|DT PCR|pcr|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. Prior|prior|RB to|to|TO sequencing|sequencing|NN ,|,|, the|the|DT DNA|dna|NN fragment|fragment|NN sizes|size|NNS were|be|VBD checked|check|VBN and|and|CC gene-specific|gene-specific|JJ quantitative|quantitative|JJ PCR|pcr|NN -LRB-|-lrb-|-LRB- qPCR|qpcr|NN -RRB-|-rrb-|-RRB- was|be|VBD carried|carry|VBN out|out|RP .|.|. Prior|prior|RB and|and|CC post|post|VB library|library|NN construction|construction|NN ,|,|, the|the|DT concentration|concentration|NN of|of|IN the|the|DT immunoprecipitated|immunoprecipitate|VBN DNA|dna|NN samples|sample|NNS was|be|VBD measured|measure|VBN using|use|VBG the|the|DT Qubit|Qubit|NNP HS|hs|NN DNA|dna|NN kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|. Library|Library|NNP construction|construction|NN and|and|CC sequencing|sequencing|NN was|be|VBD done|do|VBN using|use|VBG the|the|DT ChIP-Seq|chip-seq|NN Sample|Sample|NNP Prep|Prep|NNP kit|kit|NN ,|,|, Reagent|Reagent|NNP Preparation|Preparation|NNP kit|kit|NN and|and|CC Cluster|Cluster|NNP Station|Station|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS were|be|VBD loaded|load|VBN at|at|IN a|a|DT concentration|concentration|NN of|of|IN 10|10|CD pM|pm|NN .|.|.
Sequencing|sequencing|NN libraries|library|NNS were|be|VBD constructed|construct|VBN using|use|VBG the|the|DT NEBNext|nebnext|NN Ultra|ultra|NN DNA|dna|NN Library|Library|NNP Prep|Prep|NNP Kit|kit|NN for|for|IN Illumina|Illumina|NNP -LRB-|-lrb-|-LRB- #E7370|#E7370|NNP ,|,|, NEB|NEB|NNP -RRB-|-rrb-|-RRB- for|for|IN samples|sample|NNS 1|1|CD to|to|TO 3|3|CD -LRB-|-lrb-|-LRB- 37|37|CD C|c|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT WaferGen|WaferGen|NNP PrepX|PrepX|NNP ILM|ILM|NNP ChiP-Seq|ChiP-Seq|NNP Library|Library|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- #|#|# 400075|400075|CD ,|,|, WaferGen|WaferGen|NNP -RRB-|-rrb-|-RRB- on|on|IN the|the|DT Apollo|Apollo|NNP 324|324|CD System|System|NNP for|for|IN samples|sample|NNS 4|4|CD to|to|TO 10|10|CD -LRB-|-lrb-|-LRB- 22|22|CD C|c|NN -RRB-|-rrb-|-RRB- .|.|.
Sequencing|sequencing|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN with|with|IN Accel|Accel|NNP NGS|NGS|NNP 1S|1s|NN kit|kit|NN -LRB-|-lrb-|-LRB- Swift|Swift|NNP Bioscience|Bioscience|NNP -RRB-|-rrb-|-RRB- in|in|IN accordanse|accordanse|NN with|with|IN manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
sequencing|sequencing|NN mode|mode|NN :|:|: 50|50|CD nt|nt|NNS single-end|single-end|JJ read|read|NN protocol|protocol|NN
sequencing|sequencing|NN mode|mode|NN :|:|: paired-end|paired-end|NN 2|2|CD *|*|SYM 150|150|CD nt|nt|NNS protocol|protocol|NN
Sequencing|sequencing|NN reads|read|VBZ -LRB-|-lrb-|-LRB- approximately|approximately|RB 13|13|CD to|to|TO 25|25|CD million|million|CD per|per|IN sample|sample|NN -RRB-|-rrb-|-RRB- were|be|VBD imported|import|VBN into|into|IN Geneious|geneious|JJ Pro|pro|FW -LRB-|-lrb-|-LRB- Biomatters|biomatter|NNS -RRB-|-rrb-|-RRB- and|and|CC assembled|assemble|VBN to|to|TO the|the|DT reference|reference|NN chromosome|chromosome|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN Accession|Accession|NNP Number|number|NN 000913.2|000913.2|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT assembly|assembly|NN process|process|NN was|be|VBD set|set|VBN to|to|TO medium/low|medium/low|VB sensitivity|sensitivity|NN on|on|IN Geneious|Geneious|NNP ,|,|, with|with|IN the|the|DT following|follow|VBG parameters|parameter|NNS :|:|: 10|10|CD %|%|NN gaps|gap|NNS allowed|allow|VBD per|per|IN read|read|NN ;|;|: word|word|NN length|length|NN of|of|IN 18|18|CD ;|;|: index|index|NN word|word|NN length|length|NN of|of|IN 13|13|CD ;|;|: words|word|NNS repeated|repeat|VBN more|more|JJR than|than|IN 12|12|CD times|time|NNS ignored|ignore|VBN ;|;|: 20|20|CD %|%|NN maximum|maximum|NN mismatches|mismatch|NNS per|per|IN read|read|NN ;|;|: and|and|CC maximum|maximum|JJ ambiguity|ambiguity|NN of|of|IN 4|4|CD
Sequencing|sequencing|NN reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO the|the|DT mg1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913.2|000913.2|CD -RRB-|-rrb-|-RRB- or|or|CC a|a|DT list|list|NN of|of|IN the|the|DT designed|design|VBN signal|signal|NN peptide|peptide|NN fusions|fusion|NNS using|use|VBG bowtie|bowtie|NN 0.12.9|0.12.9|CD
Sequencing|sequencing|NN reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW genome|genome|NN with|with|IN bowtie2|bowtie2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t10|t10|NN _|_|CD t11|t11|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t10|t10|NN _|_|CD t11|t11|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t1|t1|NN _|_|CD t2|t2|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t1|t1|NN _|_|CD t2|t2|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t2|t2|NN _|_|CD t3|t3|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t2|t2|NN _|_|CD t3|t3|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t3|t3|NN _|_|CD t4|t4|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t3|t3|NN _|_|CD t4|t4|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t4|t4|NN _|_|CD t5|t5|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t4|t4|NN _|_|CD t5|t5|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t5|t5|NN _|_|CD t6|t6|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t5|t5|NN _|_|CD t6|t6|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t6|t6|NN _|_|CD t7|t7|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t6|t6|NN _|_|CD t7|t7|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t7|t7|NN _|_|CD t8|t8|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t7|t7|NN _|_|CD t8|t8|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t8|t8|NN _|_|CD t9|t9|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t8|t8|NN _|_|CD t9|t9|NN .2|.2|NN
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t9|t9|NN _|_|CD t10|t10|NN .1|.1|CD
Sequential|sequential|JJ Design|design|NN timecourse|timecourse|NN t9|t9|NN _|_|CD t10|t10|NN .2|.2|NN
Serine|serine|NN addition|addition|NN
Serine|serine|NN Hydroxamate|hydroxamate|NN stressed|stress|VBD ,|,|, replicate|replicate|VB #|#|# 1|1|CD
Serine|serine|NN Hydroxamate|hydroxamate|NN stressed|stress|VBD ,|,|, replicate|replicate|VB #|#|# 2|2|CD
Serine|serine|NN Hydroxamate|hydroxamate|NN stressed|stress|VBD ,|,|, replicate|replicate|VB #|#|# 3|3|CD
Serine|serine|NN hydrxamate|hydrxamate|NN -LRB-|-lrb-|-LRB- 100|100|CD mg/L|mg/l|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT cultures|culture|NNS in|in|IN the|the|DT late-exponential|late-exponential|JJ phase|phase|NN at|at|IN ~|~|CD 11|11|CD OD|od|NN -LRB-|-lrb-|-LRB- ~|~|NN 5.5|5.5|CD g|g|NN g|g|NN dry|dry|JJ cell|cell|NN weight|weight|NN per|per|IN liter|liter|NN -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS for|for|IN DNA|dna|NN microarray|microarray|NN analysis|analysis|NN were|be|VBD taken|take|VBN 1|1|CD hour|hour|NN after|after|IN the|the|DT beginning|begin|VBG the|the|DT serine|serine|NN hydrxamate|hydrxamate|NN addition|addition|NN -LRB-|-lrb-|-LRB- 13.2|13.2|CD OD|od|NN ,|,|, ~|~|NN 6.6|6.6|CD g|g|NN dry|dry|JJ cell|cell|NN weight|weight|NN per|per|IN liter|liter|NN ,|,|, growth|growth|NN rate|rate|NN 0.15|0.15|CD 1/h|1/h|NN -RRB-|-rrb-|-RRB- .|.|.
serotype|serotype|NN O157|o157|NN :|:|: H7|h7|NN
serotype|serotype|NN O157|o157|NN :|:|: H7|h7|NN
serotype|serotype|NN :|:|: O157|o157|NN :|:|: H7|h7|NN
serotype|serotype|NN :|:|: o157|o157|NN :|:|: H7|h7|NN clade|clade|NN 2|2|CD ,|,|, stx|stx|NN 1|1|CD and|and|CC 2|2|CD
serotype|serotype|NN :|:|: o157|o157|NN :|:|: H7|h7|NN clade|clade|NN 2|2|CD ,|,|, stx|stx|NN 2|2|CD
serotype|serotype|NN :|:|: o157|o157|NN :|:|: H7|h7|NN clade|clade|NN 8|8|CD ,|,|, stx|stx|NN 2|2|CD
serotype|serotype|NN :|:|: o157|o157|NN :|:|: H7|h7|NN clade|clade|NN 8|8|CD ,|,|, stx|stx|NN 2|2|CD and|and|CC 2c|2c|JJ
serotype|serotype|NN O175|o175|NN :|:|: H16|h16|NN
serovar|serovar|NN O157|o157|NN :|:|: H7|h7|NN strain|strain|NN EDL933|edl933|NN ;|;|: GenBank|genbank|NN accession|accession|NN NC|nc|NN _|_|CD 002655.2|002655.2|CD
setwd|setwd|NN -LRB-|-lrb-|-LRB- \|\|CD
Seven|seven|CD mililiter|mililiter|NN of|of|IN phenol/water|phenol/water|NN were|be|VBD added|add|VBN before|before|IN incubating|incubate|VBG 10|10|CD min|min|NN at|at|IN 67|67|CD °C|°c|NN with|with|IN occasional|occasional|JJ stirring|stir|VBG .|.|. The|the|DT samples|sample|NNS were|be|VBD cooled|cool|VBN on|on|IN ice|ice|NN and|and|CC spun|spin|VBD 10|10|CD min|min|NN at|at|IN 5000|5000|CD rpm|rpm|NN at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT aqueous|aqueous|JJ phase|phase|NN was|be|VBD separated|separate|VBN and|and|CC extracted|extract|VBN again|again|RB once|once|RB the|the|DT same|same|JJ way|way|NN and|and|CC then|then|RB once|once|RB with|with|IN phenol/chloroform|phenol/chloroform|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN 1:1|1:1|CD -RRB-|-rrb-|-RRB- .|.|. One|one|CD tenth|tenth|NN of|of|IN the|the|DT volume|volume|NN of|of|IN 4M|4m|NN NaCl|nacl|NN and|and|CC 2.5|2.5|CD volumes|volume|NNS of|of|IN cold|cold|JJ ethanol|ethanol|NN were|be|VBD then|then|RB added|add|VBN to|to|TO the|the|DT aqueous|aqueous|JJ phase|phase|NN .|.|. The|the|DT tubes|tube|NNS were|be|VBD left|leave|VBN at|at|IN -20|-20|CD °C|°c|NN for|for|IN two|two|CD hours|hour|NNS then|then|RB spun|spin|VBD at|at|IN 8500rpm|8500rpm|NN at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD washed|wash|VBN with|with|IN 70|70|CD %|%|NN ethanol|ethanol|NN ,|,|, dried|dry|VBN under|under|IN vacuum|vacuum|NN and|and|CC resuspened|resuspen|VBN in|in|IN 300|300|CD l|l|NN sterile|sterile|JJ water|water|NN and|and|CC transferred|transfer|VBN to|to|TO an|a|DT eppendord|eppendord|NN tube|tube|NN .|.|. An|a|DT amount|amount|NN of|of|IN 34.5|34.5|CD l|l|NN Qiagen|Qiagen|NNP RDD|RDD|NNP buffer|buffer|NN and|and|CC 9.37|9.37|CD l|l|NN of|of|IN RNase|rnase|NN free|free|JJ DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN .|.|. After|after|IN 15|15|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN ,|,|, the|the|DT tubes|tube|NNS were|be|VBD mixed|mix|VBN by|by|IN inversion|inversion|NN and|and|CC deproteinized|deproteinize|VBN as|as|IN shown|show|VBN above|above|IN with|with|IN 300|300|CD l|l|NN phenol/H2O|phenol/h2o|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. The|the|DT RNA|rna|NN was|be|VBD then|then|RB precipitated|precipitate|VBN with|with|IN 37.5|37.5|CD µl|µl|NN NaCl|nacl|NN 4M|4m|NN and|and|CC 823µl|823µl|NN cold|cold|JJ ethanol|ethanol|NN .|.|. After|after|IN 2|2|CD hours|hour|NNS at|at|IN -20|-20|CD °C|°c|NN ,|,|, the|the|DT tubes|tube|NNS were|be|VBD centrifuged|centrifuge|VBN 30|30|CD min|min|NN at|at|IN 10,000|10,000|CD G|g|NN at|at|IN 4|4|CD °C|°c|NN ,|,|, the|the|DT pellets|pellet|NNS were|be|VBD then|then|RB washed|wash|VBN with|with|IN 70|70|CD %|%|NN ethanol|ethanol|NN then|then|RB dried|dry|VBD under|under|IN vacuum|vacuum|NN and|and|CC resuspended|resuspend|VBN in|in|IN 60µl|60µl|JJ sterile|sterile|JJ water|water|NN .|.|. The|the|DT RNAs|rna|NNS were|be|VBD stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|.
SF1a|sf1a|NN _|_|NN 1|1|CD
SF1a|sf1a|NN _|_|NN 2|2|CD
SF1a|sf1a|NN _|_|CD 3|3|CD
SF1b|sf1b|NN _|_|NN 1|1|CD
SF1b|sf1b|NN _|_|NN 2|2|CD
SF1b|sf1b|NN _|_|CD 3|3|CD
SF2b|sf2b|NN _|_|NN 1|1|CD
SF2b|sf2b|NN _|_|NN 2|2|CD
SF2b|sf2b|NN _|_|CD 3|3|CD
SF3|sf3|NN _|_|NN 1|1|CD
SF3|sf3|NN _|_|NN 2|2|CD
SF3|sf3|NN _|_|CD 3|3|CD
SF4a|sf4a|NN _|_|NN 1|1|CD
SF4a|sf4a|NN _|_|NN 2|2|CD
SF4a|sf4a|NN _|_|CD 3|3|CD
SF4b|sf4b|NN _|_|NN 1|1|CD
SF4b|sf4b|NN _|_|NN 2|2|CD
SF4b|sf4b|NN _|_|CD 3|3|CD
SF5|sf5|NN
SF5|sf5|NN _|_|NN 2|2|CD
SF5|sf5|NN _|_|CD 3|3|CD
SF6|sf6|NN _|_|NN 1|1|CD
SF6|sf6|NN _|_|NN 2|2|CD
SF6|sf6|NN _|_|CD 3|3|CD
SFx|sfx|NN
SFx|sfx|NN _|_|NN 2|2|CD
SFx|SFx|NNP _|_|SYM 3|3|CD
SFy|sfy|NN _|_|NN 1|1|CD
SFy|sfy|NN _|_|NN 2|2|CD
SFy|sfy|NN _|_|CD 3|3|CD
SgrR|sgrr|NN _|_|NN 1|1|CD
SgrR|sgrr|NN _|_|NN 2|2|CD
SgrR|sgrr|NN _|_|CD 3|3|CD
sgrS|sgrs|NN _|_|CD T|t|NN _|_|NN 1|1|CD
sgrS|sgrs|NN _|_|CD T|t|NN _|_|NN 2|2|CD
sgrS|sgrs|NN _|_|CD T|t|NN _|_|NN 3|3|CD
sgrS|sgrs|NN _|_|CD un|un|NN _|_|NN 1|1|CD
sgrS|sgrs|NN _|_|CD un|un|NN _|_|NN 2|2|CD
sgrS|sgrs|NN _|_|CD un|un|NN _|_|NN 3|3|CD
SH0003|sh0003|NN 30h|30h|CD
SH0012|sh0012|NN 20h|20h|JJ
SH0012|sh0012|NN 30h|30h|CD
Sh0012|sh0012|NN 40h|40h|CD
SH0012|sh0012|NN and|and|CC SH0003|sh0003|NN were|be|VBD fermented|ferment|VBN in|in|IN a|a|DT 5.0|5.0|CD L|l|NN jar-fermenter|jar-fermenter|NN with|with|IN a|a|DT 2.0|2.0|CD working|work|VBG voulume|voulume|NN of|of|IN modified|modify|VBN R|r|NN medium|medium|NN -LRB-|-lrb-|-LRB- 20g/L|20g/l|NN glucose|glucose|NN ,|,|, 80|80|CD g/L|g/l|NN glycerol|glycerol|NN ,|,|, 1.4|1.4|CD g/L|g/l|NN MgSDo4|mgsdo4|NN ,|,|, 13.5|13.5|CD g/L|g/l|NN KH2PO4|kh2po4|NN ,|,|, 4.0|4.0|CD g/L|g/l|NN -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2HPO4|2hpo4|NN and|and|CC 1.7|1.7|CD g/L|g/l|NN citric|citric|JJ acid|acid|NN at|at|IN 35|35|CD °C|°c|NN .|.|. The|the|DT agitation|agitation|NN was|be|VBD at|at|IN 1200|1200|CD rpm|rpm|NN and|and|CC pH|ph|NN was|be|VBD maintained|maintain|VBN at|at|IN 7.0|7.0|CD with|with|IN 5N|5n|NN NH4OH|nh4oh|NN .|.|. with|with|IN the|the|DT depletion|depletion|NN of|of|IN initial|initial|JJ glucose|glucose|NN ,|,|, feeding|feed|VBG medium|medium|NN of|of|IN glycerol|glycerol|NN -LRB-|-lrb-|-LRB- 700g/L|700g/l|NN -RRB-|-rrb-|-RRB- was|be|VBD throughout|throughout|IN fermentation|fermentation|NN .|.|.
SH0012|sh0012|NN no|no|DT rpm|rpm|NN change|change|NN
SH0012|sh0012|NN no|no|DT vitamin|vitamin|NN B12|b12|NN
Shigella|shigella|NN boydii|boydii|NN
Shigella|shigella|NN boydii|boydii|NN 13|13|CD
Shigella|shigella|NN boydii|boydii|NN 14|14|CD
Shigella|shigella|NN boydii|boydii|NN 15|15|CD
Shigella|shigella|NN boydii|boydii|NN 15|15|CD
Shigella|shigella|NN boydii|boydii|NN 16|16|CD
Shigella|shigella|NN boydii|boydii|NN 17|17|CD
Shigella|shigella|NN boydii|boydii|NN 18|18|CD
Shigella|shigella|NN boydii|boydii|NN serogroup|serogroup|NN 1|1|CD
Shigella|shigella|NN boydii|boydii|NN serogroup|serogroup|NN 2|2|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 1|1|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 10|10|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 11|11|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 12|12|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 13|13|CD
Shigella|shigella|NN boydii|boydii|NN serotype2|serotype2|NN
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 2|2|CD
Shigella|shigella|NN boydii|boydii|NN serotype3|serotype3|NN
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 3|3|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 5|5|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 6|6|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 7|7|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 7|7|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 8|8|CD
Shigella|shigella|NN boydii|boydii|NN serotype|serotype|NN 9|9|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN
Shigella|shigella|NN dysenteriae|dysenteriae|NN 10|10|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 11|11|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 12|12|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 13|13|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 2|2|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 3|3|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 4|4|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 5|5|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 6|6|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 7|7|CD
Shigella|shigella|NN dysenteriae|dysenteriae|NN 8|8|CD
Shigella|shigella|NN dysenteriae|dysenteria|NNS 9|9|CD
Shigella|shigella|NN flexneri|flexneri|NN
Shigella|shigella|NN flexneri|flexneri|NN 1a|1a|NN
Shigella|shigella|NN flexneri|flexneri|NN 1b|1b|NN
Shigella|shigella|NN flexneri|flexneri|NN 2b|2b|JJ
Shigella|shigella|NN flexneri|flexneri|NN 3|3|CD
Shigella|shigella|NN flexneri|flexneri|NN 4a|4a|NN
Shigella|shigella|NN flexneri|flexneri|NN 4b|4b|NN
Shigella|shigella|NN flexneri|flexneri|NN 5|5|CD
Shigella|shigella|NN flexneri|flexneri|NN 6|6|CD
Shigella|shigella|NN flexneri|flexneri|NN variant|variant|JJ x|x|NN
Shigella|shigella|NN flexneri|flexneri|NN variant|variant|JJ y|y|NN
SHX-treated|shx-treated|JJ Delta|delta|NN dksA|dksa|NN Cells|cell|NNS
SHX-treated|shx-treated|JJ Delta|delta|NN dksA|dksa|NN Cells|cell|NNS Replicate|replicate|VB 1|1|CD
SHX-treated|shx-treated|JJ Delta|delta|NN dksA|dksa|NN Cells|cell|NNS Replicate|replicate|VB 2|2|CD
SHX-treated|shx-treated|JJ Delta|delta|NN dksA|dksa|NN Cells|cell|NNS Replicate|replicate|VB 3|3|CD
SHX-treated|shx-treated|JJ Wild-type|wild-type|JJ Cells|cell|NNS
SHX-treated|shx-treated|JJ Wild-type|wild-type|JJ Cells|cell|NNS Replicate|replicate|VB 1|1|CD
SHX-treated|shx-treated|JJ Wild-type|wild-type|JJ Cells|cell|NNS Replicate|replicate|VB 2|2|CD
SHX-treated|shx-treated|JJ Wild-type|wild-type|JJ Cells|cell|NNS Replicate|replicate|VB 3|3|CD
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW _|_|SYM exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN _|_|IN no|no|DT rifampicin|rifampicin|NN
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, no|no|DT rifampicin|rifampicin|NN applied|apply|VBD replicate|replicate|VB 1|1|CD -LRB-|-lrb-|-LRB- run|run|NN 299|299|CD -RRB-|-rrb-|-RRB-
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, no|no|DT rifampicin|rifampicin|NN applied|apply|VBD replicate|replicate|VB 1|1|CD -LRB-|-lrb-|-LRB- run|run|NN 423|423|CD -RRB-|-rrb-|-RRB-
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, no|no|DT rifampicin|rifampicin|NN applied|apply|VBD replicate|replicate|VB 2|2|CD -LRB-|-lrb-|-LRB- run|run|NN 299|299|CD -RRB-|-rrb-|-RRB-
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, no|no|DT rifampicin|rifampicin|NN applied|apply|VBD replicate|replicate|VB 2|2|CD -LRB-|-lrb-|-LRB- run|run|NN 423|423|CD -RRB-|-rrb-|-RRB-
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW _|_|SYM exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN _|_|NN rifampicin|rifampicin|NN
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, rifampicin|rifampicin|NN applied|apply|VBD for|for|IN 20|20|CD minutes|minute|NNS ,|,|, replicate|replicate|VBP 1|1|CD -LRB-|-lrb-|-LRB- run|run|NN 423|423|CD -RRB-|-rrb-|-RRB-
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, exponential|exponential|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, rifampicin|rifampicin|NN applied|apply|VBD for|for|IN 20|20|CD minutes|minute|NNS ,|,|, replicate|replicate|VBP 2|2|CD -LRB-|-lrb-|-LRB- run|run|NN 423|423|CD -RRB-|-rrb-|-RRB-
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW _|_|SYM static|static|JJ aerobic|aerobic|JJ growth|growth|NN _|_|IN no|no|DT rifampicin|rifampicin|NN
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, static|static|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, no|no|DT rifampicin|rifampicin|NN applied|apply|VBD replicate|replicate|VB 1|1|CD -LRB-|-lrb-|-LRB- run|run|NN 299|299|CD -RRB-|-rrb-|-RRB-
Sig70|sig70|NN in|in|IN E.|e.|FW coli|coli|FW ,|,|, static|static|JJ aerobic|aerobic|JJ growth|growth|NN ,|,|, no|no|DT rifampicin|rifampicin|NN applied|apply|VBD replicate|replicate|VB 2|2|CD -LRB-|-lrb-|-LRB- run|run|NN 299|299|CD -RRB-|-rrb-|-RRB-
Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|CD A|a|DT _|_|NN cy5|cy5|NN
Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|NN B|b|NN _|_|CD cy5|cy5|NN
Sigma70|sigma70|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 56859|56859|CD -RRB-|-rrb-|-RRB-
Sigma70|sigma70|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 62214|62214|CD -RRB-|-rrb-|-RRB-
Sigma70|sigma70|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS -LRB-|-lrb-|-LRB- Dataset|Dataset|NNP 64194|64194|CD -RRB-|-rrb-|-RRB-
Sigma70|sigma70|NN ChIP-chip|chip-chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 100ug/ml|100ug/ml|JJ rifampicin|rifampicin|NN -LRB-|-lrb-|-LRB- Dataset|dataset|NN 84847|84847|CD -RRB-|-rrb-|-RRB-
Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|NN control|control|NN _|_|CD A|a|DT _|_|NN cy3|cy3|NN
Sigma70|sigma70|NN _|_|CD ChIP|chip|NN _|_|NN control|control|NN _|_|NN B|b|NN _|_|CD cy3|cy3|NN
Sigma70|sigma70|NN ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS
Sigma70|sigma70|NN ChIP|chip|NN in|in|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN cells|cell|NNS treated|treat|VBN with|with|IN 100ug/ml|100ug/ml|JJ rifampicin|rifampicin|NN
Sigma70|sigma70|NN _|_|CD IP|IP|NNP _|_|SYM ChIP-seq|ChIP-seq|NNP _|_|NNP Aerobic|Aerobic|NNP _|_|SYM A|a|DT _|_|JJ SET|SET|NNP _|_|SYM WIG.wig|WIG.wig|NNP :|:|: U00096|u00096|NN .2|.2|NN
Sigma70|sigma70|NN _|_|CD IP|IP|NNP _|_|SYM ChIP-seq|ChIP-seq|NNP _|_|SYM Anaerobic|anaerobic|JJ _|_|NN A|a|DT _|_|JJ SET|SET|NNP _|_|SYM WIG.wig|WIG.wig|NNP :|:|: U00096|u00096|NN .2|.2|NN
Sigma70|sigma70|NN LB|lb|NN
Sigma70|sigma70|NN LB-1|lb-1|NN
Sigma70|sigma70|NN LB-2|lb-2|NN
Sigma70|sigma70|NN LB-3|lb-3|NN
Sigma70|sigma70|NN LP|lp|NN
Sigma70|sigma70|NN LP-1|lp-1|NN
Sigma70|sigma70|NN LP-2|lp-2|NN
Sigma70|sigma70|NN LP-3|lp-3|NN
Signal|signal|NN and|and|CC p-values|p-value|NNS for|for|IN each|each|DT genomic|genomic|JJ position|position|NN interrogated|interrogate|VBN .|.|.
Signal|signal|NN intensities|intensity|NNS were|be|VBD averaged|average|VBN among|among|IN the|the|DT technical|technical|JJ replicates|replicate|VBZ .|.|. Two|two|CD types|type|NNS of|of|IN data|data|NN analysis|analysis|NN were|be|VBD performed|perform|VBN :|:|: to|to|TO indentify|indentify|VB density-dependent|density-dependent|JJ changes|change|NNS in|in|IN gene|gene|NN expression|expression|NN ,|,|, single|single|JJ averaged|average|VBD normalized|normalize|VBN signal|signal|NN intensities|intensity|NNS for|for|IN each|each|DT treatment|treatment|NN point|point|NN were|be|VBD compared|compare|VBN to|to|TO the|the|DT average|average|NN of|of|IN corresponding|corresponding|JJ unstressed|unstressed|JJ control|control|NN signal|signal|NN intensities|intensity|NNS .|.|. Genes|gene|NNS which|which|WDT showed|show|VBD a|a|DT relative|relative|JJ signal|signal|NN log2ratio|log2ratio|NN -LRB-|-lrb-|-LRB- SLR|slr|NN -RRB-|-rrb-|-RRB- value|value|NN above|above|IN 1.0|1.0|CD or|or|CC below|below|IN -1.0|-1.0|CD were|be|VBD selected|select|VBN for|for|IN further|further|JJ analysis|analysis|NN .|.|.
Signal|signal|NN intensities|intensity|NNS were|be|VBD averaged|average|VBN among|among|IN the|the|DT technical|technical|JJ replicates|replicate|VBZ .|.|. Two|two|CD types|type|NNS of|of|IN data|data|NN analysis|analysis|NN were|be|VBD performed|perform|VBN :|:|: to|to|TO indentify|indentify|VB density-dependent|density-dependent|JJ changes|change|NNS in|in|IN gene|gene|NN expression|expression|NN ,|,|, single|single|JJ averaged|average|VBD normalized|normalize|VBN signal|signal|NN intensities|intensity|NNS for|for|IN each|each|DT treatment|treatment|NN point|point|NN were|be|VBD compared|compare|VBN to|to|TO the|the|DT average|average|NN of|of|IN corresponding|corresponding|JJ unstressed|unstressed|JJ control|control|NN signal|signal|NN intensities|intensity|NNS .|.|. Genes|gene|NNS which|which|WDT showed|show|VBD a|a|DT relative|relative|JJ signal|signal|NN log2ratio|log2ratio|NN -LRB-|-lrb-|-LRB- SLR|slr|NN -RRB-|-rrb-|-RRB- value|value|NN above|above|IN 1.0|1.0|CD or|or|CC below|below|IN -1.0|-1.0|CD were|be|VBD selected|select|VBN for|for|IN further|further|JJ analysis|analysis|NN .|.|.
Signal|signal|NN intensities|intensity|NNS were|be|VBD normalized|normalize|VBN for|for|IN spot|spot|NN and|and|CC slide|slide|NN abnormalities|abnormality|NNS with|with|IN the|the|DT spatial|spatial|JJ Lowess|lowess|NN algorithm|algorithm|NN and|and|CC analyzed|analyze|VBN by|by|IN mixed-effect|mixed-effect|JJ ANOVA|ANOVA|NNP -LRB-|-lrb-|-LRB- MAANOVA|MAANOVA|NNP -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Kerr|Kerr|NNP et|et|FW al.|al.|FW 2000|2000|CD -RRB-|-rrb-|-RRB- .|.|. Both|both|DT Lowess|lowess|NN and|and|CC MAANOVA|maanova|NN are|be|VBP part|part|NN of|of|IN the|the|DT R/MAANOVA|r/maanova|NN microarray|microarray|NN statistical|statistical|JJ package|package|NN ,|,|, available|available|JJ at|at|IN -LRB-|-lrb-|-LRB- http://www.jax.org/staff/churchill/labsite/|http://www.jax.org/staff/churchill/labsite/|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT resulting|result|VBG variety-by-gene|variety-by-gene|JJ interaction|interaction|NN -LRB-|-lrb-|-LRB- VG|vg|NN -RRB-|-rrb-|-RRB- values|value|NNS of|of|IN the|the|DT control|control|NN and|and|CC experimental|experimental|JJ spot|spot|NN intensities|intensity|NNS were|be|VBD combined|combine|VBN with|with|IN the|the|DT residual|residual|JJ noise|noise|NN from|from|IN each|each|DT spot|spot|NN to|to|TO obtain|obtain|VB the|the|DT filtered|filter|VBN and|and|CC adjusted|adjust|VBN expression|expression|NN values|value|NNS -LRB-|-lrb-|-LRB- Cui|cuus|NNS .|.|. et|et|FW .|.|. al|al|NNP -RRB-|-rrb-|-RRB- .|.|. Duplicate|duplicate|VB expression|expression|NN values|value|NNS from|from|IN each|each|DT array|array|NN were|be|VBD combined|combine|VBN ,|,|, averaged|average|VBD and|and|CC values|value|NNS from|from|IN MAANOVA|MAANOVA|NNP were|be|VBD subsequently|subsequently|RB subjected|subject|VBN to|to|TO significance|significance|NN analysis|analysis|NN of|of|IN microarray|microarray|NN -LRB-|-lrb-|-LRB- SAM|sam|NN -RRB-|-rrb-|-RRB- data|datum|NNS with|with|IN the|the|DT SAM|SAM|NNP package|package|NN -LRB-|-lrb-|-LRB- Tusher|tusher|NN .|.|. et.al|et.al|NN -RRB-|-rrb-|-RRB- .|.|. Significantly|significantly|RB up|up|IN -|-|: and|and|CC down-regulated|down-regulate|VBD genes|gene|NNS were|be|VBD identified|identify|VBN based|base|VBN on|on|IN a|a|DT 1.5|1.5|CD cutoff|cutoff|NN threshold|threshold|NN ,|,|, a|a|DT global|global|JJ false|false|JJ discovery|discovery|NN rate|rate|NN lower|lower|JJR than|than|IN 5|5|CD %|%|NN -LRB-|-lrb-|-LRB- p|p|NN <|<|JJR 0.05|0.05|CD -RRB-|-rrb-|-RRB- .|.|. Six|six|CD arrays|array|NNS representing|represent|VBG a|a|DT total|total|NN of|of|IN 12|12|CD replicates|replicate|VBZ were|be|VBD analyzed|analyze|VBN between|between|IN a|a|DT treatment|treatment|NN and|and|CC a|a|DT control|control|NN .|.|.
Signal|signal|NN intensities|intensity|NNS with|with|IN all|all|DT probes|probe|NNS are|be|VBP shown|show|VBN in|in|IN Sample|Sample|NNP data|datum|NNS table|table|NN .|.|. The|the|DT `|`|`` expressed_present_probes.txt|expressed_present_probes.txt|NN -LRB-|-lrb-|-LRB- available|available|JJ on|on|IN Series|Series|NNP records|record|NNS -RRB-|-rrb-|-RRB- contains|contain|VBZ Signal|signal|NN intensities|intensity|NNS with|with|IN present|present|JJ probes|probe|NNS .|.|. Average|average|JJ signal|signal|NN intensities|intensity|NNS from|from|IN 3|3|CD experiments|experiment|NNS were|be|VBD used|use|VBN to|to|TO calculate|calculate|VB fold|fold|JJ increases|increase|NNS in|in|IN gene|gene|NN expression|expression|NN between|between|IN treated|treated|JJ and|and|CC control|control|JJ groups|group|NNS ,|,|, with|with|IN signal|signal|NN intensity|intensity|NN of|of|IN 39|39|CD used|use|VBN as|as|IN a|a|DT minimum|minimum|JJ intensity|intensity|NN ,|,|, using|use|VBG the|the|DT formula|formula|NN :|:|: average|average|JJ intensity|intensity|NN in|in|IN treated|treat|VBN group/average|group/average|NN intensity|intensity|NN in|in|IN control|control|NN group|group|NN -LRB-|-lrb-|-LRB- the|the|DT `|`|`` Avg|avg|NN '|'|'' columns|column|NNS -RRB-|-rrb-|-RRB- .|.|. Transformed|transform|VBN Ln|ln|NN -LRB-|-lrb-|-LRB- signal|signal|NN intensity|intensity|NN -RRB-|-rrb-|-RRB- values|value|NNS ,|,|, shown|show|VBN in|in|IN columns|column|NNS `|`|`` Ln|ln|NN '|'|'' ,|,|, were|be|VBD used|use|VBN for|for|IN direct|direct|JJ statistical|statistical|JJ comparisons|comparison|NNS of|of|IN expression|expression|NN signals|signal|NNS between|between|IN treated|treated|JJ and|and|CC control|control|JJ groups|group|NNS by|by|IN t-test|t-test|NN -LRB-|-lrb-|-LRB- columns|column|NNS `|`|`` t-test|t-test|NN '|'|'' -RRB-|-rrb-|-RRB- .|.|. The|the|DT probes|probe|NNS in|in|IN the|the|DT expressed_present_probes.txt|expressed_present_probes.txt|NN are|be|VBP arranged|arrange|VBN in|in|IN descending|descend|VBG order|order|NN from|from|IN the|the|DT highest|highest|JJS to|to|TO the|the|DT lowest|lowest|JJS ratio|ratio|NN of|of|IN gene|gene|NN induction|induction|NN in|in|IN PGRP/control|pgrp/control|NN -LRB-|-lrb-|-LRB- column|column|NN `|`|`` Ratio|ratio|NN '|'|'' in|in|IN `|`|`` expressed_present_probes.txt|expressed_present_probes.txt|NN '|'|'' -RRB-|-rrb-|-RRB- .|.|.
Signals|signal|NNS mapping|map|VBG to|to|TO non-coding|non-coding|JJ RNA|rna|NN regions|region|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT datasets|dataset|NNS -LRB-|-lrb-|-LRB- see|see|VB supplementary|supplementary|JJ file|file|NN -RRB-|-rrb-|-RRB- .|.|.
Signals|signal|NNS of|of|IN each|each|DT slide|slide|NN were|be|VBD smoothed|smooth|VBN using|use|VBG the|the|DT NMPP|nmpp|NN program|program|NN -LRB-|-lrb-|-LRB- Wang|Wang|NNP et|et|FW al.|al.|FW ,|,|, 2006|2006|CD -RRB-|-rrb-|-RRB- .|.|. Normalisation|Normalisation|NNP per|per|IN chip|chip|NN to|to|TO 50th|50th|JJ percentile|percentile|NN and|and|CC further|further|JJ analyses|analysis|NNS were|be|VBD performed|perform|VBN in|in|IN GeneSpring|GeneSpring|NNP GX|GX|NNP v7|v7|NN .3.1|.3.1|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Basel|Basel|NNP ,|,|, Switzerland|Switzerland|NNP -RRB-|-rrb-|-RRB- .|.|.
Single|single|JJ colonies|colony|NNS of|of|IN P.|P.|NNP putida|putida|NN strain|strain|NN DOT-T1E|dot-t1e|NN and|and|CC E.|e.|FW coli|coli|FW MG1655|mg1655|NN were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN Luria|Luria|NNP --|--|: Bertani|Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- medium|medium|NN at|at|IN 30|30|CD °C|°c|NN .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN to|to|TO a|a|DT starting|start|VBG OD600|od600|NN of|of|IN 0.01|0.01|CD in|in|IN the|the|DT same|same|JJ medium|medium|NN and|and|CC 50|50|CD ml|ml|NN aliquots|aliquot|NNS were|be|VBD disposed|dispose|VBN in|in|RP separate|separate|JJ 250|250|CD ml|ml|NN Erlenmeyer|erlenmeyer|NN flasks|flask|NNS and|and|CC incubated|incubate|VBN with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN .|.|. When|when|WRB cultures|culture|NNS reached|reach|VBD exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- 0.5|0.5|CD at|at|IN OD600|od600|NN -RRB-|-rrb-|-RRB- ,|,|, antibiotics|antibiotic|NNS were|be|VBD added|add|VBN at|at|IN sub-lethal|sub-lethal|JJ concentrations|concentration|NNS to|to|TO the|the|DT culture|culture|NN medium|medium|NN to|to|TO reach|reach|VB a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 1|1|CD µg/ml|µg/ml|NN kanamycin|kanamycin|NN ,|,|, 300|300|CD µg/ml|µg/ml|JJ ampicillin|ampicillin|NN ,|,|, 150|150|CD µg/ml|µg/ml|JJ chloramphenicol|chloramphenicol|NN ,|,|, 4|4|CD µg/ml|µg/ml|NN tetracycline|tetracycline|NN ,|,|, 0.5|0.5|CD µg/ml|µg/ml|JJ ciprofloxacin|ciprofloxacin|NN ,|,|, 300|300|CD µg/ml|µg/ml|NN spectinomycin|spectinomycin|NN ,|,|, 500|500|CD µg/ml|µg/ml|JJ rifampicin|rifampicin|NN and|and|CC 2|2|CD µg/ml|µg/ml|JJ gentamicin|gentamicin|NN .|.|. Then|then|RB cultures|culture|NNS were|be|VBD incubated|incubate|VBN under|under|IN the|the|DT same|same|JJ conditions|condition|NNS for|for|IN one|one|CD hour|hour|NN more|more|RBR .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 8000|8000|CD g|g|NN for|for|IN 10|10|CD min|min|NN and|and|CC suspended|suspend|VBN immediately|immediately|RB in|in|IN stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- ethanol|ethanol|NN ,|,|, 5|5|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- phenol|phenol|NN -RRB-|-rrb-|-RRB- and|and|CC pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN .|.|. After|after|IN that|that|DT ,|,|, total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN with|with|IN Trizol|trizol|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|. Removal|removal|NN of|of|IN DNA|dna|NN was|be|VBD carried|carry|VBN out|out|RP by|by|IN treatment|treatment|NN with|with|IN DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Fermentas|fermentas|NN -RRB-|-rrb-|-RRB- in|in|IN combination|combination|NN with|with|IN the|the|DT RNase|rnase|NN inhibitor|inhibitor|NN RiboLock|ribolock|NN -LRB-|-lrb-|-LRB- Fermentas|fermentas|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT integrity|integrity|NN and|and|CC quality|quality|NN of|of|IN total|total|JJ RNA|rna|NN was|be|VBD assessed|assess|VBN with|with|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|.
Single|single|JJ colonies|colony|NNS were|be|VBD inoculated|inoculate|VBN into|into|IN 15x100|15x100|CD mm|mm|NN tubes|tube|NNS containing|contain|VBG 4|4|CD ml|ml|NN LB|lb|NN ,|,|, and|and|CC grown|grow|VBN at|at|IN 30ºC|30ºc|NN and|and|CC 250|250|CD rpm|rpm|NN overnight|overnight|JJ .|.|. 100|100|CD μl|μl|NN seed|seed|NN culture|culture|NN was|be|VBD inoculated|inoculate|VBN into|into|IN a|a|DT 100|100|CD ml|ml|NN flask|flask|NN containing|contain|VBG 10|10|CD ml|ml|NN LB|lb|NN medium|medium|NN ,|,|, and|and|CC grown|grow|VBN at|at|IN 30ºC|30ºc|NN and|and|CC 250|250|CD rpm|rpm|NN for|for|IN 5|5|CD h.|h.|NN
single|single|JJ mutant|mutant|NN in|in|IN exopolyphosphatase|exopolyphosphatase|NN -LRB-|-lrb-|-LRB- PPX|ppx|NN -RRB-|-rrb-|-RRB-
single|single|JJ mutant|mutant|NN in|in|IN polyphosphate|polyphosphate|NN kinase|kinase|NN 1|1|CD -LRB-|-lrb-|-LRB- PPK1|ppk1|NN -RRB-|-rrb-|-RRB-
Singleton|Singleton|NNP peaks|peak|NNS -LRB-|-lrb-|-LRB- standard|standard|JJ deviation|deviation|NN =|=|JJ 0|0|CD -RRB-|-rrb-|-RRB- and|and|CC peaks|peak|VBZ without|without|IN matched|match|VBN peaks|peak|NNS on|on|IN the|the|DT opposing|oppose|VBG strand|strand|NN where|where|WRB discarded|discard|VBN
Size|size|NN filtering|filter|VBG :|:|: discarding|discard|VBG reads|read|VBZ shorter|shorter|JJR than|than|IN 12|12|CD nt|nt|NNS -LRB-|-lrb-|-LRB- TRAPL|trapl|NN -RRB-|-rrb-|-RRB-
Size|size|NN filtering|filter|VBG :|:|: discarding|discard|VBG reads|read|VBZ shorter|shorter|JJR than|than|IN 12|12|CD nt|nt|NNS -LRB-|-lrb-|-LRB- via|via|IN READemption|reademption|NN -RRB-|-rrb-|-RRB-
Slide|slide|NN 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|Slide|NNP 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 10|10|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 11|11|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|Slide|NNP 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 12|12|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 120|120|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 120|120|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 60|60|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 13|13|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 120|120|CD
Slide|Slide|NNP 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 60|60|CD
Slide|Slide|NNP 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|SYM Cy3|cy3|NN 120|120|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 14|14|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 60|60|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 15|15|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|SYM Cy3|cy3|NN 120|120|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 15|15|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 15|15|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 15|15|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 60|60|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 15|15|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 15|15|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|Slide|NNP 15|15|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 15|15|CD _|_|CD Wild|Wild|NNP type|type|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 60|60|CD
Slide|slide|NN 16|16|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 120|120|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 16|16|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 60|60|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 16|16|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 16|16|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 120|120|CD
Slide|slide|NN 16|16|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 16|16|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 16|16|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 60|60|CD
Slide|slide|NN 16|16|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 17|17|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 17|17|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 120|120|CD
Slide|slide|NN 17|17|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 17|17|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 17|17|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 60|60|CD
Slide|slide|NN 17|17|CD _|_|NN hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 17|17|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 17|17|CD _|_|SYM hemA|hema|NN _|_|CD CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 18|18|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 19|19|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 20|20|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM CORM-3|corm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 25|25|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 26|26|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 27|27|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 28|28|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 29|29|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 30|30|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|SYM iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 31|31|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 33|33|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 34|34|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 34|34|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 120|120|CD
Slide|slide|NN 34|34|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 34|34|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 34|34|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 60|60|CD
Slide|slide|NN 34|34|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 34|34|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 34|34|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 35|35|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 120|120|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 35|35|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 60|60|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 35|35|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 35|35|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 120|120|CD
Slide|slide|NN 35|35|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 35|35|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 35|35|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 60|60|CD
Slide|slide|NN 35|35|CD _|_|NN hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 36|36|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|SYM Cy3|cy3|NN 120|120|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 36|36|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 36|36|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 36|36|CD _|_|SYM hemA|hema|NN _|_|CD iCORM-3|icorm-3|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 60|60|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 36|36|CD _|_|SYM hemA|hema|NN vs.|vs.|FW WT|wt|FW t|t|NN =|=|JJ 0|0|CD _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN hemA|hema|NN Cy5|cy5|NN WT|WT|NNP
Slide|Slide|NNP 36|36|CD _|_|SYM hemA|hema|NN vs.|vs.|FW WT|wt|FW t|t|NN =|=|JJ 0|0|CD _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN hemA|hema|NN Cy5|cy5|NN WT|wt|JJ
Slide|slide|NN 36|36|CD _|_|CD WT|WT|NNP vs.|vs.|CC hemA|hemA|NNP t|t|NN =|=|JJ 0|0|CD _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN WT|WT|NNP Cy5|Cy5|NNP hemA|hemA|NNP
Slide|Slide|NNP 36|36|CD _|_|CD WT|WT|NNP vs.|vs.|CC hemA|hemA|NNP t|t|NN =|=|JJ 0|0|CD _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN WT|wt|JJ Cy5|cy5|NN hemA|hema|NN
Slide|slide|NN 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|slide|NN 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|slide|NN 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 37|37|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 39|39|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 46|46|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 46|46|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 46|46|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 46|46|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|slide|VBP 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 48|48|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 53|53|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|slide|NN 53|53|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 53|53|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 53|53|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 53|53|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 53|53|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 53|53|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 53|53|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 54|54|CD _|_|SYM Aerobic|aerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD 2|2|CD
Slide|Slide|NNP 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|Slide|NNP 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 55|55|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 3|3|CD _|_|NN Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|slide|NN 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 56|56|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|CD CO|CO|NNP gas|gas|NN _|_|NN biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 58|58|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 10|10|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 20|20|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 40|40|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 59|59|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 2|2|CD _|_|CD Cy3|cy3|NN 80|80|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 10|10|CD
Slide|Slide|NNP 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 20|20|CD
Slide|Slide|NNP 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 2.5|2.5|CD
Slide|Slide|NNP 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 40|40|CD
Slide|slide|NN 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 5|5|CD
Slide|Slide|NNP 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|NN Cy3|cy3|NN 0|0|CD Cy5|cy5|NN 80|80|CD
Slide|Slide|NNP 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 2.5|2.5|CD Cy5|cy5|NN 0|0|CD
Slide|Slide|NNP 70|70|CD _|_|SYM Anaerobic|anaerobic|JJ culture|culture|NN _|_|NN CORM-401|corm-401|NN _|_|CD biol|biol|NN rep|rep|NN 1|1|CD _|_|CD Cy3|cy3|NN 5|5|CD Cy5|cy5|NN 0|0|CD
Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ ,|,|, and|and|CC aerobic|aerobic|JJ or|or|CC anaerobic|anaerobic|JJ sparging|sparging|NN was|be|VBD continued|continue|VBN for|for|IN 10|10|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN aerobic|aerobic|JJ or|or|CC anaerobic|anaerobic|JJ sparging|sparging|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 3500|3500|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|.
Sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- 1/100|1/100|CD vol|vol|NN .|.|. of|of|IN 1M|1m|NN ,|,|, pH|ph|NN 7.6|7.6|CD ;|;|: 10|10|CD mM|mm|NN final|final|JJ -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT mid-log|mid-log|JJ cultures|culture|NNS followed|follow|VBN by|by|IN formaldehyde|formaldehyde|NN to|to|TO 1|1|CD %|%|NN final|final|JJ and|and|CC anaerobic|anaerobic|JJ sparging|sparging|NN was|be|VBD continued|continue|VBN for|for|IN 10|10|CD min|min|NN .|.|. Cold|Cold|NNP 2.5|2.5|CD M|m|NN glycine|glycine|NN was|be|VBD added|add|VBN to|to|TO 100mM|100mm|NN and|and|CC the|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN 4|4|CD °C|°c|NN with|with|IN anaerobic|anaerobic|JJ sparging|sparging|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO stop|stop|VB the|the|DT crosslinking|crosslinking|NN .|.|. Cells|cell|NNS were|be|VBD spun|spin|VBN at|at|IN 3500|3500|CD x|x|CC g|g|NN ,|,|, and|and|CC washed|wash|VBN repeatedly|repeatedly|RB with|with|IN phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -80|-80|CD °C|°c|NN .|.|. Cell|cell|NN pellets|pellet|NNS -LRB-|-lrb-|-LRB- from|from|IN initial|initial|JJ 250|250|CD mL|ml|NN of|of|IN culture|culture|NN -RRB-|-rrb-|-RRB- were|be|VBD thawed|thaw|VBN and|and|CC resuspended|resuspend|VBN in|in|IN 250|250|CD μL|μl|NN of|of|IN IP|IP|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 1|1|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- and|and|CC sonicated|sonicate|VBN using|use|VBG a|a|DT microtip|microtip|NN sonicator|sonicator|NN set|set|VBN at|at|IN 10|10|CD %|%|NN output|output|NN for|for|IN 20|20|CD second|second|JJ intervals|interval|NNS with|with|IN periods|period|NNS of|of|IN cooling|cool|VBG in|in|IN between|between|IN .|.|. Cells|cell|NNS were|be|VBD then|then|RB treated|treat|VBN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN with|with|IN RNase|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- 2|2|CD ng/ml|ng/ml|NN -RRB-|-rrb-|-RRB- ,|,|, micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- 50|50|CD units|unit|NNS -RRB-|-rrb-|-RRB- ,|,|, 20|20|CD μM|μm|NN CaCl2|cacl2|NN ,1.2|,1.2|CD mM|mm|NN KCl|kcl|NN ,|,|, 0.3|0.3|CD mM|mm|NN NaCl|nacl|NN ,|,|, 6|6|CD mM|mm|NN sucrose|sucrose|NN ,|,|, and|and|CC 10|10|CD μM|μm|NN DTT|dtt|NN .|.|. EDTA|edta|NN was|be|VBD added|add|VBN to|to|TO 10|10|CD mM|mm|NN to|to|TO stop|stop|VB the|the|DT micrococcal|micrococcal|JJ nuclease|nuclease|NN and|and|CC the|the|DT samples|sample|NNS were|be|VBD spun|spin|VBN down|down|RP to|to|TO remove|remove|VB cell|cell|NN debris|debris|NN .|.|. The|the|DT lysate|lysate|NN was|be|VBD then|then|RB precleared|preclear|VBN through|through|IN incubation|incubation|NN with|with|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN for|for|IN 2-3|2-3|CD hours|hour|NNS at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT beads|bead|NNS were|be|VBD removed|remove|VBN by|by|IN centrifugation|centrifugation|NN and|and|CC antibody|antibody|NN was|be|VBD added|add|VBN to|to|TO the|the|DT pre-cleared|pre-cleared|JJ lysate|lysate|NN for|for|IN an|a|DT overnight|overnight|JJ incubation|incubation|NN .|.|. The|the|DT next|next|JJ day|day|NN ,|,|, 30|30|CD μl|μl|NN of|of|IN a|a|DT 50/50|50/50|CD slurry|slurry|NN of|of|IN sepharose|sepharose|NN protein|protein|NN A|a|NN beads|bead|NNS in|in|IN IP|IP|NNP buffer|buffer|NN was|be|VBD added|add|VBN to|to|TO the|the|DT lysate|lysate|NN to|to|TO capture|capture|VB antibody-protein-DNA|antibody-protein-dna|JJ complex|complex|NN for|for|IN one|one|CD hour|hour|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Beads|bead|NNS were|be|VBD then|then|RB washed|wash|VBN once|once|RB with|with|IN 1|1|CD ml|ml|NN of|of|IN LiCl|licl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 250|250|CD mM|mm|NN LiCl|licl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 600|600|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 600|600|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, twice|twice|RB with|with|IN 300|300|CD mM|mm|NN NaCl|nacl|NN wash|wash|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 300|300|CD mM|mm|NN NaCl|nacl|NN ,|,|, 2|2|CD %|%|NN TritonX-100|tritonx-100|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC twice|twice|RB with|with|IN TE|te|NN .|.|. Elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 50|50|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 8|8|CD ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN ,|,|, 1|1|CD %|%|NN SDS|sds|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN after|after|IN the|the|DT final|final|JJ wash|wash|NN step|step|NN ,|,|, and|and|CC beads|bead|NNS were|be|VBD incubated|incubate|VBN at|at|IN 65|65|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS to|to|TO remove|remove|VB the|the|DT crosslinked|crosslink|VBN protein-DNA|protein-dna|JJ complexes|complex|NNS from|from|IN the|the|DT beads|bead|NNS .|.|. After|after|IN centrifugation|centrifugation|NN to|to|TO remove|remove|VB the|the|DT beads|bead|NNS ,|,|, the|the|DT samples|sample|NNS were|be|VBD incubated|incubate|VBN overnight|overnight|RB at|at|IN 65|65|CD °C|°c|NN to|to|TO reverse|reverse|VB the|the|DT protein-DNA|protein-dna|JJ formaldehyde|formaldehyde|NN crosslinks|crosslink|NNS .|.|. DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS PCR|pcr|NN Purification|purification|NN kit|kit|NN and|and|CC eluted|elute|VBN to|to|TO a|a|DT final|final|JJ volume|volume|NN of|of|IN 50|50|CD μl|μl|NN with|with|IN EB|EB|NNP .|.|.
Soil|soil|NN DNA|dna|NN was|be|VBD extracted|extract|VBN from|from|IN a|a|DT 0.5|0.5|CD g|g|NN soil|soil|NN sub-sample|sub-sample|NN using|use|VBG the|the|DT MoBio|mobio|NN DNA|dna|NN Power|power|NN Soil|soil|NN kit|kit|NN -LRB-|-lrb-|-LRB- MoBio|mobio|NN Laboratories|Laboratories|NNPS ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|.
Solvent|Solvent|NNP control|control|NN ,|,|, biological|biological|JJ rep1|rep1|NN
Solvent|solvent|JJ control|control|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Solvent|solvent|JJ control|control|NN ,|,|, biological|biological|JJ rep3|rep3|NN
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN culture|culture|NN 1|1|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN culture|culture|NN 2|2|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN dual-species|dual-species|JJ biofilms|biofilm|NNS 1|1|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN dual-species|dual-species|JJ biofilms|biofilm|NNS 2|2|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN dual-species|dual-species|JJ planktonic|planktonic|JJ culture|culture|NN 1|1|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN dual-species|dual-species|JJ planktonic|planktonic|JJ culture|culture|NN 2|2|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN mono-species|mono-species|JJ biofilms|biofilm|NNS 1|1|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN mono-species|mono-species|JJ biofilms|biofilm|NNS 2|2|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN mono-species|mono-species|NNS pure|pure|JJ planktonic|planktonic|JJ culture|culture|NN 1|1|CD
sorted|sort|VBD E.|e.|FW coli|coli|FW cells|cell|NNS from|from|IN mono-species|mono-species|NNS pure|pure|JJ planktonic|planktonic|JJ culture|culture|NN 2|2|CD
sorted|sort|VBD vs.|vs.|CC non-sorted|non-sorted|JJ cells|cell|NNS bioreplicate|bioreplicate|VBP 1|1|CD technical|technical|JJ replicate|replicate|VBP 1|1|CD
sorted|sort|VBD vs.|vs.|CC non-sorted|non-sorted|JJ cells|cell|NNS bioreplicate|bioreplicate|VBP 1|1|CD technical|technical|JJ replicate|replicate|VB 2|2|CD
sorted|sort|VBD vs.|vs.|CC non-sorted|non-sorted|JJ cells|cell|NNS bioreplicate|bioreplicate|VBP 2|2|CD technical|technical|JJ replicate|replicate|VBP 1|1|CD
sorted|sort|VBD vs.|vs.|CC non-sorted|non-sorted|JJ cells|cell|NNS bioreplicate|bioreplicate|VBP 2|2|CD technical|technical|JJ replicate|replicate|VB 2|2|CD
source|source|NN :|:|: Bustamante|Bustamante|NNP et|et|FW al.|al.|FW ,|,|, 2011|2011|CD
source|source|NN :|:|: Peripheral|peripheral|JJ blood|blood|NN
soxR-8myc-tagged|soxr-8myc-tagged|JJ _|_|NN PQ|pq|NN treated|treat|VBN
SoxR|soxr|NN PQ|pq|NN 1|1|CD
SoxR|soxr|NN PQ|pq|NN 2|2|CD
soxS-8myc-tagged|soxs-8myc-tagged|JJ _|_|NN PQ|pq|NN treated|treat|VBN
SoxS|soxs|NN PQ|pq|NN 1|1|CD
SoxS|soxs|NN PQ|pq|NN 2|2|CD
sp1|sp1|NN
sp2|sp2|NN
Specifically|specifically|RB ,|,|, data|datum|NNS were|be|VBD treated|treat|VBN as|as|IN two|two|CD experiments|experiment|NNS constituting|constitute|VBG either|either|CC two|two|CD -LRB-|-lrb-|-LRB- \|\|CD
specific|specific|JJ growth|growth|NN rate|rate|NN 0.11|0.11|CD 1/h|1/h|JJ
specific|specific|JJ growth|growth|NN rate|rate|NN 0.21|0.21|CD 1/h|1/h|JJ
specific|specific|JJ growth|growth|NN rate|rate|NN 0.26|0.26|CD 1/h|1/h|JJ
specific|specific|JJ growth|growth|NN rate|rate|NN 0.31|0.31|CD 1/h|1/h|JJ
specific|specific|JJ growth|growth|NN rate|rate|NN 0.36|0.36|CD 1/h|1/h|JJ
specific|specific|JJ growth|growth|NN rate|rate|NN :|:|: 0.3|0.3|CD h-1|h-1|NN
Specific|specific|JJ growth|growth|NN rate|rate|NN 0.3|0.3|CD h-1|h-1|NN
specific|specific|JJ growth|growth|NN rate|rate|NN 0.40|0.40|CD 1/h|1/h|JJ
specific|specific|JJ growth|growth|NN rate|rate|NN :|:|: 0.47|0.47|CD h-1|h-1|NN
Specific|specific|JJ growth|growth|NN rate|rate|NN 0.47|0.47|CD h-1|h-1|NN
specific|specific|JJ growth|growth|NN rate|rate|NN 0.48|0.48|CD 1/h|1/h|JJ
specific|specific|JJ growth|growth|NN rate|rate|NN :|:|: 0.5h-1|0.5h-1|JJ
SPET-seq|spet-seq|NN -LRB-|-lrb-|-LRB- Ribo|Ribo|NNP -|-|: RNA|rna|NN -RRB-|-rrb-|-RRB-
SPET-seq|spet-seq|NN -LRB-|-lrb-|-LRB- Ribo|Ribo|NNP -|-|: RNA|rna|NN -RRB-|-rrb-|-RRB- ,|,|, Replicate|replicate|VB #|#|# 1|1|CD
SPET-seq|spet-seq|NN -LRB-|-lrb-|-LRB- Ribo|Ribo|NNP -|-|: RNA|rna|NN -RRB-|-rrb-|-RRB- ,|,|, Replicate|replicate|VB #|#|# 2|2|CD
SPET-seq|spet-seq|NN -LRB-|-lrb-|-LRB- Total|total|JJ RNA|rna|NN -RRB-|-rrb-|-RRB-
Sphingomonas|sphingomonas|FW sp.|sp.|FW .|.|. NM05|nm05|NN
S.|S.|NNP pneumoniae|pneumoniae|FW reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT D39|d39|NN whole|whole|JJ genome|genome|NN with|with|IN Rockhopper|rockhopper|JJ version|version|NN 1.21|1.21|CD ,|,|, using|use|VBG default|default|NN parameters|parameter|NNS .|.|. E.|e.|FW coli|coli|FW reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT K-12|k-12|NN ,|,|, substr|substr|NN .|.|. MG1655|mg1655|NN whole|whole|JJ genome|genome|NN with|with|IN Bowtie|bowtie|NN 2|2|CD ,|,|, using|use|VBG parameters|parameter|NNS --|--|: mixed|mixed|JJ --|--|: discordant|discordant|JJ -|-|: D|d|NN 10|10|CD -|-|: R|r|NN 2|2|CD -|-|: N|n|NN 0|0|CD -|-|: L|l|NN 22|22|CD -|-|: i|i|FW S|s|NN ,0,2.50|,0,2.50|CD .|.|.
Spot|Spot|NNP intensities|intensity|NNS and|and|CC corresponding|corresponding|JJ background|background|NN signals|signal|NNS were|be|VBD quantified|quantify|VBN with|with|IN Genepix|Genepix|NNP Pro|pro|FW -LRB-|-lrb-|-LRB- version|version|NN 6|6|CD ;|;|: Axon|Axon|NNP Instruments|Instruments|NNPS -LSB-|-lsb-|-LRB- http://www.moleculardevices.com/pages/software/gn_genepix_pro.html|http://www.moleculardevices.com/pages/software/gn_genepix_pro.html|NN -RSB-|-rsb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. Spots|spot|NNS which|which|WDT had|have|VBD signal-to-noise|signal-to-noise|JJ ratio|ratio|NN less|less|JJR than|than|IN three|three|CD were|be|VBD filtered|filter|VBN .|.|. Further|further|JJ analysis|analysis|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN R|r|NN environment|environment|NN -LRB-|-lrb-|-LRB- version|version|NN 2.6.1|2.6.1|CD ;|;|: -LSB-|-lsb-|-LRB- http://www.r-project.org/|http://www.r-project.org/|NN -RSB-|-rsb-|-RRB- -RRB-|-rrb-|-RRB- using|use|VBG KTH|kth|NN package|package|NN -LRB-|-lrb-|-LRB- KTH|kth|NN Microarray|microarray|NN Center|center|NN ;|;|: -LSB-|-lsb-|-LRB- http://www.biotech.kth.se/molbio/microarray/dataanalysis/index.html|http://www.biotech.kth.se/molbio/microarray/dataanalysis/index.html|NN -RSB-|-rsb-|-RRB- -RRB-|-rrb-|-RRB- .|.|. Flagged|flag|VBN spots|spot|NNS and|and|CC background|background|NN were|be|VBD extracted|extract|VBN before|before|IN ``|``|`` printTipLoess|printtiploess|NN ''|''|'' normalization|normalization|NN .|.|.
Spot|Spot|NNP intensities|intensity|NNS and|and|CC locations|location|NNS were|be|VBD determined|determine|VBN using|use|VBG TIGR|TIGR|NNP Spotfinder|Spotfinder|NNP ,|,|, Version|Version|NNP 3.1.1|3.1.1|CD .|.|. All|all|DT subsequent|subsequent|JJ analyses|analysis|NNS were|be|VBD performed|perform|VBN using|use|VBG the|the|DT ma-anova|ma-anova|JJ package|package|NN in|in|IN the|the|DT open-source|open-source|JJ statistical|statistical|JJ software|software|NN package|package|NN ,|,|, R|r|NN -LRB-|-lrb-|-LRB- www.r-project.org|www.r-project.org|NN -RRB-|-rrb-|-RRB- ,|,|, Version|Version|NNP 2.4.1|2.4.1|CD .|.|. The|the|DT data|datum|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT regional|regional|JJ lowess|lowess|NN method|method|NN .|.|.
Spot|Spot|NNP intensities|intensity|NNS and|and|CC locations|location|NNS were|be|VBD determined|determine|VBN using|use|VBG TIGR|TIGR|NNP Spotfinder|Spotfinder|NNP ,|,|, Version|Version|NNP 3.1.1|3.1.1|CD .|.|. All|all|DT subsequent|subsequent|JJ analyses|analysis|NNS were|be|VBD performed|perform|VBN using|use|VBG the|the|DT ma-anova|ma-anova|JJ package|package|NN in|in|IN the|the|DT open-source|open-source|JJ statistical|statistical|JJ software|software|NN package|package|NN ,|,|, R|r|NN -LRB-|-lrb-|-LRB- www.r-project.org|www.r-project.org|NN -RRB-|-rrb-|-RRB- ,|,|, Version|Version|NNP 2.4.1|2.4.1|CD .|.|. The|the|DT data|datum|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT regional|regional|JJ lowess|lowess|NN method|method|NN .|.|.
Spot|Spot|NNP intensities|intensity|NNS were|be|VBD extracted|extract|VBN using|use|VBG the|the|DT Feature|Feature|NNP Extraction|extraction|NN software|software|NN 10.5.1.1|10.5.1.1|CD from|from|IN Applied|Applied|NNP Biosystems|Biosystems|NNPS with|with|IN a|a|DT linear|linear|JJ dye|dye|VB normalization|normalization|NN correction|correction|NN method|method|NN .|.|. The|the|DT gProcessedSignal|gprocessedsignal|NN and|and|CC rProcessedSignal|rprocessedsignal|NN was|be|VBD used|use|VBN for|for|IN further|further|JJ analysis|analysis|NN with|with|IN the|the|DT statistics|statistics|NNS software|software|NN R.|R.|NNP Ratios|Ratios|NNP of|of|IN g|g|NN -LRB-|-lrb-|-LRB- sample|sample|NN -RRB-|-rrb-|-RRB- to|to|TO r|r|NN -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN after|after|IN background|background|NN substraction|substraction|NN and|and|CC normalized|normalize|VBD to|to|TO the|the|DT array|array|NN wide|wide|JJ average|average|NN .|.|. Data|datum|NNS points|point|NNS with|with|IN a|a|DT value|value|NN below|below|IN 0|0|CD after|after|IN background|background|NN subtraction|subtraction|NN were|be|VBD set|set|VBN `|`|`` null|null|NN '|'|'' .|.|. Data|datum|NNS points|point|NNS form|form|VBP non-unique|non-unique|JJ regions|region|NNS on|on|IN the|the|DT chromosome|chromosome|NN were|be|VBD excluded|exclude|VBN from|from|IN analysis|analysis|NN .|.|.
Spot|Spot|NNP intensities|intensity|NNS were|be|VBD extracted|extract|VBN using|use|VBG the|the|DT Feature|Feature|NNP Extraction|extraction|NN software|software|NN 10.5.1.1|10.5.1.1|CD from|from|IN Applied|Applied|NNP Biosystems|Biosystems|NNPS with|with|IN a|a|DT linear|linear|JJ dye|dye|VB normalization|normalization|NN correction|correction|NN method|method|NN .|.|. The|the|DT gProcessedSignal|gprocessedsignal|NN and|and|CC rProcessedSignal|rprocessedsignal|NN was|be|VBD used|use|VBN for|for|IN further|further|JJ analysis|analysis|NN with|with|IN the|the|DT statistics|statistics|NNS software|software|NN R.|R.|NNP Ratios|Ratios|NNP of|of|IN g|g|NN -LRB-|-lrb-|-LRB- sample|sample|NN -RRB-|-rrb-|-RRB- to|to|TO r|r|NN -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN after|after|IN background|background|NN substraction|substraction|NN .|.|. Data|datum|NNS points|point|NNS with|with|IN a|a|DT value|value|NN below|below|IN 0|0|CD after|after|IN background|background|NN subtraction|subtraction|NN were|be|VBD set|set|VBN `|`|`` null|null|NN '|'|'' .|.|. Data|datum|NNS points|point|NNS form|form|VBP non-unique|non-unique|JJ regions|region|NNS on|on|IN the|the|DT chromosome|chromosome|NN were|be|VBD excluded|exclude|VBN from|from|IN analysis|analysis|NN .|.|.
Spots|spot|NNS automatically|automatically|RB flagged|flag|VBD as|as|IN bad|bad|JJ ,|,|, negative|negative|JJ or|or|CC poor|poor|JJ in|in|IN the|the|DT Imagene|imagene|NN software|software|NN were|be|VBD removed|remove|VBN before|before|IN the|the|DT statistical|statistical|JJ analysis|analysis|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN GeneSight|GeneSight|NNP .|.|. The|the|DT mean|mean|NN values|value|NNS from|from|IN each|each|DT channel|channel|NN were|be|VBD log2|log2|NN transformed|transform|VBN and|and|CC normalised|normalise|VBN using|use|VBG the|the|DT Lowess|lowess|NN method|method|NN to|to|TO remove|remove|VB intensity-dependent|intensity-dependent|JJ effects|effect|NNS in|in|IN the|the|DT log2|log2|NN -LRB-|-lrb-|-LRB- ratios|ratio|NNS -RRB-|-rrb-|-RRB- values|value|NNS .|.|. The|the|DT Cy3/Cy5|cy3/cy5|NN fluorescent|fluorescent|JJ ratios|ratio|NNS were|be|VBD calculated|calculate|VBN from|from|IN the|the|DT normalized|normalize|VBN values|value|NNS .|.|.
Spots|spot|NNS automatically|automatically|RB flagged|flag|VBD as|as|IN bad|bad|JJ ,|,|, negative|negative|JJ or|or|CC poor|poor|JJ in|in|IN the|the|DT Imagene|imagene|NN software|software|NN were|be|VBD removed|remove|VBN before|before|IN the|the|DT statistical|statistical|JJ analysis|analysis|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN GeneSight|GeneSight|NNP .|.|. The|the|DT mean|mean|NN values|value|NNS from|from|IN each|each|DT channel|channel|NN were|be|VBD log2|log2|NN transformed|transform|VBN and|and|CC normalised|normalise|VBN using|use|VBG the|the|DT Lowess|lowess|NN method|method|NN to|to|TO remove|remove|VB intensity-dependent|intensity-dependent|JJ effects|effect|NNS in|in|IN the|the|DT log2|log2|NN -LRB-|-lrb-|-LRB- ratios|ratio|NNS -RRB-|-rrb-|-RRB- values|value|NNS .|.|. The|the|DT Cy3/Cy5|cy3/cy5|NN or|or|CC Cy5/Cy3|cy5/cy3|NN -LRB-|-lrb-|-LRB- test/reference|test/reference|NN -RRB-|-rrb-|-RRB- fluorescent|fluorescent|JJ ratios|ratio|NNS were|be|VBD calculated|calculate|VBN from|from|IN the|the|DT normalized|normalize|VBN values|value|NNS .|.|.
Spots|spot|NNS with|with|IN reference|reference|NN signal|signal|NN intensities|intensity|NNS lower|lower|JJR than|than|IN the|the|DT local|local|JJ background|background|NN -LRB-|-lrb-|-LRB- LBG|lbg|NN -RRB-|-rrb-|-RRB- plus|plus|CC 5|5|CD standard|standard|JJ deviations|deviation|NNS or|or|CC with|with|IN some|some|DT spotting|spot|VBG abnormalities|abnormality|NNS were|be|VBD removed|remove|VBN from|from|IN analysis|analysis|NN .|.|. Signal|signal|NN intensities|intensity|NNS of|of|IN other|other|JJ spots|spot|NNS were|be|VBD corrected|correct|VBN by|by|IN subtracting|subtract|VBG the|the|DT LBG|LBG|NNP .|.|.
srain|srain|NN :|:|: K12|k12|NN MG1655|mg1655|NN
srain|srain|NN :|:|: K12|k12|NN MG1656|mg1656|NN
srain|srain|NN :|:|: K12|k12|NN MG1657|mg1657|NN
srain|srain|NN :|:|: K12|k12|NN MG1658|mg1658|NN
srain|srain|NN :|:|: K12|k12|NN MG1659|mg1659|NN
srain|srain|NN :|:|: K12|k12|NN MG1660|mg1660|NN
srain|srain|NN :|:|: K12|k12|NN MG1661|mg1661|NN
srain|srain|NN :|:|: K12|k12|NN MG1662|mg1662|NN
srain|srain|NN :|:|: K12|k12|NN MG1663|mg1663|NN
srain|srain|NN :|:|: K12|k12|NN MG1664|mg1664|NN
srain|srain|NN :|:|: K12|k12|NN MG1665|mg1665|NN
srain|srain|NN :|:|: K12|k12|NN MG1666|mg1666|NN
srain|srain|NN :|:|: K12|k12|NN MG1667|mg1667|NN
srain|srain|NN :|:|: K12|k12|NN MG1668|mg1668|NN
srain|srain|NN :|:|: K12|k12|NN MG1669|mg1669|NN
srain|srain|NN :|:|: K12|k12|NN MG1670|mg1670|NN
srain|srain|NN :|:|: K12|k12|NN MG1671|mg1671|NN
srain|srain|NN :|:|: K12|k12|NN MG1672|mg1672|NN
srain|srain|NN :|:|: K12|k12|NN MG1673|mg1673|NN
srain|srain|NN :|:|: K12|k12|NN MG1674|mg1674|NN
ß|ß|SYM -|-|: Aerobic|aerobic|JJ -|-|: A|a|NN
ß|ß|SYM -|-|: Aerobic|aerobic|JJ -|-|: B|b|NN
ß|ß|SYM -|-|: Anaerobic|anaerobic|JJ -|-|: A|a|NN
ß|ß|SYM -|-|: Anaerobic|anaerobic|JJ -|-|: B|b|NN
ß|ß|NN ChIP|chip|NN DNA|dna|NN from|from|IN WT|WT|NNP Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN K-12|k-12|NN
ssRNA-seq|ssrna-seq|JJ
ssrS|ssrs|NN _|_|NN 1|1|CD _|_|NN input|input|NN
ssrS|ssrs|NN _|_|NN 1|1|CD _|_|CD IP|IP|NNP
ssrS|ssrs|NN _|_|CD EE|ee|NN _|_|NN 1|1|CD
ssrS|ssrs|NN _|_|CD EE|ee|NN _|_|NN 2|2|CD
ssrS|ssrs|NN _|_|NN LS|ls|NN _|_|NN 1|1|CD
ssrS|ssrs|NN _|_|NN LS|ls|NN _|_|NN 2|2|CD
ssrS|ssrs|NN _|_|CD ME|me|NN _|_|NN 1|1|CD
ssrS|ssrs|NN _|_|CD ME|me|NN _|_|NN 2|2|CD
ssrS|ssrs|NN _|_|CD S|s|NN _|_|NN 1|1|CD
ssrS|ssrs|NN _|_|CD S|s|NN _|_|NN 2|2|CD
ssrS|ssrs|NN _|_|CD TS|ts|NN _|_|NN 1|1|CD
ssrS|ssrs|NN _|_|CD TS|ts|NN _|_|NN 2|2|CD
Stage|Stage|NNP :|:|: logarithm|logarithm|NN phase|phase|NN
Standard|Standard|NNP Affymetrix|Affymetrix|NNP procedure|procedure|NN
Standard|Standard|NNP hot-phenol|hot-phenol|NN method|method|NN
Standard|Standard|NNP illumina|illumina|NNP library|library|NN construction|construction|NN protocol|protocol|NN for|for|IN ChIP|chip|NN
standard|standard|NN in|in|FW vitro|vitro|FW -LRB-|-lrb-|-LRB- Mg2|mg2|NN +|+|CC -RRB-|-rrb-|-RRB-
standard|standard|NN in|in|FW vitro|vitro|FW MgCl2|mgcl2|NN
Standard|standard|JJ library|library|NN construction|construction|NN for|for|IN Illumina|Illumina|NNP Hiseq2500|hiseq2500|NN sequencing|sequencing|NN platform|platform|NN
Standard|Standard|NNP Paired-End|Paired-End|NNP Illumina|Illumina|NNP Library|Library|NNP Construction|Construction|NNP Protocol|Protocol|NNP was|be|VBD used|use|VBN with|with|IN modified|modify|VBN adapters|adapter|NNS containing|contain|VBG optimized|optimize|VBN 20|20|CD bp|bp|NN barcode|barcode|NN sequences|sequence|NNS -LRB-|-lrb-|-LRB- see|see|VB original|original|JJ paper|paper|NN -RRB-|-rrb-|-RRB- .|.|. Samples|sample|NNS with|with|IN barcoded|barcoded|JJ adapters|adapter|NNS were|be|VBD sequenced|sequence|VBN on|on|IN an|a|DT Illumina|Illumina|NNP HiSeq|HiSeq|NNP 2000|2000|CD with|with|IN a|a|DT 2x101|2x101|NN -LRB-|-lrb-|-LRB- for|for|IN the|the|DT first|first|JJ sequencing|sequencing|NN run|run|NN -RRB-|-rrb-|-RRB- and|and|CC 2x51|2x51|NN -LRB-|-lrb-|-LRB- for|for|IN the|the|DT second|second|JJ -RRB-|-rrb-|-RRB- base|base|NN paired-end|paired-end|NN reads|read|VBZ in|in|IN one|one|CD lane|lane|NN .|.|.
Starter|Starter|NNP was|be|VBD cultivated|cultivate|VBN at|at|IN 32|32|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 180|180|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, then|then|RB was|be|VBD inoculated|inoculate|VBN into|into|IN 100|100|CD ml|ml|NN of|of|IN 2YT|2yt|NN without|without|IN antibiotics|antibiotic|NNS and|and|CC cultivation|cultivation|NN was|be|VBD proceeded|proceed|VBN under|under|IN the|the|DT same|same|JJ conditions|condition|NNS until|until|IN culture|culture|NN reaching|reach|VBG mid-logphase|mid-logphase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.6-0.8|0.6-0.8|CD -RRB-|-rrb-|-RRB- .|.|.
Starting|start|VBG from|from|IN single|single|JJ colonies|colony|NNS ,|,|, the|the|DT following|follow|VBG cultures|culture|NNS were|be|VBD set|set|VBN up|up|RP in|in|IN triplicate|triplicate|NN for|for|IN overnight|overnight|JJ incubation|incubation|NN :|:|: GJ13507|gj13507|NN ,|,|, GJ13531|gj13531|NN ,|,|, and|and|CC GJ13533|gj13533|NN in|in|IN glucose-minimal|glucose-minimal|JJ A|a|NN ;|;|: and|and|CC GJ13519|gj13519|NN also|also|RB in|in|IN 0.2|0.2|CD %|%|NN glycerol-minimal|glycerol-minimal|JJ A.|a.|NN All|all|PDT the|the|DT cultures|culture|NNS were|be|VBD supplemented|supplement|VBN with|with|IN 200|200|CD μM|μm|NN IPTG|iptg|NN ,|,|, with|with|IN the|the|DT exception|exception|NN of|of|IN the|the|DT cultures|culture|NNS of|of|IN GJ13507|gj13507|NN whose|whose|WP$ supplementation|supplementation|NN with|with|IN IPTG|iptg|NN was|be|VBD at|at|IN 3|3|CD μM|μm|NN .|.|. The|the|DT overnight-grown|overnight-grown|JJ cultures|culture|NNS were|be|VBD each|each|DT subcultured|subculture|VBN into|into|IN 20|20|CD ml|ml|NN of|of|IN fresh|fresh|JJ medium|medium|NN of|of|IN the|the|DT same|same|JJ composition|composition|NN ,|,|, with|with|IN an|a|DT inoculum|inoculum|NN of|of|IN 1:50|1:50|CD for|for|IN GJ13507|gj13507|NN and|and|CC GJ13531|gj13531|NN and|and|CC of|of|IN 1:100|1:100|CD for|for|IN the|the|DT remainder|remainder|NN ,|,|, and|and|CC grown|grow|VBN to|to|TO an|a|DT A600|a600|NN of|of|IN 0.4|0.4|CD to|to|TO 0.45|0.45|CD ,|,|, before|before|IN the|the|DT cells|cell|NNS were|be|VBD harvested|harvest|VBN for|for|IN making|make|VBG the|the|DT RNA|rna|NN preparations|preparation|NNS
stationary|stationary|JJ culture|culture|NN
stationary|stationary|JJ phase|phase|NN
Stationary|stationary|JJ phase|phase|NN culture|culture|NN of|of|IN EDL933|edl933|NN rpoS|rpos|NN mutants|mutant|NNS in|in|IN LB|lb|NN at|at|IN OD600|od600|NN of|of|IN 1.5|1.5|CD
Stationary|stationary|JJ phase|phase|NN culture|culture|NN of|of|IN EDL933|edl933|NN wild|wild|JJ type|type|NN in|in|IN LB|lb|NN at|at|IN OD600|od600|NN of|of|IN 1.5|1.5|CD
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0.5|0.5|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 15|15|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0.5|0.5|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 30|30|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0.5|0.5|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 5|5|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0.5|0.5|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 60|60|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0.5|0.5|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- sodium|sodium|NN benozate|benozate|NN
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0|0|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 15|15|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0|0|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 30|30|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0|0|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 5|5|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN 0|0|CD %|%|NN sodium|sodium|NN benozate|benozate|NN for|for|IN 60|60|CD minutes|minute|NNS
Stationary|stationary|JJ phase|phase|NN growth|growth|NN -LRB-|-lrb-|-LRB- 24|24|CD hr|hr|NN -RRB-|-rrb-|-RRB- ~|~|NN 8|8|CD log|log|NN CFU/ml|cfu/ml|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000xg|8000xg|CD 4C|4c|NN and|and|CC resuspended|resuspend|VBN in|in|IN Luria-Bertaini|Luria-Bertaini|NNP broth|broth|NN with|with|IN no|no|DT sodium|sodium|NN benozate|benozate|NN
Stationary|stationary|JJ phase|phase|NN t|t|NN =|=|JJ 0|0|CD
Statistical|statistical|JJ analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG R|r|NN Limma|limma|NN package|package|NN -LRB-|-lrb-|-LRB- Linear|linear|JJ Models|model|NNS for|for|IN Microarrays|Microarrays|NNP Data|Data|NNP -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Smyth|Smyth|NNP 2004|2004|CD -RRB-|-rrb-|-RRB- ,|,|, where|where|WRB the|the|DT two|two|CD microarrays|microarray|NNS per|per|IN sample|sample|NN were|be|VBD normalized|normalize|VBN using|use|VBG lowess|lowess|JJ normalization|normalization|NN method|method|NN .|.|. Multiple-gene|multiple-gene|JJ probes|probe|NNS results|result|NNS were|be|VBD merged|merge|VBN and|and|CC normalized|normalize|VBN using|use|VBG the|the|DT MA|MA|NNP table|table|NN conversion|conversion|NN tool|tool|NN available|available|JJ on|on|IN the|the|DT MOLGEN|MOLGEN|NNP Bioinformatics|Bioinformatics|NNPS Server|server|NN -LRB-|-lrb-|-LRB- http://server.molgenrug.nl/|http://server.molgenrug.nl/|NN -|-|: Molecular|molecular|JJ genetics|genetics|NNS ,|,|, university|university|NN of|of|IN Groningen|Groningen|NNP ,|,|, the|the|DT Netherlands|Netherlands|NNP -RRB-|-rrb-|-RRB- .|.|.
Statistical|statistical|JJ comparisons|comparison|NNS were|be|VBD performed|perform|VBN using|use|VBG multiple|multiple|JJ testing|testing|NN procedures|procedure|NNS to|to|TO evaluate|evaluate|VB statistical|statistical|JJ significance|significance|NN for|for|IN differentially|differentially|RB expressed|express|VBN genes|gene|NNS .|.|. A|a|DT modified|modify|VBN t-test|t-test|NN -LRB-|-lrb-|-LRB- p-value|p-value|NN -RRB-|-rrb-|-RRB- was|be|VBD computed|compute|VBN to|to|TO measure|measure|VB the|the|DT significance|significance|NN associated|associate|VBN with|with|IN each|each|DT differential|differential|JJ expression|expression|NN value|value|NN .|.|. A|a|DT gene|gene|NN expression|expression|NN value|value|NN was|be|VBD decided|decide|VBN to|to|TO be|be|VB significantly|significantly|RB different|different|JJ in|in|IN the|the|DT mutant|mutant|JJ and|and|CC over-expression|over-expression|NN strains|strain|NNS when|when|WRB the|the|DT p-value|p-value|NN was|be|VBD less|less|JJR than|than|IN 0.05|0.05|CD -LRB-|-lrb-|-LRB- except|except|IN otherwise|otherwise|RB mentioned|mention|VBN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT expression|expression|NN ratio|ratio|NN was|be|VBD ≥|≥|CD 2.0|2.0|CD or|or|CC ≤|≤|CD 0.5|0.5|CD .|.|. Gene|Gene|NNP functions|function|NNS were|be|VBD assigned|assign|VBN using|use|VBG data|datum|NNS from|from|IN EcoCyc|ecocyc|NN -LRB-|-lrb-|-LRB- http://ecocyc.org/|http://ecocyc.org/|NN -RRB-|-rrb-|-RRB- .|.|.
Statistical|statistical|JJ preprocessing|preprocessing|NN steps|step|NNS were|be|VBD conducted|conduct|VBN with|with|IN ArrayPipe|arraypipe|NN -LRB-|-lrb-|-LRB- version|version|NN 1.7|1.7|CD -RRB-|-rrb-|-RRB- ,|,|, a|a|DT web-based|web-based|JJ software|software|NN designed|design|VBN for|for|IN processing|processing|NN of|of|IN microarray|microarray|NN data|datum|NNS -LRB-|-lrb-|-LRB- www.pathogenomics.ca/arraypipe|www.pathogenomics.ca/arraypipe|NN ,|,|, Hokamp|Hokamp|NNP et|et|FW al.|al.|FW 2004|2004|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT following|follow|VBG pre-processing|pre-processing|JJ steps|step|NNS were|be|VBD applied|apply|VBN :|:|: 1|1|LS -RRB-|-rrb-|-RRB- flagging|flagging|JJ of|of|IN markers|marker|NNS and|and|CC control|control|NN spots|spot|NNS ,|,|, 2|2|LS -RRB-|-rrb-|-RRB- subgrid-wise|subgrid-wise|JJ background|background|NN correction|correction|NN ,|,|, using|use|VBG the|the|DT median|median|NN of|of|IN the|the|DT lower|lower|JJR 10|10|CD %|%|NN foreground|foreground|NN intensity|intensity|NN as|as|IN an|a|DT estimate|estimate|NN for|for|IN the|the|DT background|background|NN noise|noise|NN ,|,|, 3|3|LS -RRB-|-rrb-|-RRB- data-shifting|data-shifting|NN ,|,|, 4|4|LS -RRB-|-rrb-|-RRB- limma|limma|NN 's|'s|POS LOESS|loess|JJ normalization|normalization|NN by|by|IN print|print|NN tip|tip|NN ,|,|, 5|5|CD -RRB-|-rrb-|-RRB- merging|merge|VBG of|of|IN duplicate|duplicate|VB spots|spot|NNS .|.|.
Stat-rpoS-rep1|stat-rpos-rep1|NN
Stat-rpoS-Rep1|stat-rpos-rep1|NN
Stat-rpoS-rep2|stat-rpos-rep2|NN
Stat-rpoS-Rep2|stat-rpos-rep2|NN
Stat-rpoS-rep3|stat-rpos-rep3|NN
Stat-rpoS-Rep3|stat-rpos-rep3|NN
Stat-WT-rep1|stat-wt-rep1|NN
Stat-WT-Rep1|stat-wt-rep1|NN
Stat-WT-rep2|stat-wt-rep2|NN
Stat-WT-Rep2|stat-wt-rep2|NN
Stat-WT-rep3|stat-wt-rep3|NN
Stat-WT-Rep3|stat-wt-rep3|NN
Steady-state|steady-state|JJ continuously-cultured|continuously-cultured|JJ control|control|NN samples|sample|NNS in|in|IN the|the|DT presence|presence|NN of|of|IN adequate|adequate|JJ Zn|zn|NN
Steady-state|steady-state|JJ continuously-cultured|continuously-cultured|JJ experiment|experiment|NN samples|sample|NNS in|in|IN the|the|DT total|total|JJ absence|absence|NN of|of|IN Zn|zn|NN
Steady-state|steady-state|JJ continuously-cultured|continuously-cultured|JJ experiment|experiment|NN samples|sample|NNS in|in|IN total|total|JJ absence|absence|NN of|of|IN Zn|zn|NN
Steady-state|steady-state|JJ continuously-cultured|continuously-cultured|JJ MG1655|mg1655|NN in|in|IN the|the|DT presence|presence|NN of|of|IN adequate|adequate|JJ Zn|zn|NN
Steady-state|steady-state|JJ continuously-cultured|continuously-cultured|JJ MG1655|mg1655|NN in|in|IN the|the|DT total|total|JJ absence|absence|NN of|of|IN Zn|zn|NN
STEC|stec|NN EC472/01|ec472/01|NN ,|,|, conditioned|conditioned|JJ medium|medium|NN
STEC|STEC|NNP EC472/01|ec472/01|NN ,|,|, fresh|fresh|JJ medium|medium|NN
STEC|STEC|NNP EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 1|1|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 2|2|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 3|3|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 4|4|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 1|1|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 2|2|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 3|3|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EC472|ec472|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 4|4|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 1|1|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 2|2|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 3|3|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN conditioned|conditioned|JJ medium|medium|NN ,|,|, replicate|replicate|VB 4|4|CD -LSB-|-lsb-|-LRB- COND|cond|NN -RSB-|-rsb-|-RRB-
STEC|stec|NN EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 1|1|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 2|2|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 3|3|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EH41|eh41|NN after|after|IN 3|3|CD hrs|hr|NNS incubation|incubation|NN in|in|IN fresh|fresh|JJ medium|medium|NN ,|,|, replicate|replicate|VB 4|4|CD -LSB-|-lsb-|-LRB- FRESH|fresh|JJ -RSB-|-rsb-|-RRB-
STEC|STEC|NNP EH41|eh41|NN ,|,|, conditioned|conditioned|JJ medium|medium|NN
STEC|STEC|NNP EH41|eh41|NN ,|,|, fresh|fresh|JJ medium|medium|NN
STEC|STEC|NNP strains|strain|NNS were|be|VBD lysate|lysate|NN using|use|VBG lysozyme|lysozyme|NN -LRB-|-lrb-|-LRB- 1|1|CD mg/mL|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC proteinase|proteinase|NN K|k|NN -LRB-|-lrb-|-LRB- 2|2|CD mg/mL|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN for|for|IN 10|10|CD min|min|NN at|at|IN 20|20|CD °C|°c|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD obtained|obtain|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP cat|cat|NN no.|no.|NN 74104|74104|CD ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. The|the|DT purity|purity|NN and|and|CC quantification|quantification|NN for|for|IN all|all|DT RNA|rna|NN samples|sample|NNS were|be|VBD done|do|VBN using|use|VBG the|the|DT NanoVue|NanoVue|NNP spectrophotometer|spectrophotometer|NN and|and|CC the|the|DT RNA|rna|NN quality|quality|NN was|be|VBD assessed|assess|VBN on|on|IN the|the|DT Agilent|Agilent|NNP BioAnalyzer|BioAnalyzer|NNP 2100|2100|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. All|all|DT samples|sample|NNS that|that|WDT present|present|VBP RIN|RIN|NNP >|>|JJR 7.0|7.0|CD were|be|VBD stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN until|until|IN used|use|VBN in|in|IN hybridization|hybridization|NN experiments|experiment|NNS .|.|.
stimulus|stimulus|NN :|:|: 1|1|CD MPa|mpa|NN for|for|IN 15|15|CD min|min|NN
stimulus|stimulus|NN :|:|: Control|Control|NNP
S|s|NN ,|,|, TP1|tp1|NN
S|s|NN ,|,|, TP2|tp2|NN
S|s|NN ,|,|, TP3|tp3|NN
S|s|NN ,|,|, TP4|tp4|NN
strain|strain|NN :|:|: 173150|173150|CD
strain|strain|NN :|:|: 174750|174750|CD
strain|strain|NN :|:|: 174900|174900|CD
strain|strain|NN :|:|: 178200|178200|CD
strain|strain|NN :|:|: 178850|178850|CD
strain|strain|NN :|:|: 178900|178900|CD
strain|strain|NN :|:|: 179100|179100|CD
strain|strain|NN :|:|: 179550|179550|CD
strain|strain|NN :|:|: 180050|180050|CD
strain|strain|NN :|:|: 180200|180200|CD
strain|strain|NN :|:|: 180600|180600|CD
strain|strain|NN :|:|: 2-1|2-1|CD
strain|strain|NN :|:|: 214-4|214-4|CD
strain|strain|NN :|:|: 2230|2230|CD
strain|strain|NN :|:|: 229-1|229-1|CD
strain|strain|NN :|:|: 2429|2429|CD
strain|strain|NN :|:|: 278485-1|278485-1|CD
strain|strain|NN :|:|: 292-1|292-1|CD
strain|strain|NN :|:|: 350C1A|350c1a|NN
strain|strain|NN :|:|: 3780|3780|CD
strain|strain|NN :|:|: 42-1|42-1|CD C1|c1|NN
strain|strain|NN 520|520|CD
strain|strain|NN 521|521|CD
strain|strain|NN :|:|: 86-24|86-24|CD
strain|strain|NN :|:|: AH28|ah28|NN
Strain|strain|NN A|a|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1224|1224|CD hours|hour|NNS .|.|.
Strain|strain|NN A|a|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1824|1824|CD hours|hour|NNS .|.|.
Strain|strain|NN A|a|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 2496|2496|CD hours|hour|NNS .|.|.
Strain|strain|NN A|a|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 384|384|CD hours|hour|NNS .|.|.
Strain|strain|NN A|a|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 744|744|CD hours|hour|NNS .|.|.
strain|strain|NN :|:|: APEC|apec|NN SCI-07|sci-07|NN -LRB-|-lrb-|-LRB- O|o|NN nontypeable|nontypeable|JJ :|:|: H31|h31|NN -RRB-|-rrb-|-RRB- isolated|isolate|VBN from|from|IN lesions|lesion|NNS -LRB-|-lrb-|-LRB- gelatinous|gelatinous|JJ edema|edema|NN -RRB-|-rrb-|-RRB- on|on|IN the|the|DT skin|skin|NN of|of|IN the|the|DT head|head|NN and|and|CC periorbital|periorbital|JJ tissues|tissue|NNS from|from|IN a|a|DT laying|lay|VBG hen|hen|NN showing|show|VBG clinical|clinical|JJ signs|sign|NNS of|of|IN swollen|swollen|JJ head|head|NN syndrome|syndrome|NN
strain|strain|NN :|:|: ArcA8myc|arca8myc|NN
strain|strain|NN :|:|: ARG-2|arg-2|NN
strain|strain|NN :|:|: ARG-3|arg-3|NN
strain|strain|NN :|:|: ATCC|atcc|NN 4157|4157|CD
strain|strain|NN :|:|: AW1|aw1|NN .7|.7|CD
strain|strain|NN :|:|: B|b|NN
strain|strain|NN B02|b02|NN
strain|strain|NN B05|b05|NN
strain|strain|NN :|:|: B2C|b2c|NN
strain|strain|NN :|:|: B7A|b7a|NN
strain|strain|NN background|background|NN :|:|: B|b|NN
strain|strain|NN background|background|NN :|:|: BW25113|bw25113|NN
strain/background|strain/background|NN :|:|: BW25113|bw25113|NN
strain|strain|NN background|background|NN :|:|: EDL933|edl933|NN
strain|strain|NN background|background|NN :|:|: K-12|k-12|NN
strain|strain|NN background|background|NN :|:|: MG1655|mg1655|NN
strain/background|strain/background|NN :|:|: MG1655|mg1655|NN
strain|strain|NN :|:|: BCE001|bce001|NN ,|,|, MS16|ms16|NN
strain|strain|NN :|:|: BCE002|bce002|NN ,|,|, MS12|ms12|NN
strain|strain|NN :|:|: BCE003|bce003|NN ,|,|, DS5|ds5|NN
strain|strain|NN :|:|: BCE005|bce005|NN ,|,|, MS23|ms23|NN
strain|strain|NN :|:|: BCE007|bce007|NN
strain|strain|NN :|:|: BCE007|bce007|NN ,|,|, MS11|ms11|NN
strain|strain|NN :|:|: BCE008|bce008|NN _|_|CD MS1|ms1|NN
strain|strain|NN :|:|: BCE008|bce008|NN ,|,|, MS13|ms13|NN
strain|strain|NN :|:|: BCE011|bce011|NN ,|,|, DS3|ds3|NN
strain|strain|NN :|:|: BCE013|bce013|NN ,|,|, DS1|ds1|NN
strain|strain|NN :|:|: BCE018|bce018|NN ,|,|, DS6|ds6|NN
strain|strain|NN :|:|: BCE019|bce019|NN ,|,|, MS16|ms16|NN
strain|strain|NN :|:|: BCE021|bce021|NN ,|,|, DS7|ds7|NN
strain|strain|NN :|:|: BCE022DS6|bce022ds6|NN
strain|strain|NN :|:|: BCE035|bce035|NN ,|,|, DS6|ds6|NN
strain|strain|NN :|:|: BCE035|bce035|NN ,|,|, MS8|ms8|NN
strain|strain|NN :|:|: BCE039|bce039|NN ,|,|, DS2|ds2|NN
strain|strain|NN :|:|: BCE039|bce039|NN ,|,|, MS13|ms13|NN
strain|strain|NN :|:|: BCE041|bce041|NN ,|,|, MS11|ms11|NN
strain|strain|NN :|:|: BCE046|bce046|NN ,|,|, DS2|ds2|NN
strain|strain|NN :|:|: BCE046|bce046|NN ,|,|, DS7|ds7|NN
strain|strain|NN :|:|: BCE046|bce046|NN ,|,|, MS16|ms16|NN
strain|strain|NN :|:|: BCE049|bce049|NN ,|,|, DS3|ds3|NN
strain|strain|NN :|:|: BCE049|bce049|NN ,|,|, MS9|ms9|NN
strain|strain|NN :|:|: BCE054|bce054|NN ,|,|, DS4|ds4|NN
strain|strain|NN :|:|: BCE054|bce054|NN ,|,|, MS24|ms24|NN
strain|strain|NN :|:|: BCE055|bce055|NN ,|,|, DS1|ds1|NN
strain|strain|NN :|:|: BCE058|bce058|NN ,|,|, MS13|ms13|NN
strain|strain|NN :|:|: BCE061|bce061|NN ,|,|, DS1|ds1|NN
strain|strain|NN :|:|: BCE062|bce062|NN ,|,|, DS2|ds2|NN
strain|strain|NN :|:|: BCE062|bce062|NN ,|,|, MS24|ms24|NN
strain|strain|NN :|:|: BCE063|bce063|NN ,|,|, DS4|ds4|NN
strain|strain|NN :|:|: BCE063|bce063|NN ,|,|, MS14|ms14|NN
strain|strain|NN :|:|: BCE066|bce066|NN ,|,|, DS5|ds5|NN
strain|strain|NN :|:|: BCE068|bce068|NN ,|,|, MS10|ms10|NN
strain|strain|NN :|:|: BCE068|bce068|NN ,|,|, MS23|ms23|NN
strain|strain|NN :|:|: BCE069|bce069|NN ,|,|, DS2|ds2|NN
strain|strain|NN :|:|: BCE069|bce069|NN ,|,|, MS15|ms15|NN
strain|strain|NN :|:|: BCE069|bce069|NN ,|,|, MS9|ms9|NN
strain|strain|NN :|:|: BCE129|bce129|NN ,|,|, DS2|ds2|NN
strain|strain|NN :|:|: Bear|Bear|NNP feces|fece|VBZ isolate|isolate|JJ B1|b1|NN
strain|strain|NN :|:|: Bear|Bear|NNP feces|fece|VBZ isolate|isolate|JJ B3|b3|NN
strain|strain|NN :|:|: Bear|Bear|NNP feces|fece|VBZ isolate|isolate|JJ B5|b5|NN
strain|strain|NN :|:|: beta-lactamase|beta-lactamase|NN -LRB-|-lrb-|-LRB- ESBL|esbl|NN -RRB-|-rrb-|-RRB- -|-|: producing|produce|VBG UPEC|upec|NN -LRB-|-lrb-|-LRB- ESBL019|esbl019|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: BJW9|bjw9|NN w|w|NN /|/|: recoded|recode|VBN ompF|ompf|NN
strain|strain|NN :|:|: BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- rne131|rne131|NN DrhlB|drhlb|NN
strain|strain|NN B|b|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1224|1224|CD hours|hour|NNS .|.|.
strain|strain|NN B|b|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1824|1824|CD hours|hour|NNS .|.|.
strain|strain|NN B|b|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 2496|2496|CD hours|hour|NNS .|.|.
strain|strain|NN B|b|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 384|384|CD hours|hour|NNS .|.|.
strain|strain|NN B|b|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 744|744|CD hours|hour|NNS .|.|.
strain|strain|NN BW25113|bw25113|NN
strain|strain|NN :|:|: BW25113|bw25113|NN
Strain|strain|NN BW25113|bw25113|NN
Strain|strain|NN BW25113|bw25113|NN
Strain|strain|NN :|:|: BW25113|bw25113|NN
Strain|strain|NN :|:|: BW25113|bw25113|NN
Strain|strain|NN :|:|: BW25113/arcA|bw25113/arca|NN -|-|:
Strain|strain|NN :|:|: BW25113/arcA|bw25113/arca|NN -|-|:
Strain|strain|NN :|:|: BW25113/fur|bw25113/fur|NN -|-|:
Strain|strain|NN :|:|: BW25113/fur|bw25113/fur|NN -|-|:
strain|strain|NN :|:|: BW25113|bw25113|NN hha|hha|NN hns|hn|NNS /|/|: pCA24N-hns|pca24n-hn|NNS
strain|strain|NN :|:|: BW25113|bw25113|NN hha|hha|NN hns|hn|NNS /|/|: pCA24N-hnsK57N|pca24n-hnsk57n|JJ
Strain|strain|NN :|:|: BW25113/ihfA|bw25113/ihfa|NN -|-|:
Strain|strain|NN :|:|: BW25113/ihfA|bw25113/ihfa|NN -|-|:
Strain|strain|NN :|:|: BW25113/phoB|bw25113/phob|NN -|-|:
Strain|strain|NN :|:|: BW25113/phoB|bw25113/phob|NN -|-|:
strain|strain|NN BW25113|bw25113|NN ppsA|ppsa|NN deletion|deletion|NN
strain|strain|NN :|:|: BW25113/ubiE|bw25113/ubie|NN -|-|:
strain|strain|NN :|:|: BW27786|bw27786|NN -LRB-|-lrb-|-LRB- K-12|k-12|NN derivative|derivative|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: BW38028|bw38028|NN
strain|strain|NN C01|c01|NN
strain|strain|NN C02|c02|NN
strain|strain|NN :|:|: C-34666|c-34666|NN
strain|strain|NN :|:|: C-35134|c-35134|NN
strain|strain|NN :|:|: C-35209|c-35209|NN
strain|strain|NN :|:|: C-35213|c-35213|NN
strain|strain|NN :|:|: C-35605|c-35605|NN
strain|strain|NN :|:|: C-35662|c-35662|NN
strain|strain|NN :|:|: C-35776|c-35776|NN
strain|strain|NN :|:|: C-35959|c-35959|NN
strain|strain|NN :|:|: C-36255|c-36255|NN
strain|strain|NN :|:|: CAR005|car005|NN
strain|strain|NN :|:|: Cattle|Cattle|NNP feces|fece|NNS isolate|isolate|VBP C1A|c1a|NN
strain|strain|NN :|:|: Cattle|Cattle|NNP feces|fece|NNS isolate|isolate|VBP C4A|c4a|NN
strain|strain|NN :|:|: Cattle|Cattle|NNP feces|fece|NNS isolate|isolate|VBP C6D|c6d|NN
strain|strain|NN :|:|: CFT073|cft073|NN
strain|strain|NN CFT073|cft073|NN ;|;|: GenBank|genbank|NN accession|accession|NN AE014075|ae014075|NN .1|.1|CD
strain|strain|NN :|:|: CFT073|cft073|NN nsrR|nsrr|NN :|:|: :|:|: 3X-Flag|3x-flag|NN tag|tag|NN
strain|strain|NN :|:|: clinical|clinical|JJ isolate|isolate|JJ LB226692|lb226692|NN
strain|strain|NN :|:|: CMA540|cma540|NN -LRB-|-lrb-|-LRB- MG1693|mg1693|NN delta|delta|NN _|_|NN hfq|hfq|NN :|:|: :|:|: cat|cat|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: CMCC|cmcc|NN -LRB-|-lrb-|-LRB- B|b|NN -RRB-|-rrb-|-RRB- 44102|44102|CD
strain|strain|NN :|:|: cocar|cocar|NN 07-043|07-043|CD
strain|strain|NN :|:|: cocar|cocar|NN 07-40|07-40|CD
strain|strain|NN C|c|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1224|1224|CD hours|hour|NNS .|.|.
strain|strain|NN C|c|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1824|1824|CD hours|hour|NNS .|.|.
strain|strain|NN C|c|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 2496|2496|CD hours|hour|NNS .|.|.
strain|strain|NN C|c|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 384|384|CD hours|hour|NNS .|.|.
strain|strain|NN C|c|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 744|744|CD hours|hour|NNS .|.|.
strain|strain|NN :|:|: cosin|cosin|NN 07-14|07-14|CD
strain|strain|NN :|:|: cosin|cosin|NN 07-36|07-36|CD
strain|strain|NN :|:|: cosin|cosin|NN 07-61|07-61|CD
strain|strain|NN :|:|: cosin|cosin|NN 07-88|07-88|CD
strain|strain|NN :|:|: cosin|cosin|NN 07-92|07-92|CD
strain|strain|NN :|:|: Crooks|crook|NNS
strain|strain|NN :|:|: Crp|Crp|NNP _|_|SYM delAr1|delar1|NN
strain|strain|NN :|:|: Crp|Crp|NNP _|_|SYM delAr1delAr2|delar1delar2|NN
strain|strain|NN :|:|: Crp|Crp|NNP _|_|SYM delAr2|delar2|NN
strain|strain|NN :|:|: CSH50|csh50|NN
strain|strain|NN :|:|: CVCC2943|cvcc2943|NN
strain|strain|NN :|:|: D02-2|d02-2|NN
strain|strain|NN :|:|: Deer|deer|NNS feces|fece|NNS isolate|isolate|VBP D1|d1|NN
strain|strain|NN :|:|: Deer|deer|NNS feces|fece|NNS isolate|isolate|NN D3|d3|NN
strain|strain|NN :|:|: Deer|deer|NNS feces|fece|NNS isolate|isolate|VBP W6A|w6a|NN
strain|strain|NN :|:|: delta|delta|NN Crp|crp|NN
strain|strain|NN description|description|NN :|:|: E.|e.|FW coli|coli|FW BW25113|bw25113|NN with|with|IN an|a|DT integrated|integrate|VBN F|f|NN tra|tra|NN operon|operon|NN at|at|IN the|the|DT trp|trp|NN locus|locus|NN ,|,|, plus|plus|CC additional|additional|JJ F|f|NN oriT|orit|NN sequences|sequence|NNS integrated|integrate|VBN at|at|IN mbhA|mbha|NN and|and|CC hyfC|hyfc|NN
strain|strain|NN description|description|NN :|:|: E.|e.|FW coli|coli|FW BW25113|bw25113|NN with|with|IN F|f|NN oriTs|orit|NNS integrated|integrate|VBN at|at|IN mbhA|mbha|NN and|and|CC hyfC|hyfc|NN
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χχχ|χχχ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN rph|rph|NN +|+|CC
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: lacZ|lacz|NN :|:|: :|:|: 246pal|246pal|JJ cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χ|χ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN codBχ|codbχ|NN -|-|: prpEχ|prpeχ|NN -|-|: mhpCχ|mhpcχ|NN -|-|: cynXχ|cynxχ|NN -|-|: rph|rph|NN +|+|CC
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: lacZ|lacz|NN :|:|: :|:|: 246pal|246pal|JJ cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χχ|χχ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN codBχ|codbχ|NN -|-|: prpEχ|prpeχ|NN -|-|: mhpCχ|mhpcχ|NN -|-|: cynXχ|cynxχ|NN -|-|: rph|rph|NN +|+|CC
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: lacZ|lacz|NN :|:|: :|:|: 246pal|246pal|JJ cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χχχ|χχχ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN codBχ|codbχ|NN -|-|: prpEχ|prpeχ|NN -|-|: mhpCχ|mhpcχ|NN -|-|: cynXχ|cynxχ|NN -|-|: rph|rph|NN +|+|CC
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: lacZ|lacz|NN :|:|: :|:|: 246pal|246pal|JJ cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χχχ|χχχ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN rph|rph|NN +|+|CC
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: lacZ|lacz|NN :|:|: :|:|: 246pal|246pal|JJ cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χχχχ|χχχχ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN codBχ|codbχ|NN -|-|: prpEχ|prpeχ|NN -|-|: mhpCχ|mhpcχ|NN -|-|: cynXχ|cynxχ|NN -|-|: rph|rph|NN +|+|CC
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: lacZ|lacz|NN :|:|: :|:|: 246pal|246pal|JJ cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χχχχχ|χχχχχ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN codBχ|codbχ|NN -|-|: prpEχ|prpeχ|NN -|-|: mhpCχ|mhpcχ|NN -|-|: cynXχ|cynxχ|NN -|-|: rph|rph|NN +|+|CC
strain|strain|NN details|detail|NNS :|:|: lacIq|laciq|NN lacZχ|laczχ|NN -|-|: lacZ|lacz|NN :|:|: :|:|: 246pal|246pal|JJ cynX|cynx|NN :|:|: :|:|: GmR|gmr|NN lacZY|laczy|NN :|:|: :|:|: χχχχχχ|χχχχχχ|NN mhpA|mhpa|NN :|:|: :|:|: χχχ|χχχ|NN codBχ|codbχ|NN -|-|: prpEχ|prpeχ|NN -|-|: mhpCχ|mhpcχ|NN -|-|: cynXχ|cynxχ|NN -|-|: rph|rph|NN +|+|CC
strain|strain|NN :|:|: DH10BGFP|dh10bgfp|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔhisA|δhisa|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔhisB|δhisb|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔhisC|δhisc|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔhisD|δhisd|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔhisF|δhisf|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔhisG|δhisg|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔhisI|δhisi|NN :|:|: :|:|: cat|cat|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1|dh1|NN ΔintC|δintc|NN :|:|: :|:|: Ptrc-dsred|ptrc-dsred|JJ .|.|. t4-tetR-PEM7-zeo|t4-tetr-pem7-zeo|NN ΔgalK|δgalk|NN :|:|: :|:|: PtetA-gfpuv5|pteta-gfpuv5|NN
strain|strain|NN :|:|: DH1ΔleuB|dh1δleub|NN :|:|: :|:|: gfpuv5-kmr|gfpuv5-kmr|JJ
strain|strain|NN :|:|: DH5a|dh5a|NN
strain|strain|NN :|:|: DH5α|dh5α|NN
strain|strain|NN :|:|: DH5α|dh5α|NN -LRB-|-lrb-|-LRB- pAR060302|par060302|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: DL4184|dl4184|NN
strain|strain|NN :|:|: DL4201|dl4201|NN
strain|strain|NN :|:|: DL5966|dl5966|NN
strain|strain|NN :|:|: DL6204|dl6204|NN
strain|strain|NN :|:|: DMS2545|dms2545|NN -LRB-|-lrb-|-LRB- K-12|k-12|NN derivative|derivative|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: DMS2564|dms2564|NN -LRB-|-lrb-|-LRB- K-12|k-12|NN derivative|derivative|NN -RRB-|-rrb-|-RRB-
strain|strain|NN D|d|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1224|1224|CD hours|hour|NNS .|.|.
strain|strain|NN D|d|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1824|1824|CD hours|hour|NNS .|.|.
strain|strain|NN D|d|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 2496|2496|CD hours|hour|NNS .|.|.
strain|strain|NN D|d|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 384|384|CD hours|hour|NNS .|.|.
strain|strain|NN D|d|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 744|744|CD hours|hour|NNS .|.|.
strain|strain|NN :|:|: DS168-1|ds168-1|NN
strain|strain|NN :|:|: DS26-1|ds26-1|NN
strain|strain|NN :|:|: DY330|dy330|NN
strain|strain|NN :|:|: DY330|dy330|NN -LRB-|-lrb-|-LRB- W3110|w3110|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: E058|e058|NN
strain|strain|NN :|:|: E1392/75|e1392/75|NN
strain|strain|NN :|:|: E1777|e1777|NN
strain|strain|NN :|:|: E1785|e1785|NN
strain|strain|NN :|:|: E1786|e1786|NN
strain|strain|NN :|:|: E1787|e1787|NN
strain|strain|NN :|:|: E1788|e1788|NN
strain|strain|NN :|:|: E1789|e1789|NN
strain|strain|NN :|:|: E1790|e1790|NN
strain|strain|NN :|:|: E1791|e1791|NN
strain|strain|NN :|:|: E1792|e1792|NN
strain|strain|NN :|:|: E20738A|e20738a|NN
strain|strain|NN :|:|: E24377A|e24377a|NN
strain|strain|NN :|:|: E2528C1|e2528c1|NN
strain|strain|NN :|:|: E7473/0|e7473/0|NN
strain|strain|NN :|:|: E7476A|e7476a|NN
strain|strain|NN :|:|: E8775|e8775|NN
strain|strain|NN :|:|: E9034A|e9034a|NN
strain|strain|NN :|:|: EC472/01|ec472/01|NN -LRB-|-lrb-|-LRB- isolated|isolate|VBN from|from|IN cattle|cattle|NNS -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: E.|e.|FW coli|coli|FW ATCC|atcc|NN 25922|25922|CD
strain|strain|NN :|:|: E.|e.|FW coli|coli|FW DH1|dh1|NN
strain|strain|NN :|:|: E.|e.|FW coli|coli|FW imp|imp|FW 4231|4231|CD -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: E.|e.|FW coli|coli|FW imp|imp|FW 4231|4231|CD -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN the|the|DT 93th|93th|JJ codon|codon|NN of|of|IN fabI|fabI|NNP
strain|strain|NN :|:|: E.|e.|FW coli|coli|FW imp|imp|FW 4231|4231|CD -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- ,|,|, substitution|substitution|NN of|of|IN the|the|DT 94th|94th|JJ codon|codon|NN of|of|IN fabI|fabI|NNP
strain|strain|NN :|:|: E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: fnr|fnr|SYM -|-|: ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: aerobic|aerobic|JJ
Strain|Strain|NNP :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: fnr|fnr|SYM -|-|: ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: fnr|fnr|SYM -|-|: ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO2|no2|NN
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: fnr|fnr|SYM -|-|: ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO3|no3|NN
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: narXL|narxl|NN ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO2|no2|NN
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: narXLP|narxlp|NN ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO2|no2|NN
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: wt|wt|JJ ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: aerobic|aerobic|JJ
Strain|Strain|NNP :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: wt|wt|JJ ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: wt|wt|JJ ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO2|no2|NN
Strain|strain|NN :|:|: E.coli|e.coli|NNS K-12|k-12|NN MG1655|mg1655|NN ,|,|, Genetic|genetic|JJ background|background|NN :|:|: wt|wt|JJ ,|,|, Growth|growth|NN conditions|condition|NNS :|:|: anaerobic|anaerobic|JJ plus|plus|CC NO3|no3|NN
strain|strain|NN :|:|: E.coli|e.coli|NNS O157|o157|NN :|:|: H7|h7|NN EDL|edl|NN 932|932|CD
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10915|tw10915|NN
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10916|tw10916|NN
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10917|tw10917|NN
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10938|tw10938|NN
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10948|tw10948|NN
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10950|tw10950|NN
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10957|tw10957|NN
strain|strain|NN :|:|: e.|e.|FW coli|coli|FW o157|o157|FW H7|h7|NN strain|strain|NN TW10967|tw10967|NN
strain|strain|NN :|:|: E.|e.|FW coli|coli|FW RP437|rp437|NN
strain|strain|NN :|:|: ECOM4|ecom4|NN
strain|strain|NN :|:|: EDL933|edl933|NN
strain|strain|NN :|:|: EDL|edl|NN 933|933|CD
strain|strain|NN :|:|: EH41|eh41|NN -LRB-|-lrb-|-LRB- isolated|isolate|VBN from|from|IN patient|patient|NN with|with|IN HUS|hus|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: EHEC|ehec|NN strain|strain|NN
Strain|strain|NN EM1453|em1453|NN wild-type|wild-type|JJ pBAD-ryhB|pbad-ryhb|NN #|#|# 1|1|CD +|+|CC arabinose|arabinose|NN
strain|strain|NN E|e|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1224|1224|CD hours|hour|NNS .|.|.
strain|strain|NN E|e|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1824|1824|CD hours|hour|NNS .|.|.
strain|strain|NN E|e|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 2496|2496|CD hours|hour|NNS .|.|.
strain|strain|NN E|e|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 384|384|CD hours|hour|NNS .|.|.
strain|strain|NN E|e|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 744|744|CD hours|hour|NNS .|.|.
strain|strain|NN :|:|: EP61|ep61|NN
strain|strain|NN :|:|: EPEC|epec|NN
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW 8624|8624|CD
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW strain|strain|NN 8624|8624|CD
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW strain|strain|NN 8624|8624|CD kdpE|kdpe|NN mutant|mutant|JJ
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW strain|strain|NN 8624|8624|CD qseB|qseb|NN mutant|mutant|JJ
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW strain|strain|NN 8624|8624|CD qseC|qseC|NNP
strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW strain|strain|NN 8624|8624|CD qseC|qsec|NN mutant|mutant|JJ
Strain|strain|NN :|:|: Escherichia|escherichia|FW coli|coli|FW W3110|w3110|NN -LSB-|-lsb-|-LRB- F|f|NN --|--|: IN|in|IN -LRB-|-lrb-|-LRB- rrnD-rrnE|rrnd-rrne|NN -RRB-|-rrb-|-RRB- 1|1|CD -RSB-|-rsb-|-RRB-
strain|strain|NN :|:|: ETEC|ETEC|NNP 10/1|10/1|CD
strain|strain|NN :|:|: ETEC|etec|NNS 18/2|18/2|CD
strain|strain|NN :|:|: ETEC|ETEC|NNP 20/10|20/10|CD
strain|strain|NN :|:|: ETEC|ETEC|NNP 8/11|8/11|CD
strain|strain|NN :|:|: ETEC|ETEC|NNP Jurua|Jurua|NNP
strain|strain|NN :|:|: ETP05-002|etp05-002|NN
strain|strain|NN :|:|: ETP05-003|etp05-003|NN
strain|strain|NN :|:|: ETP05-007|etp05-007|NN
strain|strain|NN :|:|: ETP05-008|etp05-008|NN
strain|strain|NN :|:|: ETP05-009|etp05-009|NN
strain|strain|NN :|:|: ETP05-010|etp05-010|NN
strain|strain|NN :|:|: ETP05-011|etp05-011|NN
strain|strain|NN :|:|: ETP05-012|etp05-012|NN
strain|strain|NN :|:|: ETP05-015|etp05-015|NN
strain|strain|NN :|:|: ETP05-016|etp05-016|NN
strain|strain|NN :|:|: ETP05-017|etp05-017|NN
strain|strain|NN :|:|: ETP05-019|etp05-019|NN
strain|strain|NN :|:|: ETP05-020|etp05-020|NN
strain|strain|NN :|:|: ETP05-026|etp05-026|NN
strain|strain|NN :|:|: ETP05-035|etp05-035|NN
strain|strain|NN :|:|: ETP05-038|etp05-038|NN
strain|strain|NN :|:|: ETP05-039|etp05-039|NN
strain|strain|NN :|:|: ETP05-044|etp05-044|NN
strain|strain|NN :|:|: ETP05-046|etp05-046|NN
strain|strain|NN :|:|: ETP05-047|etp05-047|NN
strain|strain|NN :|:|: ETP05-050|etp05-050|NN
strain|strain|NN :|:|: ETP98004|etp98004|NN
strain|strain|NN :|:|: ETP98015|etp98015|NN
strain|strain|NN :|:|: ETP98028|etp98028|NN
strain|strain|NN :|:|: ETP98038|etp98038|NN
strain|strain|NN :|:|: ETP98042|etp98042|NN
strain|strain|NN :|:|: ETP98053|etp98053|NN
strain|strain|NN :|:|: ETP98056|etp98056|NN
strain|strain|NN :|:|: ETP98061|etp98061|NN
strain|strain|NN :|:|: ETP98062|etp98062|NN
strain|strain|NN :|:|: ETP98066|etp98066|NN
strain|strain|NN :|:|: ETP98068|etp98068|NN
strain|strain|NN :|:|: ETP98073|etp98073|NN
strain|strain|NN :|:|: ETP98097|etp98097|NN
strain|strain|NN :|:|: ETP98103|etp98103|NN
strain|strain|NN :|:|: ETP98105|etp98105|NN
strain|strain|NN :|:|: ETP98109|etp98109|NN
strain|strain|NN :|:|: ETP98111|etp98111|NN
strain|strain|NN :|:|: ETP98112|etp98112|NN
strain|strain|NN :|:|: ETP98114|etp98114|NN
strain|strain|NN :|:|: ETP98115|etp98115|NN
strain|strain|NN F01|f01|NN
strain|strain|NN F02|f02|NN
strain|strain|NN :|:|: F5656-C1|f5656-c1|NN
strain|strain|NN :|:|: F595C|f595c|NN
strain|strain|NN :|:|: FHI12|fhi12|NN
strain|strain|NN :|:|: FHI24|fhi24|NN
strain|strain|NN :|:|: FHI25|fhi25|CD
strain|strain|NN :|:|: FHI27|fhi27|NN
strain|strain|NN :|:|: FHI36|fhi36|NN
strain|strain|NN :|:|: FHI4|fhi4|NN
strain|strain|NN :|:|: FHI43|fhi43|NN
strain|strain|NN :|:|: FHI48|fhi48|NN
strain|strain|NN :|:|: FHI6|fhi6|NN
strain|strain|NN :|:|: FHI63|fhi63|NN
strain|strain|NN :|:|: FHI66|fhi66|NN
strain|strain|NN :|:|: FHI7|fhi7|NN
strain|strain|NN :|:|: FHI79|fhi79|NN
strain|strain|NN :|:|: FHI8|fhi8|NN
strain|strain|NN :|:|: FHI83|fhi83|NN
strain|strain|NN :|:|: FHI9|fhi9|NN
strain|strain|NN :|:|: FHI95|fhi95|NN
strain|strain|NN :|:|: Fnr8myc|fnr8myc|NN
strain|strain|NN F|f|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1224|1224|CD hours|hour|NNS .|.|.
strain|strain|NN F|f|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 1824|1824|CD hours|hour|NNS .|.|.
strain|strain|NN F|f|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 2496|2496|CD hours|hour|NNS .|.|.
strain|strain|NN F|f|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 384|384|CD hours|hour|NNS .|.|.
strain|strain|NN F|f|NN of|of|IN experimental|experimental|JJ evolution|evolution|NN under|under|IN ethanol|ethanol|NN stress|stress|NN in|in|IN 744|744|CD hours|hour|NNS .|.|.
strain|strain|NN :|:|: FRIK2000|frik2000|CD
strain|strain|NN :|:|: FRIK966|frik966|NN
strain|strain|NN :|:|: G4H14|g4h14|NN
strain|strain|NN :|:|: GGG10|ggg10|NN
strain|strain|NN :|:|: GLBRCE1|glbrce1|NN
strain|strain|NN :|:|: GLBRCE1|glbrce1|NN _|_|CD pBBR|pbbr|NN
strain|strain|NN :|:|: GM11|gm11|NN
strain|strain|NN H01|h01|NN
strain|strain|NN H02|h02|NN
strain|strain|NN H03|h03|NN
strain|strain|NN H04|h04|NN
strain|strain|NN H05|h05|NN
strain|strain|NN H12|h12|NN
strain|strain|NN H23|h23|NN
strain|strain|NN H27|h27|NN
strain|strain|NN :|:|: HB101|hb101|NN
strain|strain|NN :|:|: hemA|hema|NN strain|strain|NN MG1655|mg1655|NN
strain|strain|NN :|:|: ∆|∆|CD hns|hn|NNS /|/|: ∆|∆|SYM stpA|stpa|NN
strain|strain|NN :|:|: HS|hs|NN
strain|strain|NN :|:|: HT873|ht873|NN
strain|strain|NN :|:|: HT874|ht874|NN
strain|strain|NN :|:|: HT875|ht875|NN
strain|strain|NN :|:|: Human|human|JJ sewage|sewage|NN isolate|isolate|NN H1|h1|NN
strain|strain|NN :|:|: Human|human|JJ sewage|sewage|NN isolate|isolate|NN H2|h2|NN
strain|strain|NN :|:|: Human|human|JJ sewage|sewage|NN isolate|isolate|NN H3|h3|NN
strain|strain|NN :|:|: IAI1|iai1|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p1|p1|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p10|p10|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p11|p11|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p12|p12|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p13|p13|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p2|p2|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p4|p4|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p5|p5|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|CD p6|p6|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|NN p7|p7|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|CD p8|p8|NN
strain|strain|NN :|:|: ICDDR|icddr|NN ,|,|, B|b|NN _|_|CD p9|p9|NN
strain|strain|NN information|information|NN :|:|: E.|e.|FW coli|coli|FW harboring|harboring|NN empty|empty|JJ vector|vector|NN -LRB-|-lrb-|-LRB- pRADgro|pradgro|NN -RRB-|-rrb-|-RRB- ,|,|, used|use|VBN as|as|IN a|a|DT control|control|NN strain|strain|NN
strain|strain|NN information|information|NN :|:|: E.|e.|FW coli|coli|FW harboring|harbor|VBG pRADgro|pradgro|NN :|:|: :|:|: dr1558|dr1558|NN
strain|strain|NN :|:|: IspG1|ispg1|NN
strain|strain|NN :|:|: JM109|jm109|NN
strain|strain|NN :|:|: JM83|jm83|NN
strain|strain|NN :|:|: JPEP22|jpep22|NN
strain|strain|NN :|:|: JW3367|jw3367|NN
strain|strain|NN :|:|: K12|k12|NN
strain|strain|NN :|:|: K-12|k-12|NN
Strain|strain|NN :|:|: K-12|k-12|NN
strain|strain|NN :|:|: K-12|k-12|NN MG1655|mg1655|NN
strain|strain|NN :|:|: K12|k12|NN MG1655|mg1655|NN
strain|strain|NN :|:|: K12|k12|NN -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: K12|k12|NN MG1655|mg1655|NN deltaprfC|deltaprfc|NN
strain|strain|NN :|:|: K12|k12|NN MG1655|mg1655|NN prfB-Bstrain|prfb-bstrain|JJ allele|allele|NN
strain|strain|NN :|:|: K12|k12|NN MG1655|mg1655|NN prfB-Bstrain|prfb-bstrain|JJ allele|allele|NN deltaprfC|deltaprfc|NN
strain|strain|NN :|:|: k-12|k-12|NN MG1655|mg1655|NN wild-type|wild-type|JJ
strain|strain|NN :|:|: K12-MG1693|k12-mg1693|NN
strain|strain|NN :|:|: K-12|k-12|NN PHL644/pMP4655|phl644/pmp4655|NN
Strain|strain|NN :|:|: K-12|k-12|NN reduced|reduce|VBD genome|genome|NN
strain|strain|NN :|:|: K-12|k-12|NN substrain|substrain|NN MG1655|mg1655|NN
strain|strain|NN :|:|: K-12|k-12|NN substr|substr|NN .|.|. DH10B|dh10b|NN
strain|strain|NN :|:|: K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN
strain|strain|NN :|:|: K-12|k-12|NN W3110|w3110|NN
strain|strain|NN :|:|: K12|k12|NN W3110|w3110|NN
strain|strain|NN :|:|: KCTC|KCTC|NNP 2571|2571|CD
strain|strain|NN :|:|: KMD|KMD|NNP
strain|strain|NN :|:|: L-form|l-form|JJ
strain|strain|NN :|:|: LSN02-012560|lsn02-012560|NN /|/|: A|a|DT
strain|strain|NN :|:|: LSN03-016011|lsn03-016011|NN /|/|: A|a|DT
strain|strain|NN :|:|: M408C1|m408c1|NN
strain|strain|NN :|:|: M424C1|m424c1|NN
strain|strain|NN :|:|: MC1000|mc1000|NN
strain|strain|NN :|:|: MC1061|mc1061|NN
strain|strain|NN :|:|: MC4100|mc4100|NN
strain|strain|NN :|:|: MC4100|mc4100|NN derivative|derivative|JJ
strain|strain|NN :|:|: MC4100|mc4100|NN derivative|derivative|NN ,|,|, dcd|dcd|NN :|:|: :|:|: kan|kan|FW
strain|strain|NN :|:|: MC4100|mc4100|NN derivative|derivative|NN ,|,|, ndk|ndk|NN :|:|: :|:|: cam|cam|FW
strain|strain|NN :|:|: MC4100|mc4100|NN derivative|derivative|NN ,|,|, recA730|reca730|NN
strain|strain|NN :|:|: MC4100|mc4100|NN derivative|derivative|NN ,|,|, recA730|reca730|NN ,|,|, dcd|dcd|NN :|:|: :|:|: kan|kan|FW
strain|strain|NN :|:|: MC4100|mc4100|NN derivative|derivative|NN ,|,|, recA730|reca730|NN ,|,|, ndk|ndk|NN :|:|: :|:|: cam|cam|FW
strain|strain|NN :|:|: MC4101|mc4101|NN
strain|strain|NN :|:|: MC4102|mc4102|NN
strain|strain|NN :|:|: MC4103|mc4103|NN
strain|strain|NN :|:|: MC4104|mc4104|NN
strain|strain|NN :|:|: MC4105|mc4105|NN
strain|strain|NN :|:|: MC4106|mc4106|NN
strain|strain|NN :|:|: MC4107|mc4107|NN
strain|strain|NN :|:|: MDS42|mds42|NN
strain|strain|NN :|:|: MDS42|mds42|NN -LRB-|-lrb-|-LRB- genome|genome|NN reduced|reduce|VBN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: MDS42|mds42|NN -LRB-|-lrb-|-LRB- RL1961|rl1961|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: MG1655|mg1655|NN
strain|strain|NN :|:|: MG|mg|NN 1655|1655|CD
Strain|Strain|NNP MG1655|MG1655|NNP
Strain|Strain|NNP MG1655|mg1655|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|mop|NNS minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- www.genome.wisc.edu/resources/protocols/mopsminimal.htm|www.genome.wisc.edu/resources/protocols/mopsminimal.htm|NN -RRB-|-rrb-|-RRB- .|.|.
strain|strain|NN :|:|: MG1655|mg1655|NN delta|delta|NN lac|lac|NN
strain|strain|NN :|:|: MG1655|mg1655|NN delta|delta|NN lac|lac|NN delta|delta|NN dksA|dksa|NN
strain|strain|NN :|:|: MG1655|mg1655|NN delta|delta|NN lac|lac|NN +|+|CC MG1655|mg1655|NN delta|delta|NN lac|lac|NN delta|delta|NN dksA|dksa|NN
strain|strain|NN :|:|: MG1655|mg1655|NN delta|delta|NN _|_|CD mazF|mazf|NN
strain|strain|NN :|:|: MG1655dnaC2|mg1655dnac2|NN
strain|strain|NN :|:|: MG1655GFP|mg1655gfp|NN
strain|strain|NN :|:|: MG1655|mg1655|NN K-12|k-12|NN WT|wt|JJ
Strain|strain|NN MG1655|mg1655|NN or|or|CC isogenic|isogenic|JJ strain|strain|NN MG1655|mg1655|NN HA3|ha3|NN :|:|: :|:|: nusG|nusg|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|mop|NNS minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN -LRB-|-lrb-|-LRB- www.genome.wisc.edu/resources/protocols/mopsminimal.htm|www.genome.wisc.edu/resources/protocols/mopsminimal.htm|NN -RRB-|-rrb-|-RRB- .|.|.
strain|strain|NN :|:|: MG1655|mg1655|NN -LRB-|-lrb-|-LRB- parent|parent|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: MG1655|mg1655|NN -LSB-|-lsb-|-LRB- p-CTRL|p-ctrl|NN -RSB-|-rsb-|-RRB-
strain|strain|NN :|:|: MG1655|mg1655|NN -LSB-|-lsb-|-LRB- p-CUA|p-cua|NN -RSB-|-rsb-|-RRB-
strain|strain|NN :|:|: MG1655|mg1655|NN -LSB-|-lsb-|-LRB- p-CUG|p-cug|NN -RSB-|-rsb-|-RRB-
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT1|pgit1|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ the|the|DT ytfE|ytfe|NN promoter|promoter|NN in|in|IN multicopy|multicopy|JJ ,|,|, titrates|titrate|VBZ out|out|RP NsrR|nsrr|NN to|to|TO phenocopy|phenocopy|VB an|a|DT NsrR|nsrr|NN -|-|: mutation|mutation|NN -RRB-|-rrb-|-RRB-
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT1|pgit1|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ the|the|DT ytfE|ytfe|NN promoter|promoter|NN in|in|IN multicopy|multicopy|JJ ,|,|, titrates|titrate|VBZ out|out|RP NsrR|nsrr|NN to|to|TO phenocopy|phenocopy|VB an|a|DT NsrR|nsrr|NN -|-|: mutation|mutation|NN -RRB-|-rrb-|-RRB- Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT1|pgit1|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ the|the|DT ytfE|ytfe|NN promoter|promoter|NN in|in|IN multicopy|multicopy|JJ ,|,|, titrates|titrate|VBZ out|out|RP NsrR|nsrr|NN to|to|TO phenocopy|phenocopy|VB an|a|DT NsrR|nsrr|NN -|-|: mutation|mutation|NN -RRB-|-rrb-|-RRB- Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT1|pgit1|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ the|the|DT ytfE|ytfe|NN promoter|promoter|NN in|in|IN multicopy|multicopy|JJ ,|,|, titrates|titrate|VBZ out|out|RP NsrR|nsrr|NN to|to|TO phenocopy|phenocopy|VB an|a|DT NsrR|nsrr|NN -|-|: mutation|mutation|NN -RRB-|-rrb-|-RRB- Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN +2.5|+2.5|CD mM|mm|NN sodium|sodium|NN nitrite|nitrite|JJ
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT8|pgit8|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ 1|1|CD base|base|NN pair|pair|NN deletion|deletion|NN in|in|IN the|the|DT NsrR-binding|nsrr-binding|JJ site|site|NN of|of|IN the|the|DT ytfE|ytfe|NN promoter|promoter|NN -RRB-|-rrb-|-RRB-
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT8|pgit8|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ 1|1|CD base|base|NN pair|pair|NN deletion|deletion|NN in|in|IN the|the|DT NsrR-binding|nsrr-binding|JJ site|site|NN of|of|IN the|the|DT ytfE|ytfe|NN promoter|promoter|NN -RRB-|-rrb-|-RRB- Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN +|+|CC 2.5|2.5|CD mM|mm|NN sodium|sodium|NN nitrite|nitrite|JJ
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT8|pgit8|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ 1|1|CD base|base|NN pair|pair|NN deletion|deletion|NN in|in|IN the|the|DT NsrR-binding|nsrr-binding|JJ site|site|NN of|of|IN the|the|DT ytfE|ytfe|NN promoter|promoter|NN -RRB-|-rrb-|-RRB- Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN +2.5|+2.5|CD mM|mm|NN sodium|sodium|NN nitrite|nitrite|JJ
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT8|pgit8|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ 1|1|CD base|base|NN pair|pair|NN deletion|deletion|NN in|in|IN the|the|DT NsrR-binding|nsrr-binding|JJ site|site|NN of|of|IN the|the|DT ytfE|ytfe|NN promoter|promoter|NN -RRB-|-rrb-|-RRB- Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN +|+|CC .5|.5|CD mM|mm|NN sodium|sodium|NN nitrite|nitrite|JJ
Strain|strain|NN :|:|: MG1655|mg1655|NN pGIT8|pgit8|NN -LRB-|-lrb-|-LRB- carries|carry|VBZ 1|1|CD base|base|NN pair|pair|NN deletion|deletion|NN in|in|IN the|the|DT NsrR-binding|nsrr-binding|JJ site|site|NN of|of|IN the|the|DT ytfE|ytfe|NN promoter|promoter|NN -RRB-|-rrb-|-RRB- Growth|growth|NN :|:|: Anaerobic|anaerobic|JJ to|to|TO early|early|JJ exponential|exponential|JJ growth|growth|NN Media|Media|NNP :|:|: Minimal|minimal|JJ salts|salt|NNS +|+|CC 20|20|CD mM|mm|NN trimethylamine-N-oxide|trimethylamine-n-oxide|NN Pool|Pool|NNP of|of|IN eight|eight|CD independent|independent|JJ cultures|culture|NNS
strain|strain|NN :|:|: MG1655|mg1655|NN -LRB-|-lrb-|-LRB- RL1655|rl1655|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: MG1655|mg1655|NN thyA|thya|NN -|-|:
strain|strain|NN :|:|: MG1655|mg1655|NN ΔseqA|δseqa|NN
strain|strain|NN :|:|: MG1693|mg1693|NN
strain|strain|NN :|:|: N3431|n3431|NN
strain|strain|NN :|:|: N3433|n3433|NN
strain|strain|NN :|:|: NEB|NEB|NNP 10-beta|10-beta|JJ
strain|strain|NN :|:|: NN-34-1-3|nn-34-1-3|NN
strain|strain|NN :|:|: no|no|DT tag|tag|NN
strain|strain|NN :|:|: NR-12|nr-12|NN
strain|strain|NN :|:|: NZ-502|nz-502|NN -LRB-|-lrb-|-LRB- RpoB|rpob|NN mutant|mutant|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: O08|o08|NN -LRB-|-lrb-|-LRB- O38|o38|NN :|:|: H10|h10|NN -RRB-|-rrb-|-RRB- obtained|obtain|VBN from|from|IN the|the|DT yolk|yolk|NN of|of|IN the|the|DT abdomen|abdomen|NN of|of|IN a|a|DT diseased|diseased|JJ 1-day-old|1-day-old|JJ chick|chick|NN
strain|strain|NN :|:|: O157|o157|NN :|:|: h7|h7|NN
strain|strain|NN :|:|: O157|o157|NN :|:|: H7|h7|NN
Strain|strain|NN :|:|: O157|o157|NN :|:|: H7|h7|NN
strain|strain|NN :|:|: O157|o157|NN :|:|: H7|h7|NN EHEC|ehec|NN TUV93-0|tuv93-0|NN
strain|strain|NN :|:|: O157|o157|NN :|:|: H7|h7|NN NCTC|nctc|NN 12900|12900|CD
strain|strain|NN :|:|: o157|o157|NN :|:|: H7|h7|NN -LRB-|-lrb-|-LRB- Sakai|Sakai|NNP -RRB-|-rrb-|-RRB- wild-type|wild-type|JJ
strain|strain|NN :|:|: O2|o2|CD
strain|strain|NN :|:|: O63|o63|NN :|:|: nm|nm|NN
strain|strain|NN :|:|: O78|o78|NN :|:|: h11|h11|NN
strainorline|strainorline|NN :|:|: K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN
Strain|strain|NN P4X|p4x|NN ,|,|, grown|grow|VBN on|on|IN minimal|minimal|JJ medium|medium|NN ,|,|, reference|reference|NN sample|sample|NN
strain|strain|NN :|:|: PC1012|pc1012|NN
strain|strain|NN :|:|: PE360|pe360|NN
strain|strain|NN :|:|: PK4854|pk4854|NN
strain|strain|NN :|:|: PK8263|pk8263|NN
strain|strain|NN :|:|: PK9416|pk9416|NN
strain|strain|NN :|:|: PKH5000|pkh5000|NN
strain|strain|NN :|:|: Porcine|porcine|NN EPEC|epec|NN strain|strain|NN O45|o45|NN
strain|strain|NN :|:|: Poultry|Poultry|NNP E.|E.|NNP coli|coli|NN Virulent|virulent|JJ and|and|CC multidrug|multidrug|JJ resistant|resistant|JJ
strain|strain|NN :|:|: PUTI|puti|NN O26|o26|NN UMN|umn|NN O26|o26|NN
strain|strain|NN :|:|: Rabbit|rabbit|NN EPEC|epec|NN strain|strain|NN O103|o103|NN
strain|strain|NN :|:|: REL4536|rel4536|NN
strain|strain|NN :|:|: REL606|rel606|NN
strain|strain|NN :|:|: RL2325|rl2325|NN
strain|strain|NN :|:|: RL2673|rl2673|NN
strain|strain|NN :|:|: RSW421|rsw421|NN -LRB-|-lrb-|-LRB- RL1962|rl1962|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: RSW421|rsw421|NN -LRB-|-lrb-|-LRB- RL1967|rl1967|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: RSW422|rsw422|NN -LRB-|-lrb-|-LRB- RL1963|rl1963|NN -RRB-|-rrb-|-RRB-
strain|strain|NN :|:|: RSW472|rsw472|NN -LRB-|-lrb-|-LRB- RL1966|rl1966|NN -RRB-|-rrb-|-RRB-
strain|strain|NN S04|s04|NN
strain|strain|NN S05|s05|NN
strain|strain|NN S13|s13|NN
strain|strain|NN :|:|: SE15|se15|NN
strain|strain|NN :|:|: SH0003|sh0003|NN
strain|strain|NN :|:|: SH0012|sh0012|NN
strains|strain|NNS :|:|: K-12|k-12|NN BW25113|bw25113|NN
strain|strain|NN :|:|: SK4455|sk4455|NNS
strain|strain|NN :|:|: sPRH-20|sprh-20|NN
strain|strain|NN :|:|: sPRH-21|sprh-21|NN
strain|strain|NN :|:|: sPRH-25|sprh-25|NN
strain|strain|NN :|:|: sPRH-372|sprh-372|NN
strain|strain|NN :|:|: sPRH-403|sprh-403|NN
strain|strain|NN :|:|: sPRH-414|sprh-414|NN
strain|strain|NN :|:|: sPRH-418|sprh-418|NN
strain|strain|NN :|:|: sPRH-420|sprh-420|NN
strain|strain|NN :|:|: sPRH-421|sprh-421|NN
strain|strain|NN :|:|: sPRH-443|sprh-443|NN
strain|strain|NN :|:|: sPRH-445|sprh-445|NN
strain|strain|NN :|:|: sPRH-450|sprh-450|NN
strain|strain|NN :|:|: sPRH-604|sprh-604|NN
strain|strain|NN :|:|: sPRH-605|sprh-605|NN
strain|strain|NN :|:|: sPRH-606|sprh-606|NN
strain|strain|NN :|:|: sPRH-609|sprh-609|NN
strain|strain|NN :|:|: sPRH-610|sprh-610|NN
strain|strain|NN :|:|: sPRH-612|sprh-612|NN
strain|strain|NN :|:|: sPRH-613|sprh-613|NN
strain|strain|NN :|:|: St.|St.|NNP Olav104|Olav104|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav157|Olav157|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav164|Olav164|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav17|Olav17|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav172|Olav172|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav173|Olav173|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav174|Olav174|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav176|Olav176|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav178|Olav178|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav179|Olav179|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav39|Olav39|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav40|Olav40|NNP
strain|strain|NN :|:|: St.|St.|NNP Olav63|Olav63|NNP
strain|strain|NN :|:|: strain|strain|NN K12|k12|NN substrain|substrain|NN MG1655|mg1655|NN
strain|strain|NN :|:|: strain|strain|NN O157|o157|NN :|:|: H7|h7|NN
strains|strain|NNS TW014359|tw014359|NN vs|vs|CC TW04863|tw04863|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW014359|tw014359|NN vs|vs|CC TW11037|tw11037|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW02883|tw02883|NN vs|vs|CC TW11028|tw11028|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW04863|tw04863|NN vs|vs|CC TW14279|tw14279|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW07591|tw07591|NN vs|vs|CC TW09098|tw09098|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW07937|tw07937|NN vs|vs|CC TW11185|tw11185|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW07961|tw07961|NN vs|vs|CC TW08610|tw08610|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW07961|tw07961|NN vs|vs|CC TW11029|tw11029|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08030|tw08030|NN vs|vs|CC TW10045|tw10045|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08609|tw08609|NN vs|vs|CC TW08030|tw08030|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08609|tw08609|NN vs|vs|CC TW08623|tw08623|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08609|tw08609|NN vs|vs|CC TW11110|tw11110|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08610|tw08610|NN vs|vs|CC TW11110|tw11110|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08623|tw08623|NN vs|vs|CC TW02883|tw02883|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08623|tw08623|NN vs|vs|CC TW08030|tw08030|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW08635|tw08635|NN vs|vs|CC TW09098|tw09098|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW09098|tw09098|NN vs|vs|CC TW11308|tw11308|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW09189|tw09189|NN vs|vs|CC TW11032|tw11032|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW09189|tw09189|NN vs|vs|CC TW14279|tw14279|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW10012|tw10012|NN vs|vs|CC TW11037|tw11037|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW10012|tw10012|NN vs|vs|CC TW14313|tw14313|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW10045|tw10045|NN vs|vs|CC TW07937|tw07937|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11028|tw11028|NN vs|vs|CC TW07937|tw07937|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11028|tw11028|NN vs|vs|CC TW11308|tw11308|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11029|tw11029|NN vs|vs|CC TW02883|tw02883|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11029|tw11029|NN vs|vs|CC TW08610|tw08610|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11032|tw11032|NN vs|vs|CC TW04863|tw04863|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11032|tw11032|NN vs|vs|CC TW09189|tw09189|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11037|tw11037|NN vs|vs|CC TW08635|tw08635|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11110|tw11110|NN vs|vs|CC TW10012|tw10012|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11185|tw11185|NN vs|vs|CC TW014313|tw014313|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11185|tw11185|NN vs|vs|CC TW08635|tw08635|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW11308|tw11308|NN vs|vs|CC TW07591|tw07591|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW14279|tw14279|NN vs|vs|CC TW10045|tw10045|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW14313|tw14313|NN vs|vs|CC TW07591|tw07591|NN epithelial|epithelial|JJ exposure|exposure|NN
strains|strain|NNS TW14359|tw14359|NN vs|vs|CC TW07961|tw07961|NN epithelial|epithelial|JJ exposure|exposure|NN
strain|strain|NN :|:|: Suc-T110|suc-t110|NN -LRB-|-lrb-|-LRB- parental|parental|JJ strain|strain|NN -RRB-|-rrb-|-RRB-
Strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD rpm|rpm|NN .|.|. 16|16|CD h|h|NN overnight|overnight|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN to|to|TO OD600|od600|NN =|=|JJ 0.05|0.05|CD in|in|IN HEPES-glucose|hepes-glucose|NN -LRB-|-lrb-|-LRB- 0.4|0.4|CD %|%|NN -RRB-|-rrb-|-RRB- ,|,|, grown|grow|VBN to|to|TO OD600|od600|NN ~|~|NN 0.6|0.6|CD ,|,|, and|and|CC exposed|expose|VBN to|to|TO 4.5|4.5|CD %|%|NN deoxycholate|deoxycholate|NN for|for|IN 30|30|CD min|min|NN .|.|.
Strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN LBCm30|lbcm30|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD rpm|rpm|NN .|.|. 16|16|CD h|h|NN overnight|overnight|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN at|at|IN 1:1000|1:1000|CD into|into|IN fresh|fresh|JJ LBCm30|lbcm30|NN ,|,|, grown|grow|VBN to|to|TO OD600|od600|NN ~|~|NN 1.0|1.0|CD ,|,|, and|and|CC induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN for|for|IN 90|90|CD min|min|NN .|.|.
Strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN LBCm30|lbcm30|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD rpm|rpm|NN .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN into|into|IN fresh|fresh|JJ LBCm30|lbcm30|NN ,|,|, grown|grow|VBN for|for|IN 2.5|2.5|CD h|h|NN ,|,|, and|and|CC induced|induce|VBN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN for|for|IN 90|90|CD min|min|NN -LRB-|-lrb-|-LRB- final|final|JJ OD600|od600|NN =|=|JJ 1.6|1.6|CD -RRB-|-rrb-|-RRB- .|.|.
Strains|strain|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN medium|medium|NN -LRB-|-lrb-|-LRB- Difco|Difco|NNP -RRB-|-rrb-|-RRB- supplemented|supplement|VBN with|with|IN thymine|thymine|NN -LRB-|-lrb-|-LRB- 50|50|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- at|at|IN 37ºC|37ºc|NN ,|,|, unless|unless|IN otherwise|otherwise|RB stated|state|VBN .|.|. Overnight|overnight|JJ cultures|culture|NNS of|of|IN single|single|JJ fresh|fresh|JJ grown|grown|JJ colonies|colony|NNS were|be|VBD diluted|dilute|VBN to|to|TO an|a|DT initial|initial|JJ OD600|od600|NN appr|appr|NN .|.|. 0.03|0.03|CD .|.|. Cultures|culture|NNS were|be|VBD collected|collect|VBN at|at|IN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN appr|appr|NN .|.|. 0.5|0.5|CD -RRB-|-rrb-|-RRB- .|.|.
Strains|strain|NNS were|be|VBD grown|grow|VBN overnight|overnight|RB in|in|IN LB|lb|NN broth|broth|NN and|and|CC then|then|RB equalised|equalise|VBD to|to|TO 0.15|0.15|CD optical|optical|JJ density|density|NN -LRB-|-lrb-|-LRB- OD600nm|od600nm|NN -RRB-|-rrb-|-RRB- units|unit|NNS .|.|. Cells|cell|NNS were|be|VBD collected|collect|VBN and|and|CC washed|wash|VBN in|in|IN EG|eg|NN minimal|minimal|JJ medium|medium|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.2|7.2|CD -RRB-|-rrb-|-RRB- .|.|. This|this|DT wash|wash|NN step|step|NN was|be|VBD repeated|repeat|VBN twice|twice|RB more|more|RBR with|with|IN centrifugation|centrifugation|NN to|to|TO collect|collect|VB the|the|DT cells|cell|NNS .|.|. The|the|DT final|final|JJ pellet|pellet|NN was|be|VBD resuspended|resuspend|VBN in|in|IN 1|1|CD ml|ml|NN of|of|IN 1X|1x|NN EG|eg|NN minimal|minimal|JJ -LRB-|-lrb-|-LRB- pH|ph|NN 7.2|7.2|CD -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO OD600|od600|NN ~|~|NN 0.5-0.6|0.5-0.6|CD in|in|IN a|a|DT 40|40|CD ml|ml|NN volume|volume|NN in|in|IN a|a|DT 250|250|CD ml|ml|NN flask|flask|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC 200|200|CD rpm|rpm|NN .|.|.
Strains|strain|NNS were|be|VBD harvested|harvest|VBN in|in|IN MH|mh|NN broth|broth|NN at|at|IN log|log|NN phase|phase|NN
strain|strain|NN :|:|: T175|t175|NN
strain|strain|NN :|:|: T177|t177|NN
strain|strain|NN :|:|: T3|t3|NN 5H5|5h5|NN
strain|strain|NN :|:|: T3|t3|NN 5H5|5h5|NN M|m|NN
strain|strain|NN :|:|: T75|t75|NN
strain|strain|NN :|:|: TB1|tb1|NN
strain|strain|NN :|:|: TB16|tb16|NN
strain|strain|NN :|:|: TG-1|tg-1|NN
strain|strain|NN :|:|: TG-2|tg-2|NN
strain|strain|NN TW02883|tw02883|NN
strain|strain|NN TW02883|tw02883|NN
strain|strain|NN :|:|: TW03439|tw03439|NN
strain|strain|NN :|:|: TW03452|tw03452|NN
strain|strain|NN :|:|: TW03574|tw03574|NN
strain|strain|NN :|:|: TW03576|tw03576|NN
strain|strain|NN :|:|: TW03585|tw03585|NN
strain|strain|NN :|:|: TW03741|tw03741|NN
strain|strain|NN TW04863|tw04863|NN
strain|strain|NN TW07591|tw07591|NN
strain|strain|NN TW07937|tw07937|NN
strain|strain|NN TW07961|tw07961|NN
strain|strain|NN TW07961|tw07961|NN
strain|strain|NN TW08030|tw08030|NN
strain|strain|NN TW08609|tw08609|NN
strain|strain|NN TW08609|tw08609|NN
strain|strain|NN TW08610|tw08610|NN
strain|strain|NN TW08623|tw08623|NN
strain|strain|NN TW08635|tw08635|NN
strain|strain|NN TW08635|tw08635|NN
strain|strain|NN TW09098|tw09098|NN
strain|strain|NN TW09098|tw09098|NN
strain|strain|NN TW09189|tw09189|NN
strain|strain|NN :|:|: TW09308|tw09308|NN
strain|strain|NN TW10012|tw10012|NN
strain|strain|NN TW10045|tw10045|NN
strain|strain|NN TW10045|tw10045|NN
strain|strain|NN TW11028|tw11028|NN
strain|strain|NN TW11029|tw11029|NN
strain|strain|NN TW11029|tw11029|NN
strain|strain|NN TW11032|tw11032|NN
strain|strain|NN TW11032|tw11032|NN
strain|strain|NN TW11037|tw11037|NN
strain|strain|NN TW11110|tw11110|NN
strain|strain|NN TW11110|tw11110|NN
strain|strain|NN TW11185|tw11185|NN
strain|strain|NN TW11185|tw11185|NN
strain|strain|NN TW11308|tw11308|NN
strain|strain|NN TW11308|tw11308|NN
strain|strain|NN :|:|: TW11588|tw11588|NN
strain|strain|NN TW14279|tw14279|NN
strain|strain|NN TW14279|tw14279|NN
strain|strain|NN TW14313|tw14313|NN
strain|strain|NN TW14359|tw14359|NN
strain|strain|NN :|:|: TWx30|twx30|NN
strain|strain|NN :|:|: TWx31|twx31|NN
strain|strain|NN :|:|: TWx34|twx34|NN
strain|strain|NN :|:|: TWx48|twx48|NN
strain|strain|NN :|:|: unevolved|unevolved|JJ parent|parent|NN strain|strain|NN
strain|strain|NN :|:|: W3110|w3110|NN
Strain|strain|NN W3110|w3110|NN
Strain|strain|NN :|:|: W3110|w3110|NN
Strain|strain|NN :|:|: W3110|w3110|NN
Strain|strain|NN :|:|: W3110|w3110|NN
strain|strain|NN :|:|: W3110hns|w3110hn|NNS ∆|∆|VBP 93-1|93-1|CD
strain|strain|NN :|:|: wildtype|wildtype|JJ
strain|strain|NN :|:|: Wild|Wild|NNP Type|type|NN K-12|k-12|NN
strain|strain|NN :|:|: Wild|Wild|NNP type|type|NN strain|strain|NN MG1655|mg1655|NN
strain|strain|NN :|:|: WS|ws|NN 0115A|0115a|NN
strain|strain|NN :|:|: WS1896A|ws1896a|NN
strain|strain|NN :|:|: WS1896|ws1896|NN A-1|a-1|NN
strain|strain|NN :|:|: WS|ws|NN 1933D|1933d|NN
strain|strain|NN :|:|: WS2068A|ws2068a|NN
strain|strain|NN :|:|: WS|ws|NN 2173A|2173a|NN
strain|strain|NN :|:|: WS2741|ws2741|NN A-1|a-1|NN
strain|strain|NN :|:|: WS3080A|ws3080a|NN
strain|strain|NN :|:|: WS|ws|NN 3294A|3294a|NN
strain|strain|NN :|:|: WS|w|NNS 3572|3572|CD A-1|a-1|NN
strain|strain|NN :|:|: WS|w|NNS 3596|3596|CD A-4|a-4|NN
strain|strain|NN :|:|: WS4087|ws4087|NN A-1|a-1|NN
strain|strain|NN :|:|: WS4264|ws4264|NN A-1|a-1|NN
strain|strain|NN :|:|: WS5874|ws5874|NN A-1|a-1|NN
strain|strain|NN :|:|: WS6582|ws6582|NN A-1|a-1|NN
strain|strain|NN :|:|: WS|ws|NN 6866B-1|6866b-1|NN
strain|strain|NN :|:|: WS|w|NNS 7162|7162|CD A-1|a-1|NN
strain|strain|NN :|:|: WS7179|ws7179|NN A-2|a-2|NN
strain|strain|NN :|:|: wt|wt|JJ
strain|strain|NN :|:|: wt|wt|JJ 3xflag|3xflag|NN strain|strain|NN
strain|strain|NN :|:|: Xuzhou21|xuzhou21|NN
strain|strain|NN :|:|: Xuzhou21m|xuzhou21m|NN
strain|strain|NN :|:|: ZD1|zd1|NN
strain|strain|NN :|:|: ZD26|zd26|NN
strain|strain|NN :|:|: ZD51|zd51|NN
strain|strain|NN :|:|: ZD56|zd56|NN
strain|strain|NN :|:|: ZD59|zd59|NN
strain|strain|NN :|:|: ZD60|zd60|NN
strain|strain|NN :|:|: ZD8|zd8|NN
Strand|strand|NN specific|specific|JJ base|base|NN read|read|VBD counts|count|NNS were|be|VBD determined|determine|VBN for|for|IN each|each|DT of|of|IN 4091|4091|CD ORFs|orf|NNS for|for|IN the|the|DT 15|15|CD samples|sample|NNS
Strand-specific|strand-specific|JJ cDNA|cdna|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN from|from|IN 50|50|CD ng|ng|NN of|of|IN rRNA-depleted|rrna-depleted|JJ samples|sample|NNS following|follow|VBG the|the|DT TruSeq|TruSeq|NNP RNA|rna|NN protocol|protocol|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, San|San|NNP Diego|Diego|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP ,|,|, without|without|IN purification|purification|NN -RRB-|-rrb-|-RRB- with|with|IN modification|modification|NN of|of|IN the|the|DT 2nd|2nd|JJ strand|strand|NN cDNA|cdna|NN synthesis|synthesis|NN as|as|IN previously|previously|RB described|describe|VBN -LRB-|-lrb-|-LRB- Parkhomchuk|Parkhomchuk|NNP et|et|FW al.|al.|FW 2009|2009|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT libraries|library|NNS were|be|VBD prepared|prepare|VBN using|use|VBG multiplex|multiplex|JJ primers|primer|NNS to|to|TO allow|allow|VB simultaneous|simultaneous|JJ sequencing|sequencing|NN in|in|IN a|a|DT single|single|JJ lane|lane|NN .|.|. Sequencing|sequencing|NN was|be|VBD performed|perform|VBN on|on|IN a|a|DT HiSeq1500|hiseq1500|NN using|use|VBG SBS|SBS|NNP v3|v3|NN kits|kit|NNS -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- to|to|TO generate|generate|VB paired-end|paired-end|NN reads|read|VBZ of|of|IN 2|2|CD x|x|CC 50|50|CD nucleotides|nucleotide|NNS .|.|.
Strand-specific|strand-specific|JJ RNA-Seq|rna-seq|NN data|datum|NNS were|be|VBD generated|generate|VBN ,|,|, following|follow|VBG rRNA|rrna|NN depletion|depletion|NN with|with|IN a|a|DT Ribo-Zero|Ribo-Zero|NNP kit|kit|NN ,|,|, with|with|IN the|the|DT aid|aid|NN of|of|IN the|the|DT di-tagged|di-tagged|JJ cDNA|cdna|NN strategy|strategy|NN -LRB-|-lrb-|-LRB- ScriptSeq|scriptseq|NN -RRB-|-rrb-|-RRB- on|on|IN an|a|DT Illumina|Illumina|NNP NextSeq|NextSeq|NNP platform|platform|NN
Strand|Strand|NNP specific|specific|JJ RNAtag-seq|rnatag-seq|NN libraries|library|NNS were|be|VBD created|create|VBN by|by|IN the|the|DT Broad|Broad|NNP Technology|Technology|NNP Labs|Labs|NNPS specialized|specialized|JJ service|service|NN facility|facility|NN -LRB-|-lrb-|-LRB- SSF|ssf|NN -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT standard|standard|JJ protocol|protocol|NN described|describe|VBN in|in|IN Shishkin|Shishkin|NNP et|et|FW al.|al.|FW .|.|. Nature|Nature|NNP Methods|method|NNS 2016|2016|CD .|.|.
streptomycin|streptomycin|NN treatment|treatment|NN
Streptomycin|Streptomycin|NNP _|_|NN treatment|treatment|NN _|_|NN plasmidmappedreads|plasmidmappedread|NNS _|_|VBP statistical|statistical|JJ _|_|NN output.txt|output.txt|NN :|:|: NC|nc|NN _|_|SYM 012692.1|012692.1|CD
Strep|strep|JJ _|_|NN treatment|treatment|NN _|_|NN genomemappedreads|genomemappedread|NNS _|_|VBP statistical|statistical|JJ _|_|NN output.txt|output.txt|NN :|:|: NC|nc|NN _|_|SYM 000913.2|000913.2|CD
stress|stress|NN :|:|: acidic|acidic|JJ
stress|stress|NN :|:|: Adenosine|Adenosine|NNP addition|addition|NN
stress|stress|NN :|:|: Alanine|alanine|NN addition|addition|NN
stress|stress|NN :|:|: Arginine|arginine|NN addition|addition|NN
stress|stress|NN :|:|: Aspartate|Aspartate|NNP addition|addition|NN
stress|stress|NN :|:|: control|control|NN
stress|stress|NN :|:|: control|control|NN -LRB-|-lrb-|-LRB- before|before|IN perturbation|perturbation|NN -RRB-|-rrb-|-RRB-
stress|stress|NN :|:|: Cysteine|cysteine|NN addition|addition|NN
stress|stress|NN :|:|: Cytidine|cytidine|NN addition|addition|NN
stress|stress|NN :|:|: Glutamate|glutamate|JJ addition|addition|NN
stress|stress|NN :|:|: Glutamine|glutamine|NN addition|addition|NN
stress|stress|NN :|:|: Glycine|glycine|NN addition|addition|NN
stress|stress|NN :|:|: Guanosine|Guanosine|NNP addition|addition|NN
stress|stress|NN :|:|: heptanoic|heptanoic|JJ acid|acid|NN
stress|stress|NN :|:|: Histidine|histidine|NN addition|addition|NN
stress|stress|NN :|:|: Isoleucine|isoleucine|NN addition|addition|NN
stress|stress|NN :|:|: Lysine|lysine|NN addition|addition|NN
stress|stress|NN :|:|: Methionine|methionine|NN addition|addition|NN
stress|stress|NN :|:|: Minimal|minimal|JJ medium|medium|NN
stress|stress|NN :|:|: n-butanol|n-butanol|NN
stress|stress|NN :|:|: osmotic|osmotic|JJ
stress|stress|NN :|:|: oxidative|oxidative|JJ
stress|stress|NN :|:|: Phenylalanine|phenylalanine|NN addition|addition|NN
stress|stress|NN :|:|: Proline|Proline|NNP addition|addition|NN
stress|stress|NN :|:|: Serine|serine|NN addition|addition|NN
stress|stress|NN :|:|: Threonine|threonine|NN addition|addition|NN
stress|stress|NN :|:|: Thymidine|Thymidine|NNP addition|addition|NN
stress|stress|NN :|:|: Tryptophan|tryptophan|NN addition|addition|NN
stress|stress|NN :|:|: Uridine|uridine|NN addition|addition|NN
stress|stress|NN :|:|: Valine|Valine|NNP addition|addition|NN
Strian|Strian|NNP :|:|: W3110|w3110|NN
S.|S.|NNP Typhimurium|Typhimurium|NNP cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN LB|lb|NN -LRB-|-lrb-|-LRB- supplemented|supplement|VBN with|with|IN 10mM|10mm|NN glucose|glucose|NN -RRB-|-rrb-|-RRB- to|to|TO mid-exponential|mid-exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ ~|~|NN 0.6|0.6|CD -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN and|and|CC shaking|shake|VBG 250rpm|250rpm|JJ
Subsequent|subsequent|JJ data|datum|NNS visualizations|visualization|NNS were|be|VBD performed|perform|VBN in|in|IN R|r|NN -LRB-|-lrb-|-LRB- version|version|NN 3.1.2|3.1.2|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT cummeRbund|cummerbund|NN package|package|NN -LRB-|-lrb-|-LRB- version|version|NN 3.0|3.0|CD -RRB-|-rrb-|-RRB-
substrain|substrain|NN :|:|: ATCC|atcc|NN 25922|25922|CD
sub|sub|NN strain|strain|NN :|:|: BW38028|bw38028|NN
sub|sub|NN strain|strain|NN :|:|: BW39452|bw39452|NN
substrain|substrain|NN :|:|: DH1|dh1|NN
substrain|substrain|NN :|:|: EC14|ec14|NN
substrain|substrain|NN :|:|: EC19|ec19|NN
substrain|substrain|NN :|:|: EC24|ec24|NN
substrain|substrain|NN :|:|: GJ13507|gj13507|NN
substrain|substrain|NN :|:|: GJ13519|gj13519|NN
substrain|substrain|NN :|:|: GJ13531|gj13531|NN
substrain|substrain|NN :|:|: GJ13533|gj13533|NN
substrain|substrain|NN :|:|: MG1655|mg1655|NN
substr|substr|NN :|:|: MG1655|mg1655|NN
sucrose|sucrose|NN status|status|NN :|:|: no|no|DT sucrose|sucrose|NN
sucrose|sucrose|NN status|status|NN :|:|: with|with|IN 15|15|CD %|%|NN sucrose|sucrose|NN
SucT110|suct110|NN _|_|CD 12|12|CD %|%|NN Glu|glu|NN
SucT110|suct110|NN _|_|CD 5|5|CD %|%|NN Glu|glu|NN
sulA|sula|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r1|r1|FW
sulA|sula|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r2|r2|FW
sulA|sula|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
sulA|sula|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
Summarize|summarize|VB the|the|DT read|read|NN count|count|NN to|to|TO each|each|DT annotated|annotated|JJ gene|gene|NN
Supplementary|supplementary|JJ files|file|NNS contain|contain|VBP the|the|DT following|following|NN :|:|: Raw|raw|NN Signal|signal|NN Values|value|NNS :|:|: The|the|DT term|term|NN ``|``|`` raw|raw|JJ ''|''|'' signal|signal|NN values|value|NNS refer|refer|VBP to|to|TO the|the|DT linear|linear|JJ data|datum|NNS after|after|IN thresholding|threshold|VBG and|and|CC summarization|summarization|NN Summarization|summarization|NN is|be|VBZ performed|perform|VBN by|by|IN computing|compute|VBG the|the|DT geometric|geometric|JJ mean|mean|NN .|.|. Raw|raw|NN data|datum|NNS filtered|filter|VBN on|on|IN Expression|expression|NN -LRB-|-lrb-|-LRB- 20.0|20.0|CD -|-|: 343943.344|343943.344|CD -RRB-|-rrb-|-RRB- •|•|SYM Normalized|normalize|VBN Signal|signal|NN Values|value|NNS :|:|: ``|``|`` Normalized|normalize|VBN ''|''|'' value|value|NN is|be|VBZ the|the|DT value|value|NN generated|generate|VBN after|after|IN log|log|NN transformation|transformation|NN and|and|CC normalization|normalization|NN -LRB-|-lrb-|-LRB- Shift|shift|NN to|to|TO 75|75|CD percentile|percentile|NN -RRB-|-rrb-|-RRB- and|and|CC baseline|baseline|NN transformation|transformation|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: 5m_ribozero_counts_cleavage_ratio.csv.gz|5m_ribozero_counts_cleavage_ratio.csv.gz|NN is|be|VBZ a|a|DT log-transformed|log-transformed|JJ list|list|NN of|of|IN sequencing|sequencing|NN depth-normalized|depth-normalized|JJ counts|count|NNS for|for|IN every|every|DT genomic|genomic|JJ position|position|NN at|at|IN both|both|DT strands|strand|NNS for|for|IN each|each|DT ribozero|ribozero|NN treated|treat|VBN sample|sample|NN as|as|RB well|well|RB as|as|IN the|the|DT average|average|JJ cleavage|cleavage|NN ratio|ratio|NN calculated|calculate|VBN from|from|IN all|all|DT samples|sample|NNS .|.|. total_RNA_rpm.csv.gz|total_rna_rpm.csv.gz|NN is|be|VBZ a|a|DT list|list|NN of|of|IN sequencing|sequencing|NN depth-normalized|depth-normalized|JJ counts|count|NNS for|for|IN every|every|DT genomic|genomic|JJ position|position|NN at|at|IN both|both|DT strans|stran|NNS for|for|IN all|all|DT total|total|JJ RNA|rna|NN samples|sample|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: All|all|DT in|in|IN tab-delimited|tab-delimited|JJ ASCII|ASCII|NNP format|format|NN .|.|. raw_count.txt|raw_count.txt|NN -LRB-|-lrb-|-LRB- pre-normalized|pre-normalized|JJ read|read|NN count|count|NN -RRB-|-rrb-|-RRB- ,|,|, normalized_count.txt|normalized_count.txt|NN ,|,|, panGeneMap.txt|pangenemap.txt|NN -LRB-|-lrb-|-LRB- geneID|geneid|NN map|map|NN between|between|IN the|the|DT strains|strain|NNS and|and|CC pangene|pangene|NN ID|id|NN -RRB-|-rrb-|-RRB- ,|,|, Gene_annotations.txt|gene_annotations.txt|NN -LRB-|-lrb-|-LRB- annotation|annotation|NN of|of|IN genes|gene|NNS -RRB-|-rrb-|-RRB-
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: A|a|DT tab|tab|NN deliminited|deliminit|VBN file|file|NN with|with|IN counts|count|NNS for|for|IN each|each|DT gene|gene|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: bed|bed|NN format|format|NN peak|peak|NN file|file|NN generated|generate|VBN from|from|IN MACS2|macs2|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: bedgraph|bedgraph|NN :|:|: Data|datum|NNS presented|present|VBN in|in|IN a|a|DT 4|4|CD column|column|NN BED|bed|NN format|format|NN ,|,|, of|of|IN which|which|WDT the|the|DT first|first|JJ column|column|NN is|be|VBZ the|the|DT chromosome|chromosome|NN ,|,|, the|the|DT second|second|JJ column|column|NN is|be|VBZ the|the|DT start|start|NN position|position|NN of|of|IN the|the|DT chromosome|chromosome|NN ,|,|, the|the|DT third|third|JJ column|column|NN is|be|VBZ the|the|DT end|end|NN position|position|NN ,|,|, and|and|CC the|the|DT fourth|fourth|JJ column|column|NN is|be|VBZ the|the|DT fragments|fragment|NNS per|per|IN kilobase|kilobase|NN mapped|map|VBN -LRB-|-lrb-|-LRB- FPKM|fpkm|NN -RRB-|-rrb-|-RRB- for|for|IN that|that|DT sample|sample|NN .|.|. Chromosome|chromosome|NN positions|position|NNS are|be|VBP specified|specify|VBN as|as|IN 0-relative|0-relative|JJ .|.|. The|the|DT first|first|JJ chromosome|chromosome|NN position|position|NN is|be|VBZ 0|0|CD .|.|. The|the|DT last|last|JJ position|position|NN in|in|IN a|a|DT chromosome|chromosome|NN of|of|IN length|length|NN N|n|NN would|would|MD be|be|VB N|n|NN -|-|: 1|1|CD .|.|. Only|only|RB positions|position|NNS specified|specify|VBN have|have|VBP data|datum|NNS .|.|. Positions|position|NNS not|not|RB specified|specify|VBN do|do|VBP not|not|RB have|have|VB data|datum|NNS and|and|CC will|will|MD not|not|RB be|be|VB graphed|graph|VBN .|.|. All|all|DT positions|position|NNS specified|specify|VBN in|in|IN the|the|DT input|input|NN data|datum|NNS are|be|VBP in|in|IN numerical|numerical|JJ order|order|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Bedgraphs|bedgraph|NNS files|file|NNS representing|represent|VBG the|the|DT extracted|extract|VBN peak|peak|NN data|datum|NNS
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: BedGraphs|bedgraph|NNS of|of|IN the|the|DT reads|read|VBZ before|before|IN and|and|CC after|after|IN TAP|tap|NN treatment|treatment|NN for|for|IN each|each|DT of|of|IN the|the|DT samples|sample|NNS .|.|. Separate|separate|JJ files|file|NNS are|be|VBP provided|provide|VBN for|for|IN the|the|DT forward|forward|JJ and|and|CC reverse|reverse|JJ strands|strand|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Bedgraph|Bedgraph|NNP wiggle|wiggle|NN files|file|NNS were|be|VBD created|create|VBN for|for|IN each|each|DT sample|sample|NN and|and|CC replicate|replicate|VB for|for|IN all|all|DT reads|read|VBZ aligned|align|VBN to|to|TO the|the|DT genome|genome|NN after|after|IN computational|computational|JJ rRNA|rrna|NN and|and|CC tRNA|trna|NN subtraction|subtraction|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: BIGWIG|bigwig|NN file|file|NN containing|contain|VBG coverage|coverage|NN tracks|track|NNS from|from|IN 3|3|CD '|'|'' RACE|race|NN data|datum|NNS
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: BigWIG|bigwig|NN files|file|NNS are|be|VBP provided|provide|VBN showing|show|VBG uniquely|uniquely|RB mapped|map|VBN sequence|sequence|NN reads|read|VBZ .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: BigWig|BigWig|NNP files|file|VBZ for|for|IN whole-genome|whole-genome|JJ reads|read|VBZ coverage|coverage|NN -LRB-|-lrb-|-LRB- including|include|VBG number|number|NN of|of|IN mapped|map|VBN reads|read|VBZ -RRB-|-rrb-|-RRB- for|for|IN each|each|DT sample|sample|NN .|.|. Each|each|DT sample|sample|NN has|have|VBZ two|two|CD files|file|NNS ,|,|, one|one|CD for|for|IN plus|plus|CC strand|strand|NN ,|,|, and|and|CC the|the|DT other|other|JJ for|for|IN minus|minus|CC strand|strand|NN .|.|. Therefore|therefore|RB ,|,|, there|there|EX are|be|VBP 14|14|CD BigWig|BigWig|NNP files|file|NNS for|for|IN 7|7|CD samples|sample|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: chromosome|chromosome|NN chromosomeStartPosition|chromosomestartposition|NN chromosomeStopPosition|chromosomestopposition|NN readCoverage|readcoverage|NN -LRB-|-lrb-|-LRB- positive|positive|JJ values|value|NNS on|on|IN +|+|CC strand|strand|NN ,|,|, negative|negative|JJ on|on|IN -|-|: strand|strand|NN -RRB-|-rrb-|-RRB-
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: CoK12|cok12|NN _|_|CD LB.xlsx|lb.xlsx|NN :|:|: Average|average|JJ expression|expression|NN values|value|NNS of|of|IN reads|read|VBZ related|related|JJ with|with|IN MG1655|mg1655|NN strain|strain|NN in|in|IN samples|sample|NNS Co-culture|co-culture|NN _|_|CD LB1|lb1|NN and|and|CC LB2|lb2|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Column|Column|NNP 1|1|CD names|name|NNS the|the|DT nucleotide|nucleotide|NN in|in|IN the|the|DT genome|genome|NN ,|,|, column|column|NN 2|2|CD gives|give|VBZ counts|count|NNS for|for|IN the|the|DT forward|forward|JJ strand|strand|NN ,|,|, column|column|NN 3|3|CD for|for|IN the|the|DT reverse|reverse|JJ strand|strand|NN ,|,|, columns|column|NNS are|be|VBP tab|tab|NN separated|separated|JJ
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Comma-delimited|comma-delimited|JJ text|text|NN file|file|NN includes|include|VBZ RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: comma-delimited|comma-delimited|JJ text|text|NN files|file|NNS include|include|VBP FPKM|fpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: comma-delimited|comma-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Comma|comma|NN separated|separated|JJ value|value|NN files|file|NNS include|include|VBP log-fold|log-fold|JJ changes|change|NNS and|and|CC associated|associate|VBN p-values|p-value|NNS for|for|IN each|each|DT comparison|comparison|NN made|make|VBD
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: contents|contents|NNS :|:|: reference|reference|NN seq,co-ordinate|seq,co-ordinate|JJ start|start|NN position,co-ordinate|position,co-ordinate|JJ end|end|NN position|position|NN ,|,|, counts|count|VBZ for|for|IN the|the|DT position|position|NN ,|,|, mapping|map|VBG quality|quality|NN ,|,|, strand|strand|NN position|position|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: CoT1E|cot1e|NN _|_|CD LB.xlsx|lb.xlsx|NN :|:|: Average|average|JJ expression|expression|NN values|value|NNS of|of|IN reads|read|VBZ related|related|JJ with|with|IN DOT-T1E|dot-t1e|NN strain|strain|NN in|in|IN samples|sample|NNS Co-culture|co-culture|NN _|_|CD LB1|lb1|NN and|and|CC LB2|lb2|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: counts|count|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: CSV|CSV|NNP file|file|NN contains|contain|VBZ counts|count|NNS generated|generate|VBN using|use|VBG RSEM|rsem|NN software|software|NN .|.|. Ribosomal|ribosomal|JJ RNA|rna|NN transcripts|transcript|NNS excluded|exclude|VBN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: csv|csv|NN files|file|NNS ,|,|, FPKM|fpkm|NN values|value|NNS from|from|IN pairwise|pairwise|JJ comparisons|comparison|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: CSV|CSV|NNP files|file|NNS of|of|IN raw|raw|JJ read|read|NN counts|count|NNS and|and|CC normalized|normalize|VBN gene|gene|NN expression|expression|NN in|in|IN FPKM|FPKM|NNP units|unit|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: CSV|CSV|NNP files|file|VBZ providing|provide|VBG the|the|DT number|number|NN of|of|IN reads|read|VBZ mapping|map|VBG to|to|TO each|each|DT genomic|genomic|JJ gene|gene|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: DMS-seq|dms-seq|NN data|datum|NNS -LRB-|-lrb-|-LRB- pooled|pooled|JJ Total|total|JJ and|and|CC Ribo|Ribo|NNP -|-|: RNA|rna|NN -RRB-|-rrb-|-RRB- is|be|VBZ provided|provide|VBN in|in|IN the|the|DT form|form|NN of|of|IN RNA|rna|NN Framework|framework|NN 's|'s|POS -LRB-|-lrb-|-LRB- http://www.rnaframework.com|http://www.rnaframework.com|NN -RRB-|-rrb-|-RRB- RNA|rna|NN Count|count|NN -LRB-|-lrb-|-LRB- RC|rc|NN -RRB-|-rrb-|-RRB- files|file|NNS .|.|. For|for|IN a|a|DT detailed|detailed|JJ description|description|NN of|of|IN the|the|DT RC|rc|NN format|format|NN ,|,|, please|please|VB refer|refer|VB to|to|TO :|:|: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Each|each|DT wig|wig|NN file|file|NN contains|contain|VBZ the|the|DT alignd|alignd|NN reads|read|VBZ of|of|IN each|each|DT ChIP-exo|ChIP-exo|NNP sample|sample|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: ecoli|ecolus|NNS _|_|VBP heatshock|heatshock|NN _|_|NN normalizedcounts.txt|normalizedcounts.txt|NN :|:|: Tab-delimited|tab-delimited|JJ text|text|NN file|file|NN has|have|VBZ EdgeR-normalized|edger-normalize|VBN counts|count|NNS per|per|IN kilobase|kilobase|NN million|million|CD for|for|IN each|each|DT E.|e.|FW coli|coli|FW gene|gene|NN -LRB-|-lrb-|-LRB- EcoCyc|ecocyc|NN gene|gene|NN names|name|NNS -RRB-|-rrb-|-RRB- .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: ecoli|ecolus|NNS _|_|VBP heatshock|heatshock|NN _|_|NN rawcounts.txt|rawcounts.txt|NN :|:|: Tab-delimited|tab-delimited|JJ text|text|NN file|file|NN has|have|VBZ raw|raw|JJ read|read|NN counts|count|VBZ per|per|FW kilobase|kilobase|NN million|million|CD for|for|IN each|each|DT E.|e.|FW coli|coli|FW gene|gene|NN -LRB-|-lrb-|-LRB- EcoCyc|ecocyc|NN gene|gene|NN names|name|NNS -RRB-|-rrb-|-RRB- .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Enrichement|enrichement|NN -LRB-|-lrb-|-LRB- IP/input|ip/input|NN -RRB-|-rrb-|-RRB- wig|wig|NN files|file|NNS were|be|VBD generated|generate|VBN using|use|VBG homemade|homemade|NN matlab|matlab|NN code|code|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Excel|Excel|NNP file|file|NN include|include|VBP FPKM|fpkm|NN values|value|NNS of|of|IN different|different|JJ genes|gene|NNS for|for|IN each|each|DT sample|sample|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: excel|excel|VB file|file|NN include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Excel|Excel|NNP files|file|NNS include|include|VBP FPKM|fpkm|NN values|value|NNS for|for|IN each|each|DT sample|sample|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: excel|excel|VB file|file|NN with|with|IN coverage|coverage|NN and|and|CC FPKM|fpkm|NN measurements|measurement|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Excel|Excel|NNP formatted|format|VBD matrix|matrix|NN table|table|NN containing|contain|VBG transcript|transcript|NN coordinates|coordinate|VBZ ,|,|, normalized|normalize|VBD abundance|abundance|NN estimates|estimate|NNS across|across|IN the|the|DT biological|biological|JJ replicates|replicate|VBZ and|and|CC fold-changes|fold-change|VBZ in|in|IN gene|gene|NN expression|expression|NN between|between|IN cells|cell|NNS expressing|express|VBG Vector|Vector|NNP and|and|CC DicF|dicf|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: expression|expression|NN level|level|NN files|file|NNS are|be|VBP tab-delimited|tab-delimited|JJ text|text|NN with|with|IN columns|column|NNS as|as|IN follows|follow|VBZ :|:|: index|index|NN ,|,|, hits|hit|VBZ ,|,|, RPKM|rpkm|NN ,|,|, RPM|RPM|NNP ,|,|, start|start|VB _|_|SYM position|position|NN ,|,|, end|end|NN _|_|NN position|position|NN ,|,|, strand|strand|NN ,|,|, feature|feature|NN _|_|CD type|type|NN ,|,|, reference|reference|NN _|_|NN replicon|replicon|NN -LRB-|-lrb-|-LRB- type|type|NN -RRB-|-rrb-|-RRB- ,|,|, locus|locus|NN _|_|NN tag|tag|NN ,|,|, gene|gene|NN _|_|NN name|name|NN ,|,|, product|product|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: expression|expression|NN of|of|IN genes|gene|NNS in|in|IN time|time|NN ,|,|, rows|row|NNS =|=|JJ genes|gene|NNS ,|,|, cols|col|NNS =|=|JJ time|time|NN points|point|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Files|file|NNS ending|end|VBG with|with|IN _|_|CD coverage.txt|coverage.txt|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN file|file|NN of|of|IN nucleotide-resolution|nucleotide-resolution|JJ coverage|coverage|NN from|from|IN RNA-seq|rna-seq|JJ data|datum|NNS -LRB-|-lrb-|-LRB- column|column|NN 1|1|CD :|:|: genome|genome|NN ID|id|NN ,|,|, column|column|NN 2|2|CD :|:|: nucleotide|nucleotide|NN position|position|NN ,|,|, column|column|NN 3|3|CD :|:|: coverage|coverage|NN -RRB-|-rrb-|-RRB-
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: format|format|NN :|:|: bed|bed|NN format|format|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Gene|Gene|NNP _|_|NNP lists|list|VBZ _|_|SYM GEO.xls|geo.xls|NNS ;|;|: The|the|DT supplementary|supplementary|JJ file|file|NN contains|contain|VBZ gene|gene|NN lists|list|NNS used|use|VBN in|in|IN data|data|NN analysis|analysis|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: GFF|gff|NN file|file|NN containing|contain|VBG 3|3|CD '|'|'' end|end|NN annotations|annotation|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: gff|gff|NN file|file|NN is|be|VBZ generated|generate|VBN by|by|IN in-house|in-house|JJ script|script|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: htcount|htcount|NN :|:|: expression|expression|NN count|count|NN for|for|IN each|each|DT gene|gene|NN and|and|CC its|its|PRP$ name|name|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: In|in|IN the|the|DT .|.|. txt|txt|NN files|file|VBZ the|the|DT first|first|JJ column|column|NN is|be|VBZ the|the|DT coordinate|coordinate|NN of|of|IN the|the|DT base|base|NN corresponding|correspond|VBG to|to|TO NC|NC|NNP _|_|SYM 000913.3|000913.3|CD and|and|CC the|the|DT second|second|JJ column|column|NN is|be|VBZ the|the|DT number|number|NN of|of|IN normalized|normalize|VBN reads|read|VBZ at|at|IN that|that|DT position|position|NN .|.|. All|all|DT 0|0|CD values|value|NNS were|be|VBD given|give|VBN a|a|DT pseudocount|pseudocount|NN of|of|IN 0.01|0.01|CD .|.|. Counts|count|NNS are|be|VBP normalized|normalize|VBN so|so|IN that|that|IN the|the|DT averages|average|NNS of|of|IN ssrA|ssra|NN ,|,|, ssrS|ssrs|NN ,|,|, and|and|CC rnpB|rnpb|NN are|be|VBP stable|stable|JJ throughout|throughout|IN the|the|DT decay|decay|NN from|from|IN 0|0|CD to|to|TO 20|20|CD minutes|minute|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: K12|k12|NN _|_|CD LB.xlsx|lb.xlsx|NN :|:|: Average|average|NN of|of|IN expression|expression|NN values|value|NNS of|of|IN samples|sample|NNS MG1655|mg1655|NN _|_|CD LB1|lb1|NN and|and|CC LB2|lb2|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: MACS|macs|NN v2|v2|NN .0.10.20131216|.0.10.20131216|CD peaks|peak|VBZ file|file|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Mapped|map|VBN reads|read|VBZ were|be|VBD rescaled|rescale|VBN to|to|TO a|a|DT size|size|NN of|of|IN 10|10|CD bp|bp|NN ,|,|, and|and|CC BEDGraph|bedgraph|NN files|file|NNS were|be|VBD generated|generate|VBN using|use|VBG the|the|DT genomeCoverageBed|genomecoveragebed|JJ utility|utility|NN of|of|IN the|the|DT BEDTools|bedtool|NNS suite|suite|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Microsoft|Microsoft|NNP Excel|Excel|NNP File|file|VB with|with|IN normalized|normalize|VBN sequencing|sequencing|NN coverage|coverage|NN of|of|IN all|all|DT annotated|annotated|JJ genes|gene|NNS and|and|CC statistical|statistical|JJ comparison|comparison|NN of|of|IN expression|expression|NN in|in|IN antibiotic|antibiotic|JJ treated|treat|VBN to|to|TO untreated|untreated|JJ cells|cell|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Microsoft|Microsoft|NNP excel|excel|VB spreadsheet|spreadsheet|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT gene|gene|NN of|of|IN sample|sample|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: .|.|. narrowPeak|narrowpeak|NN files|file|NNS output|output|NN by|by|IN macs2|macs2|NN ,|,|, giving|give|VBG peak|peak|JJ start|start|NN and|and|CC end|end|NN positions|position|NNS ,|,|, as|as|RB well|well|RB as|as|IN fold-change|fold-change|NN ,|,|, -|-|: log10pvalue|log10pvalue|NN ,|,|, -|-|: log10qvalue|log10qvalue|NN ,|,|, and|and|CC relative|relative|JJ summit|summit|NN position|position|NN to|to|TO peak|peak|VB start|start|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: .|.|. narrowPeak|narrowpeak|NN files|file|NNS output|output|NN by|by|IN MACS|mac|NNS ,|,|, giving|give|VBG peak|peak|JJ start|start|NN and|and|CC end|end|NN positions|position|NNS ,|,|, as|as|RB well|well|RB as|as|IN fold-change|fold-change|NN ,|,|, -|-|: log10pvalue|log10pvalue|NN ,|,|, -|-|: log10qvalue|log10qvalue|NN ,|,|, and|and|CC relative|relative|JJ summit|summit|NN position|position|NN to|to|TO peak|peak|VB start|start|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: peaks.bed|peaks.bed|JJ
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN data|datum|NNS files|file|NNS are|be|VBP WIG|WIG|NNP files|file|NNS normalized|normalize|VBD to|to|TO reads|read|VBZ per|per|IN million|million|CD per|per|IN position|position|NN .|.|. Those|those|DT designated|designate|VBN \|\|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN data|datum|NNS files|file|NNS are|be|VBP WIG|WIG|NNP files|file|NNS with|with|IN non-coding|non-coding|JJ RNAs|rna|NNS removed|remove|VBD ,|,|, normalized|normalize|VBD to|to|TO reads|read|VBZ per|per|IN million|million|CD per|per|IN position|position|NN .|.|. Those|those|DT with|with|IN a|a|DT \|\|JJ
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN data|datum|NNS files|file|NNS contain|contain|VBP raw|raw|JJ counts|count|NNS for|for|IN CDS|cd|NNS genomic|genomic|JJ features|feature|NNS ,|,|, locations|location|NNS of|of|IN genomic|genomic|JJ features|feature|NNS are|be|VBP provided|provide|VBN in|in|IN associated|associate|VBN .|.|. gtf|gtf|NN files|file|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN data|datum|NNS files|file|NNS contain|contain|VBP the|the|DT number|number|NN of|of|IN reads|read|VBZ mapped|map|VBN to|to|TO each|each|DT base|base|NN pair|pair|NN after|after|IN the|the|DT total|total|JJ number|number|NN of|of|IN reads|read|VBZ were|be|VBD scaled|scale|VBN to|to|TO 20|20|CD million|million|CD reads|read|VBZ per|per|IN experiment|experiment|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN data|datum|NNS include|include|VBP read|read|VBN pileups|pileup|NNS obtained|obtain|VBN in|in|IN two|two|CD ChIP-seq|chip-seq|JJ experiments|experiment|NNS by|by|IN two|two|CD different|different|JJ approaches|approach|NNS -LRB-|-lrb-|-LRB- files|file|NNS 1-4|1-4|CD -RRB-|-rrb-|-RRB- ,|,|, the|the|DT set|set|NN of|of|IN regions|region|NNS bound|bind|VBN by|by|IN Dps|dp|NNS in|in|IN both|both|DT experiments|experiment|NNS -LRB-|-lrb-|-LRB- file|file|NN 5|5|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT set|set|NN of|of|IN regions|region|NNS unbound|unbound|JJ by|by|IN Dps|dp|NNS in|in|IN both|both|DT experiments|experiment|NNS -LRB-|-lrb-|-LRB- file|file|NN 6|6|CD -RRB-|-rrb-|-RRB- .|.|. All|all|DT processed|process|VBN data|datum|NNS are|be|VBP provided|provide|VBN as|as|IN tab-delimited|tab-delimited|JJ .|.|. txt|txt|NN files|file|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN data|datum|NNS is|be|VBZ presented|present|VBN in|in|IN a|a|DT cuff|cuff|NN diff|diff|NN analysis|analysis|NN format|format|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN data|datum|NNS is|be|VBZ presented|present|VBN in|in|IN gff|gff|NN files|file|NNS containing|contain|VBG a|a|DT pileup|pileup|NN of|of|IN 5|5|CD '|'|'' tags|tag|NNS .|.|. GFF|gff|NN column|column|NN headers|header|NNS \|\|VBP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed|process|VBN files|file|NNS are|be|VBP in|in|IN tab|tab|NN delimited|delimit|VBD format|format|NN .|.|. Separate|separate|JJ files|file|NNS are|be|VBP provided|provide|VBN for|for|IN the|the|DT forward|forward|JJ and|and|CC reverse|reverse|JJ strands|strand|NNS .|.|. The|the|DT start|start|NN and|and|CC end|end|NN coordinates|coordinate|VBZ should|should|MD be|be|VB the|the|DT same|same|JJ .|.|. Each|each|DT line|line|NN in|in|IN the|the|DT data|data|NN set|set|NN represents|represent|VBZ the|the|DT position|position|NN of|of|IN the|the|DT first|first|JJ nucleotide|nucleotide|NN at|at|IN the|the|DT 5|5|CD '|'|'' end|end|NN of|of|IN a|a|DT sequence|sequence|NN that|that|WDT could|could|MD be|be|VB mapped|map|VBN to|to|TO the|the|DT E.|e.|FW coli|coli|FW genome|genome|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed-VectorvsDicF-operon|Processed-VectorvsDicF-operon|NNP .|.|. txt|txt|NN :|:|: .|.|. txt|txt|NN tab|tab|NN delimited|delimit|VBD file|file|NN with|with|IN operons|operon|NNS expressed|express|VBN differently|differently|RB between|between|IN vector|vector|NN and|and|CC DicF|dicf|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP .|.|. txt|txt|NN :|:|: .|.|. txt|txt|NN raw|raw|JJ output|output|NN file|file|NN from|from|IN Rockhopper|Rockhopper|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Processed-VectorvsDicF-transcripts|Processed-VectorvsDicF-transcripts|NNP .|.|. xlsx|xlsx|NN :|:|: Excel|Excel|NNP file|file|NN with|with|IN transcription|transcription|NN start|start|NN and|and|CC stop|stop|VB ,|,|, expression|expression|NN values|value|NNS of|of|IN all|all|DT genes|gene|NNS in|in|IN the|the|DT E.|e.|FW coli|coli|FW genome|genome|NN in|in|IN vector|vector|NN and|and|CC DicF|dicf|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: raw|raw|JJ read|read|NN counts|count|VBZ as|as|RB determined|determine|VBN by|by|IN HTseq-Count|htseq-count|NN ,|,|, provided|provide|VBN in|in|IN .|.|. csv|csv|NN format|format|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Read|Read|NNP counts|count|VBZ aligned|align|VBN to|to|TO genes|gene|NNS and|and|CC noncoding|noncoding|JJ Rfam|rfam|NN features|feature|NNS in|in|IN CSV|CSV|NNP format|format|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Read|read|VB counts|count|NNS were|be|VBD normalized|normalize|VBN by|by|IN the|the|DT length|length|NN of|of|IN the|the|DT unique|unique|JJ CDS|cds|NN per|per|IN kilobase|kilobase|NN -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT total|total|JJ mapped|map|VBN reads|read|VBZ per|per|IN million|million|CD -LRB-|-lrb-|-LRB- RPM|rpm|NN -RRB-|-rrb-|-RRB-
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Reads|read|NNS ,|,|, RPKM|rpkm|NN ,|,|, and|and|CC RCV|RCV|NNP mapped|map|VBD to|to|TO NC|NC|NNP _|_|SYM 002655|002655|CD -LRB-|-lrb-|-LRB- RCV|rcv|NN =|=|JJ Ribosomal|ribosomal|JJ Coverage|Coverage|NNP Value|value|NN =|=|JJ RPKM-footprint|rpkm-footprint|NN over|over|IN RPKM-transcription|rpkm-transcription|NN -RRB-|-rrb-|-RRB-
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: rna-seq|rna-seq|NN :|:|: genomic|genomic|JJ position|position|NN -LRB-|-lrb-|-LRB- middle|middle|NN of|of|IN the|the|DT 5kb-bin|5kb-bin|NN -RRB-|-rrb-|-RRB- to|to|TO each|each|DT count|count|NN .|.|. 3C|3c|NN seq|seq|NN :|:|: contact|contact|NN maps|map|NNS -LRB-|-lrb-|-LRB- 2D|2d|NN array|array|NN of|of|IN 928|928|CD 5kb-bins|5kb-bin|NNS x|x|CC 928|928|CD 5kb-bins|5kb-bin|NNS -RRB-|-rrb-|-RRB- .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: RPG|rpg|NN -LRB-|-lrb-|-LRB- reads|read|VBZ per|per|IN gene|gene|NN -RRB-|-rrb-|-RRB- files|file|NNS were|be|VBD created|create|VBN using|use|VBG HTSeq|htseq|NN ,|,|, mapping|map|VBG raw|raw|JJ reads|read|VBZ -LRB-|-lrb-|-LRB- fastq|fastq|NN format|format|NN -RRB-|-rrb-|-RRB- against|against|IN the|the|DT E.|e.|FW coli|coli|FW K12|k12|NN genome|genome|NN and|and|CC using|use|VBG a|a|DT GFF|gff|NN file|file|NN derived|derive|VBN from|from|IN the|the|DT annotation|annotation|NN of|of|IN NC|NC|NNP _|_|SYM 000913.3|000913.3|CD available|available|JJ from|from|IN NCBI|NCBI|NNP .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: RPKM|RPKM|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: RPKM|rpkm|NN is|be|VBZ generated|generate|VBN by|by|IN in-house|in-house|JJ script|script|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: sam|sam|NN containing|contain|VBG aligned|align|VBN sequences|sequence|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: SPET-seq|spet-seq|NN data|datum|NNS is|be|VBZ provided|provide|VBN in|in|IN the|the|DT form|form|NN of|of|IN RNA|rna|NN Framework|framework|NN 's|'s|POS -LRB-|-lrb-|-LRB- http://www.rnaframework.com|http://www.rnaframework.com|NN -RRB-|-rrb-|-RRB- RNA|rna|NN Count|count|NN -LRB-|-lrb-|-LRB- RC|rc|NN -RRB-|-rrb-|-RRB- files|file|NNS .|.|. A|a|DT file|file|NN corresponding|correspond|VBG to|to|TO each|each|DT transcription|transcription|NN intermediate|intermediate|NN is|be|VBZ provided|provide|VBN .|.|. For|for|IN a|a|DT detailed|detailed|JJ description|description|NN of|of|IN the|the|DT RC|rc|NN format|format|NN ,|,|, please|please|VB refer|refer|VB to|to|TO :|:|: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: SPET-seq|spet-seq|NN data|datum|NNS is|be|VBZ provided|provide|VBN in|in|IN the|the|DT form|form|NN of|of|IN RNA|rna|NN Framework|framework|NN 's|'s|POS -LRB-|-lrb-|-LRB- http://www.rnaframework.com|http://www.rnaframework.com|NN -RRB-|-rrb-|-RRB- RNA|rna|NN Count|count|NN -LRB-|-lrb-|-LRB- RC|rc|NN -RRB-|-rrb-|-RRB- files|file|NNS .|.|. A|a|DT file|file|NN corresponding|correspond|VBG to|to|TO each|each|DT transcription|transcription|NN intermediate|intermediate|NN is|be|VBZ provided|provide|VBN .|.|. For|for|IN a|a|DT detailed|detailed|JJ description|description|NN of|of|IN the|the|DT RC|rc|NN format|format|NN ,|,|, please|please|VB refer|refer|VB to|to|TO :|:|: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|NN .|.|. For|for|IN rRNA|rrna|NN 23S|23s|NN -LRB-|-lrb-|-LRB- rrlB|rrlb|NN gene|gene|NN -RRB-|-rrb-|-RRB- ,|,|, SPET-seq|spet-seq|JJ data|datum|NNS is|be|VBZ provided|provide|VBN in|in|IN the|the|DT form|form|NN of|of|IN RC|RC|NNP files|file|NNS ,|,|, each|each|DT one|one|CD corresponding|correspond|VBG to|to|TO individual|individual|JJ transcription|transcription|NN intermediates|intermediate|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: SPET-seq|spet-seq|NN data|datum|NNS -LRB-|-lrb-|-LRB- pooled|pooled|JJ Total|total|JJ and|and|CC Ribo|Ribo|NNP -|-|: RNA|rna|NN from|from|IN both|both|DT replicates|replicate|VBZ -RRB-|-rrb-|-RRB- is|be|VBZ provided|provide|VBN in|in|IN the|the|DT form|form|NN of|of|IN RNA|rna|NN Framework|framework|NN 's|'s|POS -LRB-|-lrb-|-LRB- http://www.rnaframework.com|http://www.rnaframework.com|NN -RRB-|-rrb-|-RRB- RNA|rna|NN Count|count|NN -LRB-|-lrb-|-LRB- RC|rc|NN -RRB-|-rrb-|-RRB- files|file|NNS .|.|. For|for|IN each|each|DT analyzed|analyze|VBN transcript|transcript|NN ,|,|, 10|10|CD files|file|NNS corresponding|correspond|VBG to|to|TO SPET-seq|spet-seq|JJ data|datum|NNS for|for|IN the|the|DT 10|10|CD transcription|transcription|NN deciles|decile|NNS are|be|VBP provided|provide|VBN .|.|. For|for|IN a|a|DT detailed|detailed|JJ description|description|NN of|of|IN the|the|DT RC|rc|NN format|format|NN ,|,|, please|please|VB refer|refer|VB to|to|TO :|:|: http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|http://rnaframework.readthedocs.io/en/latest/rf-count/#rc-rna-count-format|JJ
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Strain-expression|strain-expression|NN .|.|. xlsx|xlsx|NN archive|archive|NN contains|contain|VBZ expression|expression|NN values|value|NNS in|in|IN RPKM|rpkm|NN -LRB-|-lrb-|-LRB- Reads|read|NNS Per|per|IN Kb|kb|NN exon|exon|NN -LRB-|-lrb-|-LRB- contig|contig|NN -RRB-|-rrb-|-RRB- per|per|IN Million|Million|NNP mapped|map|VBD reads|read|VBZ -LRB-|-lrb-|-LRB- see|see|VB Mortazavi|Mortazavi|NNP et|et|FW al.|al.|FW 2008|2008|CD ,|,|, Nat|Nat|NNP Methods|method|NNS .|.|. 5|5|CD -LRB-|-lrb-|-LRB- 7|7|CD -RRB-|-rrb-|-RRB- :|:|: 621-8|621-8|CD -RRB-|-rrb-|-RRB- and|and|CC can|can|MD be|be|VB directly|directly|RB compared|compare|VBN to|to|TO each|each|DT other|other|JJ -RRB-|-rrb-|-RRB- tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: T1E|t1e|NN _|_|CD LB.xlsx|lb.xlsx|NN :|:|: Average|average|NN of|of|IN expression|expression|NN values|value|NNS of|of|IN samples|sample|NNS DOT-T1E|dot-t1e|NN _|_|CD LB1|lb1|NN and|and|CC LB2|lb2|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Tab-delimited|tab-delimited|JJ text|text|NN file|file|NN ;|;|: genes|gene|NNS in|in|IN rows|row|NNS and|and|CC samples|sample|NNS in|in|IN columns|column|NNS ;|;|: each|each|DT entry|entry|NN corresponds|correspond|VBZ to|to|TO the|the|DT number|number|NN of|of|IN reads|read|VBZ mapping|map|VBG to|to|TO the|the|DT given|give|VBN gene|gene|NN in|in|IN the|the|DT given|give|VBN sample|sample|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Tab|tab|NN delimited|delimit|VBN text|text|NN file|file|NN ;|;|: includes|include|VBZ :|:|: gene|gene|NN differential|differential|JJ expression|expression|NN levels|level|NNS relative|relative|JJ to|to|TO the|the|DT G500|g500|NN strain|strain|NN with|with|IN corresponding|corresponding|JJ p-values|p-value|NNS and|and|CC processed|process|VBN counts|count|NNS for|for|IN each|each|DT biological|biological|JJ replicate|replicate|VB -LRB-|-lrb-|-LRB- each|each|DT normolized|normolized|NN and|and|CC averaged|average|VBD between|between|IN 2|2|CD technical|technical|JJ replicates|replicate|VBZ -RRB-|-rrb-|-RRB- .|.|. Linked|link|VBN as|as|IN supplementary|supplementary|JJ file|file|NN on|on|IN Series|Series|NNP record|record|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Tab-delimited|tab-delimited|JJ text|text|NN file|file|NN includes|include|VBZ Rockhopper|Rockhopper|NNP -LRB-|-lrb-|-LRB- McClure|McClure|NNP et|et|FW al.|al.|FW ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- normalized|normalize|VBD transcript|transcript|NN abundance|abundance|NN measurements|measurement|NNS -LRB-|-lrb-|-LRB- Expression|expression|NN -RRB-|-rrb-|-RRB- ,|,|, transcript|transcript|NN abundance|abundance|NN ratios|ratio|NNS -LRB-|-lrb-|-LRB- Expression|expression|NN Ratio|ratio|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC qValues|qvalue|NNS -LRB-|-lrb-|-LRB- qValue|qvalue|NN -RRB-|-rrb-|-RRB- for|for|IN raw|raw|JJ data|datum|NNS that|that|WDT were|be|VBD treated|treat|VBN as|as|IN two|two|CD experiments|experiment|NNS constituting|constitute|VBG either|either|CC two|two|CD -LRB-|-lrb-|-LRB- \|\|CD
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN file|file|NN of|of|IN transition|transition|NN error|error|NN rate|rate|NN per|per|IN position|position|NN .|.|. The|the|DT position|position|NN is|be|VBZ corresponding|correspond|VBG to|to|TO the|the|DT position|position|NN of|of|IN \|\|CD
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Tab|tab|NN delimited|delimit|VBN text|text|NN files|file|NNS containing|contain|VBG transcription|transcription|NN coordinates|coordinate|VBZ and|and|CC abundance|abundance|NN estimates|estimate|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP count|count|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP CPM|CPM|NNP values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP gene|gene|NN expresion|expresion|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP normalized|normalize|VBN FPKM|fpkm|NN values|value|NNS and|and|CC raw|raw|JJ fragment|fragment|NN counts|count|NNS for|for|IN each|each|DT Sample|Sample|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP ...|...|:
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT sample|sample|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT sample|sample|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP the|the|DT average|average|NN of|of|IN the|the|DT expression|expression|NN values|value|NNS obtained|obtain|VBN in|in|IN Rockhopper|Rockhopper|NNP for|for|IN the|the|DT replicates|replicate|VBZ of|of|IN each|each|DT condition|condition|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP TPM|tpm|NN values|value|NNS for|for|IN each|each|DT Sample|sample|NN ;|;|: column1|column1|NN :|:|: transcript|transcript|NN id|id|NN ;|;|: column2|column2|NN :|:|: TPM|tpm|NN value|value|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS in|in|IN gff|gff|NN format|format|NN which|which|WDT has|have|VBZ 8|8|CD columns|column|NNS :|:|: sequence|sequence|NN id|id|NN ,|,|, source|source|NN -LRB-|-lrb-|-LRB- empty|empty|JJ -RRB-|-rrb-|-RRB- ,|,|, feature|feature|NN -LRB-|-lrb-|-LRB- +|+|CC /|/|: -|-|: strand|strand|NN -RRB-|-rrb-|-RRB- ,|,|, start|start|VB position|position|NN ,|,|, end|end|NN position|position|NN ,|,|, intensity|intensity|NN score|score|NN ,|,|, strand|strand|NN -LRB-|-lrb-|-LRB- +|+|CC /|/|: -|-|: -RRB-|-rrb-|-RRB- ,|,|, frame|frame|NN -LRB-|-lrb-|-LRB- .|.|. -RRB-|-rrb-|-RRB- ,|,|, attribute|attribute|NN -LRB-|-lrb-|-LRB- .|.|. -RRB-|-rrb-|-RRB- .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab|tab|NN delimited|delimit|VBD text|text|NN files|file|NNS ,|,|, with|with|IN feature|feature|NN annotation|annotation|NN ,|,|, REC|rec|NN _|_|CD seq|seq|NN score|score|NN ,|,|, gene|gene|NN name|name|NN and|and|CC description|description|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tab-delimitted|tab-delimitted|JJ text|text|NN files|file|NNS contain|contain|VBP TPM|tpm|NN -LRB-|-lrb-|-LRB- transcripts|transcript|NNS per|per|IN million|million|CD -RRB-|-rrb-|-RRB- values|value|NNS for|for|IN each|each|DT sample|sample|NN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Table|Table|NNP of|of|IN read|read|VBN counts|count|NNS with|with|IN genes|gene|NNS as|as|IN rows|row|NNS and|and|CC samples|sample|NNS as|as|IN columns|column|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tabular|tabular|JJ :|:|: Tabular|tabular|JJ data|datum|NNS that|that|WDT informs|inform|VBZ the|the|DT excel|excel|VB spreadsheet|spreadsheet|NN .|.|. The|the|DT data|datum|NNS are|be|VBP averaged|average|VBN across|across|IN the|the|DT three|three|CD samples|sample|NNS per|per|IN strain|strain|NN .|.|. Both|both|DT averaged|average|VBD strain|strain|NN data|datum|NNS are|be|VBP presented|present|VBN for|for|IN each|each|DT gene|gene|NN on|on|IN the|the|DT same|same|JJ line|line|NN .|.|. Data|datum|NNS contain|contain|VBP gene|gene|NN ID|id|NN ,|,|, gene|gene|NN number|number|NN ,|,|, locus|locus|NN ,|,|, fragments|fragment|NNS per|per|IN kilobase|kilobase|NN mapped|map|VBN -LRB-|-lrb-|-LRB- FPKM|fpkm|NN -RRB-|-rrb-|-RRB- for|for|IN WT|WT|NNP and|and|CC mutant|mutant|JJ strains|strain|NNS ,|,|, log2|log2|NN -LRB-|-lrb-|-LRB- fold-change|fold-change|NN -RRB-|-rrb-|-RRB- relative|relative|JJ epxression|epxression|NN of|of|IN WT|WT|NNP over|over|IN mutant|mutant|JJ strains|strain|NNS ,|,|, test-statistic|test-statistic|JJ ,|,|, p-value|p-value|NN ,|,|, q-value|q-value|NN ,|,|, and|and|CC significance|significance|NN analyzed|analyze|VBD via|via|IN the|the|DT cummeRbund|cummerbund|NN package|package|NN in|in|IN R|r|NN whereby|whereby|WRB a|a|DT q-value|q-value|NN of|of|IN <|<|JJR 0.05|0.05|CD is|be|VBZ considered|consider|VBN significant|significant|JJ .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: tar|tar|NN archives|archive|NNS contain|contain|VBP the|the|DT following|following|NN :|:|:
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: text|text|NN files|file|NNS containing|contain|VBG gene|gene|NN counts|count|VBZ output|output|NN by|by|IN htseq-count|htseq-count|JJ
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: The|the|DT columns|column|NNS in|in|IN the|the|DT processed|process|VBN files|file|NNS are|be|VBP the|the|DT following|follow|VBG in|in|IN order|order|NN :|:|: GeneID|geneid|NN ,|,|, Length|length|NN ,|,|, ORF1|orf1|NN _|_|NN 1|1|CD _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 7655775|7655775|CD -RRB-|-rrb-|-RRB- ,|,|, ORF1|orf1|NN _|_|NN 1|1|CD _|_|CD IPTG|iptg|NN _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 7178582|7178582|CD -RRB-|-rrb-|-RRB- ,|,|, ORF1|orf1|NN _|_|NN 2|2|CD _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 7706927|7706927|CD -RRB-|-rrb-|-RRB- ,|,|, ORF1|orf1|NN _|_|NN 2|2|CD _|_|CD IPTG|iptg|NN _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 7070827|7070827|CD -RRB-|-rrb-|-RRB- ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 1|1|CD _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 8018710|8018710|CD -RRB-|-rrb-|-RRB- ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 1|1|CD _|_|CD IPTG|iptg|NN _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 8299205|8299205|CD -RRB-|-rrb-|-RRB- ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 2|2|CD _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 7313736|7313736|CD -RRB-|-rrb-|-RRB- ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 2|2|CD _|_|CD IPTG|iptg|NN _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 8344539|8344539|CD -RRB-|-rrb-|-RRB- ,|,|, WT1|wt1|NN _|_|CD IPTG|iptg|NN _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 8074159|8074159|CD -RRB-|-rrb-|-RRB- ,|,|, WT2|wt2|NN _|_|CD IPTG|iptg|NN _|_|NN mapped|map|VBD _|_|CD reads|read|VBZ -LRB-|-lrb-|-LRB- 8103887|8103887|CD -RRB-|-rrb-|-RRB- ,|,|, ORF1|orf1|NN _|_|NN 1|1|CD _|_|NN coverage|coverage|NN ,|,|, ORF1|orf1|NN _|_|NN 1|1|CD _|_|SYM IPTG|iptg|SYM _|_|SYM coverage|coverage|NN ,|,|, ORF1|orf1|NN _|_|NN 2|2|CD _|_|CD coverage|coverage|NN ,|,|, ORF1|orf1|NN _|_|NN 2|2|CD _|_|SYM IPTG|iptg|SYM _|_|SYM coverage|coverage|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 1|1|CD _|_|NN coverage|coverage|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 1|1|CD _|_|SYM IPTG|iptg|SYM _|_|SYM coverage|coverage|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 2|2|CD _|_|CD coverage|coverage|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 2|2|CD _|_|SYM IPTG|iptg|SYM _|_|SYM coverage|coverage|NN ,|,|, WT1|wt1|NN _|_|CD IPTG|IPTG|NNP _|_|CD coverage|coverage|NN ,|,|, WT2|wt2|NN _|_|CD IPTG|IPTG|NNP _|_|CD coverage|coverage|NN ,|,|, ORF1|orf1|NN _|_|NN 1|1|CD _|_|NN rpkm|rpkm|NN ,|,|, ORF1|orf1|NN _|_|NN 1|1|CD _|_|CD IPTG|iptg|NN _|_|NN rpkm|rpkm|NN ,|,|, ORF1|orf1|NN _|_|NN 2|2|CD _|_|CD rpkm|rpkm|NN ,|,|, ORF1|orf1|NN _|_|NN 2|2|CD _|_|CD IPTG|iptg|NN _|_|NN rpkm|rpkm|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 1|1|CD _|_|NN rpkm|rpkm|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 1|1|CD _|_|CD IPTG|iptg|NN _|_|NN rpkm|rpkm|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 2|2|CD _|_|CD rpkm|rpkm|NN ,|,|, Svi3|svi3|NN _|_|NN 3|3|CD _|_|NN 2|2|CD _|_|CD IPTG|iptg|NN _|_|NN rpkm|rpkm|NN ,|,|, WT1|wt1|NN _|_|CD IPTG|iptg|NN _|_|NN rpkm|rpkm|NN ,|,|, WT2|wt2|NN _|_|CD IPTG|iptg|NN _|_|NN rpkm|rpkm|NN ,|,|, Symbol|symbol|NN -LRB-|-lrb-|-LRB- gene|gene|NN name|name|NN -RRB-|-rrb-|-RRB- ,|,|, Description|description|NN ,|,|, KEGG|KEGG|NNP Orthology|Orthology|NNP ,|,|, GO|GO|NNP Component|Component|NNP ,|,|, GO|GO|NNP Function|function|NN ,|,|, and|and|CC GO|GO|NNP Process|process|VBP
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: The|the|DT file|file|NN format|format|NN is|be|VBZ .|.|. xlsx|xlsx|NN .|.|. The|the|DT file|file|NN contains|contain|VBZ the|the|DT raw|raw|JJ gene|gene|NN counts|count|NNS of|of|IN all|all|DT samples|sample|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: The|the|DT tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP raw|raw|JJ read|read|NN values|value|NNS for|for|IN each|each|DT time-point|time-point|NN for|for|IN both|both|DT biol|biol|NN .|.|. replicates|replicate|VBZ of|of|IN control|control|NN and|and|CC Carolacton-treated|carolacton-treated|JJ samples|sample|NNS as|as|IN obtained|obtain|VBN from|from|IN Rockhopper|Rockhopper|NNP .|.|. A|a|DT FASTA|fasta|NN file|file|NN on|on|IN the|the|DT series|series|NN record|record|NN contains|contain|VBZ the|the|DT transcript|transcript|NN sequences|sequence|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: The|the|DT text|text|NN file|file|NN contains|contain|VBZ sense|sense|NN and|and|CC antisense|antisense|JJ raw|raw|JJ base|base|NN read|read|VBD counts|count|NNS for|for|IN each|each|DT of|of|IN the|the|DT 4091|4091|CD ORFs|orf|NNS for|for|IN all|all|PDT the|the|DT 15|15|CD samples|sample|NNS ,|,|, and|and|CC the|the|DT explanation|explanation|NN key|key|NN is|be|VBZ included|include|VBN in|in|IN the|the|DT file|file|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: The|the|DT txt|txt|NN file|file|NN includes|include|VBZ the|the|DT gene|gene|NN expression|expression|NN profiles|profile|NNS of|of|IN all|all|PDT the|the|DT samples|sample|NNS .|.|. The|the|DT xlsx|xlsx|NN file|file|NN contains|contain|VBZ the|the|DT PC1|pc1|NN and|and|CC PC2|pc2|NN values|value|NNS of|of|IN all|all|PDT the|the|DT samples|sample|NNS .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: .|.|. txt|txt|NN file|file|NN file|file|NN with|with|IN raw|raw|JJ and|and|CC normalized|normalize|VBD counts|count|NNS of|of|IN coverage|coverage|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Txt|txt|NN files|file|NNS are|be|VBP processed|process|VBN data|datum|NNS for|for|IN DMS-MaPseq|dms-mapseq|NN with|with|IN two|two|CD columns|column|NNS :|:|: first|first|JJ column|column|NN containing|contain|VBG chromosome|chromosome|NN positions|position|NNS -LRB-|-lrb-|-LRB- relative|relative|JJ to|to|TO transcription|transcription|NN start|start|NN site|site|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- of|of|IN cspA|cspa|NN -RRB-|-rrb-|-RRB- and|and|CC second|second|JJ column|column|NN containing|contain|VBG the|the|DT mutation|mutation|NN rate|rate|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: txt|txt|NN files|file|NNS including|include|VBG count|count|NN data|datum|NNS for|for|IN the|the|DT whole|whole|JJ genome|genome|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: txt|txt|NN files|file|NNS including|include|VBG count|count|NN numbers|number|NNS of|of|IN RNA|rna|NN 's|'s|POS and|and|CC quality|quality|NN control|control|NN were|be|VBD generated|generate|VBN
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: txt|txt|NN files|file|NNS of|of|IN a|a|DT matrix|matrix|NN containing|contain|VBG genome|genome|NN position|position|NN in|in|IN column|column|NN 1|1|CD and|and|CC number|number|NN of|of|IN depth|depth|NN of|of|IN mapped|map|VBN reads|read|VBZ in|in|IN column|column|NN 2|2|CD .|.|. Also|also|RB ,|,|, in|in|IN a|a|DT CSV|CSV|NNP file|file|NN of|of|IN a|a|DT matrix|matrix|NN containing|contain|VBG genome|genome|NN position|position|NN in|in|IN column|column|NN 1|1|CD and|and|CC subsequent|subsequent|JJ coloumns|coloumn|NNS with|with|IN normalised|normalised|JJ number|number|NN of|of|IN depth|depth|NN of|of|IN mapped|map|VBN reads|read|VBZ -LRB-|-lrb-|-LRB- column|column|NN names|name|NNS have|have|VBP the|the|DT strain|strain|NN number|number|NN -RRB-|-rrb-|-RRB- .|.|. CSV|CSV|NNP file|file|NN is|be|VBZ on|on|IN the|the|DT series|series|NN record|record|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: .|.|. txt|txt|NN -LRB-|-lrb-|-LRB- log2|log2|NN fold|fold|JJ change|change|NN values|value|NNS ,|,|, p-values|p-value|NNS -RRB-|-rrb-|-RRB-
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: -LSB-|-lsb-|-LRB- .|.|. txt|txt|NN -RSB-|-rsb-|-RRB- tab-delimited|tab-delimited|JJ text|text|NN file|file|NN includes|include|VBZ RPKM|rpkm|NN values|value|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: txt|txt|NN :|:|: tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS include|include|VBP RPKM|rpkm|NN values|value|NNS for|for|IN each|each|DT Sample|Sample|NNP
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: *|*|SYM txt|txt|NN ,|,|, *|*|SYM xml|xml|NN :|:|: These|these|DT files|file|NNS contain|contain|VBP the|the|DT raw|raw|JJ counts|count|NNS ,|,|, normalized|normalize|VBD counts|count|NNS ,|,|, RPKM|rpkm|NN values|value|NNS ,|,|, expression|expression|NN values|value|NNS ,|,|, P-values|p-value|NNS and|and|CC Q-values|q-value|NNS .|.|. Each|each|DT file|file|NN contains|contain|VBZ the|the|DT values|value|NNS for|for|IN both|both|DT samples|sample|NNS at|at|IN the|the|DT indicated|indicate|VBN timepoint|timepoint|NN .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: WIG|wig|NN files|file|NNS are|be|VBP provided|provide|VBN showing|show|VBG uniquely|uniquely|RB mapped|map|VBN sequence|sequence|NN reads|read|VBZ -LRB-|-lrb-|-LRB- normalized|normalize|VBN -RRB-|-rrb-|-RRB- .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: wig|wig|NN files|file|NNS representing|represent|VBG the|the|DT normalized|normalize|VBN number|number|NN of|of|IN pAA-associated|paa-associated|JJ mapped|map|VBN reads|read|VBZ per|per|IN nucleotide|nucleotide|NN .|.|. Files|file|NNS contain|contain|VBP wiggle-formatted|wiggle-formatted|JJ files|file|NNS data|datum|NNS for|for|IN accessions|accession|NNS NC|NC|NNP _|_|SYM 018658.1|018658.1|CD ,|,|, NC|NC|NNP _|_|NNP 018659.1|018659.1|CD ,|,|, NC|NC|NNP _|_|NNP 018660.1|018660.1|CD ,|,|, and|and|CC NC|NC|NNP _|_|SYM 018666.1|018666.1|CD .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: wiggle|wiggle|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: wiggle|wiggle|NN files|file|NNS with|with|IN two|two|CD columns|column|NNS :|:|: first|first|JJ column|column|NN containing|contain|VBG chromosome|chromosome|NN positions|position|NNS and|and|CC second|second|JJ column|column|NN containing|contain|VBG the|the|DT number|number|NN of|of|IN reads|read|VBZ mapped|map|VBN to|to|TO the|the|DT position|position|NN -LRB-|-lrb-|-LRB- see|see|VB publication|publication|NN for|for|IN details|detail|NNS -RRB-|-rrb-|-RRB- .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: Wiggle|Wiggle|NNP files|file|VBZ with|with|IN two|two|CD columns|column|NNS :|:|: first|first|JJ column|column|NN containing|contain|VBG chromosome|chromosome|NN positions|position|NNS and|and|CC second|second|JJ column|column|NN containing|contain|VBG the|the|DT number|number|NN of|of|IN reads|read|VBZ mapped|map|VBN to|to|TO the|the|DT position|position|NN -LRB-|-lrb-|-LRB- see|see|VB publication|publication|NN for|for|IN details|detail|NNS -RRB-|-rrb-|-RRB- .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: .|.|. xls|xl|NNS ,|,|, spreadsheet|spreadsheet|NN of|of|IN normalized|normalize|VBN read|read|NN counts|count|NNS for|for|IN each|each|DT gene|gene|NN for|for|IN each|each|DT sample|sample|NN ,|,|, differential|differential|JJ expression|expression|NN data|datum|NNS ,|,|, and|and|CC annotation|annotation|NN
Supplementary|supplementary|JJ _|_|NN files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: xls|xl|NNS :|:|: The|the|DT data|datum|NNS are|be|VBP averaged|average|VBN across|across|IN the|the|DT three|three|CD samples|sample|NNS per|per|IN strain|strain|NN .|.|. Both|both|DT averaged|average|VBD strain|strain|NN data|datum|NNS are|be|VBP presented|present|VBN for|for|IN each|each|DT gene|gene|NN on|on|IN the|the|DT same|same|JJ line|line|NN .|.|. Excel|Excel|NNP spreadsheet|spreadsheet|NN containing|contain|VBG gene|gene|NN ID|id|NN ,|,|, gene|gene|NN number|number|NN ,|,|, locus|locus|NN ,|,|, fragments|fragment|NNS per|per|IN kilobase|kilobase|NN mapped|map|VBN -LRB-|-lrb-|-LRB- FPKM|fpkm|NN -RRB-|-rrb-|-RRB- for|for|IN WT|WT|NNP and|and|CC mutant|mutant|JJ strains|strain|NNS ,|,|, log2|log2|NN -LRB-|-lrb-|-LRB- fold-change|fold-change|NN -RRB-|-rrb-|-RRB- relative|relative|JJ epxression|epxression|NN of|of|IN WT|WT|NNP over|over|IN mutant|mutant|JJ strains|strain|NNS ,|,|, test-statistic|test-statistic|JJ ,|,|, p-value|p-value|NN ,|,|, q-value|q-value|NN ,|,|, and|and|CC significance|significance|NN analyzed|analyze|VBD via|via|IN the|the|DT cummeRbund|cummerbund|NN package|package|NN in|in|IN R|r|NN whereby|whereby|WRB a|a|DT q-value|q-value|NN of|of|IN <|<|JJR 0.05|0.05|CD is|be|VBZ considered|consider|VBN significant|significant|JJ .|.|.
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: xlsx|xlsx|NN file|file|NN format|format|NN includes|include|VBZ raw|raw|JJ gene|gene|NN counts|count|VBZ for|for|IN each|each|DT sample|sample|NN before|before|IN and|and|CC after|after|IN filtering|filter|VBG for|for|IN low|low|JJ coverage|coverage|NN genes|gene|NNS
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: .|.|. xlsx|xlsx|NN files|file|NNS contain|contain|VBP peak|peak|JJ region|region|NN locations|location|NNS and|and|CC gene|gene|NN expression|expression|NN value|value|NN for|for|IN ChIP-Seq|chip-seq|NN and|and|CC RNA-Seq|rna-seq|NN respectively|respectively|RB
Supplementary|Supplementary|NNP _|_|VBD files|file|NNS _|_|IN format|format|NN _|_|NN and|and|CC _|_|NN content|content|NN :|:|: xlsx|xlsx|NN :|:|: logFC|logfc|NN and|and|CC p-value|p-value|JJ
supplementation|supplementation|NN :|:|: adenine|adenine|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN -RRB-|-rrb-|-RRB-
supplementation|supplementation|NN :|:|: L-tryptophan|l-tryptophan|NN -LRB-|-lrb-|-LRB- 20|20|CD mg/L|mg/l|NN -RRB-|-rrb-|-RRB-
supplementation|supplementation|NN :|:|: None|none|NN
Suspended|suspend|VBN cells|cell|NNS were|be|VBD then|then|RB removed|remove|VBN and|and|CC biofilms|biofilm|NNS were|be|VBD washed|wash|VBN 3|3|CD times|time|NNS with|with|IN 1|1|CD ml|ml|NN 10|10|CD %|%|NN LB|lb|NN broth|broth|NN .|.|. Biofilms|biofilm|NNS from|from|IN each|each|DT petri|petri|NN dish|dish|NN were|be|VBD then|then|RB scraped|scrape|VBN into|into|IN a|a|DT vial|vial|NN containing|contain|VBG 1|1|CD ml|ml|NN 10|10|CD %|%|NN LB|lb|NN .|.|. Scraped|scraped|JJ biofilms|biofilm|NNS in|in|IN each|each|DT vial|vial|NN were|be|VBD concentrated|concentrate|VBN from|from|IN 1|1|CD ml|ml|NN into|into|IN 50|50|CD ul|ul|NN by|by|IN centrifugation|centrifugation|NN .|.|. 500|500|CD ul|ul|NN RNAlater|rnalater|NN was|be|VBD added|add|VBN and|and|CC mixed|mix|VBN well|well|RB .|.|. Samples|sample|NNS in|in|IN RNAlater|rnalater|NN were|be|VBD kept|keep|VBN in|in|IN 4C|4c|NN fridge|fridge|NN overnight|overnight|JJ .|.|. Each|each|DT vial|vial|NN was|be|VBD homogenized|homogenize|VBN with|with|IN OMNI|OMNI|NNP TH|th|NN homogenizer|homogenizer|NN for|for|IN 2|2|CD min|min|NN on|on|IN ice|ice|NN and|and|CC further|further|JJ aliquoted|aliquote|VBN into|into|IN small|small|JJ vials|vial|NNS .|.|. Cells|cell|NNS in|in|IN each|each|DT vial|vial|NN were|be|VBD then|then|RB re-suspended|re-suspended|JJ in|in|IN nuclease-free|nuclease-free|JJ phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN ,|,|, incubated|incubate|VBN with|with|IN anti-E|anti-e|JJ .|.|. coli|coli|NN antibody|antibody|NN -LRB-|-lrb-|-LRB- ViroStat|virostat|NN -RRB-|-rrb-|-RRB- and|and|CC microbeads|microbead|NNS -LRB-|-lrb-|-LRB- Miltenyi|miltenyi|NN -RRB-|-rrb-|-RRB- ,|,|, followed|follow|VBN by|by|IN separation|separation|NN on|on|IN a|a|DT MACS|macs|NN separator|separator|NN -LRB-|-lrb-|-LRB- Miltenyi|Miltenyi|NNP ,|,|, Auburn|Auburn|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- at|at|IN 4|4|CD degree|degree|NN C.|c.|NN Sorted|sort|VBN cells|cell|NNS were|be|VBD re-suspended|re-suspended|JJ into|into|IN RNAlater|rnalater|NN until|until|IN RNA|rna|NN extractions|extraction|NNS .|.|.
Svi3|svi3|NN _|_|CD 3|3|CD _|_|NN 1|1|CD
Svi3|svi3|NN _|_|CD 3|3|CD _|_|NN 1|1|CD _|_|CD IPTG|iptg|NN
Svi3|svi3|NN _|_|CD 3|3|CD _|_|NN 2|2|CD
Svi3|svi3|NN _|_|CD 3|3|CD _|_|NN 2|2|CD _|_|CD IPTG|iptg|NN
symbioflor|symbioflor|NN status|status|NN :|:|: without|without|IN Symbioflor|Symbioflor|NNP
symbioflor|symbioflor|NN status|status|NN :|:|: with|with|IN Symbioflor|Symbioflor|NNP
Synchronization|synchronization|NN was|be|VBD achieved|achieve|VBN by|by|IN passaging|passaging|NN cells|cell|NNS through|through|IN one|one|CD or|or|CC two|two|CD rounds|round|NNS of|of|IN stationary|stationary|JJ phase|phase|NN according|accord|VBG to|to|TO Cutler|Cutler|NNP and|and|CC Evans|Evans|NNP 1966|1966|CD .|.|. Briefly|briefly|RB :|:|: Individual|individual|JJ colonies|colony|NNS -LRB-|-lrb-|-LRB- LB|lb|NN plate|plate|NN ,|,|, 37|37|CD °C|°c|NN ,|,|, 24|24|CD h|h|NN -RRB-|-rrb-|-RRB- were|be|VBD inoculated|inoculate|VBN into|into|IN M9|m9|NN media|media|NNS and|and|CC grown|grow|VBN O/N|o/n|NN -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN ,|,|, 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- .|.|. M9|m9|NN media|media|NNS was|be|VBD inoculated|inoculate|VBN to|to|TO a|a|DT final|final|JJ OD600|od600|NN =|=|JJ 0.25|0.25|CD -LRB-|-lrb-|-LRB- early-logarithmic|early-logarithmic|JJ phase|phase|NN -RRB-|-rrb-|-RRB- .|.|. Cultures|culture|NNS were|be|VBD grown|grow|VBN -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN ,|,|, 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- and|and|CC maintained|maintain|VBN in|in|IN stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN 1.8|1.8|CD -RRB-|-rrb-|-RRB- for|for|IN approximately|approximately|RB 2|2|CD hours|hour|NNS .|.|. An|a|DT appropriate|appropriate|JJ amount|amount|NN of|of|IN each|each|DT culture|culture|NN was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB pre-warmed|pre-warmed|JJ -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN -RRB-|-rrb-|-RRB- M9|m9|NN media|media|NNS to|to|TO a|a|DT final|final|JJ OD600|od600|NN =|=|JJ 0.25|0.25|CD -LRB-|-lrb-|-LRB- approximate|approximate|JJ 7-fold|7-fold|JJ dilution|dilution|NN -RRB-|-rrb-|-RRB- .|.|. Released|release|VBN cultures|culture|NNS were|be|VBD grown|grow|VBN -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN ,|,|, 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- and|and|CC harvested|harvest|VBN -LRB-|-lrb-|-LRB- time|time|NN =|=|JJ 0|0|CD ,|,|, 1|1|CD hr|hr|NN ,|,|, or|or|CC 2|2|CD hr|hr|NN -RRB-|-rrb-|-RRB- for|for|IN GCC|gcc|NN and|and|CC RNA|rna|NN isolation|isolation|NN .|.|. Samples|sample|NNS -LRB-|-lrb-|-LRB- 1|1|CD mL|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD also|also|RB taken|take|VBN for|for|IN FACS|facs|NN analysis|analysis|NN and|and|CC fluorescence|fluorescence|NN microscopy|microscopy|NN -LRB-|-lrb-|-LRB- t|t|NN =|=|JJ 0|0|CD ,|,|, 1|1|CD hr|hr|NN ,|,|, and|and|CC 2|2|CD hr|hr|NN -RRB-|-rrb-|-RRB- .|.|.
SynH|synh|NN _|_|CD Exp|exp|NN _|_|CD BXHU|bxhu|NN
SynH|synh|NN _|_|CD Exp|exp|NN _|_|CD CBYS|cbys|NN
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Exp|exp|NN _|_|CD BXNX|bxnx|NN
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Exp|exp|NN _|_|CD CBYU|cbyu|NN
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Exp|exp|NN _|_|CD CCOG|ccog|NN
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Stat1|stat1|NN _|_|CD BXNB|bxnb|NN
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Stat1|stat1|NN _|_|CD BXNZ|bxnz|NN
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Stat1|stat1|NN _|_|CD CHBW|chbw|NN
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Trans|Trans|NNP _|_|CD BXNC|BXNC|NNP
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Trans|Trans|NNP _|_|CD BXXC|BXXC|NNP
SynH|synh|NN _|_|CD LT|lt|NN _|_|CD Trans|Trans|NNP _|_|CD CBYW|CBYW|NNP
SynH|synh|NN _|_|CD Stat1|stat1|NN _|_|CD CBYN|cbyn|NN
SynH|synh|NN _|_|CD Stat1|stat1|NN _|_|CD CUOC|cuoc|NN
SynH|synh|NN _|_|CD Trans|Trans|NNP _|_|CD CUNZ|CUNZ|NNP
SynH|synh|NN _|_|CD Trans|Trans|NNP _|_|SYM CUOB|cuob|NN
synthetic|synthetic|JJ circuit|circuit|NN :|:|: H3|h3|NN
synthetic|synthetic|JJ circuit|circuit|NN :|:|: LACZ|lacz|NN
synthetic|synthetic|JJ circuit|circuit|NN :|:|: Lux|lux|FW
synthetic|synthetic|JJ circuit|circuit|NN :|:|: M1|m1|NN
synthetic|synthetic|JJ circuit|circuit|NN :|:|: None|none|NN
T0|t0|NN _|_|SYM N0025|n0025|CD _|_|CD r1|r1|NN
T0|t0|NN _|_|SYM N0025|n0025|CD _|_|CD r2|r2|NN
T0|t0|NN _|_|SYM N0025|n0025|CD _|_|CD r3|r3|NN
T12|t12|NN _|_|SYM N0025|n0025|CD _|_|CD r1|r1|NN
T12|t12|NN _|_|SYM N0025|n0025|CD _|_|CD r2|r2|NN
T12|t12|NN _|_|SYM N0025|n0025|CD _|_|CD r3|r3|NN
T170V|t170v|NN 0|0|CD min|min|NN
T170V|t170v|NN 10|10|CD min|min|NN
T18-ParB|t18-parb|NN -LRB-|-lrb-|-LRB- G101S|g101s|NN -RRB-|-rrb-|-RRB- were|be|VBD produced|produce|VBN by|by|IN addition|addition|NN of|of|IN 0.5|0.5|CD mM|mm|NN IPTG|iptg|NN for|for|IN an|a|DT hour|hour|NN before|before|IN formadehyde|formadehyde|NN to|to|TO 1|1|CD %|%|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO fix|fix|VB cells|cell|NNS for|for|IN ChIP-seq|ChIP-seq|NNP
T18-ParB|t18-parb|NN -LRB-|-lrb-|-LRB- WT|wt|NN -RRB-|-rrb-|-RRB- were|be|VBD produced|produce|VBN by|by|IN addition|addition|NN of|of|IN 0.5|0.5|CD mM|mm|NN IPTG|iptg|NN for|for|IN an|a|DT hour|hour|NN before|before|IN formadehyde|formadehyde|NN to|to|TO 1|1|CD %|%|NN -LRB-|-lrb-|-LRB- final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO fix|fix|VB cells|cell|NNS for|for|IN ChIP-seq|ChIP-seq|NNP
T24|t24|NN _|_|CD N0000|n0000|NN _|_|CD r1|r1|NN
T24|t24|NN _|_|CD N0000|n0000|NN _|_|CD r2|r2|NN
T24|t24|NN _|_|CD N0000|n0000|NN _|_|CD r3|r3|NN
T24|t24|NN _|_|SYM N0025|n0025|CD _|_|CD r1|r1|NN
T24|t24|NN _|_|SYM N0025|n0025|CD _|_|CD r2|r2|NN
T24|t24|NN _|_|SYM N0025|n0025|CD _|_|CD r3|r3|NN
T24|t24|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD first|first|JJ replicate|replicate|VB
T24|t24|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD second|second|JJ replicate|replicate|VBP
T24|t24|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD first|first|JJ replicate|replicate|VB
T24|t24|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD second|second|JJ replicate|replicate|VBP
T2|t2|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD first|first|RB replicate|replicate|VB
T2|t2|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD second|second|JJ replicate|replicate|VBP
T2|t2|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD first|first|JJ replicate|replicate|VB
T2|t2|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD second|second|JJ replicate|replicate|VB
T36|t36|NN _|_|SYM N0025|n0025|CD _|_|CD r1|r1|NN
T36|t36|NN _|_|SYM N0025|n0025|CD _|_|SYM r2|r2|FW
T36|t36|FW _|_|SYM N0025|n0025|CD _|_|CD r3|r3|NN
T48|t48|NN _|_|SYM N0025|n0025|CD _|_|CD r1|r1|NN
T48|t48|NN _|_|SYM N0025|n0025|CD _|_|CD r2|r2|NN
T48|t48|NN _|_|SYM N0025|n0025|CD _|_|CD r3|r3|NN
T5|t5|NN _|_|CD 1x|1x|NN _|_|NN 4|4|CD
T5|t5|NN _|_|CD 27x|27x|CD _|_|NN 1|1|CD
T60|t60|NN _|_|CD N0000|n0000|NN _|_|CD r1|r1|NN
T60|t60|NN _|_|CD N0000|n0000|NN _|_|CD r2|r2|NN
T60|t60|NN _|_|CD N0000|n0000|NN _|_|CD r3|r3|NN
T60|t60|NN _|_|SYM N0025|n0025|CD _|_|CD r1|r1|NN
T60|t60|NN _|_|SYM N0025|n0025|CD _|_|CD r2|r2|NN
T60|t60|NN _|_|SYM N0025|n0025|CD _|_|CD r3|r3|NN
t7|t7|NN genotype|genotype|NN :|:|: evolved|evolve|VBD ,|,|, codon-deoptimized|codon-deoptimized|JJ gene|gene|NN 10|10|CD
t7|t7|NN genotype|genotype|NN :|:|: wild-type|wild-type|JJ gene|gene|NN 10|10|CD
t7|t7|NN strain|strain|NN :|:|: evolved|evolve|VBD
t7|t7|NN strain|strain|NN :|:|: wild|wild|JJ type|type|NN
T8|t8|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD first|first|RB replicate|replicate|VB
T8|t8|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 1|1|CD second|second|JJ replicate|replicate|VBP
T8|t8|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD first|first|JJ replicate|replicate|VB
T8|t8|NN THP-1|thp-1|NN infection|infection|NN ,|,|, Microarray|Microarray|NNP #|#|# 2|2|CD second|second|JJ replicate|replicate|VBP
tab-delimited|tab-delimited|JJ text|text|NN files|file|NNS with|with|IN GCSs|gcss|NNS coordinates|coordinate|VBZ ,|,|, N3E|n3e|NN values|value|NNS -LRB-|-lrb-|-LRB- \|\|CD
tagged|tag|VBD gyrase|gyrase|NN subunit|subunit|NN :|:|: GyrA-SPA|gyra-spa|JJ
tag|tag|NN :|:|: MG1655|mg1655|NN K-12|k-12|NN WT|wt|JJ
Tagwise|tagwise|JJ dispersion|dispersion|NN was|be|VBD estimated|estimate|VBN using|use|VBG the|the|DT weighted|weighted|JJ likelihood|likelihood|NN empirical|empirical|JJ Bayes|baye|NNS method|method|NN
technical|technical|JJ replicate|replicate|VB :|:|: 1|1|CD
technical|technical|JJ replicate|replicate|VB :|:|: 2|2|CD
technical|technical|JJ replicates|replicate|VBZ :|:|: 2|2|CD
temp|temp|NN :|:|: 37ºC|37ºc|NN
temperature|temperature|NN :|:|: 10|10|CD °C|°c|NN
temperature|temperature|NN :|:|: 37|37|CD °C|°c|NN
temperature|temperature|NN _|_|CD down|down|IN _|_|CD 0|0|CD min|min|NN
temperature|temperature|NN _|_|CD down|down|IN _|_|CD 12|12|CD min|min|NN
temperature|temperature|NN _|_|CD down|down|IN _|_|CD 20|20|CD min|min|NN
temperature|temperature|NN _|_|CD down|down|IN _|_|CD 28|28|CD min|min|NN
temperature|temperature|NN _|_|CD down|down|IN _|_|CD 44|44|CD min|min|NN
temperature|temperature|NN _|_|CD down|down|IN _|_|CD 4|4|CD min|min|NN
temperature|temperature|NN _|_|CD down|down|IN _|_|CD 8|8|CD min|min|NN
temperature|temperature|NN down|down|IN shift|shift|NN ,|,|, 0|0|CD min|min|NN
temperature|temperature|NN down|down|IN shift|shift|NN ,|,|, 12|12|CD min|min|NN
temperature|temperature|NN down|down|IN shift|shift|NN ,|,|, 20|20|CD min|min|NN
temperature|temperature|NN down|down|IN shift|shift|NN ,|,|, 28|28|CD min|min|NN
temperature|temperature|NN down|down|IN shift|shift|NN ,|,|, 44|44|CD min|min|NN
temperature|temperature|NN down|down|IN shift|shift|NN ,|,|, 4|4|CD min|min|NN
temperature|temperature|NN down|down|IN shift|shift|NN ,|,|, 8|8|CD min|min|NN
temperature|temperature|NN _|_|CD Up|up|IN _|_|CD 0|0|CD min|min|NN
temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 12|12|CD min|min|NN
temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 20|20|CD min|min|NN
temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 28|28|CD min|min|NN
temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 44|44|CD min|min|NN
temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 4|4|CD min|min|NN
temperature|temperature|NN _|_|VBD Up|up|RP _|_|SYM 8|8|CD min|min|NN
temperature|temperature|NN up|up|IN shift|shift|NN ,|,|, 0|0|CD min|min|NN
temperature|temperature|NN up|up|IN shift|shift|NN ,|,|, 12|12|CD min|min|NN
temperature|temperature|NN up|up|IN shift|shift|NN ,|,|, 20|20|CD min|min|NN
temperature|temperature|NN up|up|IN shift|shift|NN ,|,|, 28|28|CD min|min|NN
temperature|temperature|NN up|up|IN shift|shift|NN ,|,|, 44|44|CD min|min|NN
temperature|temperature|NN up|up|IN shift|shift|NN ,|,|, 4|4|CD min|min|NN
temperature|temperature|NN up|up|IN shift|shift|NN ,|,|, 8|8|CD min|min|NN
test|test|NN :|:|: ChIP|chip|NN DNA|dna|NN
test|test|NN :|:|: E.|e.|FW coli|coli|FW TOP10|top10|NN containing|contain|VBG pBAD18|pbad18|NN vector|vector|NN exposed|expose|VBN to|to|TO arabinose|arabinose|VB inducer|inducer|NN
TEX|tex|SYM -|-|: _|_|SYM E.|e.|FW coli|coli|FW O104|o104|NN :|:|: H4|h4|NN
TEX|tex|NN +|+|CC _|_|SYM E.|e.|FW coli|coli|FW O104|o104|NN :|:|: H4|h4|NN
text|text|NN wig|wig|NN files|file|NNS contain|contain|VBP coverage|coverage|NN depth|depth|NN data|datum|NNS
text|text|NN wig|wig|NN files|file|NNS contain|contain|VBP N3E|n3e|NN values|value|NNS -LRB-|-lrb-|-LRB- number|number|NN of|of|IN DNA|dna|NN fragments|fragment|NNS 3|3|CD '|'|'' ends|end|VBZ for|for|IN each|each|DT position|position|NN of|of|IN the|the|DT genome|genome|NN -RRB-|-rrb-|-RRB-
TG1/pBS|tg1/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- /|/|: pMMB277|pmmb277|NN 2nd|2nd|JJ
TG1/pBS|tg1/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- /|/|: pMMB277|pmmb277|NN ,|,|, cis-DCE|cis-dce|JJ
TG1/pBS|tg1/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: TOM-Green/pMMB277-IsoILR|tom-green/pmmb277-isoilr|NN 1-GSHI|1-gshi|NN 2nd|2nd|JJ
TG1/pBS|tg1/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: TOM-Green/pMMB277-IsoILR|tom-green/pmmb277-isoilr|NN 1-GSHI|1-gshi|NN ,|,|, cis-DCE|cis-dce|JJ
TG1|tg1|NN /|/|: pMMB206-TOM-Green/pBS|pmmb206-tom-green/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- ,|,|, cis-DCE|cis-dce|JJ
TG1/pMMB206-TOM-Green/pBS|tg1/pmmb206-tom-green/pbs|NN -LRB-|-lrb-|-LRB- Kan|Kan|NNP -RRB-|-rrb-|-RRB- -|-|: EchA|echa|NN F108L/I219L/C248I|f108l/i219l/c248i|NN ,|,|, cis-DCE|cis-dce|JJ
than|than|IN or|or|CC equal|equal|JJ to|to|TO the|the|DT intensity|intensity|NN of|of|IN the|the|DT foreground|foreground|NN ,|,|, the|the|DT resulting|result|VBG log|log|NN ratios|ratio|NNS became|become|VBD complex|complex|JJ or|or|CC
The|the|DT 200|200|CD ml|ml|NN eluate|eluate|NN from|from|IN the|the|DT Ni-NTA|ni-nta|NN agarose|agarose|NN was|be|VBD mixed|mix|VBN with|with|IN equal|equal|JJ volume|volume|NN of|of|IN pre-warmed|pre-warmed|JJ PCI|pci|NN and|and|CC incubated|incubate|VBN for|for|IN 2|2|CD min|min|NN at|at|IN 70|70|CD ˚C|˚c|NN .|.|. The|the|DT mixture|mixture|NN was|be|VBD centrifuged|centrifuge|VBN ,|,|, and|and|CC RNA|rna|NN and|and|CC DNA|dna|NN were|be|VBD precipitated|precipitate|VBN with|with|IN isopropanol|isopropanol|NN from|from|IN the|the|DT supernatant|supernatant|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD dissolved|dissolve|VBN in|in|IN 30|30|CD ml|ml|NN DNase|dnase|NN I|i|CD buffer|buffer|NN with|with|IN 5|5|CD U|U|NNP DNaseI|dnasei|NN -LRB-|-lrb-|-LRB- Takara|Takara|NNP Bio|Bio|NNP -RRB-|-rrb-|-RRB- and|and|CC 20|20|CD U|U|NNP SUPERase|SUPERase|NNP ,|,|, incubated|incubate|VBN for|for|IN 10|10|CD min|min|NN at|at|IN RT.|RT.|NNP .|.|. RNA|rna|NN was|be|VBD separated|separate|VBN from|from|IN the|the|DT digested|digest|VBN DNA|dna|NN by|by|IN the|the|DT PCI|pci|NN extraction|extraction|NN and|and|CC RNA|rna|NN was|be|VBD precipitated|precipitate|VBN with|with|IN isopropanol|isopropanol|NN .|.|. The|the|DT pellet|pellet|NN was|be|VBD dissolved|dissolve|VBN in|in|IN diethylpyrocarbonate-treated|diethylpyrocarbonate-treated|JJ water|water|NN and|and|CC used|use|VBN for|for|IN cDNA|cdna|NN synthesis|synthesis|NN .|.|.
The|the|DT aligned|align|VBN reads|read|VBZ were|be|VBD converted|convert|VBN to|to|TO BAM|BAM|NNP files|file|NNS and|and|CC sorted|sort|VBN and|and|CC indexed|index|VBN using|use|VBG SAMtools|samtool|NNS
The|the|DT .|.|. align|align|VB files|file|NNS have|have|VBP been|be|VBN processed|process|VBN using|use|VBG tagalign|tagalign|NN .|.|. Reads|read|NNS were|be|VBD aligned|align|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- Bowtie|Bowtie|NNP v.|v.|CC 0.12.0|0.12.0|CD -RRB-|-rrb-|-RRB- by|by|IN the|the|DT first|first|JJ 25|25|CD nt|nt|NNS and|and|CC extended|extend|VBN to|to|TO account|account|VB for|for|IN the|the|DT linker|linker|NN .|.|.
The|the|DT alignment|alignment|NN Bam|bam|UH files|file|NNS were|be|VBD compared|compare|VBN against|against|IN the|the|DT gene|gene|NN annotation|annotation|NN general|general|JJ feature|feature|NN format|format|NN -LRB-|-lrb-|-LRB- GFF|gff|NN -RRB-|-rrb-|-RRB- file|file|NN ,|,|, and|and|CC raw|raw|JJ counts|count|NNS for|for|IN each|each|DT gene|gene|NN were|be|VBD generated|generate|VBN using|use|VBG the|the|DT featureCounts|featureCounts|NNPS tool|tool|NN from|from|IN Subread|Subread|NNP .|.|. The|the|DT raw|raw|JJ counts|count|NNS data|datum|NNS of|of|IN the|the|DT expressed|express|VBN genes|gene|NNS was|be|VBD normalized|normalize|VBN for|for|IN RNA|rna|NN composition|composition|NN using|use|VBG the|the|DT trimmed|trimmed|RBR mean|mean|VB of|of|IN M|m|NN values|value|NNS -LRB-|-lrb-|-LRB- TMM|tmm|NN -RRB-|-rrb-|-RRB- method|method|NN -LRB-|-lrb-|-LRB- http://www.ncbi.nlm.nih.gov/pubmed/20196867|http://www.ncbi.nlm.nih.gov/pubmed/20196867|NN -RRB-|-rrb-|-RRB- from|from|IN the|the|DT Empirical|empirical|JJ analysis|analysis|NN of|of|IN Digital|Digital|NNP Gene|Gene|NNP Expression|expression|NN Data|datum|NNS in|in|IN R|r|NN -LRB-|-lrb-|-LRB- EdgeR|edger|NN -RRB-|-rrb-|-RRB- package|package|NN -LRB-|-lrb-|-LRB- https://bioconductor.org/packages/release/bioc/html/edgeR.html|https://bioconductor.org/packages/release/bioc/html/edger.html|NN -RRB-|-rrb-|-RRB- ,|,|, then|then|RB transformed|transform|VBN to|to|TO log2CPM|log2cpm|NN -LRB-|-lrb-|-LRB- counts|count|NNS per|per|IN million|million|CD -RRB-|-rrb-|-RRB- values|value|NNS using|use|VBG the|the|DT voom|voom|NN method|method|NN -LRB-|-lrb-|-LRB- http://www.ncbi.nlm.nih.gov/pubmed/24485249|http://www.ncbi.nlm.nih.gov/pubmed/24485249|NN -RRB-|-rrb-|-RRB- from|from|IN the|the|DT R|r|NN LIMMA|limma|NN package|package|NN -LRB-|-lrb-|-LRB- https://bioconductor.org/packages/release/bioc/html/limma.html|https://bioconductor.org/packages/release/bioc/html/limma.html|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT amplified|amplify|VBN cDNA|cdna|NN libraries|library|NNS from|from|IN two|two|CD biological|biological|JJ replicates|replicate|VBZ for|for|IN each|each|DT E.|e.|FW coli|coli|FW were|be|VBD sequenced|sequence|VBN on|on|IN an|a|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP .|.|. Sequence|sequence|NN reads|read|VBZ for|for|IN cDNA|cdna|NN libraries|library|NNS were|be|VBD aligned|align|VBN onto|onto|IN E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN genome|genome|NN ,|,|, using|use|VBG Mosaik|mosaik|NN with|with|IN following|follow|VBG arguments|argument|NNS :|:|: hash|hash|VB size|size|NN =|=|JJ 10|10|CD ,|,|, mismatch|mismatch|NN =|=|JJ 0|0|CD .|.|. Only|only|RB reads|read|VBZ that|that|IN aligned|align|VBN to|to|TO the|the|DT unique|unique|JJ genomic|genomic|JJ location|location|NN were|be|VBD retained|retain|VBN .|.|. Two|two|CD biological|biological|JJ replicates|replicate|VBZ were|be|VBD processed|process|VBN seperatedly|seperatedly|RB ,|,|, and|and|CC only|only|RB sequence|sequence|NN reads|read|VBZ presented|present|VBN in|in|IN both|both|CC biological|biological|JJ replciates|replciate|NNS were|be|VBD considered|consider|VBN for|for|IN further|further|JJ process|process|NN .|.|. The|the|DT genomic|genomic|JJ coordinates|coordinate|VBZ of|of|IN the|the|DT 5|5|CD '|'|'' -|-|: end|end|NN of|of|IN these|these|DT uniquely|uniquely|RB aligned|align|VBN reads|read|VBZ were|be|VBD defined|define|VBN as|as|IN potential|potential|JJ TSSs|tsss|NNS .|.|. Among|among|IN potential|potential|JJ TSSs|tsss|NNS ,|,|, only|only|RB TSSs|tsss|NNS with|with|IN the|the|DT strongest|strongest|JJS signal|signal|NN within|within|IN 10|10|CD bp|bp|NN window|window|NN were|be|VBD kept|keep|VBN to|to|TO remove|remove|VB possible|possible|JJ noise|noise|NN signals|signal|NNS ,|,|, and|and|CC TSSs|tsss|NNS with|with|IN greater|greater|JJR than|than|IN or|or|CC equal|equal|JJ to|to|TO 40|40|CD %|%|NN of|of|IN the|the|DT strongest|strongest|JJS signal|signal|NN upstream|upstream|RB of|of|IN an|a|DT annotated|annotated|JJ gene|gene|NN were|be|VBD considered|consider|VBN as|as|IN multiple|multiple|JJ TSSs|tsss|NNS .|.|.
The|the|DT analysis|analysis|NN of|of|IN the|the|DT data|datum|NNS is|be|VBZ based|base|VBN on|on|IN cross|cross|NN validation|validation|NN with|with|IN datasets|dataset|NNS generated|generate|VBN by|by|IN Monte-Carlo|Monte-Carlo|NNP simulation|simulation|NN .|.|. The|the|DT null|null|JJ hypothesis|hypothesis|NN was|be|VBD that|that|IN the|the|DT gene|gene|NN expression|expression|NN changes|change|NNS monotonously|monotonously|RB as|as|IN a|a|DT function|function|NN of|of|IN NaCl|nacl|NN concentration|concentration|NN .|.|. The|the|DT existence|existence|NN of|of|IN a|a|DT deviation|deviation|NN from|from|IN monotony|monotony|NN was|be|VBD tested|test|VBN by|by|IN F-tests|f-test|NNS for|for|IN each|each|DT gene|gene|NN probe|probe|NN .|.|. By|by|IN comparing|compare|VBG the|the|DT number|number|NN of|of|IN probes|probe|NNS with|with|IN the|the|DT lowest|lowest|JJS p|p|NN -LRB-|-lrb-|-LRB- F|f|NN -RRB-|-rrb-|-RRB- values|value|NNS for|for|IN each|each|DT NaCl|nacl|NN concentrations|concentration|NNS with|with|IN analogous|analogous|JJ results|result|NNS generated|generate|VBN from|from|IN Monte-Carlo|Monte-Carlo|NNP sampling|sampling|NN of|of|IN the|the|DT null|null|JJ hypothesis|hypothesis|NN ,|,|, we|we|PRP show|show|VBP that|that|IN it|it|PRP is|be|VBZ very|very|RB unlikely|unlikely|JJ that|that|IN a|a|DT switch|switch|NN between|between|IN 4.5|4.5|CD and|and|CC 5|5|CD %|%|NN NaCl|nacl|NN could|could|MD have|have|VB happened|happen|VBN by|by|IN chance|chance|NN -LRB-|-lrb-|-LRB- in|in|IN fact|fact|NN p|p|NN <<|<<|CD 0.01|0.01|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT analyzed|analyze|VBN data|datum|NNS were|be|VBD imported|import|VBN to|to|TO ArrayTrack|ArrayTrack|NNP -LRB-|-lrb-|-LRB- NCTR|NCTR|NNP Center|Center|NNP for|for|IN Toxicoinformatics|Toxicoinformatics|NNPS ;|;|: http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/arraytrack_webaccess.htm|http://www.fda.gov/nctr/science/centers/toxicoinformatics/arraytrack/arraytrack_webaccess.htm|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT raw|raw|JJ data|datum|NNS were|be|VBD normalized|normalize|VBN by|by|IN using|use|VBG median|median|NN channel|channel|NN -LRB-|-lrb-|-LRB- intensity|intensity|NN -RRB-|-rrb-|-RRB- scaling|scale|VBG with|with|IN no|no|DT background|background|NN subtraction|subtraction|NN .|.|.
The|the|DT analyzed|analyze|VBN data|datum|NNS were|be|VBD imported|import|VBN to|to|TO ArrayTrack|ArrayTrack|NNP -LRB-|-lrb-|-LRB- NCTR|NCTR|NNP Center|Center|NNP for|for|IN Toxicoinformatics|Toxicoinformatics|NNPS .|.|. The|the|DT raw|raw|JJ data|datum|NNS were|be|VBD normalized|normalize|VBN by|by|IN using|use|VBG median|median|NN channel|channel|NN -LRB-|-lrb-|-LRB- intensity|intensity|NN -RRB-|-rrb-|-RRB- scaling|scale|VBG with|with|IN no|no|DT background|background|NN subtraction|subtraction|NN .|.|.
The|the|DT appropriate|appropriate|JJ protocols|protocol|NNS were|be|VBD performed|perform|VBN using|use|VBG standard|standard|JJ Illumina|Illumina|NNP procedures|procedure|NNS
The|the|DT average|average|JJ fluorescence|fluorescence|NN intensity|intensity|NN for|for|IN each|each|DT spot|spot|NN was|be|VBD calculated|calculate|VBN and|and|CC local|local|JJ background|background|NN was|be|VBD subtracted|subtract|VBN .|.|. All|all|DT data|datum|NNS normalization|normalization|NN and|and|CC selection|selection|NN of|of|IN fold-changed|fold-changed|JJ genes|gene|NNS were|be|VBD performed|perform|VBN using|use|VBG GeneSpringGX|GeneSpringGX|NNP 7.3.1|7.3.1|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technology|Technology|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. Normalization|normalization|NN for|for|IN Agilent|Agilent|NNP one-color|one-color|JJ method|method|NN was|be|VBD performed|perform|VBN ,|,|, which|which|WDT is|be|VBZ Data|Data|NNP transformation|transformation|NN :|:|: Set|set|VB measurements|measurement|NNS less|less|JJR than|than|IN 5.0|5.0|CD to|to|TO 5.0|5.0|CD and|and|CC Per|per|IN Chip|chip|NN :|:|: Normalize|normalize|VB to|to|TO 50th|50th|JJ percentage|percentage|NN .|.|.
The|the|DT average|average|JJ fluorescent|fluorescent|JJ signal|signal|NN intensity|intensity|NN and|and|CC local|local|JJ background|background|NN correction|correction|NN for|for|IN each|each|DT spot|spot|NN were|be|VBD obtained|obtain|VBN using|use|VBG commercially|commercially|RB available|available|JJ software|software|NN from|from|IN Biodiscovery|Biodiscovery|NNP Inc|Inc|NNP -LRB-|-lrb-|-LRB- Imagene|Imagene|NNP ,|,|, version|version|NN 4.0|4.0|CD and|and|CC Genesight|Genesight|NNP ,|,|, version|version|NN 3.5|3.5|CD -RRB-|-rrb-|-RRB- .|.|. Spots|spot|NNS with|with|IN a|a|DT signal|signal|NN intensity|intensity|NN lower|lower|JJR than|than|IN the|the|DT background|background|NN signal|signal|NN or|or|CC those|those|DT with|with|IN blemishes|blemish|NNS were|be|VBD omitted|omit|VBN from|from|IN subsequent|subsequent|JJ analysis|analysis|NN .|.|. The|the|DT mean|mean|NN values|value|NNS from|from|IN each|each|DT channel|channel|NN were|be|VBD then|then|RB log2|log2|NN transformed|transform|VBN and|and|CC normalised|normalise|VBN using|use|VBG the|the|DT LOWESS|lowess|NN method|method|NN to|to|TO remove|remove|VB intensity-dependent|intensity-dependent|JJ effects|effect|NNS in|in|IN the|the|DT log2|log2|NN -LRB-|-lrb-|-LRB- ratios|ratio|NNS -RRB-|-rrb-|-RRB- values|value|NNS .|.|. The|the|DT Cy3/Cy5|cy3/cy5|NN -LRB-|-lrb-|-LRB- or|or|CC ,|,|, for|for|IN replicates|replicate|VBZ 3|3|CD and|and|CC 4|4|CD ,|,|, Cy3/Cy3|cy3/cy3|NN ratio|ratio|NN -RRB-|-rrb-|-RRB- fluorescent|fluorescent|JJ ratios|ratio|NNS were|be|VBD calculated|calculated|JJ form|form|NN the|the|DT normalised|normalised|JJ values|value|NNS .|.|. Data|datum|NNS from|from|IN independent|independent|JJ experiments|experiment|NNS were|be|VBD combined|combine|VBN .|.|. Significance|significance|NN analysis|analysis|NN of|of|IN the|the|DT data|datum|NNS used|use|VBD the|the|DT Student|student|NN 's|'s|POS t|t|NN test|test|NN to|to|TO determine|determine|VB the|the|DT probability|probability|NN that|that|IN the|the|DT average|average|NN of|of|IN the|the|DT experimental|experimental|JJ replicates|replicate|VBZ was|be|VBD significantly|significantly|RB different|different|JJ from|from|IN the|the|DT average|average|NN of|of|IN the|the|DT control|control|NN replicates|replicate|VBZ .|.|. p-values|p-value|NNS for|for|IN the|the|DT data|datum|NNS were|be|VBD calculated|calculate|VBN by|by|IN treating|treat|VBG each|each|DT slide|slide|NN as|as|IN a|a|DT repeat|repeat|NN using|use|VBG Genesight|Genesight|NNP .|.|.
The|the|DT average|average|JJ signal|signal|NN intensity|intensity|NN and|and|CC local|local|JJ background|background|NN correction|correction|NN were|be|VBD obtained|obtain|VBN using|use|VBG a|a|DT commercially|commercially|RB available|available|JJ software|software|NN package|package|NN from|from|IN Biodiscovery|Biodiscovery|NNP ,|,|, Inc|Inc|NNP -LRB-|-lrb-|-LRB- Imagene|Imagene|NNP ,|,|, version|version|NN 4.0|4.0|CD and|and|CC GeneSight|GeneSight|NNP ,|,|, version|version|NN 3.5|3.5|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT bacterial|bacterial|JJ cells|cell|NNS from|from|IN 5L|5l|NN fermentation|fermentation|NN were|be|VBD collected|collect|VBN at|at|IN 20h|20h|CD ,|,|, 30h|30h|CD ,|,|, 40h|40h|NN and|and|CC centrifuged|centrifuge|VBN for|for|IN 5|5|CD min|min|NN to|to|TO pellet|pellet|VB the|the|DT cells|cell|NNS .|.|. The|the|DT cells|cell|NNS then|then|RB mixed|mix|VBN with|with|IN 500mL|500ml|NN of|of|IN RNA|rna|NN protectant|protectant|NN bacterial|bacterial|JJ reagents|reagent|NNS to|to|TO stabilize|stabilize|VB RNA|rna|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD °C|°c|NN until|until|IN use|use|NN .|.|. Total|total|JJ RNAs|rna|NNS were|be|VBD isolated|isolate|VBN using|use|VBG RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN and|and|CC were|be|VBD treated|treat|VBN with|with|IN DNase|dnase|NN to|to|TO remove|remove|VB DNA|dna|NN .|.|.
The|the|DT bacterial|bacterial|JJ cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD ℃|℃|NN for|for|IN 17|17|CD hours|hour|NNS on|on|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- agar|agar|NN plate|plate|NN .|.|. An|a|DT isolated|isolate|VBN colony|colony|NN was|be|VBD picked|pick|VBN and|and|CC inoculated|inoculate|VBN into|into|IN 100|100|CD ml|ml|NN of|of|IN sterilized|sterilize|VBN LB|lb|NN broth|broth|NN -LRB-|-lrb-|-LRB- 10g|10g|CD of|of|IN tryptone|tryptone|NN ,|,|, 5g|5g|NN of|of|IN yeast|yeast|NN extract|extract|NN and|and|CC 10g|10g|NN of|of|IN sodium|sodium|NN chloride|chloride|NN per|per|IN liter|liter|NN -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN overnight|overnight|JJ for|for|IN 17|17|CD hours|hour|NNS at|at|IN 37|37|CD ℃|℃|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD rpm|rpm|NN .|.|. A|a|DT 1:100|1:100|CD dilution|dilution|NN of|of|IN the|the|DT culture|culture|NN was|be|VBD performed|perform|VBN using|use|VBG pre-warmed|pre-warmed|JJ LB|lb|NN broth|broth|NN .|.|. The|the|DT diluted|diluted|JJ culture|culture|NN was|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD ℃|℃|NN with|with|IN shaking|shake|VBG at|at|IN 250rpm|250rpm|NN until|until|IN a|a|DT final|final|JJ optical|optical|JJ density|density|NN -LRB-|-lrb-|-LRB- OD600|od600|NN -RRB-|-rrb-|-RRB- of|of|IN 0.8|0.8|CD -LRB-|-lrb-|-LRB- early|early|JJ logarithmic|logarithmic|JJ phase|phase|NN -RRB-|-rrb-|-RRB- was|be|VBD attained|attain|VBN .|.|. A|a|DT further|further|JJ 1:10|1:10|CD dilution|dilution|NN was|be|VBD performed|perform|VBN using|use|VBG LB|lb|NN broth|broth|NN and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD ℃|℃|NN with|with|IN shaking|shake|VBG at|at|IN 250|250|CD rpm|rpm|NN .|.|.
The|the|DT bacterial|bacterial|JJ culture|culture|NN pellets|pellet|NNS were|be|VBD grown|grow|VBN according|accord|VBG to|to|TO the|the|DT instructions|instruction|NNS from|from|IN ATCC|atcc|NN .|.|.
The|the|DT bacteria|bacterium|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 4000|4000|CD ×|×|CD g|g|NN at|at|IN 4|4|CD °C|°c|NN for|for|IN 5|5|CD min|min|NN and|and|CC then|then|RB washed|wash|VBN with|with|IN PBS|PBS|NNP .|.|.
The|the|DT bacteria|bacterium|NNS were|be|VBD routinely|routinely|RB grown|grow|VBN in|in|IN Luria-Bertani|Luria-Bertani|NNP -LRB-|-lrb-|-LRB- LB|LB|NNP -RRB-|-rrb-|-RRB- broth|broth|NN or|or|CC on|on|IN LB|LB|NNP agar|agar|NN plates|plate|NNS -LRB-|-lrb-|-LRB- pH|ph|NN 7.2|7.2|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT bcl2fastq|bcl2fastq|NN Conversion|conversion|NN Software|Software|NNP v.|v.|CC 1.8.4|1.8.4|CD from|from|IN Illumina|Illumina|NNP -LRB-|-lrb-|-LRB- http://support.illumina.com/downloads.html|http://support.illumina.com/downloads.html|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO translate|translate|VB cluster|cluster|NN intensity|intensity|NN values|value|NNS into|into|IN fastq|fastq|NN files|file|NNS .|.|.
The|the|DT binding|binding|NN regions|region|NNS were|be|VBD considered|consider|VBN by|by|IN taking|take|VBG into|into|IN account|account|NN base|base|NN position|position|NN with|with|IN z-score|z-score|NN greater|greater|JJR than|than|IN threshold|threshold|NN and|and|CC merging|merge|VBG adjacent|adjacent|JJ binding|binding|NN regions|region|NNS seperated|seperate|VBN by|by|IN a|a|DT distance|distance|NN of|of|IN less|less|JJR than|than|IN 200bo|200bo|CD into|into|IN the|the|DT single|single|JJ binding|binding|NN regions|region|NNS
The|the|DT CEL|cel|NN files|file|VBZ generated|generate|VBN for|for|IN each|each|DT array|array|NN were|be|VBD analyzed|analyze|VBN using|use|VBG Affymetrix|Affymetrix|NNP Expression|expression|NN Console|console|NN software|software|NN .|.|.
The|the|DT cell|cell|NN cultures|culture|NNS were|be|VBD interrupted|interrupt|VBN by|by|IN placing|place|VBG them|they|PRP directly|directly|RB into|into|IN a|a|DT cold|cold|JJ phenol-ethanol|phenol-ethanol|NN solution|solution|NN -LRB-|-lrb-|-LRB- 0.1g-phenol|0.1g-phenol|NN /|/|: mL-ethanol|ml-ethanol|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT cells|cell|NNS were|be|VBD collected|collect|VBN using|use|VBG centrifugation|centrifugation|NN at|at|IN 12,000|12,000|CD g|g|NN for|for|IN 5|5|CD min|min|NN at|at|IN 4C|4c|NN ,|,|, and|and|CC the|the|DT pelleted|pelleted|JJ cells|cell|NNS were|be|VBD once|once|RB stored|store|VBN at|at|IN -80|-80|CD C|c|NN prior|prior|JJ to|to|TO use|use|VB .|.|.
The|the|DT cell|cell|NN culture|culture|NN was|be|VBD put|put|VBN into|into|IN cold|cold|JJ phenol-ethanol|phenol-ethanol|JJ solution|solution|NN -LRB-|-lrb-|-LRB- 1|1|CD g|g|NN of|of|IN phenol|phenol|NN in|in|IN 10|10|CD mL|ml|NN of|of|IN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- prepared|prepare|VBN in|in|IN advance|advance|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 16,000|16,000|CD ×|×|CD g|g|NN for|for|IN 5|5|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN ,|,|, and|and|CC the|the|DT pelleted|pelleted|JJ cells|cell|NNS were|be|VBD stored|store|VBN at|at|IN --|--|: 80|80|CD °C|°c|NN prior|prior|RB to|to|TO use|use|VB .|.|.
The|the|DT cell|cell|NN culture|culture|NN was|be|VBD put|put|VBN into|into|IN cold|cold|JJ phenol-ethanol|phenol-ethanol|JJ solution|solution|NN -LRB-|-lrb-|-LRB- 1|1|CD g|g|NN of|of|IN phenol|phenol|NN in|in|IN 10|10|CD mL|ml|NN of|of|IN ethanol|ethanol|NN -RRB-|-rrb-|-RRB- prepared|prepare|VBN in|in|IN advance|advance|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 7,000|7,000|CD ×|×|CD g|g|NN for|for|IN 3|3|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN ,|,|, and|and|CC the|the|DT pelleted|pelleted|JJ cells|cell|NNS were|be|VBD stored|store|VBN at|at|IN --|--|: 80|80|CD °C|°c|NN prior|prior|RB to|to|TO use|use|VB .|.|.
The|the|DT cell|cell|NN culture|culture|NN was|be|VBD treated|treat|VBN with|with|IN the|the|DT RNAprotect|rnaprotect|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT cell|cell|NN samples|sample|NNS were|be|VBD collected|collect|VBN directly|directly|RB into|into|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- to|to|TO avoid|avoid|VB RNA|rna|NN degradation|degradation|NN .|.|. The|the|DT samples|sample|NNS were|be|VBD centrifuged|centrifuge|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN and|and|CC frozen|freeze|VBN at|at|IN -|-|: 80|80|CD °C|°c|NN until|until|IN RNA|rna|NN isolation|isolation|NN .|.|.
The|the|DT cells|cell|NNS culture|culture|NN were|be|VBD harvested|harvest|VBN and|and|CC resuspended|resuspend|VBN with|with|IN a|a|DT solution|solution|NN containing|contain|VBG 0.5|0.5|CD %|%|NN SDS|sds|NN ,|,|, 20|20|CD mM|mm|NN sodium|sodium|NN acetate|acetate|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.5|5.5|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC 10|10|CD mM|mm|NN EDTA|edta|NN .|.|. The|the|DT suspended|suspend|VBN cells|cell|NNS were|be|VBD mixed|mix|VBN with|with|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN pre-warmed|pre-warmed|JJ saturated|saturated|JJ phenol|phenol|NN -LRB-|-lrb-|-LRB- 20|20|CD mM|mm|NN sodium|sodium|NN acetate|acetate|NN ,|,|, 10|10|CD mM|mm|NN EDTA|edta|NN pH|ph|NN 5.5|5.5|CD -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN for|for|IN 5|5|CD min|min|NN at|at|IN 60|60|CD ˚C|˚c|NN .|.|.
The|the|DT cells|cell|NNS for|for|IN RNA|rna|NN extraction|extraction|NN were|be|VBD immediately|immediately|RB mixed|mix|VBN with|with|IN RNA|rna|NN Protect|protect|VB Bacterial|bacterial|JJ reagent|reagent|NN ®|®|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC processed|process|VBN by|by|IN the|the|DT RNAeasy|RNAeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturers|manufacturer|NNS instructions|instruction|NNS .|.|. The|the|DT cells|cell|NNS for|for|IN whole|whole|JJ cell|cell|NN proteomics|proteomic|NNS were|be|VBD chilled|chill|VBN in|in|IN ice-slush|ice-slush|JJ ,|,|, pelleted|pelleted|JJ at|at|IN 14000|14000|CD rpm|rpm|NN ,|,|, 4|4|CD °C|°c|NN and|and|CC the|the|DT media|media|NNS was|be|VBD aspirated|aspirate|VBN .|.|. The|the|DT cells|cell|NNS were|be|VBD washed|wash|VBN with|with|IN 3|3|CD ×|×|NN 1.5|1.5|CD mL|ml|NN PBS|PBS|NNP with|with|IN pelleting|pelleting|NN at|at|IN as|as|IN above|above|IN in|in|IN between|between|IN .|.|. The|the|DT final|final|JJ pellet|pellet|NN was|be|VBD stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN until|until|IN being|be|VBG shipped|ship|VBN to|to|TO the|the|DT Proteomics|Proteomics|NNP Core|Core|NNP Facility|Facility|NNP at|at|IN University|University|NNP of|of|IN Gothenburg|Gothenburg|NNP for|for|IN processing|processing|NN .|.|. The|the|DT RNA|rna|NN was|be|VBD shipped|ship|VBN to|to|TO BGI|BGI|NNP for|for|IN total|total|JJ RNA|rna|NN sequencing|sequencing|NN .|.|.
The|the|DT cells|cell|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000|8000|CD rpm|rpm|NN for|for|IN 5|5|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. The|the|DT cell|cell|NN pellets|pellet|NNS were|be|VBD snap-frozen|snap-frozen|JJ in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC kept|keep|VBD at|at|IN -80|-80|CD °C|°c|NN
The|the|DT cells|cell|NNS were|be|VBD centrifuged|centrifuge|VBN when|when|WRB they|they|PRP reached|reach|VBD the|the|DT log|log|NN phase|phase|NN ,|,|, and|and|CC then|then|RB rapidly|rapidly|RB chilled|chill|VBD and|and|CC stored|store|VBD in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN until|until|IN used|use|VBN for|for|IN the|the|DT DNA|dna|NN microarray|microarray|NN assay|assay|NN
The|the|DT cells|cell|NNS were|be|VBD collected|collect|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 8,000|8,000|CD ×|×|CD g|g|NN for|for|IN 5|5|CD min|min|NN at|at|IN 25|25|CD °C|°c|NN ,|,|, and|and|CC the|the|DT pelleted|pelleted|JJ cells|cell|NNS were|be|VBD stored|store|VBN at|at|IN --|--|: 80|80|CD °C|°c|NN prior|prior|RB to|to|TO use|use|VB .|.|.
The|the|DT cells|cell|NNS were|be|VBD cultivated|cultivate|VBN in|in|IN 100|100|CD ml|ml|NN LB|lb|NN broth|broth|NN containing|contain|VBG 2|2|CD mg/L|mg/l|NN Cm|cm|NN with|with|IN 50|50|CD mg/L|mg/l|NN triclosan|triclosan|NN and|and|CC harvested|harvest|VBN in|in|IN mid-logarithmic|mid-logarithmic|JJ growth|growth|NN phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 1.1|1.1|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT cells|cell|NNS were|be|VBD cultivated|cultivate|VBN in|in|IN 100|100|CD ml|ml|NN LB|lb|NN broth|broth|NN containing|contain|VBG 2|2|CD mg/L|mg/l|NN Cm|cm|NN without|without|IN triclosan|triclosan|NN and|and|CC harvested|harvest|VBN in|in|IN mid-logarithmic|mid-logarithmic|JJ growth|growth|NN phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 1.0|1.0|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN ~|~|NN 300|300|CD ml|ml|NN LB|lb|NN broth|broth|NN +25|+25|CD mg/ml|mg/ml|NN kanamycin|kanamycin|NN with|with|IN shaking|shake|VBG at|at|IN 37|37|CD ˚C|˚c|NN until|until|IN OD600|od600|NN of|of|IN ~|~|NN 0.5|0.5|CD .|.|. The|the|DT cells|cell|NNS of|of|IN 150|150|CD mg|mg|NN -LRB-|-lrb-|-LRB- wet|wet|JJ weight|weight|NN -RRB-|-rrb-|-RRB- were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 6,500|6,500|CD ×|×|CD g|g|NN for|for|IN 4|4|CD min|min|NN at|at|IN 4|4|CD ˚C|˚c|NN ,|,|, aliquoted|aliquote|VBN in|in|IN three|three|CD 1.5|1.5|CD ml|ml|NN tubes|tube|NNS ,|,|, flash|flash|VBP frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN ,|,|, and|and|CC stored|store|VBD at|at|IN -80|-80|CD ˚C|˚c|NN .|.|.
The|the|DT cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN ~|~|NN 300|300|CD ml|ml|NN LB|lb|NN broth|broth|NN +25|+25|CD mg/ml|mg/ml|NN kanamycin|kanamycin|NN with|with|IN shaking|shake|VBG at|at|IN 37|37|CD ˚C|˚c|NN until|until|IN OD600|od600|NN of|of|IN ~|~|NN 0.5|0.5|CD .|.|. The|the|DT cells|cell|NNS of|of|IN 150|150|CD mg|mg|NN -LRB-|-lrb-|-LRB- wet|wet|JJ weight|weight|NN -RRB-|-rrb-|-RRB- were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 6,500|6,500|CD ×|×|CD g|g|NN for|for|IN 4|4|CD min|min|NN at|at|IN 4|4|CD ˚C|˚c|NN ,|,|, aliquoted|aliquote|VBN in|in|IN three|three|CD 1.5|1.5|CD ml|ml|NN tubes|tube|NNS ,|,|, flash|flash|VBP frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN ,|,|, and|and|CC stored|store|VBD at|at|IN -80|-80|CD ˚C|˚c|NN .|.|.
The|the|DT cells|cell|NNS were|be|VBD untreated|untreated|JJ ,|,|, or|or|CC treated|treat|VBN with|with|IN -LRB-|-lrb-|-LRB- 100µg/mL|100µg/ml|NN Erythromycin|erythromycin|NN or|or|CC 50|50|CD µg/mL|µg/ml|NN Clindamycin|clindamycin|NN in|in|IN 70|70|CD %|%|NN Ethanol|ethanol|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN 10|10|CD minutes|minute|NNS at|at|IN 37|37|CD °C|°c|NN ,|,|, 1|1|CD mL|ml|NN samples|sample|NNS were|be|VBD subjected|subject|VBN to|to|TO hot|hot|JJ phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN .|.|. Ref|Ref|NNP :|:|: Chuang|Chuang|NNP SE|se|NN ,|,|, Daniels|Daniels|NNP DL|DL|NNP ,|,|, and|and|CC Blattner|Blattner|NNP FR|fr|NN -LRB-|-lrb-|-LRB- 1993|1993|CD -RRB-|-rrb-|-RRB- Global|global|JJ regulation|regulation|NN of|of|IN gene|gene|NN expression|expression|NN in|in|IN Escherichia|escherichia|FW coli|coli|FW .|.|. J.|J.|NNP Bacteriol|Bacteriol|NNP .|.|. 175:2026-2036|175:2026-2036|CD .|.|.
The|the|DT ChIP-exo|chip-exo|JJ experiments|experiment|NNS were|be|VBD generated|generate|VBN by|by|IN following|follow|VBG the|the|DT steps|step|NNS presented|present|VBN by|by|IN Rhee|Rhee|NNP and|and|CC Pugh|Pugh|NNP ,|,|, 2011|2011|CD .|.|.
The|the|DT ChIP|chip|NN experiment|experiment|NN was|be|VBD performed|perform|VBN essentially|essentially|RB as|as|IN described|describe|VBN previously|previously|RB -LRB-|-lrb-|-LRB- Herring|Herring|NNP ,|,|, Raffaelle|Raffaelle|NNP et|et|FW al.|al.|FW 2005|2005|CD -RRB-|-rrb-|-RRB- .|.|. Briefly|briefly|RB ,|,|, the|the|DT cell|cell|NN cultures|culture|NNS were|be|VBD fixed|fix|VBN by|by|IN a|a|DT 1|1|CD %|%|NN formaldehyde|formaldehyde|NN and|and|CC 10|10|CD mM|mm|NN sodium|sodium|NN phosphate|phosphate|NN -LRB-|-lrb-|-LRB- pH|ph|NN 7.6|7.6|CD -RRB-|-rrb-|-RRB- solution|solution|NN for|for|IN 20|20|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. After|after|IN cell|cell|NN lysis|lysis|NN ,|,|, RNase|rnase|NN A|a|NN treatment|treatment|NN and|and|CC sonication|sonication|NN ,|,|, the|the|DT chromosome|chromosome|NN was|be|VBD fragmented|fragmented|JJ to|to|TO 100-1200|100-1200|CD bp|bp|NN .|.|. RNAP|rnap|NN binding|binding|NN DNA|dna|NN -LRB-|-lrb-|-LRB- IP|IP|NNP DNA|dna|NN -RRB-|-rrb-|-RRB- was|be|VBD immunoprecipitated|immunoprecipitate|VBN with|with|IN RNAP|rnap|NN using|use|VBG an|a|DT antibody|antibody|NN against|against|IN the|the|DT RNAP|rnap|NN β|β|NN '|'|'' subunit|subunit|NN and|and|CC pan|pan|NN mouse|mouse|NN magnetic|magnetic|JJ beads|bead|NNS .|.|. The|the|DT same|same|JJ sample|sample|NN without|without|IN the|the|DT β|β|NN '|'|'' antibody|antibody|NN was|be|VBD used|use|VBN as|as|IN mock|mock|JJ immunoprecipitation|immunoprecipitation|NN DNA|dna|NN -LRB-|-lrb-|-LRB- mock|mock|JJ IP|IP|NNP DNA|dna|NN -RRB-|-rrb-|-RRB- .|.|. After|after|IN washing|wash|VBG and|and|CC de-crosslinking|de-crosslinking|NN ,|,|, DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG the|the|DT PCR|pcr|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT clean|clean|JJ reads|read|VBZ obtained|obtain|VBN were|be|VBD aligned|align|VBN to|to|TO the|the|DT genome|genome|NN sequence|sequence|NN of|of|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN EDL933|edl933|NN using|use|VBG SOAP2|soap2|NN
The|the|DT conditioned|conditioned|JJ medium|medium|NN -LRB-|-lrb-|-LRB- C|c|NN -RRB-|-rrb-|-RRB- was|be|VBD the|the|DT DMEM|DMEM|NNP medium|medium|NN containing|contain|VBG 10|10|CD %|%|NN FBS|fbs|NN without|without|IN antibiotics|antibiotic|NNS recovered|recover|VBN after|after|IN 24|24|CD hrs|hr|NNS incubation|incubation|NN with|with|IN differentiated|differentiate|VBN Caco-2|caco-2|NN cells|cell|NNS .|.|. 400|400|CD µL|µl|NN of|of|IN STEC|stec|NN culture|culture|NN were|be|VBD inoculated|inoculate|VBN in|in|IN 4|4|CD mL|ml|NN of|of|IN C|c|NN medium|medium|NN and|and|CC incubated|incubate|VBN for|for|IN 3|3|CD hrs|hr|NNS at|at|IN 37|37|CD °C|°c|NN .|.|. After|after|IN this|this|DT period|period|NN the|the|DT bacteria|bacterium|NNS were|be|VBD recovered|recover|VBN by|by|IN centrifugation|centrifugation|NN for|for|IN 10|10|CD min|min|NN at|at|IN 5000|5000|CD xg|xg|NN and|and|CC the|the|DT pellet|pellet|NN was|be|VBD ressuspended|ressuspend|VBN in|in|IN 600|600|CD µL|µl|NN of|of|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP cat|cat|NN .|.|. no.|no.|RB 76506|76506|CD ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- for|for|IN RNA|rna|NN extraction|extraction|NN .|.|.
The|the|DT counts|count|NNS of|of|IN reads|read|VBZ 150|150|CD aligning|align|VBG to|to|TO genomic|genomic|JJ features|feature|NNS were|be|VBD obtained|obtain|VBN using|use|VBG the|the|DT `|`|`` feaureCounts|feaurecount|NNS '|'|POS function|function|NN from|from|IN the|the|DT R|r|NN package|package|NN `|`|`` Rsubread|Rsubread|NNP '|'|''
The|The|NNP cross-linked|cross-linked|JJ DNA-ArgR|dna-argr|NN complexes|complex|NNS in|in|IN the|the|DT supernatant|supernatant|NN were|be|VBD then|then|RB immunoprecipitated|immunoprecipitate|VBN by|by|IN adding|add|VBG 10|10|CD µL|µl|NN of|of|IN Anti-myc|anti-myc|NN -LRB-|-lrb-|-LRB- 9E10|9e10|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Santa|Santa|NNP Cruz|Cruz|NNP ,|,|, Dallas|Dallas|NNP ,|,|, TX|TX|NNP -RRB-|-rrb-|-RRB- .|.|. For|for|IN mock-IP|mock-ip|JJ control|control|NN ,|,|, 2|2|CD µg|µg|NN of|of|IN normal|normal|JJ mouse|mouse|NN IgG|igg|NN -LRB-|-lrb-|-LRB- Santa|Santa|NNP Cruz|Cruz|NNP -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN into|into|IN the|the|DT supernatant|supernatant|NN in|in|IN parallel|parallel|NN .|.|. They|they|PRP were|be|VBD then|then|RB incubated|incubate|VBN overnight|overnight|JJ at|at|IN 4oC|4oc|NN with|with|IN constant|constant|JJ rotation|rotation|NN .|.|. The|the|DT cross-linked|cross-linked|JJ DNA-protein|dna-protein|NN and|and|CC antibody|antibody|NN complexes|complex|NNS were|be|VBD selectively|selectively|RB captured|capture|VBN by|by|IN adding|add|VBG 50|50|CD µL|µl|NN of|of|IN Dynabeads|Dynabeads|NNP Pan|Pan|NNP Mouse|Mouse|NNP IgG|igg|NN magnetic|magnetic|JJ beads|bead|NNS -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, Grand|Grand|NNP Island|Island|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- .|.|. Then|then|RB ,|,|, DNAs|dna|NNS were|be|VBD end-polished|end-polished|JJ using|use|VBG T4|t4|NN DNA|dna|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- NEB|neb|NN ,|,|, Ipswich|Ipswich|NNP ,|,|, MA|MA|NNP -RRB-|-rrb-|-RRB- ,|,|, ligated|ligate|VBN with|with|IN the|the|DT annealed|annealed|JJ adaptor|adaptor|NN 1|1|CD -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: Phospho-AACTGCCCCGGGTTGCTCTTCCGATCT|phospho-aactgccccgggttgctcttccgatct|NN and|and|CC 5|5|CD '|'|'' -|-|: OH-AGATCGGAAGAGC-OH|oh-agatcggaagagc-oh|NN -RRB-|-rrb-|-RRB- ,|,|, nick-repaired|nick-repaired|JJ using|use|VBG phi29|phi29|NN polymerase|polymerase|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC digested|digest|VBN with|with|IN λ|λ|NN exonuclease|exonuclease|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- as|as|IN reported|report|VBN previously|previously|RB .|.|. Then|then|RB ,|,|, protein-DNA|protein-dna|JJ complexes|complex|NNS were|be|VBD reverse-cross-linked|reverse-cross-link|VBN by|by|IN heating|heating|NN at|at|IN 65|65|CD °C|°c|NN overnight|overnight|JJ and|and|CC proteins|protein|NNS were|be|VBD degraded|degrade|VBN by|by|IN 8|8|CD µg|µg|NN of|of|IN protease|protease|NN K|k|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT purified|purify|VBN DNAs|dna|NNS were|be|VBD denatured|denature|VBN at|at|IN 95|95|CD °C|°c|NN and|and|CC extended|extend|VBN by|by|IN P1|p1|NN primer|primer|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: OH-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT|oh-gtgactggagttcagacgtgtgctcttccgatct|NN -RRB-|-rrb-|-RRB- ,|,|, further|further|JJ ligated|ligate|VBN with|with|IN the|the|DT annealed|annealed|JJ adaptor|adaptor|NN 2|2|CD -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: OH-ACACTCTTTCCCTACACGACGCTCTTCCGATCT|oh-acactctttccctacacgacgctcttccgatct|NN and|and|CC 5|5|CD '|'|'' -|-|: OH-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG|oh-agatcggaagagcgtcgtgtagggaaagagtgtag|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT ligated|ligate|VBN DNA|dna|NN products|product|NNS were|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP PCR|pcr|NN purification|purification|NN kit|kit|NN and|and|CC were|be|VBD PCR-amplified|pcr-amplified|JJ by|by|IN P2|p2|NN primer|primer|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: OH-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT|oh-aatgatacggcgaccaccgagatctacactctttccctacacgacgctcttccgatct|NN -RRB-|-rrb-|-RRB- and|and|CC P3|p3|NN primer|primer|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: OH-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGT|oh-caagcagaagacggcatacgagatnnnnnngtgactggagttcagacgtgt|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT degenerative|degenerative|JJ sequence|sequence|NN -LRB-|-lrb-|-LRB- the|the|DT underlined|underline|VBN 6Ns|6n|NNS -RRB-|-rrb-|-RRB- in|in|IN the|the|DT P3|p3|NN primer|primer|NN indicates|indicate|VBZ the|the|DT index|index|NN sequence|sequence|NN for|for|IN the|the|DT Illumina|Illumina|NNP next-generation|next-generation|JJ sequencing|sequencing|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, San|San|NNP Diego|Diego|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT PCR-amplified|pcr-amplified|JJ DNA|dna|NN products|product|NNS were|be|VBD then|then|RB loaded|load|VBN onto|onto|IN 2|2|CD %|%|NN agarose|agarose|NN gel|gel|NN and|and|CC extracted|extract|VBN using|use|VBG QIAquick|qiaquick|NN gel|gel|NN purification|purification|NN columns|column|NNS .|.|.
The|the|DT cultivations|cultivation|NNS were|be|VBD performed|perform|VBN in|in|IN a|a|DT Biostat|biostat|NN C|c|NN 15|15|CD L|l|NN bioreactor|bioreactor|NN with|with|IN the|the|DT DCU-3|dcu-3|NN controlling|control|VBG unit|unit|NN and|and|CC MFCS-win|mfcs-win|NN supervisory|supervisory|JJ system|system|NN -LRB-|-lrb-|-LRB- Sartorius|sartorius|NN -RRB-|-rrb-|-RRB- with|with|IN an|a|DT initial|initial|JJ working|work|VBG volume|volume|NN of|of|IN 8|8|CD L|l|NN .|.|. The|the|DT mineral|mineral|NN salt|salt|NN medium|medium|NN contained|contain|VBD per|per|IN liter|liter|NN :|:|: 14.6|14.6|CD g|g|NN K2HPO4|k2hpo4|NN ,|,|, 3.6|3.6|CD g|g|NN NaH2PO4|nah2po4|NN ×|×|NN 2|2|CD H2O|h2o|NN ,|,|, 2.0|2.0|CD g|g|NN Na2SO4|na2so4|NN ,|,|, 2.47|2.47|CD g|g|NN -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2SO4|2so4|NN ,|,|, 0.5|0.5|CD g|g|NN NH4Cl|nh4cl|NN ,|,|, 1.0|1.0|CD g|g|NN -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2-H-citrate|2-h-citrate|NN ,|,|, 2|2|CD mM|mm|NN MgSO4|mgso4|NN ,|,|, 0.1|0.1|CD g|g|NN thiamine|thiamine|NN hydrochloride|hydrochloride|NN ,|,|, 0.1|0.1|CD mL|ml|NN antifoam|antifoam|NN 204|204|CD -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- and|and|CC 2|2|CD mL|ml|NN trace|trace|NN element|element|NN solution|solution|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT initial|initial|JJ glucose|glucose|NN concentration|concentration|NN was|be|VBD 40|40|CD g|g|NN L-1|l-1|NN .|.|. The|the|DT feed|feed|NN solution|solution|NN contained|contain|VBD 650|650|CD g|g|NN L-1|l-1|NN glucose|glucose|NN .|.|. 2|2|CD mL|ml|NN L-1|l-1|NN of|of|IN sterile|sterile|JJ filtered|filter|VBN 1M|1m|NN MgSO4|mgso4|NN were|be|VBD added|add|VBN regularly|regularly|RB per|per|IN OD600|od600|NN =|=|JJ 10|10|CD increase|increase|NN .|.|.
The|the|DT cultured|culture|VBN cells|cell|NNS were|be|VBD inoculated|inoculate|VBN with|with|IN 1:100|1:100|CD dilution|dilution|NN into|into|IN 50|50|CD mL|ml|NN of|of|IN the|the|DT fresh|fresh|JJ M9|m9|NN medium|medium|NN containing|contain|VBG 2|2|CD g/L|g/l|NN glucose|glucose|NN in|in|IN either|either|CC the|the|DT presence|presence|NN or|or|CC absence|absence|NN of|of|IN 1|1|CD g/L|g/l|NN arginine|arginine|NN and|and|CC continued|continue|VBD to|to|TO culture|culture|NN at|at|IN 37|37|CD °C|°c|NN until|until|IN reaching|reach|VBG an|a|DT appropriate|appropriate|JJ cell|cell|NN density|density|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ≈|≈|CD 0.5|0.5|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT culture|culture|NN medium|medium|NN samples|sample|NNS were|be|VBD withdrawn|withdraw|VBN with|with|IN a|a|DT capillary|capillary|JJ sampling|sampling|NN probe|probe|NN as|as|IN developed|develop|VBN by|by|IN Theobald|Theobald|NNP et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- 1997|1997|CD -RRB-|-rrb-|-RRB- ,|,|, however|however|RB ,|,|, without|without|IN using|use|VBG membrane-covered|membrane-covered|JJ glass|glass|NN tubes|tube|NNS .|.|.
The|the|DT cultures|culture|NNS were|be|VBD balanced|balanced|JJ and|and|CC grown|grow|VBN in|in|IN CAMHB|CAMHB|NNP media|media|NNS at|at|IN 37|37|CD degrees|degree|NNS Celsius|Celsius|NNP .|.|.
The|the|DT cultures|culture|NNS were|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000|8000|CD rpm|rpm|NN for|for|IN 10|10|CD minutes|minute|NNS and|and|CC the|the|DT pellet|pellet|NN was|be|VBD dissolved|dissolve|VBN in|in|IN 15|15|CD mL|ml|NN of|of|IN 10|10|CD mM|mm|NN NaCl|nacl|NN ,|,|, 20|20|CD mM|mm|NN Tris-HCl|tris-hcl|NN -LRB-|-lrb-|-LRB- pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 100|100|CD μg/mL|μg/ml|NN proteinase|proteinase|NN K|k|NN and|and|CC 0.5|0.5|CD %|%|NN SDS|sds|NN .|.|. This|this|DT suspension|suspension|NN was|be|VBD incubated|incubate|VBN at|at|IN 50oC|50oc|NN for|for|IN 2|2|CD h|h|NN and|and|CC DNA|dna|NN extracted|extract|VBN with|with|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN :|:|: isoamyl|isoamyl|NN alcohol|alcohol|NN -LRB-|-lrb-|-LRB- 25:24:1|25:24:1|CD -RRB-|-rrb-|-RRB- .|.|. Following|follow|VBG centrifugation|centrifugation|NN for|for|IN 10|10|CD min|min|NN at|at|IN 8000|8000|CD rpm|rpm|NN ,|,|, the|the|DT upper|upper|JJ phase|phase|NN was|be|VBD removed|remove|VBN and|and|CC precipitated|precipitate|VBN by|by|IN adding|add|VBG 0.1|0.1|CD volume|volume|NN of|of|IN 3|3|CD M|m|NN NaOAc|naoac|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- and|and|CC 2|2|CD volumes|volume|NNS of|of|IN 99|99|CD %|%|NN ethanol|ethanol|NN .|.|. The|the|DT DNA|dna|NN precipitate|precipitate|NN was|be|VBD then|then|RB spooled|spool|VBN out|out|IN of|of|IN the|the|DT solution|solution|NN using|use|VBG a|a|DT sterile|sterile|JJ glass|glass|NN rod|rod|NN ,|,|, washed|wash|VBN with|with|IN 70|70|CD %|%|NN ethanol|ethanol|NN ,|,|, and|and|CC dissolved|dissolve|VBN in|in|IN 5|5|CD mL|ml|NN of|of|IN TE|TE|NNP -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- buffer|buffer|NN .|.|.
The|the|DT cultures|culture|NNS were|be|VBD prepared|prepare|VBN by|by|IN inoculating|inoculate|VBG one|one|CD colony|colony|NN from|from|IN tryptone|tryptone|NN soya|soya|NN agar|agar|NN -LRB-|-lrb-|-LRB- TSA|tsa|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Oxoid|Oxoid|NNP -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- overnight|overnight|JJ growth|growth|NN at|at|IN 37|37|CD °C|°c|NN -RRB-|-rrb-|-RRB- to|to|TO 5|5|CD ml|ml|NN TSB|tsb|NN and|and|CC incubating|incubate|VBG overnight|overnight|JJ at|at|IN 37|37|CD °C|°c|NN ,|,|, with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- .|.|. This|this|DT culture|culture|NN was|be|VBD initially|initially|RB diluted|dilute|VBN 1:10|1:10|CD in|in|IN medium|medium|NN and|and|CC used|use|VBN to|to|TO inoculate|inoculate|VB room-temperature|room-temperature|JJ TSB|tsb|NN for|for|IN each|each|DT of|of|IN the|the|DT different|different|JJ stress|stress|NN factors|factor|NNS -LRB-|-lrb-|-LRB- 40|40|CD ml|ml|NN total|total|JJ volume|volume|NN -RRB-|-rrb-|-RRB- to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN approx.|approx.|RB 1|1|CD '|'|'' 107|107|CD CFU/ml|cfu/ml|NN -LRB-|-lrb-|-LRB- 1:100|1:100|CD dilution|dilution|NN of|of|IN overnight|overnight|JJ culture|culture|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN cold|cold|JJ stress|stress|NN experiment|experiment|NN the|the|DT medium|medium|NN was|be|VBD chilled|chill|VBN to|to|TO 15|15|CD °C|°c|NN prior|prior|RB to|to|TO inoculation|inoculation|NN .|.|. The|the|DT cultures|culture|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN -LRB-|-lrb-|-LRB- except|except|IN fpr|fpr|NN 15|15|CD °C|°c|NN and|and|CC 46|46|CD °C|°c|NN conditions|condition|NNS -RRB-|-rrb-|-RRB- ,|,|, shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN and|and|CC samples|sample|NNS were|be|VBD collected|collect|VBN during|during|IN exponential|exponential|JJ growth|growth|NN at|at|IN a|a|DT cell|cell|NN density|density|NN of|of|IN approx.|approx.|RB 1|1|CD '|'|'' 108|108|CD CFU/ml|cfu/ml|NN .|.|. All|all|PDT the|the|DT stress|stress|NN conditions|condition|NNS ,|,|, including|include|VBG the|the|DT control|control|NN ,|,|, were|be|VBD inoculated|inoculate|VBN with|with|IN the|the|DT same|same|JJ overnight|overnight|JJ culture|culture|NN and|and|CC started|start|VBD at|at|IN the|the|DT same|same|JJ time|time|NN point|point|NN .|.|. The|the|DT experiment|experiment|NN was|be|VBD performed|perform|VBN 3|3|CD times|time|NNS at|at|IN different|different|JJ days|day|NNS and|and|CC with|with|IN freshly|freshly|RB prepared|prepared|JJ solutions|solution|NNS ,|,|, resulting|result|VBG in|in|IN 3|3|CD biological|biological|JJ replicates|replicate|VBZ .|.|.
The|the|DT culture|culture|NN was|be|VBD divided|divide|VBN into|into|IN two|two|CD 20-ml|20-ml|JJ volumes|volume|NNS and|and|CC the|the|DT cells|cell|NNS collected|collect|VBN by|by|IN centrifugation|centrifugation|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD removed|remove|VBN and|and|CC the|the|DT two|two|CD pellets|pellet|NNS were|be|VBD subjected|subject|VBN to|to|TO different|different|JJ treatments|treatment|NNS .|.|. One|one|CD was|be|VBD resuspended|resuspend|VBN in|in|IN 1|1|CD ml|ml|NN of|of|IN pre-warmed|pre-warmed|JJ 1X|1x|NN EG-minimal|eg-minimal|JJ medium|medium|NN pH|ph|NN 7.2|7.2|CD .|.|. The|the|DT second|second|NN was|be|VBD resuspended|resuspend|VBN in|in|IN 1|1|CD ml|ml|NN of|of|IN pre-warmed|pre-warmed|JJ 1X|1x|NN EG-minimal|eg-minimal|JJ medium|medium|NN pH|ph|NN 4.5|4.5|CD .|.|. Each|each|DT suspension|suspension|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ volume|volume|NN of|of|IN 20|20|CD ml|ml|NN 1X|1x|NN EG|eg|NN minimal|minimal|JJ medium|medium|NN of|of|IN the|the|DT same|same|JJ pH|ph|NN in|in|IN a|a|DT 250|250|CD ml|ml|NN flask|flask|NN .|.|. Cells|cell|NNS were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN and|and|CC 200|200|CD rpm|rpm|NN shaking|shake|VBG for|for|IN 90|90|CD min|min|NN before|before|IN harvesting|harvest|VBG for|for|IN analysis|analysis|NN .|.|.
The|the|DT culture|culture|NN was|be|VBD incubated|incubate|VBN with|with|IN 100|100|CD µg/ml|µg/ml|NN of|of|IN chloramphenicol|chloramphenicol|NN for|for|IN 2|2|CD min|min|NN ,|,|, and|and|CC harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN .|.|. The|the|DT pellet|pellet|NN with|with|IN washed|wash|VBN and|and|CC resuspended|resuspend|VBN in|in|IN 100|100|CD mM|mm|NN NH4Cl|nh4cl|NN ,|,|, 10|10|CD mM|mm|NN MgCl2|mgcl2|NN ,|,|, 20|20|CD mM|mm|NN Tris|Tris|NNP Cl|Cl|NNP ,|,|, 0.4|0.4|CD %|%|NN Triton|Triton|NNP X100|x100|NN ,|,|, 0.1|0.1|CD %|%|NN NP-40|np-40|NN ,|,|, and|and|CC 100|100|CD µl/ml|µl/ml|JJ chloramphenicol|chloramphenicol|NN ,|,|, and|and|CC flash|flash|NN frozen|freeze|VBN over|over|IN liquid|liquid|JJ nitrogen|nitrogen|NN .|.|. The|the|DT frozen|frozen|JJ cell|cell|NN pellets|pellet|NNS were|be|VBD pulverized|pulverize|VBN by|by|IN mixer|mixer|NN milling|milling|NN and|and|CC thawed|thaw|VBN in|in|IN 2.5|2.5|CD mM|mm|NN DSP|DSP|NNP .|.|. The|the|DT crosslinking|crosslinking|NN reaction|reaction|NN was|be|VBD quenched|quench|VBN with|with|IN 100|100|CD mM|mm|NN Tris|Tris|NNP Cl|Cl|NNP 8.3|8.3|CD .|.|.
The|the|DT data|datum|NNS did|do|VBD not|not|RB undergo|undergo|VB normalization|normalization|NN across|across|IN samples|sample|NNS .|.|.
The|the|DT data|datum|NNS output|output|NN from|from|IN the|the|DT Illumina|Illumina|NNP Hiseq|Hiseq|NNP System|System|NNP was|be|VBD obtained|obtain|VBN directly|directly|RB from|from|IN Vertis|Vertis|NNP
The|the|DT data|datum|NNS provided|provide|VBN are|be|VBP the|the|DT original|original|JJ data|datum|NNS generated|generate|VBN with|with|IN the|the|DT Jaguar|Jaguar|NNP software|software|NN from|from|IN the|the|DT microarray|microarray|NN images|image|NNS .|.|. The|the|DT VALUEs|value|NNS reported|report|VBD represent|represent|VBP log10|log10|NN -LRB-|-lrb-|-LRB- Cy5/Cy3|cy5/cy3|NN -RRB-|-rrb-|-RRB- ratios|ratio|NNS for|for|IN this|this|DT experiment/sample|experiment/sample|NN .|.|. They|they|PRP were|be|VBD not|not|RB normalized|normalize|VBN across|across|IN all|all|DT samples|sample|NNS in|in|IN the|the|DT study|study|NN .|.|.
The|the|DT data|datum|NNS provided|provide|VBN are|be|VBP the|the|DT original|original|JJ data|datum|NNS generated|generate|VBN with|with|IN the|the|DT Jaguar|Jaguar|NNP software|software|NN from|from|IN the|the|DT microarray|microarray|NN images|image|NNS .|.|. The|the|DT VALUEs|value|NNS reported|report|VBD represent|represent|VBP normalized|normalize|VBN log10|log10|NN -LRB-|-lrb-|-LRB- Cy5/Cy3|cy5/cy3|NN -RRB-|-rrb-|-RRB- ratios|ratio|NNS for|for|IN this|this|DT experiment/sample|experiment/sample|NN .|.|. They|they|PRP were|be|VBD not|not|RB normalized|normalize|VBN across|across|IN all|all|DT samples|sample|NNS in|in|IN the|the|DT study|study|NN .|.|.
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG Robust|robust|JJ Multi-Array|multi-array|JJ average|average|NN as|as|IN implemented|implement|VBN in|in|IN Bioconductor|Bioconductor|NNP
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN ArrayStar|arraystar|NN 3|3|CD -LRB-|-lrb-|-LRB- DNASTAR|dnastar|NN -RRB-|-rrb-|-RRB- using|use|VBG RMA|RMA|NNP normalization|normalization|NN method|method|NN .|.|. Genes|gene|NNS with|with|IN at|at|IN least|least|JJS two-fold|two-fold|JJ expression|expression|NN level|level|NN change|change|NN and|and|CC FDR-adjusted|fdr-adjusted|JJ P-value|p-value|NN -LRB-|-lrb-|-LRB- T-test|t-test|NN -RRB-|-rrb-|-RRB- of|of|IN less|less|JJR than|than|IN 0.05|0.05|CD were|be|VBD considered|consider|VBN significant|significant|JJ .|.|.
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN FlexArray|FlexArray|NNP 1.4.1|1.4.1|CD software|software|NN program|program|NN -LRB-|-lrb-|-LRB- http://genomequebec.mcgill.ca/FlexArray/|http://genomequebec.mcgill.ca/flexarray/|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT data|datum|NNS were|be|VBD normalized|normalize|VBN using|use|VBG the|the|DT Robust|robust|JJ Multi-Array|Multi-Array|NNP Average|Average|NNP algorithm|algorithm|NN -LRB-|-lrb-|-LRB- RMA|rma|NN -RRB-|-rrb-|-RRB- .|.|. Comparison|comparison|NN between|between|IN the|the|DT two|two|CD data|datum|NNS sets|set|NNS was|be|VBD done|do|VBN using|use|VBG the|the|DT Randomized|Randomized|NNP Variance|Variance|NNP Model|Model|NNP -LRB-|-lrb-|-LRB- RVM|RVM|NNP -RRB-|-rrb-|-RRB- with|with|IN a|a|DT cut-off|cut-off|JJ of|of|IN a|a|DT fold|fold|JJ change|change|NN of|of|IN 2|2|CD -LRB-|-lrb-|-LRB- or|or|CC -2|-2|CD -RRB-|-rrb-|-RRB- and|and|CC a|a|DT P-value|p-value|NN of|of|IN 0.05|0.05|CD .|.|.
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN GCOS|gcos|NN 1.4|1.4|CD software|software|NN .|.|. All|all|DT probe|probe|NN sets|set|VBZ scaling|scale|VBG was|be|VBD performed|perform|VBN with|with|IN a|a|DT target|target|NN signal|signal|NN value|value|NN of|of|IN 500|500|CD .|.|. No|no|DT normalization|normalization|NN was|be|VBD performed|perform|VBN .|.|.
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN Microarray|Microarray|NNP Suite|Suite|NNP version|version|NN 5.0|5.0|CD -LRB-|-lrb-|-LRB- MAS|mas|NN 5.0|5.0|CD -RRB-|-rrb-|-RRB- using|use|VBG Affymetrix|Affymetrix|NNP default|default|NN analysis|analysis|NN settings|setting|NNS and|and|CC global|global|JJ scaling|scaling|NN as|as|IN normalization|normalization|NN method|method|NN .|.|.
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN Microarray|Microarray|NNP Suite|Suite|NNP version|version|NN 5.0|5.0|CD -LRB-|-lrb-|-LRB- MAS|mas|NN 5.0|5.0|CD -RRB-|-rrb-|-RRB- using|use|VBG Affymetrix|Affymetrix|NNP default|default|NN analysis|analysis|NN settings|setting|NNS and|and|CC global|global|JJ scaling|scaling|NN as|as|IN normalization|normalization|NN method|method|NN .|.|. Data|datum|NNS from|from|IN this|this|DT sample|sample|NN were|be|VBD collected|collect|VBN using|use|VBG Affy|Affy|NNP Ecoli|Ecoli|NNP anti-sense|anti-sense|JJ chip|chip|NN -LRB-|-lrb-|-LRB- 2001|2001|CD ;|;|: platform|platform|NN ID|id|NN GPL4940|gpl4940|NN -RRB-|-rrb-|-RRB- ,|,|, but|but|CC because|because|IN the|the|DT analysis|analysis|NN software|software|NN failed|fail|VBD to|to|TO recognize|recognize|VB the|the|DT correct|correct|JJ platform|platform|NN ,|,|, we|we|PRP reformatted|reformat|VBD the|the|DT data|datum|NNS to|to|TO match|match|VB the|the|DT newer|newer|JJR -LRB-|-lrb-|-LRB- and|and|CC mostly|mostly|RB equivalent|equivalent|JJ -RRB-|-rrb-|-RRB- platform|platform|NN GPL199|gpl199|NN -LRB-|-lrb-|-LRB- Affy|Affy|NNP Ecoli|Ecoli|NNP anti-sense|anti-sense|JJ chip|chip|NN version|version|NN 2|2|CD ,|,|, 2002|2002|CD -RRB-|-rrb-|-RRB- .|.|. Because|because|IN ,|,|, however|however|RB ,|,|, not|not|RB all|all|DT of|of|IN the|the|DT probes|probe|NNS on|on|IN the|the|DT new|new|JJ platform|platform|NN were|be|VBD present|present|JJ on|on|IN the|the|DT old|old|JJ platform|platform|NN ,|,|, data|datum|NNS for|for|IN some|some|DT probes|probe|NNS were|be|VBD unavailable|unavailable|JJ and|and|CC labeled|label|VBN in|in|IN the|the|DT `|`|`` remapped|remapped|NN '|'|'' dataset|dataset|NN as|as|IN `|`|`` NULL|NULL|NNP '|'|'' to|to|TO indicate|indicate|VB they|they|PRP were|be|VBD missing|miss|VBG .|.|. While|while|IN the|the|DT following|follow|VBG data|datum|NNS are|be|VBP therefore|therefore|RB formatted|format|VBN using|use|VBG ID|ID|NNP _|_|SYM REFs|ref|NNS that|that|WDT match|match|VBP GPL199|gpl199|NN ,|,|, the|the|DT CEL|CEL|NNP file|file|NN contains|contain|VBZ the|the|DT raw|raw|JJ data|data|NN -LRB-|-lrb-|-LRB- not|not|RB `|`|`` remapped|remap|VBN '|'|'' -RRB-|-rrb-|-RRB- and|and|CC thus|thus|RB corresponds|correspond|VBZ to|to|TO the|the|DT actual|actual|JJ array|array|NN used|use|VBN -LRB-|-lrb-|-LRB- GPL4940|gpl4940|NN ,|,|, Ecoli|ecoli|JJ antisense|antisense|JJ chip|chip|NN ,|,|, 2001|2001|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN Microarray|Microarray|NNP Suite|Suite|NNP version|version|NN 5.0|5.0|CD -LRB-|-lrb-|-LRB- MAS|mas|NN 5.0|5.0|CD -RRB-|-rrb-|-RRB- using|use|VBG Affymetrix|Affymetrix|NNP default|default|NN analysis|analysis|NN settings|setting|NNS and|and|CC global|global|JJ scaling|scaling|NN as|as|IN normalization|normalization|NN method|method|NN .|.|. The|the|DT trimmed|trim|VBN mean|mean|NN target|target|NN intensity|intensity|NN of|of|IN each|each|DT array|array|NN was|be|VBD arbitrarily|arbitrarily|RB set|set|VBN to|to|TO 100|100|CD .|.|.
The|the|DT data|datum|NNS were|be|VBD analyzed|analyze|VBN with|with|IN Partek|Partek|NNP Genomics|Genomics|NNP Suite|Suite|NNP using|use|VBG Affymetrix|Affymetrix|NNP default|default|NN analysis|analysis|NN settings|setting|NNS and|and|CC global|global|JJ scaling|scaling|NN as|as|IN normalization|normalization|NN method|method|NN .|.|.
The|the|DT data|datum|NNS were|be|VBD imported|import|VBN into|into|IN FlexArray|FlexArray|NNP using|use|VBG gc-RMA|gc-rma|NN preprocessing|preprocessing|NN for|for|IN analysis|analysis|NN .|.|.
The|the|DT data|datum|NNS were|be|VBD normalised|normalised|JJ manually|manually|RB in|in|IN Excel|Excel|NNP .|.|. For|for|IN each|each|DT spot|spot|NN ,|,|, the|the|DT median|median|NN of|of|IN the|the|DT spot|spot|NN intensity|intensity|NN minus|minus|CC the|the|DT background|background|NN were|be|VBD considered|consider|VBN .|.|. Because|because|IN we|we|PRP wanted|want|VBD to|to|TO compare|compare|VB different|different|JJ environmental|environmental|JJ conditions|condition|NNS ,|,|, the|the|DT cDNA|cdna|NN signal|signal|NN in|in|IN each|each|DT condition|condition|NN was|be|VBD normalised|normalised|JJ to|to|TO that|that|DT of|of|IN gDNA|gdna|NN with|with|IN M|m|NN =|=|JJ ln|ln|NN -LRB-|-lrb-|-LRB- cDNA/gDNA|cdna/gdna|NN -RRB-|-rrb-|-RRB- .|.|. To|to|TO ensure|ensure|VB that|that|IN the|the|DT fluorescence|fluorescence|NN measurements|measurement|NNS were|be|VBD independent|independent|JJ of|of|IN the|the|DT overall|overall|JJ signal|signal|NN intensity|intensity|NN of|of|IN the|the|DT spot|spot|NN ,|,|, the|the|DT values|value|NNS of|of|IN M|m|NN were|be|VBD made|make|VBN independent|independent|JJ of|of|IN A|a|NN =|=|JJ -LRB-|-lrb-|-LRB- lncDNA|lncdna|NN +|+|CC lngDNA|lngdna|NN -RRB-|-rrb-|-RRB- /|/|: 2|2|CD with|with|IN a|a|DT linear|linear|JJ shift|shift|NN .|.|. Spots|spot|NNS where|where|WRB the|the|DT A|a|NN values|value|NNS were|be|VBD less|less|JJR than|than|IN 5.5|5.5|CD were|be|VBD not|not|RB considered|consider|VBN .|.|. Finally|finally|RB the|the|DT experiments|experiment|NNS were|be|VBD aligned|align|VBN so|so|RB that|that|IN the|the|DT median|median|NN of|of|IN M|m|NN =|=|JJ 0|0|CD and|and|CC their|they|PRP$ deviation|deviation|NN was|be|VBD normalised|normalised|JJ .|.|.
The|the|DT data|datum|NNS were|be|VBD normalized|normalize|VBN by|by|IN RMA|rma|NN method|method|NN and|and|CC then|then|RB analyzed|analyze|VBN by|by|IN limma|limma|NN package|package|NN to|to|TO identify|identify|VB differentially|differentially|RB expressed|express|VBN genes|gene|NNS -LRB-|-lrb-|-LRB- bioconductor|bioconductor|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT distribution|distribution|NN of|of|IN reads|read|VBZ was|be|VBD plotted|plot|VBN by|by|IN its|its|PRP$ location|location|NN in|in|IN the|the|DT reference|reference|NN genome|genome|NN ,|,|, and|and|CC then|then|RB divided|divide|VBN into|into|IN gene|gene|NN region|region|NN and|and|CC intergenic|intergenic|JJ region|region|NN .|.|. Genome|Genome|NNP and|and|CC gene|gene|NN coverage|coverage|NN was|be|VBD calculated|calculate|VBN by|by|IN counting|count|VBG the|the|DT number|number|NN of|of|IN reads|read|VBZ mapped|map|VBN to|to|TO the|the|DT genome|genome|NN and|and|CC individual|individual|JJ genes|gene|NNS respectively|respectively|RB .|.|.
The|the|DT early-exponential|early-exponential|JJ phase|phase|NN cells|cell|NNS were|be|VBD collected|collect|VBN without|without|IN NaCl|nacl|NN treatment|treatment|NN .|.|.
The|the|DT E.|e.|FW coli|coli|FW isolate|isolate|NN ESBL019|esbl019|NN was|be|VBD originally|originally|RB isolated|isolate|VBN from|from|IN a|a|DT patient|patient|NN at|at|IN Örebro|Örebro|NNP University|University|NNP hospital|hospital|NN ,|,|, Sweden|Sweden|NNP and|and|CC was|be|VBD maintained|maintain|VBN on|on|IN tryptic|tryptic|JJ soy|soy|NN agar|agar|NN -LRB-|-lrb-|-LRB- TSA|tsa|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Becton|Becton|NNP Dickinson|Dickinson|NNP ,|,|, Le|Le|NNP Pont|Pont|NNP Claix|Claix|NNP ,|,|, France|France|NNP -RRB-|-rrb-|-RRB- .|.|. ESBL019|esbl019|NN was|be|VBD grown|grow|VBN in|in|IN Luria|Luria|NNP broth|broth|NN -LRB-|-lrb-|-LRB- Difco|Difco|NNP Laboratories|Laboratories|NNPS ,|,|, Detroit|Detroit|NNP ,|,|, MI|MI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- overnight|overnight|JJ on|on|IN shake|shake|NN at|at|IN 200|200|CD rpm|rpm|NN 37|37|CD °C|°c|NN prior|prior|RB to|to|TO experiments|experiment|NNS .|.|. The|the|DT bacteria|bacterium|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN sterile|sterile|JJ phosphate|phosphate|NN buffered|buffer|VBN saline|saline|NN prior|prior|RB to|to|TO inoculation|inoculation|NN of|of|IN CnT-21|cnt-21|NN cell|cell|NN culture|culture|NN medium|medium|NN -LRB-|-lrb-|-LRB- CCM|ccm|NN -RRB-|-rrb-|-RRB- with|with|IN or|or|CC without|without|IN ceftibuten|ceftibuten|NN -LRB-|-lrb-|-LRB- 480|480|CD ng/mL|ng/ml|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT E.|e.|FW coli|coli|FW K12|k12|NN strain|strain|NN MG1655|mg1655|NN and|and|CC its|its|PRP$ isogenic|isogenic|JJ ptsN|ptsn|NN mutant|mutant|NN were|be|VBD grown|grow|VBN in|in|IN M9|m9|NN minimal|minimal|JJ medium|medium|NN containing|contain|VBG 0.5|0.5|CD %|%|NN glucose|glucose|NN as|as|IN carbon|carbon|NN source|source|NN .|.|. Cells|cell|NNS from|from|IN duplicate|duplicate|VBP experiments|experiment|NNS were|be|VBD harvested|harvest|VBN in|in|IN exponential|exponential|JJ growth|growth|NN phase|phase|NN when|when|WRB cultures|culture|NNS reached|reach|VBD an|a|DT A600|a600|NN of|of|IN 0.4|0.4|CD .|.|.
The|the|DT E.|e.|FW coli|coli|FW strain|strain|NN BW25113|bw25113|NN -LRB-|-lrb-|-LRB- 2|2|CD x|x|CC 10|10|CD ^|^|SYM 9|9|CD -RRB-|-rrb-|-RRB- suspended|suspend|VBN with|with|IN insect|insect|JJ saline|saline|NN -LRB-|-lrb-|-LRB- 0.13|0.13|CD M|m|NN NaCl|nacl|NN ,|,|, 4.7|4.7|CD mM|mm|NN KCl|kcl|NN ,|,|, 1.9|1.9|CD mM|mm|NN CaCl2|cacl2|NN -RRB-|-rrb-|-RRB- ,|,|, was|be|VBD incubated|incubate|VBN with|with|IN GST|gst|NN or|or|CC GST-fused|gst-fused|JJ Drosophila|drosophila|FW immune|immune|JJ proteins|protein|NNS for|for|IN 10|10|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|.
The|the|DT E.|e.|FW coli|coli|FW strains|strain|NNS were|be|VBD grown|grow|VBN for|for|IN six|six|CD hours|hour|NNS under|under|IN anaerobic|anaerobic|JJ growth|growth|NN condition|condition|NN in|in|IN glucose-containing|glucose-containing|JJ complex|complex|JJ medium|medium|NN .|.|.
The|the|DT equivalent|equivalent|NN of|of|IN 5|5|CD OD600|od600|NN was|be|VBD saved|save|VBN for|for|IN RNA|rna|NN extraction|extraction|NN with|with|IN TriZOL|trizol|NN before|before|IN adding|add|VBG antibodies|antibody|NNS -LRB-|-lrb-|-LRB- lysate|lysate|NN RNA|rna|NN sample|sample|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN coIP|coip|NN samples|sample|NNS ,|,|, beads|bead|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN the|the|DT lysis|lysis|NN buffer|buffer|NN ,|,|, mixed|mix|VBN with|with|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN :|:|: isopropanol|isopropanol|NN -LRB-|-lrb-|-LRB- 25:24:1|25:24:1|CD ,|,|, pH4|ph4|NN .5|.5|CD ,|,|, Roth|Roth|NNP -RRB-|-rrb-|-RRB- for|for|IN 20|20|CD s|s|NNS and|and|CC incubated|incubate|VBN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 3|3|CD min|min|NN .|.|. After|after|IN centrifugation|centrifugation|NN ,|,|, the|the|DT aqueous|aqueous|JJ phase|phase|NN was|be|VBD precipitated|precipitate|VBN with|with|IN isopropanol|isopropanol|NN -LRB-|-lrb-|-LRB- coIP|coip|NN RNA|rna|NN sample|sample|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT purified|purify|VBN RNA|rna|NN coIP|coip|NN sample|sample|NN was|be|VBD treated|treat|VBN with|with|IN DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- to|to|TO remove|remove|VB the|the|DT residual|residual|JJ DNA|dna|NN and|and|CC reisolated|reisolate|VBN with|with|IN phenol|phenol|NN :|:|: chloroform|chloroform|NN :|:|: isopropanol|isopropanol|NN .|.|. The|the|DT spike-in|spike-in|JJ RNA|rna|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' P-CUCGUCCGACGUCACCUAGA|p-cucguccgacgucaccuaga|NN ,|,|, IBA|iba|NN -RRB-|-rrb-|-RRB- had|have|VBD been|be|VBN added|add|VBN to|to|TO 40|40|CD pg/µl|pg/µl|NN for|for|IN coIP|coip|NN samples|sample|NNS and|and|CC to|to|TO 1.6|1.6|CD ng/µl|ng/µl|NN for|for|IN lysate|lysate|NN samples|sample|NNS .|.|.
The|the|DT exponential|exponential|JJ phase|phase|NN culture|culture|NN was|be|VBD split|split|VBN in|in|IN two|two|CD ,|,|, and|and|CC one|one|CD part|part|NN was|be|VBD induced|induce|VBN with|with|IN mitomycin|mitomycin|NN C|c|NN at|at|IN a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.25|0.25|CD μg/ml|μg/ml|NN .|.|. Both|both|DT cultures|culture|NNS were|be|VBD subsequently|subsequently|RB incubated|incubate|VBN at|at|IN 37|37|CD °C|°c|NN with|with|IN agitation|agitation|NN for|for|IN 1.5|1.5|CD hours|hour|NNS .|.|. Bacterial|bacterial|JJ cells|cell|NNS were|be|VBD then|then|RB spun|spin|VBN down|down|RP and|and|CC resuspended|resuspend|VBN in|in|IN 5-10|5-10|CD volumes|volume|NNS of|of|IN RNA|rna|NN later|later|RB -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP -RRB-|-rrb-|-RRB- before|before|IN being|be|VBG frozen|freeze|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|.
The|the|DT expression|expression|NN levels|level|NNS were|be|VBD based|base|VBN upon|upon|IN the|the|DT RPKM|RPKM|NNP metric|metric|JJ obtained|obtain|VBN from|from|IN strand-specific|strand-specific|JJ manner|manner|NN .|.|.
The|the|DT fastq|fastq|NN files|file|NNS of|of|IN 36-bp|36-bp|JJ sequenced|sequence|VBN reads|read|VBZ were|be|VBD generated|generate|VBN with|with|IN the|the|DT CASAVA|CASAVA|NNP v1|v1|NN .8|.8|CD -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|. For|for|IN the|the|DT bulk|bulk|NN RNET-seq|rnet-seq|NN analysis|analysis|NN ,|,|, the|the|DT specific|specific|JJ adapter|adapter|NN sequences|sequence|NNS were|be|VBD trimmed|trim|VBN with|with|IN the|the|DT Trimmomatic|trimmomatic|JJ v0|v0|NN .25|.25|CD to|to|TO obtain|obtain|VB reads|read|VBZ ≥|≥|SYM 21-nt|21-nt|CD from|from|IN the|the|DT 5|5|CD '|'|'' end|end|NN .|.|. The|the|DT reads|read|VBZ ≥|≥|SYM 21-nt|21-nt|JJ were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN strain|strain|NN W3110|w3110|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 007779.1|007779.1|CD -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Bowtie2|bowtie2|NN v2|v2|NN .1.0|.1.0|CD with|with|IN the|the|DT default|default|NN parameter|parameter|NN .|.|. A|a|DT gene|gene|NN annotation|annotation|NN file|file|NN of|of|IN E.|e.|FW coli|coli|FW W3110|w3110|NN was|be|VBD downloaded|download|VBN from|from|IN the|the|DT ftp|ftp|NN server|server|NN of|of|IN Ensembl|ensembl|NN .|.|.
The|the|DT fed-batch|fed-batch|JJ cultivations|cultivation|NNS were|be|VBD carried|carry|VBN out|out|RP with|with|IN the|the|DT bacterial|bacterial|JJ strain|strain|NN E.|e.|FW coli|coli|FW K-12|k-12|NN W3110|w3110|NN -LRB-|-lrb-|-LRB- DSM|DSM|NNP 5911|5911|CD ,|,|, German|german|JJ Collection|collection|NN of|of|IN Microorganisms|microorganism|NNS and|and|CC Cell|cell|NN Cultures|culture|NNS -RRB-|-rrb-|-RRB- in|in|IN a|a|DT 30-l|30-l|JJ bioreactor|bioreactor|NN -LRB-|-lrb-|-LRB- Bioengineering|bioengineer|VBG AG|AG|NNP ,|,|, Wald|Wald|NNP ,|,|, Switzerland|Switzerland|NNP -RRB-|-rrb-|-RRB- .|.|. Minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN as|as|IN the|the|DT carbon|carbon|NN source|source|NN was|be|VBD used|use|VBN .|.|. The|the|DT batch|batch|NN medium|medium|NN -LRB-|-lrb-|-LRB- batch|batch|NN volume|volume|NN VR|vr|NN ,0|,0|NN =|=|JJ 17|17|CD l|l|NN -RRB-|-rrb-|-RRB- consisted|consist|VBD of|of|IN 8.8|8.8|CD g|g|NN l|l|NN −|−|CD 1|1|CD glucose|glucose|NN •|•|SYM H2O|h2o|NN ,|,|, 2.0|2.0|CD g|g|NN l|l|NN −|−|CD 1|1|CD Na2SO4|na2so4|NN •|•|SYM 10H2O|10h2o|CD ,|,|, 2.68|2.68|CD g|g|NN l|l|NN −|−|CD 1|1|CD -LRB-|-lrb-|-LRB- NH4|nh4|NN -RRB-|-rrb-|-RRB- 2SO4|2so4|NN ,|,|, 1.0|1.0|CD g|g|NN l|l|NN −|−|CD 1|1|CD NH4Cl|nh4cl|NN ,|,|, 14.6|14.6|CD g|g|NN l|l|NN −|−|CD 1|1|CD K2HPO4|k2hpo4|NN ,|,|, 4.02|4.02|CD g|g|NN l|l|NN −|−|CD 1|1|CD NaH2PO4|nah2po4|NN •|•|SYM 2H2O|2h2o|NN ,|,|, 0.01|0.01|CD g|g|NN l|l|NN −|−|CD 1|1|CD thiamine|thiamine|NN HCl|hcl|NN ;|;|: 0.3|0.3|CD mM|mm|NN CaCl2|cacl2|NN •|•|SYM 2H2O|2h2o|NN ,|,|, 2mM|2mm|NN MgSO4|mgso4|NN •|•|SYM 7H2O|7h2o|CD ;|;|: 3|3|CD ml|ml|NN l|l|NN −|−|CD 1|1|CD of|of|IN trace|trace|NN element|element|NN solution|solution|NN -LRB-|-lrb-|-LRB- TES|tes|NN :|:|: 16.7|16.7|CD g|g|NN l|l|NN −|−|CD 1|1|CD FeCl3|fecl3|NN •|•|SYM 6H2O|6h2o|CD ,|,|, 20.1|20.1|CD g|g|NN l|l|NN −|−|CD 1|1|CD
the|the|DT first|first|JJ ten|ten|CD base|base|NN pairs|pair|NNS of|of|IN each|each|DT read|read|NN were|be|VBD trimmed|trim|VBN using|use|VBG FASTXToolkit|fastxtoolkit|NN 0.0.13|0.0.13|CD .|.|.
The|the|DT five|five|CD bacterial|bacterial|JJ strains|strain|NNS -LRB-|-lrb-|-LRB- JO2057|jo2057|NN ,|,|, JO2081|jo2081|NN ,|,|, JO2083|jo2083|NN ,|,|, JO3020|jo3020|NN and|and|CC MW30|mw30|NN -RRB-|-rrb-|-RRB- were|be|VBD grown|grow|VBN in|in|IN 100|100|CD ml|ml|NN LB|lb|NN 0.5|0.5|CD %|%|NN NaCl|nacl|NN ,|,|, M9|m9|NN minimal|minimal|JJ glucose|glucose|NN or|or|CC M9|m9|NN minimal|minimal|JJ glycerol|glycerol|NN at|at|IN 200|200|CD rpm|rpm|NN in|in|IN New|New|NNP Brunswick|Brunswick|NNP laboratory|laboratory|NN shaker|shaker|NN in|in|IN 2liter|2liter|JJ flasks|flask|NNS .|.|. The|the|DT typical|typical|JJ doubling|doubling|NN time|time|NN ,|,|, observed|observe|VBN in|in|IN exponential|exponential|JJ phase|phase|NN in|in|IN LB|LB|NNP ,|,|, was|be|VBD 40|40|CD min|min|NN for|for|IN JO2057|jo2057|NN ,|,|, JO2081|jo2081|NN ,|,|, JO2083|jo2083|NN ,|,|, MW30|mw30|NN and|and|CC 75|75|CD min|min|NN for|for|IN JO3020|jo3020|NN .|.|. After|after|IN growth|growth|NN curve|curve|NN calibration|calibration|NN ,|,|, the|the|DT various|various|JJ growth|growth|NN phase|phase|NN sample|sample|NN were|be|VBD collected|collect|VBN at|at|IN the|the|DT following|following|JJ cell|cell|NN densities|density|NNS :|:|: exponential|exponential|JJ phase|phase|NN :|:|: OD600|od600|NN 0.6-0.7|0.6-0.7|CD ;|;|: transition|transition|NN :|:|: 2.2-2.5|2.2-2.5|CD and|and|CC stationary|stationary|JJ :|:|: 4.6-4.8|4.6-4.8|CD -LRB-|-lrb-|-LRB- 3.0|3.0|CD for|for|IN hupAB|hupab|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT fluorescent|fluorescent|JJ spot|spot|NN intensities|intensity|NNS were|be|VBD quantified|quantify|VBN using|use|VBG ImaGeneÔ|imageneô|NN 5.6.1|5.6.1|CD -LRB-|-lrb-|-LRB- BioDiscovery|BioDiscovery|NNP Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- software|software|NN .|.|. Background|background|NN subtraction|subtraction|NN and|and|CC normalization|normalization|NN -LRB-|-lrb-|-LRB- LOWESS|lowess|NN -RRB-|-rrb-|-RRB- was|be|VBD performed|perform|VBN in|in|IN GeneSpringä|GeneSpringä|NNP 7|7|CD -LRB-|-lrb-|-LRB- Silicon|Silicon|NNP Genetics|Genetics|NNP -RRB-|-rrb-|-RRB- .|.|. -LRB-|-lrb-|-LRB- A|a|DT lowess|lowess|NN curve|curve|NN was|be|VBD fit|fit|VBN to|to|TO the|the|DT log-intensity|log-intensity|JJ versus|versus|CC log-ratio|log-ratio|JJ plot|plot|NN .|.|. 20|20|CD %|%|NN of|of|IN the|the|DT data|datum|NNS was|be|VBD used|use|VBN to|to|TO calculate|calculate|VB the|the|DT lowess|lowess|NN fit|fit|NN at|at|IN each|each|DT point|point|NN .|.|. The|the|DT curve|curve|NN was|be|VBD used|use|VBN to|to|TO adjust|adjust|VB the|the|DT control|control|NN value|value|NN for|for|IN each|each|DT measurement|measurement|NN .|.|. If|if|IN the|the|DT control|control|NN channel|channel|NN was|be|VBD lower|lower|JJR than|than|IN 10|10|CD then|then|RB the|the|DT value|value|NN was|be|VBD set|set|VBN to|to|TO 10|10|CD -RRB-|-rrb-|-RRB- .|.|. Only|only|RB data|datum|NNS from|from|IN spots|spot|NNS representing|represent|VBG E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN genes|gene|NNS were|be|VBD analyzed|analyze|VBN in|in|IN our|we|PRP$ studies|study|NNS .|.|. All|all|DT analyses|analysis|NNS were|be|VBD based|base|VBN on|on|IN 3|3|CD biological|biological|JJ replicates|replicate|VBZ with|with|IN the|the|DT exception|exception|NN of|of|IN the|the|DT second|second|JJ biological|biological|JJ replicate|replicate|VB from|from|IN conditions|condition|NNS HCl|hcl|NN and|and|CC NaOH|naoh|NN .|.|. These|these|DT two|two|CD observations|observation|NNS were|be|VBD removed|remove|VBN due|due|JJ to|to|TO bad|bad|JJ hybridization|hybridization|NN giving|give|VBG a|a|DT total|total|NN of|of|IN 34|34|CD array|array|NN hybridizations|hybridization|NNS -LRB-|-lrb-|-LRB- observations|observation|NNS -RRB-|-rrb-|-RRB- .|.|. Genes|gene|NNS not|not|RB present|present|VB in|in|IN any|any|DT of|of|IN the|the|DT 34|34|CD observations|observation|NNS were|be|VBD filtered|filter|VBN out|out|RP ,|,|, resulting|result|VBG in|in|IN the|the|DT analysis|analysis|NN of|of|IN 4279|4279|CD out|out|IN of|of|IN 4289|4289|CD MG1655|mg1655|NN genes|gene|NNS on|on|IN the|the|DT array|array|NN .|.|. Missing|miss|VBG values|value|NNS -LRB-|-lrb-|-LRB- data|datum|NNS points|point|NNS -RRB-|-rrb-|-RRB- were|be|VBD replaced|replace|VBN by|by|IN using|use|VBG the|the|DT KNNimpute|knnimpute|NN procedure|procedure|NN -LRB-|-lrb-|-LRB- k|k|NN =|=|JJ 10|10|CD -RRB-|-rrb-|-RRB- on|on|IN log2|log2|NN transformed|transform|VBN data|datum|NNS .|.|.
The|the|DT fresh|fresh|JJ medium|medium|NN -LRB-|-lrb-|-LRB- F|f|NN -RRB-|-rrb-|-RRB- was|be|VBD the|the|DT DMEM|DMEM|NNP medium|medium|NN containing|contain|VBG 10|10|CD %|%|NN FBS|fbs|NN without|without|IN antibiotics|antibiotic|NNS .|.|. 400|400|CD µL|µl|NN of|of|IN STEC|stec|NN culture|culture|NN were|be|VBD inoculated|inoculate|VBN in|in|IN 4|4|CD mL|ml|NN of|of|IN F|f|NN medium|medium|NN and|and|CC incubated|incubate|VBN for|for|IN 3|3|CD hrs|hr|NNS at|at|IN 37|37|CD °C|°c|NN .|.|. After|after|IN this|this|DT period|period|NN the|the|DT bacteria|bacterium|NNS were|be|VBD recovered|recover|VBN by|by|IN centrifugation|centrifugation|NN for|for|IN 10|10|CD min|min|NN at|at|IN 5000|5000|CD xg|xg|NN and|and|CC the|the|DT pellet|pellet|NN was|be|VBD ressuspended|ressuspend|VBN in|in|IN 600|600|CD µL|µl|NN of|of|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP cat|cat|NN .|.|. no.|no.|RB 76506|76506|CD ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- for|for|IN RNA|rna|NN extraction|extraction|NN .|.|.
The|the|DT full|full|JJ library|library|NN construction|construction|NN protocol|protocol|NN was|be|VBD described|describe|VBN in|in|IN detail|detail|NN previously|previously|RB -LRB-|-lrb-|-LRB- Churchman|Churchman|NNP et|et|FW al.|al.|FW ,|,|, Nature|Nature|NNP 2011|2011|CD -RRB-|-rrb-|-RRB- .|.|. Purified|purify|VBN total|total|JJ RNA|rna|NN was|be|VBD fragmented|fragmented|JJ and|and|CC dephosphorylated|dephosphorylate|VBN with|with|IN T4|t4|NN PNK|pnk|NN ,|,|, and|and|CC then|then|RB ligated|ligate|VBD to|to|TO a|a|DT 5|5|CD '|'|'' adenylated|adenylate|VBN DNA|dna|NN oligo|oligo|JJ to|to|TO generate|generate|VB RNA|rna|NN ranging|range|VBG from|from|IN 30-100|30-100|CD nt|nt|NNS .|.|. The|the|DT RNA|rna|NN was|be|VBD reverse|reverse|JJ transcribed|transcribe|VBN ,|,|, and|and|CC the|the|DT single-stranded|single-stranded|JJ DNA|dna|NN circularized|circularize|VBN and|and|CC PCR|pcr|NN amplified|amplify|VBD .|.|.
The|the|DT gene|gene|NN expression|expression|NN values|value|NNS were|be|VBD calculated|calculate|VBN as|as|IN RPKM|rpkm|NN -LRB-|-lrb-|-LRB- reads|read|VBZ per|per|IN kilobase|kilobase|NN transcriptome|transcriptome|NN per|per|IN million|million|CD mapped|map|VBD reads|read|VBZ -RRB-|-rrb-|-RRB- by|by|IN the|the|DT inhouse|inhouse|NNP BGI|BGI|NNP pipeline|pipeline|NN .|.|.
The|the|DT gene|gene|NN expression|expression|NN was|be|VBD calculated|calculate|VBN using|use|VBG the|the|DT RPKM|rpkm|NN method|method|NN
The|the|DT genes|gene|NNS were|be|VBD considered|consider|VBN differentially|differentially|RB expressed|express|VBN when|when|WRB the|the|DT logarithmic|logarithmic|JJ gene|gene|NN expression|expression|NN ratios|ratio|NNS had|have|VBD a|a|DT 2-fold|2-fold|JJ difference|difference|NN in|in|IN the|the|DT expression|expression|NN level|level|NN .|.|. The|the|DT significance|significance|NN of|of|IN the|the|DT data|datum|NNS was|be|VBD determined|determine|VBN using|use|VBG Student|student|NN 's|'s|POS t|t|NN test|test|NN .|.|. P-values|p-value|NNS of|of|IN less|less|JJR than|than|IN 0.01|0.01|CD were|be|VBD considered|consider|VBN significant|significant|JJ .|.|.
The|the|DT genes|gene|NNS were|be|VBD filtered|filter|VBN by|by|IN removing|remove|VBG the|the|DT flag-out|flag-out|JJ genes|gene|NNS in|in|IN each|each|DT experiment|experiment|NN .|.|. The|the|DT gene|gene|NN expression|expression|NN was|be|VBD normalized|normalize|VBN through|through|IN LOWESS|lowess|NN regression|regression|NN for|for|IN 3|3|CD datasets|dataset|NNS obtained|obtain|VBN from|from|IN 3|3|CD biological|biological|JJ replicates|replicate|VBZ .|.|.
The|the|DT genomic|genomic|JJ DNA|dna|NN from|from|IN pure|pure|JJ and|and|CC mixed|mixed|JJ bacterial|bacterial|JJ cultures|culture|NNS was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT Wizard|Wizard|NNP genomic|genomic|JJ DNA|dna|NN isolation|isolation|NN kit|kit|NN -LRB-|-lrb-|-LRB- Promega|Promega|NNP corporation|corporation|NN ,|,|, Madison|Madison|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- as|as|IN per|per|IN manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. The|the|DT concentration|concentration|NN of|of|IN DNA|dna|NN was|be|VBD analyzed|analyze|VBN by|by|IN Nanodrop|Nanodrop|NNP spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Nanodrop|Nanodrop|NNP Technologies|Technologies|NNPS Inc|Inc|NNP ,|,|, Rockland|Rockland|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC quality|quality|NN was|be|VBD determined|determine|VBN by|by|IN analysis|analysis|NN on|on|IN DNA|dna|NN 12000|12000|CD kit|kit|NN -LRB-|-lrb-|-LRB- Caliper|Caliper|NNP Sciences|Sciences|NNPS ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Palo|Palo|NNP Alto|Alto|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT hot-phenol|hot-phenol|NN method|method|NN was|be|VBD used|use|VBN to|to|TO extract|extract|VB total|total|JJ RNA|rna|NN from|from|IN two|two|CD independent|independent|JJ cultures|culture|NNS of|of|IN cells|cell|NNS grown|grow|VBN aerobically|aerobically|RB
The|the|DT hot-phenol|hot-phenol|NN method|method|NN was|be|VBD used|use|VBN to|to|TO extract|extract|VB total|total|JJ RNA|rna|NN from|from|IN two|two|CD independent|independent|JJ cultures|culture|NNS of|of|IN cells|cell|NNS grown|grow|VBN aerobically|aerobically|RB and|and|CC treated|treat|VBN with|with|IN 250|250|CD μM|μm|NN CORM-2|corm-2|NN during|during|IN 15|15|CD min|min|NN .|.|.
The|the|DT hot-phenol|hot-phenol|NN method|method|NN was|be|VBD used|use|VBN to|to|TO extract|extract|VB total|total|JJ RNA|rna|NN from|from|IN two|two|CD independent|independent|JJ cultures|culture|NNS of|of|IN cells|cell|NNS grown|grow|VBN anaerobically|anaerobically|RB
The|the|DT hot-phenol|hot-phenol|NN method|method|NN was|be|VBD used|use|VBN to|to|TO extract|extract|VB total|total|JJ RNA|rna|NN from|from|IN two|two|CD independent|independent|JJ cultures|culture|NNS of|of|IN cells|cell|NNS grown|grow|VBN anaerobically|anaerobically|RB and|and|CC treated|treat|VBN with|with|IN 250|250|CD μM|μm|NN CORM-2|corm-2|NN during|during|IN 15|15|CD min|min|NN .|.|.
The|the|DT hybridization|hybridization|NN intensity|intensity|NN data|datum|NNS signals|signal|NNS were|be|VBD analyzed|analyze|VBN ,|,|, normalized|normalize|VBD ,|,|, and|and|CC corrected|correct|VBN for|for|IN batch|batch|NN effect|effect|NN using|use|VBG Affymetrix|Affymetrix|NNP GeneChip|GeneChip|NNP ®|®|NNP Command|command|NN Console|Console|NNP ®|®|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- AGCC|AGCC|NNP v.|v.|CC 3.0|3.0|CD -RRB-|-rrb-|-RRB- .|.|. Signal|signal|NN average|average|NN ,|,|, noise|noise|NN average|average|NN ,|,|, scaling|scaling|NN factor|factor|NN ,|,|, %|%|NN present|present|JJ ,|,|, and|and|CC %|%|NN absent|absent|JJ were|be|VBD calculated|calculate|VBN for|for|IN each|each|DT probe|probe|NN ,|,|, from|from|IN which|which|WDT the|the|DT signal|signal|NN intensity|intensity|NN of|of|IN >|>|JJR 39|39|CD was|be|VBD calculated|calculate|VBN as|as|IN reliable|reliable|JJ expression|expression|NN .|.|. Using|use|VBG this|this|DT cutoff|cutoff|NN ,|,|, 5531|5531|CD probes|probe|NNS were|be|VBD classified|classify|VBN as|as|IN present|present|JJ out|out|IN of|of|IN total|total|JJ 10208|10208|CD probes|probe|NNS on|on|IN the|the|DT array|array|NN -LRB-|-lrb-|-LRB- full_expressed_data.txt|full_expressed_data.txt|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT image|image|NN analysis|analysis|NN performed|perform|VBN using|use|VBG GenePix|GenePix|NNP Pro|pro|FW 6.0|6.0|CD Software|Software|NNP -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Devices|Devices|NNPS -RRB-|-rrb-|-RRB- ,|,|, normalized|normalize|VBN with|with|IN MIDAS|midas|NN -LRB-|-lrb-|-LRB- LOWESS|lowess|NN method|method|NN -RRB-|-rrb-|-RRB- ,|,|, with|with|IN clustering|clustering|NN analysis|analysis|NN in|in|IN MeV|mev|NN -LRB-|-lrb-|-LRB- CAST|cast|NN -RRB-|-rrb-|-RRB-
The|the|DT image|image|NN analysis|analysis|NN was|be|VBD performed|perform|VBN using|use|VBG GenePix|GenePix|NNP Pro|pro|FW 6.0|6.0|CD Software|Software|NNP -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Devices|Devices|NNPS -RRB-|-rrb-|-RRB- .|.|. Data|datum|NNS were|be|VBD normalized|normalize|VBN with|with|IN MIDAS|midas|NN -LRB-|-lrb-|-LRB- LOWESS|lowess|NN method|method|NN -RRB-|-rrb-|-RRB- ,|,|, with|with|IN clustering|clustering|NN analysis|analysis|NN in|in|IN MeV|mev|NN -LRB-|-lrb-|-LRB- CAST|cast|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT intensity|intensity|NN cell|cell|NN files|file|NNS were|be|VBD then|then|RB imported|import|VBN ,|,|, normalized|normalize|VBN for|for|IN background|background|NN correction|correction|NN -LRB-|-lrb-|-LRB- used|use|VBN RMA|rma|NN for|for|IN normalization|normalization|NN -RRB-|-rrb-|-RRB- and|and|CC data|datum|NNS analysed|analyse|VBN using|use|VBG Gene|Gene|NNP Spring|Spring|NNP 11.5|11.5|CD software|software|NN .|.|.
The|the|DT intensity|intensity|NN cell|cell|NN files|file|NNS were|be|VBD then|then|RB imported|import|VBN ,|,|, normalized|normalize|VBN for|for|IN background|background|NN correction|correction|NN using|use|VBG PLIER|plier|NN and|and|CC data|datum|NNS analysed|analyse|VBN using|use|VBG Gene|Gene|NNP Spring|Spring|NNP 11.5|11.5|CD software|software|NN .|.|.
The|the|DT intensity|intensity|NN of|of|IN each|each|DT spot|spot|NN was|be|VBD measured|measure|VBN with|with|IN ScanArray|ScanArray|NNP Express|Express|NNP using|use|VBG the|the|DT histogram|histogram|NN quantitation|quantitation|NN method|method|NN ;|;|: the|the|DT percentile|percentile|NN ranges|range|VBZ for|for|IN histograms|histogram|NNS were|be|VBD 80|80|CD %|%|NN for|for|IN low|low|JJ signal|signal|NN range|range|NN ,|,|, 95|95|CD %|%|NN for|for|IN high|high|JJ signal|signal|NN range|range|NN ,|,|, 5|5|CD %|%|NN for|for|IN low|low|JJ background|background|NN range|range|NN and|and|CC 20|20|CD %|%|NN for|for|IN high|high|JJ background|background|NN range|range|NN .|.|. The|the|DT median|median|JJ intensity|intensity|NN minus|minus|CC the|the|DT median|median|JJ background|background|NN intensity|intensity|NN was|be|VBD used|use|VBN for|for|IN further|further|JJ calculations|calculation|NNS performed|perform|VBN in|in|IN Microsoft|Microsoft|NNP Excel|Excel|NNP .|.|. The|the|DT background|background|NN measurement|measurement|NN refers|refer|VBZ to|to|TO the|the|DT local|local|JJ spot|spot|NN background|background|NN intensity|intensity|NN .|.|. Prior|prior|RB to|to|TO normalization|normalization|NN ,|,|, all|all|DT spots|spot|NNS with|with|IN a|a|DT Signal-to-Noise|Signal-to-Noise|NNP ratio|ratio|NN -LRB-|-lrb-|-LRB- SNR|snr|NN -RRB-|-rrb-|-RRB- lower|lower|JJR than|than|IN 3|3|CD were|be|VBD removed|remove|VBN .|.|. The|the|DT SNR|snr|NN was|be|VBD calculated|calculate|VBN using|use|VBG the|the|DT following|follow|VBG formula|formula|NN :|:|: -LRB-|-lrb-|-LRB- Median|median|JJ Signal|signal|NN --|--|: Median|median|JJ Background|background|NN -RRB-|-rrb-|-RRB- /|/|: Standard|standard|JJ Deviation|deviation|NN of|of|IN Background|background|NN .|.|. Normalization|normalization|NN between|between|IN each|each|DT array|array|NN was|be|VBD performed|perform|VBN using|use|VBG an|a|DT internal|internal|JJ labeling|labeling|NN control|control|NN -LRB-|-lrb-|-LRB- IC|ic|NN -RRB-|-rrb-|-RRB- consisting|consist|VBG of|of|IN a|a|DT 290|290|CD bp|bp|NN luxA|luxa|NN fragment|fragment|NN .|.|. This|this|DT fragment|fragment|NN was|be|VBD added|add|VBN to|to|TO each|each|DT labeling|labeling|NN reaction|reaction|NN at|at|IN a|a|DT ratio|ratio|NN of|of|IN 0.05|0.05|CD %|%|NN of|of|IN the|the|DT DNA|dna|NN to|to|TO be|be|VB labeled|label|VBN .|.|. The|the|DT intensity|intensity|NN of|of|IN each|each|DT Cy5-sample|cy5-sample|JJ gene|gene|NN spot|spot|NN was|be|VBD corrected|correct|VBN using|use|VBG the|the|DT average|average|JJ intensity|intensity|NN of|of|IN all|all|DT Cy3-lambda|cy3-lambda|NN signals|signal|NNS .|.|. Corrected|correct|VBN intensity|intensity|NN values|value|NNS were|be|VBD averaged|average|VBN over|over|IN triplicate|triplicate|NN spots|spot|NNS to|to|TO give|give|VB a|a|DT single|single|JJ value|value|NN per|per|IN gene|gene|NN .|.|. The|the|DT intensity|intensity|NN of|of|IN the|the|DT genes|gene|NNS for|for|IN which|which|WDT hybridization|hybridization|NN of|of|IN the|the|DT probes|probe|NNS could|could|MD not|not|RB be|be|VB visually|visually|RB detected|detect|VBN in|in|IN image|image|NN analysis|analysis|NN was|be|VBD set|set|VBN to|to|TO zero|zero|CD .|.|. Relative|relative|JJ intensity|intensity|NN values|value|NNS were|be|VBD then|then|RB calculated|calculate|VBN by|by|IN dividing|divide|VBG the|the|DT intensity|intensity|NN of|of|IN a|a|DT gene|gene|NN by|by|IN the|the|DT sum|sum|NN of|of|IN the|the|DT intensity|intensity|NN for|for|IN all|all|DT genes|gene|NNS -LRB-|-lrb-|-LRB- excluding|exclude|VBG controls|control|NNS -RRB-|-rrb-|-RRB- .|.|. This|this|DT ``|``|`` relative|relative|JJ abundance|abundance|NN ''|''|'' represents|represent|VBZ the|the|DT fraction|fraction|NN of|of|IN the|the|DT total|total|JJ intensity|intensity|NN that|that|WDT is|be|VBZ due|due|JJ to|to|TO a|a|DT particular|particular|JJ gene|gene|NN and|and|CC this|this|DT value|value|NN was|be|VBD subsequently|subsequently|RB used|use|VBN in|in|IN statistical|statistical|JJ analyses|analysis|NNS .|.|.
The|the|DT in|in|FW vitro|vitro|FW bacterial|bacterial|JJ samples|sample|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 5000|5000|CD ×|×|CD g|g|NN ,|,|, 10|10|CD min|min|NN ,|,|, 4|4|CD °C|°c|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT pellet|pellet|NN was|be|VBD frozen|freeze|VBN at|at|IN −|−|CD 70|70|CD °C|°c|NN until|until|IN RNA|rna|NN extraction|extraction|NN .|.|. The|the|DT in|in|FW vivo|vivo|FW bacterial|bacterial|JJ samples|sample|NNS were|be|VBD harvested|harvest|VBN with|with|IN two-step|two-step|JJ centrifugation|centrifugation|NN .|.|. We|we|PRP first|first|RB centrifuged|centrifuge|VBD the|the|DT collected|collect|VBN anticoagulated|anticoagulated|JJ blood|blood|NN samples|sample|NNS at|at|IN low|low|JJ speed|speed|NN to|to|TO remove|remove|VB the|the|DT abundant|abundant|JJ red|red|JJ and|and|CC white|white|JJ blood|blood|NN cells|cell|NNS and|and|CC collected|collect|VBN the|the|DT upper|upper|JJ serum|serum|NN layer|layer|NN .|.|. We|we|PRP then|then|RB used|use|VBD high-speed|high-speed|JJ centrifugation|centrifugation|NN to|to|TO precipitate|precipitate|VB the|the|DT bacteria|bacterium|NNS from|from|IN the|the|DT serum|serum|NN .|.|.
The|the|DT in|in|FW vivo|vivo|FW bacterial|bacterial|JJ samples|sample|NNS were|be|VBD harvested|harvest|VBN with|with|IN two-step|two-step|JJ centrifugation|centrifugation|NN .|.|. We|we|PRP first|first|RB centrifuged|centrifuge|VBD the|the|DT collected|collect|VBN anticoagulated|anticoagulated|JJ blood|blood|NN samples|sample|NNS at|at|IN low|low|JJ speed|speed|NN to|to|TO remove|remove|VB the|the|DT abundant|abundant|JJ red|red|JJ and|and|CC white|white|JJ blood|blood|NN cells|cell|NNS and|and|CC collected|collect|VBN the|the|DT upper|upper|JJ serum|serum|NN layer|layer|NN .|.|. We|we|PRP then|then|RB used|use|VBD high-speed|high-speed|JJ centrifugation|centrifugation|NN to|to|TO precipitate|precipitate|VB the|the|DT bacteria|bacterium|NNS from|from|IN the|the|DT serum|serum|NN .|.|.
The|the|DT isolated|isolate|VBN persisters|persister|NNS were|be|VBD incubated|incubate|VBN in|in|IN 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN for|for|IN 1|1|CD h|h|NN -LRB-|-lrb-|-LRB- 200|200|CD rpm|rpm|NN ,|,|, 37oC|37oc|NN -RRB-|-rrb-|-RRB- with|with|IN or|or|CC without|without|IN 5|5|CD µg/mL|µg/ml|NN BF8|bf8|NN .|.|.
The|the|DT laboratory|laboratory|NN strain|strain|NN E.|e.|FW coli|coli|FW K12|k12|NN MG1655|mg1655|NN was|be|VBD grown|grow|VBN for|for|IN 24|24|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN under|under|IN continuous|continuous|JJ shaking|shake|VBG -LRB-|-lrb-|-LRB- 120|120|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, in|in|IN 200|200|CD mL|ml|NN M9|m9|NN medium|medium|NN -LRB-|-lrb-|-LRB- Merck|Merck|NNP Prolabo|Prolabo|NNP -RRB-|-rrb-|-RRB- complemented|complement|VBN with|with|IN 2.5|2.5|CD g/L|g/l|NN of|of|IN anhydrous|anhydrous|JJ glucose|glucose|NN ,|,|, and|and|CC inoculated|inoculate|VBN at|at|IN 108|108|CD CFU/mL|cfu/ml|NN -LRB-|-lrb-|-LRB- corresponding|correspond|VBG to|to|TO an|a|DT optical|optical|JJ density|density|NN at|at|IN 595|595|CD nm|nm|NN -LSB-|-lsb-|-LRB- OD595|od595|CD nm|nm|NN -RSB-|-rsb-|-RRB- of|of|IN 0.12|0.12|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT inoculum|inoculum|NN for|for|IN this|this|DT culture|culture|NN was|be|VBD prepared|prepare|VBN in|in|IN 40|40|CD mL|ml|NN M9|m9|NN broth|broth|NN inoculated|inoculate|VBN with|with|IN approximately|approximately|RB 1.5|1.5|CD x107|x107|CD CFU/mL|cfu/ml|NN -LRB-|-lrb-|-LRB- corresponding|correspond|VBG to|to|TO an|a|DT OD595|od595|NN nm|nm|NN of|of|IN 0.12|0.12|CD -RRB-|-rrb-|-RRB- and|and|CC incubated|incubate|VBN overnight|overnight|JJ under|under|IN the|the|DT same|same|JJ conditions|condition|NNS -LRB-|-lrb-|-LRB- 37|37|CD °C|°c|NN ,|,|, 120|120|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- .|.|. This|this|DT inoculum|inoculum|NN was|be|VBD obtained|obtain|VBN by|by|IN adding|add|VBG 1|1|CD mL|ml|NN of|of|IN stock|stock|NN culture|culture|NN of|of|IN the|the|DT bacterial|bacterial|JJ cells|cell|NNS in|in|IN 5|5|CD mL|ml|NN of|of|IN Luria|Luria|NNP Bertani|Bertani|NNP broth|broth|NN -LRB-|-lrb-|-LRB- Biokar|biokar|JJ Diagnotics|diagnotic|NNS ,|,|, PRS|prs|NN Panreac|panreac|NN -RRB-|-rrb-|-RRB- in|in|IN a|a|DT 15-mL|15-ml|JJ half-opened|half-opened|JJ BD|bd|NN FalconTM|falcontm|NN tube|tube|NN ,|,|, followed|follow|VBN by|by|IN 8|8|CD h|h|NN of|of|IN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC 120|120|CD rpm|rpm|NN .|.|.
The|the|DT libraries|library|NNS were|be|VBD generated|generate|VBN by|by|IN Vertis|Vertis|NNP Biotechnologie|Biotechnologie|NNP AG|AG|NNP -LRB-|-lrb-|-LRB- Munich|Munich|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT samples|sample|NNS were|be|VBD poly|poly|NN -LRB-|-lrb-|-LRB- A|a|NN -RRB-|-rrb-|-RRB- -|-|: tailed|tail|VBN by|by|IN using|use|VBG poly|poly|NN -LRB-|-lrb-|-LRB- A|a|NN -RRB-|-rrb-|-RRB- polymerase|polymerase|NN .|.|. The|the|DT 5|5|CD '|'|'' -|-|: PPP|ppp|NN were|be|VBD removed|remove|VBN using|use|VBG tobacco|tobacco|NN acid|acid|NN pyrophosphatase|pyrophosphatase|NN -LRB-|-lrb-|-LRB- TAP|tap|NN -RRB-|-rrb-|-RRB- followed|follow|VBN by|by|IN the|the|DT ligation|ligation|NN of|of|IN the|the|DT RNA|rna|NN adapter|adapter|NN to|to|TO the|the|DT 5|5|CD '|'|'' -|-|: monophosphate|monophosphate|NN of|of|IN the|the|DT RNA|rna|NN .|.|. First-strand|first-strand|JJ cDNA|cdna|NN synthesis|synthesis|NN was|be|VBD performed|perform|VBN with|with|IN an|a|DT oligo|oligo|JJ -LRB-|-lrb-|-LRB- dT|dt|NN -RRB-|-rrb-|-RRB- -|-|: adapter|adapter|NN primer|primer|NN and|and|CC the|the|DT M-MLV|m-mlv|NN reverse|reverse|JJ transcriptase|transcriptase|NN .|.|. The|the|DT resulting|result|VBG cDNA|cdna|NN was|be|VBD PCR-amplified|pcr-amplified|JJ to|to|TO reach|reach|VB a|a|DT concentration|concentration|NN of|of|IN 20-30|20-30|CD ng/μl|ng/μl|NN using|use|VBG a|a|DT high|high|JJ fidelity|fidelity|NN DNA|dna|NN polymerase|polymerase|NN .|.|. The|the|DT cDNA|cdna|NN was|be|VBD purified|purify|VBN using|use|VBG the|the|DT Agencourt|Agencourt|NNP AMPure|AMPure|NNP XP|xp|NN kit|kit|NN -LRB-|-lrb-|-LRB- Beckman|Beckman|NNP Coulter|Coulter|NNP Genomics|Genomics|NNPS -RRB-|-rrb-|-RRB- and|and|CC was|be|VBD analyzed|analyze|VBN by|by|IN capillary|capillary|JJ electrophoresis|electrophoresis|NN .|.|. The|the|DT primers|primer|NNS used|use|VBN for|for|IN PCR|pcr|NN amplification|amplification|NN were|be|VBD designed|design|VBN for|for|IN TruSeq|TruSeq|NNP sequencing|sequencing|NN according|accord|VBG to|to|TO the|the|DT instructions|instruction|NNS of|of|IN Illumina|Illumina|NNP
The|The|NNP log10|log10|NN mRNA|mrna|NN concentration|concentration|NN -LRB-|-lrb-|-LRB- pM|pm|NN -RRB-|-rrb-|-RRB- data|datum|NNS are|be|VBP provided|provide|VBN as|as|IN a|a|DT supplementary|supplementary|JJ file|file|NN on|on|IN the|the|DT SERIES|series|NN record|record|NN .|.|.
The|the|DT log2-ratio|log2-ratio|NN is|be|VBZ computed|compute|VBN and|and|CC scaled|scale|VBN to|to|TO center|center|VB the|the|DT ratio|ratio|NN data|datum|NNS around|around|IN zero|zero|CD .|.|. Scaling|scaling|NN is|be|VBZ performed|perform|VBN by|by|IN subtracting|subtract|VBG the|the|DT bi-weight|bi-weight|JJ mean|mean|NN for|for|IN the|the|DT log2-ratio|log2-ratio|JJ values|value|NNS for|for|IN all|all|DT features|feature|NNS on|on|IN the|the|DT array|array|NN from|from|IN each|each|DT log2-ratio|log2-ratio|JJ value|value|NN .|.|.
The|the|DT `|`|`` LogRatio|LogRatio|NNP '|'|'' value|value|NN was|be|VBD used|use|VBN in|in|IN subsequent|subsequent|JJ analyses|analysis|NNS .|.|. All|all|DT values|value|NNS for|for|IN the|the|DT same|same|JJ ORF|orf|NN were|be|VBD averaged|average|VBN as|as|IN were|be|VBD the|the|DT values|value|NNS from|from|IN the|the|DT two|two|CD biological|biological|JJ replicates|replicate|VBZ performed|perform|VBN for|for|IN each|each|DT comparison|comparison|NN .|.|.
The|the|DT low-quality|low-quality|NN of|of|IN raw|raw|JJ reads|read|VBZ were|be|VBD trimmed|trim|VBN using|use|VBG Trimmomatic|trimmomatic|JJ -LRB-|-lrb-|-LRB- v0|v0|JJ .30|.30|CD -RRB-|-rrb-|-RRB- with|with|IN default|default|NN settings|setting|NNS .|.|.
The|the|DT lysates|lysate|NNS were|be|VBD applied|apply|VBN to|to|TO gDNA|gdna|NN removal|removal|NN columns|column|NNS and|and|CC rRNA|rrna|NN was|be|VBD removed|remove|VBN from|from|IN total|total|JJ RNA|rna|NN using|use|VBG a|a|DT Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN removal|removal|NN kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacture|manufacture|NN 's|'s|POS instruction|instruction|NN for|for|IN Gram-positive|gram-positive|JJ bacteria|bacterium|NNS .|.|. The|the|DT sequencing|sequencing|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN from|from|IN the|the|DT enriched|enriched|JJ mRNA|mrna|NN using|use|VBG the|the|DT NEBNext|nebnext|NN Ultra|ultra|NN RNA|rna|NN library|library|NN prep|prep|JJ kit|kit|NN -LRB-|-lrb-|-LRB- NEB|neb|NN ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC independently|independently|RB indexed|index|VBN using|use|VBG NEBNext|nebnext|NN multi-plex|multi-plex|JJ oligos|oligo|NNS for|for|IN Illumina|Illumina|NNP -LRB-|-lrb-|-LRB- NEB|NEB|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT libraries|library|NNS were|be|VBD pooled|pool|VBN at|at|IN equimolar|equimolar|JJ ratios|ratio|NNS before|before|IN they|they|PRP were|be|VBD sequenced|sequence|VBN using|use|VBG MiSeq|MiSeq|NNP Reagent|Reagent|NNP Kit|kit|NN v3|v3|NN 600|600|CD cycles|cycle|NNS -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT MACS|macs|NN 2.1.0|2.1.0|CD software|software|NN was|be|VBD used|use|VBN to|to|TO call|call|VB peaks|peak|NNS .|.|.
The|the|DT MACS2|macs2|NN software|software|NN was|be|VBD used|use|VBN to|to|TO call|call|VB peaks|peak|NNS .|.|.
The|the|DT mean|mean|JJ signal|signal|NN intensity|intensity|NN values|value|NNS of|of|IN the|the|DT duplicate|duplicate|VB spots|spot|NNS were|be|VBD averaged|average|VBN and|and|CC then|then|RB normalized|normalize|VBN by|by|IN the|the|DT global|global|JJ normalization|normalization|NN method|method|NN .|.|. The|the|DT genes|gene|NNS showing|show|VBG the|the|DT p-values|p-value|NNS lower|lower|JJR than|than|IN 0.05|0.05|CD were|be|VBD considered|consider|VBN to|to|TO be|be|VB significant|significant|JJ .|.|.
The|the|DT measured|measure|VBN lifetime|lifetime|NN of|of|IN mRNA|mrna|NN is|be|VBZ available|available|JJ as|as|IN a|a|DT supplementary|supplementary|JJ file|file|NN -LRB-|-lrb-|-LRB- real_rna_life.txt|real_rna_life.txt|NN -RRB-|-rrb-|-RRB- on|on|IN the|the|DT Series|Series|NNP record|record|NN .|.|.
The|the|DT medium|medium|NN for|for|IN batch|batch|NN culture|culture|NN was|be|VBD consisted|consist|VBN of|of|IN 11.3|11.3|CD g|g|NN M9|m9|NN medium|medium|NN ,|,|, 0.2|0.2|CD g|g|NN MgSO4|mgso4|NN •|•|SYM 7H2O|7H2O|NNP ,|,|, 0.1|0.1|CD g|g|NN CaCl2|cacl2|NN ,|,|, 1|1|CD mg|mg|NN thiamine|thiamine|NN ,|,|, 10|10|CD g|g|NN NaHCO3|nahco3|NN and|and|CC 9|9|CD g|g|NN glucose|glucose|NN ,|,|, 50|50|CD mg|mg|NN ampicillin|ampicillin|NN and|and|CC 0.1|0.1|CD mmole|mmole|NN IPTG|iptg|NN per|per|IN liter|liter|NN .|.|.
The|the|DT medium|medium|NN for|for|IN continuous|continuous|JJ culture|culture|NN contained|contain|VBD 20|20|CD g|g|NN LB|lb|NN ,|,|, 9|9|CD g|g|NN glucose|glucose|NN ,|,|, 10|10|CD g|g|NN NaHCO3|nahco3|NN ,|,|, 50|50|CD mg|mg|NN ampicillin|ampicillin|NN per|per|IN liter|liter|NN and|and|CC isopropyl|isopropyl|NN -|-|: -|-|: D-thiogalactopyranoside|d-thiogalactopyranoside|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN -RRB-|-rrb-|-RRB- was|be|VBD supplemented|supplement|VBN to|to|TO be|be|VB 0.1|0.1|CD mM|mm|NN .|.|. The|the|DT initial|initial|JJ pH|ph|NN of|of|IN the|the|DT medium|medium|NN was|be|VBD set|set|VBN to|to|TO be|be|VB pH|ph|NN 7.3|7.3|CD by|by|IN adding|add|VBG 1|1|CD N|n|NN HCl|hcl|NN solution|solution|NN .|.|. The|the|DT inoculation|inoculation|NN culture|culture|NN was|be|VBD transferred|transfer|VBN into|into|IN a|a|DT 250|250|CD mL-fermentor|ml-fermentor|NN containing|contain|VBG 100|100|CD mL|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- Small|small|JJ scale|scale|NN multi-chemostat|multi-chemostat|JJ fermentor|fermentor|NN ;|;|: Biotron|Biotron|NNP Inc.|Inc.|NNP ,|,|, Bucheon|Bucheon|NNP ,|,|, Korea|Korea|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT culture|culture|NN was|be|VBD performed|perform|VBN at|at|IN 37|37|CD C|c|NN ,|,|, 350|350|CD rpm|rpm|NN with|with|IN flushing|flushing|NN CO2|co2|NN gas|gas|NN at|at|IN 20|20|CD mL/min|ml/min|NN .|.|. After|after|IN 8|8|CD h|h|NN inoculation|inoculation|NN ,|,|, the|the|DT feeding|feeding|NN and|and|CC outlet|outlet|NN pumps|pump|NNS were|be|VBD started|start|VBN at|at|IN flow|flow|NN rate|rate|NN of|of|IN 0.166|0.166|CD mL/h|ml/h|NN -LRB-|-lrb-|-LRB- dilution|dilution|NN rate|rate|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT medium|medium|NN for|for|IN continuous|continuous|JJ culture|culture|NN contained|contain|VBD 20|20|CD g|g|NN LB|lb|NN ,|,|, 9|9|CD g|g|NN glucose|glucose|NN ,|,|, 10|10|CD g|g|NN NaHCO3|nahco3|NN ,|,|, 50|50|CD mg|mg|NN ampicillin|ampicillin|NN per|per|IN liter|liter|NN and|and|CC isopropyl|isopropyl|NN -|-|: -|-|: D-thiogalactopyranoside|d-thiogalactopyranoside|NN -LRB-|-lrb-|-LRB- IPTG|iptg|NN -RRB-|-rrb-|-RRB- was|be|VBD supplemented|supplement|VBN to|to|TO be|be|VB 0.1|0.1|CD mM|mm|NN .|.|. The|the|DT initial|initial|JJ pH|ph|NN of|of|IN the|the|DT medium|medium|NN was|be|VBD set|set|VBN to|to|TO be|be|VB pH|ph|NN 7.3|7.3|CD by|by|IN adding|add|VBG 1|1|CD N|n|NN HCl|hcl|NN solution|solution|NN .|.|. The|the|DT inoculation|inoculation|NN culture|culture|NN was|be|VBD transferred|transfer|VBN into|into|IN a|a|DT 250|250|CD mL-fermentor|ml-fermentor|NN containing|contain|VBG 100|100|CD mL|ml|NN medium|medium|NN -LRB-|-lrb-|-LRB- Small|small|JJ scale|scale|NN multi-chemostat|multi-chemostat|JJ fermentor|fermentor|NN ;|;|: Biotron|Biotron|NNP Inc.|Inc.|NNP ,|,|, Bucheon|Bucheon|NNP ,|,|, Korea|Korea|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT culture|culture|NN was|be|VBD performed|perform|VBN at|at|IN 37|37|CD C|c|NN ,|,|, 350|350|CD rpm|rpm|NN with|with|IN flushing|flushing|NN CO2|co2|NN gas|gas|NN at|at|IN 20|20|CD mL/min|ml/min|NN .|.|. After|after|IN 8|8|CD h|h|NN inoculation|inoculation|NN ,|,|, the|the|DT feeding|feeding|NN and|and|CC outlet|outlet|NN pumps|pump|NNS were|be|VBD started|start|VBN at|at|IN flow|flow|NN rate|rate|NN of|of|IN 0.166|0.166|CD mL/h|ml/h|NN -LRB-|-lrb-|-LRB- dilution|dilution|NN rate|rate|NN =|=|JJ 0.1|0.1|CD h-1|h-1|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT medium|medium|NN for|for|IN continuous|continuous|JJ culture|culture|NN contained|contain|VBD 3|3|CD g|g|NN glucose|glucose|NN medium|medium|NN consisted|consist|VBD with|with|IN 0.8|0.8|CD g|g|NN NH4Cl|nh4cl|NN ,|,|, 0.5|0.5|CD g|g|NN NaCl|nacl|NN ,|,|, 7.5|7.5|CD g|g|NN Na2HPO4|na2hpo4|NN •|•|SYM 2H2O|2h2o|NN ,|,|, 3|3|CD g|g|NN KH2PO4|kh2po4|NN with|with|IN separately|separately|RB added|add|VBN trace|trace|NN element|element|NN of|of|IN 0.2|0.2|CD g|g|NN MgSO4|mgso4|NN •|•|SYM 7H2O|7H2O|NNP ,|,|, 0.1|0.1|CD g|g|NN CaCl2|cacl2|NN ,|,|, 1|1|CD mg|mg|NN thiamine|thiamine|NN per|per|IN liter|liter|NN and|and|CC the|the|DT concentraiton|concentraiton|NN of|of|IN added|add|VBN succinate|succinate|JJ gradually|gradually|RB was|be|VBD raised|raise|VBN from|from|IN 30|30|CD g/L|g/l|NN to|to|TO 160|160|CD g/L|g/l|NN during|during|IN 9|9|CD months|month|NNS .|.|. The|the|DT initial|initial|JJ pH|ph|NN of|of|IN the|the|DT medium|medium|NN was|be|VBD set|set|VBN to|to|TO be|be|VB pH|ph|NN 8|8|CD .|.|. The|the|DT fermentor|fermentor|NN was|be|VBD maintained|maintain|VBN at|at|IN 37|37|CD ℃|℃|CD ,|,|, 350|350|CD rpm|rpm|NN with|with|IN air|air|NN gas|gas|NN flushing|flushing|NN and|and|CC the|the|DT feeding|feeding|NN and|and|CC outlet|outlet|NN pumps|pump|NNS were|be|VBD maintained|maintain|VBN at|at|IN flow|flow|NN rate|rate|NN of|of|IN 0.1|0.1|CD h-1|h-1|NN .|.|.
The|the|DT medium|medium|NN for|for|IN continuous|continuous|JJ culture|culture|NN contained|contain|VBD 3|3|CD g|g|NN glucose|glucose|NN medium|medium|NN consisted|consist|VBD with|with|IN 0.8|0.8|CD g|g|NN NH4Cl|nh4cl|NN ,|,|, 0.5|0.5|CD g|g|NN NaCl|nacl|NN ,|,|, 7.5|7.5|CD g|g|NN Na2HPO4|na2hpo4|NN •|•|SYM 2H2O|2h2o|NN ,|,|, 3|3|CD g|g|NN KH2PO4|kh2po4|NN with|with|IN separately|separately|RB added|add|VBN trace|trace|NN element|element|NN of|of|IN 0.2|0.2|CD g|g|NN MgSO4|mgso4|NN •|•|SYM 7H2O|7H2O|NNP ,|,|, 0.1|0.1|CD g|g|NN CaCl2|cacl2|NN ,|,|, 1|1|CD mg|mg|NN thiamine|thiamine|NN per|per|IN liter|liter|NN and|and|CC the|the|DT concentraiton|concentraiton|NN of|of|IN added|add|VBN succinate|succinate|JJ gradually|gradually|RB was|be|VBD raised|raise|VBN from|from|IN 30|30|CD g/L|g/l|NN to|to|TO 160|160|CD g/L|g/l|NN during|during|IN 9|9|CD months|month|NNS .|.|. The|the|DT initial|initial|JJ pH|ph|NN of|of|IN the|the|DT medium|medium|NN was|be|VBD set|set|VBN to|to|TO be|be|VB pH|ph|NN 8|8|CD .|.|. The|the|DT fermentor|fermentor|NN was|be|VBD maintained|maintain|VBN at|at|IN 37|37|CD ℃|℃|CD ,|,|, 350|350|CD rpm|rpm|NN with|with|IN air|air|NN gas|gas|NN flushing|flushing|NN and|and|CC the|the|DT feeding|feeding|NN and|and|CC outlet|outlet|NN pumps|pump|NNS were|be|VBD maintained|maintain|VBN at|at|IN flow|flow|NN rate|rate|NN of|of|IN 0.1|0.1|CD h-1|h-1|NN .|.|.
The|the|DT medium|medium|NN for|for|IN continuous|continuous|JJ culture|culture|NN contained|contain|VBD 3|3|CD g|g|NN glucose|glucose|NN medium|medium|NN consisted|consist|VBD with|with|IN 0.8|0.8|CD g|g|NN NH4Cl|nh4cl|NN ,|,|, 0.5|0.5|CD g|g|NN NaCl|nacl|NN ,|,|, 7.5|7.5|CD g|g|NN Na2HPO4|na2hpo4|NN •|•|SYM 2H2O|2h2o|NN ,|,|, 3|3|CD g|g|NN KH2PO4|kh2po4|NN with|with|IN separately|separately|RB added|add|VBN trace|trace|NN element|element|NN of|of|IN 0.2|0.2|CD g|g|NN MgSO4|mgso4|NN •|•|SYM 7H2O|7H2O|NNP ,|,|, 0.1|0.1|CD g|g|NN CaCl2|cacl2|NN ,|,|, 1|1|CD mg|mg|NN thiamine|thiamine|NN per|per|IN liter|liter|NN .|.|. The|the|DT fermentor|fermentor|NN was|be|VBD maintained|maintain|VBN at|at|IN 37|37|CD ℃|℃|CD ,|,|, 350|350|CD rpm|rpm|NN with|with|IN air|air|NN gas|gas|NN flushing|flushing|NN and|and|CC the|the|DT feeding|feeding|NN and|and|CC outlet|outlet|NN pumps|pump|NNS were|be|VBD maintained|maintain|VBN at|at|IN flow|flow|NN rate|rate|NN of|of|IN 0.1|0.1|CD h-1|h-1|NN .|.|.
The|the|DT medium|medium|NN for|for|IN continuous|continuous|JJ culture|culture|NN contained|contain|VBD 3|3|CD g|g|NN glucose|glucose|NN medium|medium|NN consisted|consist|VBD with|with|IN 0.8|0.8|CD g|g|NN NH4Cl|nh4cl|NN ,|,|, 0.5|0.5|CD g|g|NN NaCl|nacl|NN ,|,|, 7.5|7.5|CD g|g|NN Na2HPO4|na2hpo4|NN •|•|SYM 2H2O|2h2o|NN ,|,|, 3|3|CD g|g|NN KH2PO4|kh2po4|NN with|with|IN separately|separately|RB added|add|VBN trace|trace|NN element|element|NN of|of|IN 0.2|0.2|CD g|g|NN MgSO4|mgso4|NN •|•|SYM 7H2O|7H2O|NNP ,|,|, 0.1|0.1|CD g|g|NN CaCl2|cacl2|NN ,|,|, 1|1|CD mg|mg|NN thiamine|thiamine|NN per|per|IN liter|liter|NN .|.|. The|the|DT fermentor|fermentor|NN was|be|VBD maintained|maintain|VBN at|at|IN 37|37|CD ℃|℃|CD ,|,|, 350|350|CD rpm|rpm|NN with|with|IN air|air|NN gas|gas|NN flushing|flushing|NN and|and|CC the|the|DT feeding|feeding|NN and|and|CC outlet|outlet|NN pumps|pump|NNS were|be|VBD maintained|maintain|VBN at|at|IN flow|flow|NN rate|rate|NN of|of|IN 0.1|0.1|CD h-1|h-1|NN .|.|.
The|the|DT microarray|microarray|NN data|datum|NNS files|file|NNS were|be|VBD processed|process|VBN using|use|VBG statistical|statistical|JJ software|software|NN R|r|NN version|version|NN 3.0.1|3.0.1|CD and|and|CC Bioconductor|Bioconductor|NNP packages|package|NNS .|.|. The|the|DT Single-Channel|Single-Channel|NNP Array|Array|NNP Normalization|normalization|NN -LRB-|-lrb-|-LRB- SCAN.UPC|scan.upc|NN -RRB-|-rrb-|-RRB- package|package|NN was|be|VBD used|use|VBN to|to|TO normalize|normalize|VB the|the|DT microarray|microarray|NN data|datum|NNS .|.|. Batch|batch|NN effects|effect|NNS were|be|VBD adjusted|adjust|VBN by|by|IN using|use|VBG the|the|DT Empirical|Empirical|NNP Bayes|Bayes|NNP method|method|NN implemented|implement|VBN in|in|IN COMBAT|COMBAT|NNP software|software|NN .|.|.
The|the|DT microarray|microarray|NN data|datum|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG R|r|NN -LRB-|-lrb-|-LRB- v.|v.|CC 2.2.1|2.2.1|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT MAANOVA|MAANOVA|NNP -LRB-|-lrb-|-LRB- v.|v.|CC 0.98.8|0.98.8|CD -RRB-|-rrb-|-RRB- package|package|NN .|.|. Raw|raw|NN intensity|intensity|NN values|value|NNS from|from|IN replicate|replicate|VBP probes|probe|NNS were|be|VBD averaged|average|VBN and|and|CC log2|log2|NN transformed|transform|VBN after|after|IN normalization|normalization|NN with|with|IN the|the|DT pin-tip|pin-tip|JJ LOWESS|lowess|NN method|method|NN .|.|. The|the|DT normalized|normalize|VBN intensity|intensity|NN values|value|NNS were|be|VBD fitted|fit|VBN to|to|TO a|a|DT mixed|mixed|JJ model|model|NN ANOVA|ANOVA|NNP considering|consider|VBG array|array|NN and|and|CC biological|biological|JJ replicates|replicate|VBZ as|as|IN random|random|JJ factors|factor|NNS and|and|CC dye|dye|VB ,|,|, strain|strain|NN and|and|CC growth|growth|NN phase|phase|NN as|as|IN fixed|fixed|JJ factors|factor|NNS .|.|. The|the|DT linear|linear|JJ model|model|NN tested|test|VBN was|be|VBD Y|y|NN -LRB-|-lrb-|-LRB- intensity|intensity|NN -RRB-|-rrb-|-RRB- =|=|JJ array|array|NN +|+|CC dye|dye|VB +|+|CC strain|strain|NN -LRB-|-lrb-|-LRB- wild|wild|JJ type|type|NN or|or|CC mutant|mutant|NN -RRB-|-rrb-|-RRB- +|+|CC growth|growth|NN phase|phase|NN -LRB-|-lrb-|-LRB- exponential|exponential|JJ or|or|CC stationary|stationary|JJ -RRB-|-rrb-|-RRB- +|+|CC strain|strain|NN *|*|SYM growth|growth|NN phase|phase|NN +|+|CC sample|sample|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP -RRB-|-rrb-|-RRB- +|+|CC error|error|NN .|.|. Significant|significant|JJ differences|difference|NNS in|in|IN expression|expression|NN due|due|JJ to|to|TO strain|strain|NN ,|,|, growth|growth|NN phase|phase|NN and|and|CC strain|strain|NN *|*|SYM growth|growth|NN phase|phase|NN were|be|VBD determined|determine|VBN using|use|VBG the|the|DT Fs|f|NNS test|test|NN in|in|IN MAANOVA|MAANOVA|NNP which|which|WDT uses|use|VBZ a|a|DT shrinkage|shrinkage|NN estimator|estimator|NN for|for|IN gene-specific|gene-specific|JJ variance|variance|NN components|component|NNS that|that|WDT makes|make|VBZ no|no|DT assumption|assumption|NN about|about|IN the|the|DT variances|variance|NNS across|across|IN genes|gene|NNS with|with|IN 500|500|CD random|random|JJ permutations|permutation|NNS to|to|TO estimate|estimate|VB the|the|DT p-values|p-value|NNS .|.|. The|the|DT q-value|q-value|JJ package|package|NN in|in|IN R|r|NN was|be|VBD used|use|VBN for|for|IN determining|determine|VBG the|the|DT false|false|JJ discovery|discovery|NN rate|rate|NN -LRB-|-lrb-|-LRB- FDR|FDR|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT microarray|microarray|NN data|datum|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG R|r|NN -LRB-|-lrb-|-LRB- v.|v.|CC 2.2.1|2.2.1|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT MAANOVA|MAANOVA|NNP -LRB-|-lrb-|-LRB- v.|v.|CC 0.98.8|0.98.8|CD -RRB-|-rrb-|-RRB- package|package|NN .|.|. Raw|raw|NN intensity|intensity|NN values|value|NNS from|from|IN replicate|replicate|VBP probes|probe|NNS were|be|VBD averaged|average|VBN and|and|CC log2|log2|NN transformed|transform|VBN after|after|IN normalization|normalization|NN with|with|IN the|the|DT pin-tip|pin-tip|JJ LOWESS|lowess|NN method|method|NN .|.|. The|the|DT normalized|normalize|VBN intensity|intensity|NN values|value|NNS were|be|VBD fitted|fit|VBN to|to|TO a|a|DT mixed|mixed|JJ model|model|NN ANOVA|ANOVA|NNP considering|consider|VBG array|array|NN and|and|CC biological|biological|JJ replicates|replicate|VBZ as|as|IN random|random|JJ factors|factor|NNS and|and|CC dye|dye|VB ,|,|, strain|strain|NN as|as|IN fixed|fixed|JJ factors|factor|NNS .|.|. The|the|DT linear|linear|JJ model|model|NN tested|test|VBN was|be|VBD Y|y|NN -LRB-|-lrb-|-LRB- intensity|intensity|NN -RRB-|-rrb-|-RRB- =|=|JJ array|array|NN +|+|CC dye|dye|VB +|+|CC strain|strain|NN -LRB-|-lrb-|-LRB- clinical|clinical|JJ or|or|CC bovine-biased|bovine-biased|JJ -RRB-|-rrb-|-RRB- +|+|CC sample|sample|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP -RRB-|-rrb-|-RRB- +|+|CC error|error|NN .|.|. Significant|significant|JJ differences|difference|NNS in|in|IN expression|expression|NN due|due|JJ to|to|TO strain|strain|NN were|be|VBD determined|determine|VBN using|use|VBG the|the|DT Fs|f|NNS test|test|NN in|in|IN MAANOVA|MAANOVA|NNP which|which|WDT uses|use|VBZ a|a|DT shrinkage|shrinkage|NN estimator|estimator|NN for|for|IN gene-specific|gene-specific|JJ variance|variance|NN components|component|NNS that|that|WDT makes|make|VBZ no|no|DT assumption|assumption|NN about|about|IN the|the|DT variances|variance|NNS across|across|IN genes|gene|NNS with|with|IN 500|500|CD random|random|JJ permutations|permutation|NNS to|to|TO estimate|estimate|VB the|the|DT p-values|p-value|NNS .|.|. The|the|DT q-value|q-value|JJ package|package|NN in|in|IN R|r|NN was|be|VBD used|use|VBN for|for|IN determining|determine|VBG the|the|DT false|false|JJ discovery|discovery|NN rate|rate|NN -LRB-|-lrb-|-LRB- FDR|FDR|NNP -RRB-|-rrb-|-RRB- .|.|. SAM|SAM|NNP provided|provide|VBN by|by|IN TMEV|tmev|NN was|be|VBD also|also|RB used|use|VBN for|for|IN data|data|NN analysis|analysis|NN .|.|.
The|the|DT microarray|microarray|NN data|datum|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG R|r|NN -LRB-|-lrb-|-LRB- v.|v.|CC 2.2.1|2.2.1|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT MAANOVA|MAANOVA|NNP -LRB-|-lrb-|-LRB- v.|v.|CC 0.98.8|0.98.8|CD -RRB-|-rrb-|-RRB- package|package|NN .|.|. Raw|raw|NN intensity|intensity|NN values|value|NNS from|from|IN replicate|replicate|VBP probes|probe|NNS were|be|VBD averaged|average|VBN and|and|CC log2|log2|NN transformed|transform|VBN after|after|IN normalization|normalization|NN with|with|IN the|the|DT pin-tip|pin-tip|JJ LOWESS|lowess|NN method|method|NN .|.|. The|the|DT normalized|normalize|VBN intensity|intensity|NN values|value|NNS were|be|VBD fitted|fit|VBN to|to|TO a|a|DT mixed|mixed|JJ model|model|NN ANOVA|ANOVA|NNP considering|consider|VBG array|array|NN and|and|CC biological|biological|JJ replicates|replicate|VBZ as|as|IN random|random|JJ factors|factor|NNS and|and|CC dye|dye|VB ,|,|, strain|strain|NN as|as|IN fixed|fixed|JJ factor|factor|NN .|.|. The|the|DT linear|linear|JJ model|model|NN tested|test|VBN was|be|VBD Y|y|NN -LRB-|-lrb-|-LRB- intensity|intensity|NN -RRB-|-rrb-|-RRB- =|=|JJ array|array|NN +|+|CC dye|dye|VB +|+|CC strain|strain|NN -LRB-|-lrb-|-LRB- clinical|clinical|JJ or|or|CC bovine-biased|bovine-biased|JJ -RRB-|-rrb-|-RRB- +|+|CC sample|sample|NN -LRB-|-lrb-|-LRB- biological|biological|JJ replicate|replicate|VBP -RRB-|-rrb-|-RRB- +|+|CC error|error|NN .|.|. Significant|significant|JJ differences|difference|NNS in|in|IN expression|expression|NN due|due|JJ to|to|TO strain|strain|NN were|be|VBD determined|determine|VBN using|use|VBG the|the|DT Fs|f|NNS test|test|NN in|in|IN MAANOVA|MAANOVA|NNP which|which|WDT uses|use|VBZ a|a|DT shrinkage|shrinkage|NN estimator|estimator|NN for|for|IN gene-specific|gene-specific|JJ variance|variance|NN components|component|NNS that|that|WDT makes|make|VBZ no|no|DT assumption|assumption|NN about|about|IN the|the|DT variances|variance|NNS across|across|IN genes|gene|NNS with|with|IN 500|500|CD random|random|JJ permutations|permutation|NNS to|to|TO estimate|estimate|VB the|the|DT p-values|p-value|NNS .|.|. The|the|DT q-value|q-value|JJ package|package|NN in|in|IN R|r|NN was|be|VBD used|use|VBN for|for|IN determining|determine|VBG the|the|DT false|false|JJ discovery|discovery|NN rate|rate|NN -LRB-|-lrb-|-LRB- FDR|FDR|NNP -RRB-|-rrb-|-RRB- .|.|. SAM|SAM|NNP provided|provide|VBN by|by|IN TMEV|tmev|NN was|be|VBD also|also|RB used|use|VBN for|for|IN data|data|NN analysis|analysis|NN .|.|.
The|the|DT microarray|microarray|NN experiment|experiment|NN was|be|VBD performed|perform|VBN with|with|IN two|two|CD serotypes|serotype|NNS of|of|IN wild|wild|JJ type|type|NN E.|e.|FW coli|coli|FW and|and|CC their|they|PRP$ adhE|adhE|NNP mutants|mutant|NNS :|:|: -LRB-|-lrb-|-LRB- 1|1|LS -RRB-|-rrb-|-RRB- K-12|k-12|NN strain|strain|NN ,|,|, wild|wild|JJ type|type|NN ;|;|: -LRB-|-lrb-|-LRB- 2|2|LS -RRB-|-rrb-|-RRB- B|b|NN strain|strain|NN ,|,|, wild|wild|JJ type|type|NN ;|;|: -LRB-|-lrb-|-LRB- 3|3|LS -RRB-|-rrb-|-RRB- BW25113|bw25113|NN ,|,|, adhE|adhe|NN mutants|mutant|NNS ;|;|: -LRB-|-lrb-|-LRB- 4|4|LS -RRB-|-rrb-|-RRB- BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- ,|,|, adhE|adhe|NN mutants|mutant|NNS .|.|.
The|the|DT MiSeq|MiSeq|NNP Reporter|reporter|NN MiSeq|miseq|NN Reporter|reporter|NN 2.4.60.8|2.4.60.8|CD was|be|VBD used|use|VBN for|for|IN basecalling|basecalling|NN and|and|CC demultiplexing|demultiplex|VBG
The|the|DT normalized|normalize|VBN data|datum|NNS can|can|MD be|be|VB found|find|VBN on|on|IN the|the|DT series|series|NN record|record|NN in|in|IN the|the|DT file|file|NN \|\|SYM
The|the|DT number|number|NN of|of|IN R1|r1|NN reads|read|VBZ mapping|map|VBG to|to|TO each|each|DT gene|gene|NN were|be|VBD counted|count|VBN using|use|VBG HTSeq|htseq|NN 0.6.0|0.6.0|CD
The|the|DT number|number|NN of|of|IN reads|read|VBZ at|at|IN each|each|DT position|position|NN in|in|IN the|the|DT genome|genome|NN was|be|VBD counted|count|VBN using|use|VBG in-house|in-house|JJ Python|Python|NNP scripts|script|NNS .|.|.
The|the|DT number|number|NN of|of|IN reads|read|VBZ mapping|map|VBG to|to|TO each|each|DT gene|gene|NN was|be|VBD counted|count|VBN and|and|CC normalized|normalize|VBN using|use|VBG EdgeR|edger|NN .|.|.
The|the|DT number|number|NN of|of|IN reads|read|VBZ overlapping|overlap|VBG each|each|DT gene|gene|NN was|be|VBD recorded|record|VBN and|and|CC normalized|normalize|VBN based|base|VBN on|on|IN reads|read|VBZ per|per|IN kilobase|kilobase|NN per|per|IN million|million|CD -LRB-|-lrb-|-LRB- RPKM|rpkm|NN -RRB-|-rrb-|-RRB- uniquely|uniquely|RB mapped|map|VBD reads|read|VBZ .|.|.
The|the|DT number|number|NN of|of|IN sequence|sequence|NN reads|read|VBZ that|that|IN aligned|align|VBN to|to|TO features|feature|NNS in|in|IN annotation|annotation|NN file|file|NN -LRB-|-lrb-|-LRB- Escherichia|escherichia|FW _|_|FW coli|coli|FW _|_|SYM str|str|FW _|_|FW k|k|NN _|_|SYM 12|12|CD _|_|SYM substr|substr|FW _|_|FW mg1655.GCA|mg1655.gca|NN _|_|SYM 000005845.2.24|000005845.2.24|CD .|.|. gtf|gtf|NN from|from|IN http://bacteria.ensembl.org|http://bacteria.ensembl.org|NN -RRB-|-rrb-|-RRB- were|be|VBD tabulated|tabulate|VBN from|from|IN the|the|DT resulting|result|VBG SAM|SAM|NNP alignment|alignment|NN files|file|NNS using|use|VBG the|the|DT HTSeq-count|htseq-count|JJ program|program|NN -LRB-|-lrb-|-LRB- Anders|Anders|NNP et|et|FW al.|al.|FW ,|,|, 2015|2015|CD ,|,|, Bioinformatics|bioinformatic|NNS -RRB-|-rrb-|-RRB- with|with|IN intersection|intersection|NN non-empty|non-empty|JJ mode|mode|NN .|.|.
The|the|DT number|number|NN read|read|VBD pairs|pair|NNS mapped|map|VBN to|to|TO each|each|DT gene|gene|NN was|be|VBD counted|count|VBN with|with|IN HTSeq|htseq|NN 0.6.1|0.6.1|CD
The|the|DT numbers|number|NNS of|of|IN 4|4|CD bases|basis|NNS A|a|DT ,|,|, T|t|NN ,|,|, G|g|NN ,|,|, C|c|NN ,|,|, and|and|CC N|n|NN were|be|VBD counted|count|VBN in|in|IN each|each|DT position|position|NN of|of|IN the|the|DT mapped|map|VBN reads|read|VBZ by|by|IN using|use|VBG the|the|DT program|program|NN SAMtools|samtool|NNS 0.1.18|0.1.18|CD with|with|IN supplemental|supplemental|JJ use|use|NN of|of|IN a|a|DT Perl|Perl|NNP script|script|NN .|.|.
Theobald|Theobald|NNP ,|,|, U.|U.|NNP ,|,|, Mailinger|Mailinger|NNP ,|,|, W.|W.|NNP ,|,|, Baltes|Baltes|NNP ,|,|, M.|M.|NNP ,|,|, Rizzi|Rizzi|NNP ,|,|, M.|M.|NNP ,|,|, Reuss|Reuss|NNP ,|,|, M.|M.|NNP ,|,|, 1997|1997|CD .|.|. In|in|FW vivo|vivo|FW analysis|analysis|NN of|of|IN metabolic|metabolic|JJ dynamics|dynamics|NNS in|in|IN Saccharomyces|saccharomyces|FW cerevisiae|cerevisiae|FW .|.|. 1|1|LS .|.|. Experimental|experimental|JJ observations|observation|NNS .|.|. Biotechnol|Biotechnol|NNP .|.|. Bioeng|Bioeng|NNP .|.|. 55|55|CD ,|,|, 305|305|CD --|--|: 316|316|CD .|.|.
The|the|DT obtained|obtain|VBN reads|read|VBZ were|be|VBD aligned|align|VBN and|and|CC mapped|map|VBN to|to|TO the|the|DT pPR9|ppr9|NN plasmid|plasmid|NN DNA|dna|NN sequences|sequence|NNS using|use|VBG Bowtie|Bowtie|NNP 0.12.7|0.12.7|CD .|.|.
The|the|DT optical|optical|JJ density|density|NN was|be|VBD measured|measure|VBN every|every|DT 30|30|CD min|min|NN and|and|CC expression|expression|NN of|of|IN the|the|DT heterologous|heterologous|JJ sigma|sigma|NN factor|factor|NN was|be|VBD induced|induce|VBN with|with|IN 1mM|1mm|NN IPTG|iptg|NN at|at|IN an|a|DT optical|optical|JJ density|density|NN of|of|IN 0.1|0.1|CD .|.|. Samples|sample|NNS for|for|IN RNA|rna|NN extractions|extraction|NNS -LRB-|-lrb-|-LRB- 1|1|CD ml|ml|NN -RRB-|-rrb-|-RRB- were|be|VBD taken|take|VBN after|after|IN 4.5|4.5|CD ,|,|, 6|6|CD and|and|CC 9|9|CD hours|hour|NNS after|after|IN induction|induction|NN .|.|. Cell|cell|NN pellets|pellet|NNS were|be|VBD stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN until|until|IN total|total|JJ RNA|rna|NN extraction|extraction|NN was|be|VBD performed|perform|VBN .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 0.25|0.25|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- to|to|TO OD600|od600|CD 0.5|0.5|CD ,|,|, 100|100|CD uM|um|NN AI-2|ai-2|NN was|be|VBD added|add|VBN in|in|IN .|.|. after|after|IN further|further|JJ 3-h|3-h|JJ incubation|incubation|NN ,|,|, 2.0|2.0|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD removed|remove|VBN and|and|CC cells|cell|NNS were|be|VBD pelleted|pelleted|JJ and|and|CC frozen|frozen|JJ in|in|IN -80|-80|CD C|c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 0.25|0.25|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- to|to|TO OD600|od600|CD 0.5|0.5|CD ,|,|, no|no|DT AI-2|ai-2|NN was|be|VBD added|add|VBN in|in|IN .|.|. after|after|IN further|further|JJ 3-h|3-h|JJ incubation|incubation|NN ,|,|, 2.0|2.0|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD removed|remove|VBN and|and|CC cells|cell|NNS were|be|VBD pelleted|pelleted|JJ and|and|CC frozen|frozen|JJ in|in|IN -80|-80|CD C|c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 0.25|0.25|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- to|to|TO OD600|od600|CD 4.0|4.0|CD ,|,|, 2.0|2.0|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD removed|remove|VBN and|and|CC cells|cell|NNS were|be|VBD pelleted|pelleted|JJ and|and|CC frozen|frozen|JJ in|in|IN -80|-80|CD C|c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 0.25|0.25|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- to|to|TO OD600|od600|CD 0.5|0.5|CD ,|,|, 100|100|CD uM|um|NN AI-2|ai-2|NN was|be|VBD added|add|VBN in|in|IN .|.|. after|after|IN further|further|JJ 3-h|3-h|JJ incubation|incubation|NN ,|,|, 2.0|2.0|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD removed|remove|VBN and|and|CC cells|cell|NNS were|be|VBD pelleted|pelleted|JJ and|and|CC frozen|frozen|JJ in|in|IN -80|-80|CD C|c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 0.25|0.25|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- to|to|TO OD600|od600|CD 0.5|0.5|CD ,|,|, no|no|DT AI-2|ai-2|NN was|be|VBD added|add|VBN in|in|IN .|.|. after|after|IN further|further|JJ 3-h|3-h|JJ incubation|incubation|NN ,|,|, 2.0|2.0|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD removed|remove|VBN and|and|CC cells|cell|NNS were|be|VBD pelleted|pelleted|JJ and|and|CC frozen|frozen|JJ in|in|IN -80|-80|CD C|c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 0.25|0.25|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. Planktonic|planktonic|JJ cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO a|a|DT turbidity|turbidity|NN of|of|IN 0.5|0.5|CD at|at|IN 600|600|CD nm|nm|NN in|in|IN LB|lb|NN medium|medium|NN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN at|at|IN 37|37|CD °C|°c|NN ,|,|, adjusted|adjust|VBN the|the|DT turbidity|turbidity|NN to|to|TO 1|1|CD ,|,|, and|and|CC exposed|expose|VBN to|to|TO 20|20|CD μg/mL|μg/ml|NN ampicillin|ampicillin|NN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN for|for|IN 1|1|CD h.|h.|NN Cells|cell|NNS were|be|VBD isolated|isolate|VBN by|by|IN centrifuging|centrifuge|VBG at|at|IN 0|0|CD °C|°c|NN ,|,|, and|and|CC RNALater|rnalater|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Cat|Cat|NNP #|#|# AM7021|am7021|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO stabilize|stabilize|VB RNA|rna|NN during|during|IN the|the|DT RNA|rna|NN preparation|preparation|NN steps|step|NNS .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 0.25|0.25|CD mL|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD mL|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. Planktonic|planktonic|JJ cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO a|a|DT turbidity|turbidity|NN of|of|IN 0.5|0.5|CD at|at|IN 600|600|CD nm|nm|NN in|in|IN LB|lb|NN medium|medium|NN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN at|at|IN 37|37|CD °C|°c|NN ,|,|, adjusted|adjust|VBN the|the|DT turbidity|turbidity|NN to|to|TO 1|1|CD ,|,|, and|and|CC exposed|expose|VBN to|to|TO 20|20|CD μg/mL|μg/ml|NN ampicillin|ampicillin|NN with|with|IN 1|1|CD mM|mm|NN IPTG|iptg|NN for|for|IN 1|1|CD h.|h.|NN Cells|cell|NNS were|be|VBD isolated|isolate|VBN by|by|IN centrifuging|centrifuge|VBG at|at|IN 0|0|CD °C|°c|NN ,|,|, and|and|CC RNALater|rnalater|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Cat|Cat|NNP #|#|# AM7021|am7021|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO stabilize|stabilize|VB RNA|rna|NN during|during|IN the|the|DT RNA|rna|NN preparation|preparation|NN steps|step|NNS .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN glu|glu|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 15|15|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN glu|glu|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 15|15|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- for|for|IN 7|7|CD hours|hour|NNS ,|,|, 2.0|2.0|CD ml|ml|NN of|of|IN cell|cell|NN culture|culture|NN was|be|VBD removed|remove|VBN from|from|IN suspension|suspension|NN part|part|NN and|and|CC cells|cell|NNS were|be|VBD pelleted|pelleted|JJ and|and|CC frozen|frozen|JJ in|in|IN -80|-80|CD C|c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- and|and|CC 1|1|CD mM|mm|NN indole|indole|NN for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- and|and|CC DMF|dmf|NN for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- and|and|CC DMF|dmf|NN for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- and|and|CC DMF|dmf|NN for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- and|and|CC with|with|IN 100|100|CD uM|um|NN indole|indole|NN for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- and|and|CC with|with|IN 100|100|CD uM|um|NN indole|indole|NN for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
``|``|`` The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 15|15|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 15|15|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 24|24|CD h|h|NN at|at|IN 37oC|37oc|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0oC|0oc|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0oC|0oc|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 30|30|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB-
The|the|DT overnight|overnight|JJ culture|culture|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD ml|ml|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 250|250|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN of|of|IN submerged|submerged|JJ glass|glass|NN wool|wool|NN -LRB-|-lrb-|-LRB- Corning|Corning|NNP Glass|Glass|NNP Works|Works|NNP ,|,|, Corning|Corning|NNP ,|,|, NY|NY|NNP -RRB-|-rrb-|-RRB- for|for|IN forming|form|VBG biofilm|biofilm|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN 7|7|CD h|h|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT glass|glass|NN wool|wool|NN was|be|VBD carefully|carefully|RB and|and|CC quickly|quickly|RB removed|remove|VBD and|and|CC rinsed|rinse|VBD with|with|IN 100|100|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. Biofilm|biofilm|NN cells|cell|NNS were|be|VBD removed|remove|VBN by|by|IN sonicating|sonicate|VBG the|the|DT glass|glass|NN wool|wool|NN in|in|IN 200|200|CD ml|ml|NN of|of|IN sterile|sterile|JJ 0.85|0.85|CD %|%|NN NaCl|nacl|NN solution|solution|NN at|at|IN 0|0|CD °C|°c|NN .|.|. After|after|IN breaking|break|VBG the|the|DT cells|cell|NNS with|with|IN a|a|DT bead|bead|NN beater|beater|NN ,|,|, and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ cultures|culture|NNS of|of|IN bacteria|bacterium|NNS in|in|IN LB|lb|NN broth|broth|NN were|be|VBD refreshed|refresh|VBN with|with|IN the|the|DT ratio|ratio|NN of|of|IN 1:100|1:100|CD into|into|IN fresh|fresh|JJ LB|lb|NN broth|broth|NN ,|,|, and|and|CC incubated|incubate|VBN at|at|IN 30|30|CD ℃|℃|NN with|with|IN continuous|continuous|JJ shaking|shake|VBG until|until|IN the|the|DT absorbance|absorbance|NN at|at|IN 590|590|CD nm|nm|NN reached|reach|VBD 0.5|0.5|CD to|to|TO 0.6|0.6|CD .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD at|at|IN 37oC|37oc|NN under|under|IN 2|2|CD mM|mm|NN IPTG|iptg|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT planktonic|planktonic|JJ cells|cell|NNS were|be|VBD quickly|quickly|RB removed|remove|VBN and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN OD600|od600|NN =|=|JJ 0.5|0.5|CD at|at|IN 37oC|37oc|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, the|the|DT planktonic|planktonic|JJ cells|cell|NNS were|be|VBD quickly|quickly|RB removed|remove|VBN and|and|CC the|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP mini|minus|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT overnight|overnight|JJ culture|culture|NN was|be|VBD used|use|VBN to|to|TO inoculate|inoculate|VB 25|25|CD ml|ml|NN of|of|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN .|.|. After|after|IN incubation|incubation|NN for|for|IN OD600|od600|NN =|=|JJ 0.8|0.8|CD at|at|IN 37oC|37oc|NN with|with|IN shaking|shake|VBG -LRB-|-lrb-|-LRB- 250|250|CD rpm|rpm|NN -RRB-|-rrb-|-RRB- ,|,|, adding|add|VBG 0.5|0.5|CD %|%|NN L-arabinose|l-arabinose|NN and|and|CC incubated|incubate|VBN for|for|IN 24|24|CD h|h|NN
The|the|DT parent|parent|NN strain|strain|NN ,|,|, AG102|ag102|NN ,|,|, was|be|VBD previously|previously|RB derived|derive|VBN from|from|IN AG100|ag100|NN -LRB-|-lrb-|-LRB- K-12|k-12|NN -RRB-|-rrb-|-RRB- .|.|. AG102|ag102|NN is|be|VBZ drug|drug|NN hyper-resistant|hyper-resistant|JJ due|due|JJ to|to|TO a|a|DT mutation|mutation|NN in|in|IN marR|marr|NN -LRB-|-lrb-|-LRB- marR1|marr1|NN -RRB-|-rrb-|-RRB- which|which|WDT increases|increase|VBZ expression|expression|NN of|of|IN MarA|mara|NN ,|,|, a|a|DT global|global|JJ regulator|regulator|NN ,|,|, which|which|WDT in|in|IN turn|turn|NN results|result|VBZ in|in|IN overexpression|overexpression|NN of|of|IN the|the|DT AcrAB-TolC|acrab-tolc|NN multidrug|multidrug|JJ efflux|efflux|NN system|system|NN .|.|.
The|the|DT pCA24N,-gfp|pca24n,-gfp|NN /|/|: DA4201|da4201|NN cultures|culture|NNS and|and|CC two|two|CD cultures|culture|NNS each|each|DT of|of|IN Svi3-3|svi3-3|NN comp|comp|NN .|.|. -LRB-|-lrb-|-LRB- recoded|recode|VBN Svi3-3|svi3-3|NN -RRB-|-rrb-|-RRB- /|/|: DA4201|da4201|NN and|and|CC pORF1/DA4201|porf1/da4201|NN were|be|VBD supplemented|supplement|VBN by|by|IN 50|50|CD μM|μm|NN IPTG|iptg|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO OD|od|NN 0.15-0.2|0.15-0.2|CD and|and|CC cells|cell|NNS were|be|VBD withdrawn|withdraw|VBN for|for|IN RNA|rna|NN extraction|extraction|NN and|and|CC whole|whole|JJ cell|cell|NN proteomics|proteomic|NNS .|.|.
The|the|DT pre-culture|pre-culture|JJ was|be|VBD the|the|DT overnight|overnight|JJ propagated|propagate|VBN cells|cell|NNS in|in|IN 5|5|CD ml|ml|NN of|of|IN LB|lb|NN medium|medium|NN at|at|IN 37ºC|37ºc|NN and|and|CC 180|180|CD rpm|rpm|NN .|.|. The|the|DT main|main|JJ bacterial|bacterial|JJ culture|culture|NN was|be|VBD prepared|prepare|VBN by|by|IN 1|1|CD %|%|NN inoculation|inoculation|NN from|from|IN pre-culture|pre-culture|JJ when|when|WRB optical|optical|JJ densities|density|NNS at|at|IN 600|600|CD nm|nm|NN -LRB-|-lrb-|-LRB- i.e.|i.e.|FW ,|,|, OD600|od600|NN -RRB-|-rrb-|-RRB- reached|reach|VBD 0.7|0.7|CD .|.|. Growth|growth|NN was|be|VBD achieved|achieve|VBN in|in|IN 50|50|CD ml|ml|NN of|of|IN LB|lb|NN medium|medium|NN .|.|.
The|the|DT probe|probe|NN intensity|intensity|NN data|datum|NNS was|be|VBD analyzed|analyze|VBN using|use|VBG Genetraffic|genetraffic|JJ software|software|NN -LRB-|-lrb-|-LRB- Iobion|Iobion|NNP Informatics|Informatics|NNPS LLC|LLC|NNP ,|,|, La|La|NNP Jolla|Jolla|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT probe|probe|NN intensity|intensity|NN data|datum|NNS was|be|VBD normalized|normalize|VBN using|use|VBG GC-RMA|gc-rma|NN algorithm|algorithm|NN .|.|.
The|the|DT processed|process|VBN data|datum|NNS file|file|NN -LRB-|-lrb-|-LRB- csv|csv|NN -RRB-|-rrb-|-RRB- includes|include|VBZ information|information|NN about|about|IN genomic|genomic|JJ position|position|NN ,|,|, reference/non-reference|reference/non-reference|NN bases|basis|NNS ,|,|, read|read|VBD count|count|NN ,|,|, the|the|DT fraction|fraction|NN of|of|IN 3|3|CD '|'|'' RNA|rna|NN end|end|NN ,|,|, DNA|dna|NN strand|strand|NN -LRB-|-lrb-|-LRB- +|+|CC /|/|: -|-|: -RRB-|-rrb-|-RRB- ,|,|, gene|gene|NN name|name|NN ,|,|, and|and|CC mapping/base|mapping/base|NN qualities|quality|NNS in|in|IN transcriptional|transcriptional|JJ pause|pause|NN sites|site|NNS that|that|WDT are|be|VBP defined|define|VBN by|by|IN the|the|DT parameters|parameter|NNS P|p|NN -LRB-|-lrb-|-LRB- 0.9,100|0.9,100|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT processed|process|VBN data|datum|NNS file|file|NN -LRB-|-lrb-|-LRB- csv|csv|NN -RRB-|-rrb-|-RRB- includes|include|VBZ information|information|NN about|about|IN genomic|genomic|JJ position|position|NN ,|,|, reference/non-reference|reference/non-reference|NN bases|basis|NNS ,|,|, read|read|VBD count|count|NN ,|,|, the|the|DT fraction|fraction|NN of|of|IN 3|3|CD '|'|'' RNA|rna|NN end|end|NN ,|,|, DNA|dna|NN strand|strand|NN -LRB-|-lrb-|-LRB- +|+|CC /|/|: -|-|: -RRB-|-rrb-|-RRB- ,|,|, gene|gene|NN name|name|NN ,|,|, and|and|CC mapping/base|mapping/base|NN qualities|quality|NNS in|in|IN transcriptional|transcriptional|JJ pause|pause|NN sites|site|NNS that|that|WDT are|be|VBP defined|define|VBN by|by|IN the|the|DT parameters|parameter|NNS P|p|NN -LRB-|-lrb-|-LRB- 0.9|0.9|CD ,|,|, 160|160|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT processed|process|VBN gene|gene|NN expression|expression|NN data|datum|NNS in|in|IN log10|log10|NN scale|scale|NN are|be|VBP provided|provide|VBN in|in|IN the|the|DT supplementary|supplementary|JJ file|file|NN \|\|SYM
The|the|DT program|program|NN Rockhopper|rockhopper|NN -LRB-|-lrb-|-LRB- described|describe|VBN in|in|IN Mc|mc|NN Clure|clure|NN ,|,|, et|et|FW al.|al.|FW .|.|. Nucleic|nucleic|JJ Acids|Acids|NNP Research|Research|NNP .|.|. 2013|2013|CD ,|,|, 41|41|CD -LRB-|-lrb-|-LRB- 14|14|CD -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN alignment|alignment|NN ,|,|, normalization|normalization|NN ,|,|, and|and|CC quantification|quantification|NN .|.|. Genome|Genome|NNP _|_|SYM builg|builg|NN :|:|: K-12|k-12|NN subst|subst|NN .|.|. MG1655|mg1655|NN genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913.3|000913.3|CD -RRB-|-rrb-|-RRB- /|/|: ASM584v1|asm584v1|NN
The|the|DT program|program|NN used|use|VBN to|to|TO generate|generate|VB the|the|DT bed/bar|bed/bar|JJ files|file|NNS is|be|VBZ ``|``|`` Affymetrix|Affymetrix|NNP Tiling|Tiling|NNP Analysis|Analysis|NNP Software|Software|NNP .|.|. ''|''|'' Standardized|standardized|JJ signals|signal|NNS ,|,|, for|for|IN each|each|DT probe|probe|NN in|in|IN the|the|DT arrays|array|NNS ,|,|, were|be|VBD generated|generate|VBN using|use|VBG the|the|DT MAT|mat|NN software|software|NN -LRB-|-lrb-|-LRB- Johnson|Johnson|NNP WE|WE|NNP et|et|FW al.|al.|FW 2006|2006|CD -RRB-|-rrb-|-RRB- ,|,|, which|which|WDT provides|provide|VBZ a|a|DT model-based|model-based|JJ ,|,|, sequence-specific|sequence-specific|JJ ,|,|, background|background|NN correction|correction|NN for|for|IN each|each|DT sample|sample|NN .|.|. A|a|DT gene-specific|gene-specific|JJ score|score|NN was|be|VBD then|then|RB calculated|calculate|VBN for|for|IN each|each|DT gene|gene|NN by|by|IN averaging|average|VBG all|all|DT MAT|mat|NN scores|score|NNS -LRB-|-lrb-|-LRB- natural|natural|JJ log|log|NN -RRB-|-rrb-|-RRB- for|for|IN all|all|DT probes|probe|NNS under|under|IN the|the|DT annotated|annotated|JJ gene|gene|NN coordinates|coordinate|VBZ .|.|. Gene|Gene|NNP annotation|annotation|NN was|be|VBD from|from|IN the|the|DT ASAP|asap|NN database|database|NN -LRB-|-lrb-|-LRB- Glasner|glasner|FW JD|jd|FW et|et|FW al.|al.|FW 2003|2003|CD -RRB-|-rrb-|-RRB- at|at|IN the|the|DT University|University|NNP of|of|IN Wisconsin-Madison|Wisconsin-Madison|NNP ,|,|, for|for|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN version|version|NN m56|m56|NN .|.|. Differences|difference|NNS of|of|IN two|two|CD log|log|NN scale|scale|NN values|value|NNS in|in|IN the|the|DT absence|absence|NN or|or|CC presence|presence|NN of|of|IN D-galactose|d-galactose|NN were|be|VBD calculated|calculate|VBN in|in|IN galT|galT|NNP mutant|mutant|JJ cells|cell|NNS .|.|. Finally|finally|RB ,|,|, the|the|DT transcriptome|transcriptome|JJ results|result|NNS -LRB-|-lrb-|-LRB- log|log|NN scale|scale|NN values|value|NNS -RRB-|-rrb-|-RRB- with|with|IN or|or|CC without|without|IN D-galactose|d-galactose|NN were|be|VBD compared|compare|VBN graphically|graphically|RB -LSB-|-lsb-|-LRB- References|reference|NNS :|:|: Johnson|Johnson|NNP WE|WE|NNP ,|,|, et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- 2006|2006|CD -RRB-|-rrb-|-RRB- Model-based|model-based|JJ analysis|analysis|NN of|of|IN tiling-arrays|tiling-array|NNS for|for|IN ChIP-chip|ChIP-chip|NNP .|.|. Proc|Proc|NNP Natl|Natl|NNP Acad|Acad|NNP Sci|Sci|NNP USA|USA|NNP 103:12457|103:12457|CD --|--|: 12462|12462|CD ;|;|: Glasner|glasner|FW JD|jd|FW ,|,|, et|et|FW al.|al.|FW -LRB-|-lrb-|-LRB- 2003|2003|CD -RRB-|-rrb-|-RRB- ASAP|asap|RB ,|,|, a|a|DT systematic|systematic|JJ annotation|annotation|NN package|package|NN for|for|IN community|community|NN analysis|analysis|NN of|of|IN genomes|genome|NNS .|.|. Nucleic|nucleic|JJ Acids|acid|NNS Res|Res|NNP 31:147|31:147|CD --|--|: 151|151|CD -RSB-|-rsb-|-RRB-
The|the|DT quality|quality|NN and|and|CC quantity|quantity|NN of|of|IN rRNA-depleted|rrna-depleted|JJ RNA|rna|NN was|be|VBD assessed|assess|VBN on|on|IN a|a|DT 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP RNA|rna|NN pico|pico|NN chip|chip|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- using|use|VBG manufacturer|manufacturer|NN 's|'s|POS recommendations|recommendation|NNS .|.|. Next|next|JJ generation|generation|NN sequencing|sequencing|NN -LRB-|-lrb-|-LRB- NGS|ngs|NN -RRB-|-rrb-|-RRB- libraries|library|NNS were|be|VBD prepared|prepare|VBN using|use|VBG the|the|DT Kapa|Kapa|NNP biosystems|biosystem|NNS NGS|NGS|NNP stranded|strand|VBD library|library|NN prep|prep|JJ kit|kit|NN for|for|IN RNA-Seq|rna-seq|NN with|with|IN dual|dual|JJ indexed|index|VBN Illumina|Illumina|NNP adapters|adapter|NNS .|.|. The|the|DT mode|mode|NN library|library|NN insert|insert|NN size|size|NN was|be|VBD ~|~|CD 150|150|CD bp|bp|NN ,|,|, as|as|IN determined|determine|VBN by|by|IN high|high|JJ sensitivity|sensitivity|NN NGS|ngs|NN fragment|fragment|NN analysis|analysis|NN kit|kit|NN for|for|IN Fragment|fragment|NN Analyzer|analyzer|NN ™|™|NN -LRB-|-lrb-|-LRB- Advanced|Advanced|NNP Analytical|Analytical|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- using|use|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Quantification|quantification|NN of|of|IN each|each|DT library|library|NN was|be|VBD done|do|VBN by|by|IN qPCR|qpcr|NN and|and|CC all|all|DT 30|30|CD libraries|library|NNS were|be|VBD pooled|pool|VBN in|in|IN equal|equal|JJ concentrations|concentration|NNS .|.|.
The|the|DT quality|quality|NN of|of|IN reads|read|VBZ was|be|VBD assessed|assess|VBN by|by|IN using|use|VBG FastQC|fastqc|NN -LRB-|-lrb-|-LRB- Andrews|Andrews|NNP S|s|NN ,|,|, 2010|2010|CD -RRB-|-rrb-|-RRB- and|and|CC any|any|DT reads|read|VBZ with|with|IN a|a|DT quality|quality|NN score|score|NN ≤|≤|CD Q28|q28|NN were|be|VBD trimmed|trim|VBN using|use|VBG Trim|Trim|NNP Galore|Galore|NNP !|!|. -LRB-|-lrb-|-LRB- Krueger|krueger|NN F|f|NN ,|,|, 2013|2013|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT quality|quality|NN of|of|IN sequencing|sequencing|NN data|datum|NNS was|be|VBD assessed|assess|VBN using|use|VBG FastQC|fastqc|NN ,|,|, -LRB-|-lrb-|-LRB- V11|v11|NN .2|.2|NN -RRB-|-rrb-|-RRB- before|before|IN the|the|DT reads|read|VBZ were|be|VBD trimmed|trim|VBN using|use|VBG Trimmomatic|trimmomatic|JJ -LRB-|-lrb-|-LRB- V0|v0|NN .33|.33|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT raw|raw|JJ data|datum|NNS output|output|NN -LRB-|-lrb-|-LRB- XSEQ|xseq|NN files|file|NNS -RRB-|-rrb-|-RRB- from|from|IN the|the|DT SOLiD|solid|NN 4|4|CD Genetic|genetic|JJ Analyzer|Analyzer|NNP System|System|NNP are|be|VBP passed|pass|VBN through|through|IN the|the|DT ABI|ABI|NNP Sequence|sequence|NN Accuracy|Accuracy|NNP Enhancement|enhancement|NN Tool|Tool|NNP -LRB-|-lrb-|-LRB- SAET|SAET|NNP -RRB-|-rrb-|-RRB-
The|the|DT raw|raw|JJ data|data|NN -LRB-|-lrb-|-LRB- .|.|. pair|pair|NN file|file|NN -RRB-|-rrb-|-RRB- was|be|VBD subjected|subject|VBN to|to|TO per|per|IN channel|channel|NN quantile|quantile|NN normalization|normalization|NN -LRB-|-lrb-|-LRB- Bolstad|Bolstad|NNP et|et|FW al.|al.|FW .|.|. Bioinformatics|bioinformatic|NNS 19|19|CD -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- :|:|: 185|185|CD -RRB-|-rrb-|-RRB- ,|,|, IP/mock-IP|ip/mock-ip|JJ ratio|ratio|NN computation|computation|NN and|and|CC enriched|enriched|JJ region|region|NN identification|identification|NN as|as|IN implemented|implement|VBN in|in|IN the|the|DT NimbleScan|NimbleScan|NNP software|software|NN package|package|NN ,|,|, version|version|NN 2.4.27|2.4.27|CD -LRB-|-lrb-|-LRB- www.nimblegen.com|www.nimblegen.com|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT raw|raw|JJ data|data|NN -LRB-|-lrb-|-LRB- .|.|. pair|pair|NN file|file|NN -RRB-|-rrb-|-RRB- was|be|VBD subjected|subject|VBN to|to|TO RMA|rma|NN -LRB-|-lrb-|-LRB- Robust|robust|JJ Multi-Array|multi-array|JJ Analysis|analysis|NN ;|;|: Irizarry|Irizarry|NNP et|et|FW al.|al.|FW .|.|. Biostatistics|biostatistic|NNS 4|4|CD -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- :|:|: 249|249|CD -RRB-|-rrb-|-RRB- ,|,|, quantile|quantile|JJ normalization|normalization|NN -LRB-|-lrb-|-LRB- Bolstad|Bolstad|NNP et|et|FW al.|al.|FW .|.|. Bioinformatics|bioinformatic|NNS 19|19|CD -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- :|:|: 185|185|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC background|background|NN correction|correction|NN as|as|IN implemented|implement|VBN in|in|IN the|the|DT NimbleGen|NimbleGen|NNP Deva|Deva|NNP software|software|NN ,|,|, version|version|NN 1.2|1.2|CD -LRB-|-lrb-|-LRB- Roche|Roche|NNP NimbleGen|NimbleGen|NNP ,|,|, Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT raw|raw|JJ data|data|NN -LRB-|-lrb-|-LRB- .|.|. pair|pair|NN file|file|NN -RRB-|-rrb-|-RRB- was|be|VBD subjected|subject|VBN to|to|TO RMA|rma|NN -LRB-|-lrb-|-LRB- Robust|robust|JJ Multi-Array|multi-array|JJ Analysis|analysis|NN ;|;|: Irizarry|Irizarry|NNP et|et|FW al.|al.|FW .|.|. Biostatistics|biostatistic|NNS 4|4|CD -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- :|:|: 249|249|CD -RRB-|-rrb-|-RRB- ,|,|, quantile|quantile|JJ normalization|normalization|NN -LRB-|-lrb-|-LRB- Bolstad|Bolstad|NNP et|et|FW al.|al.|FW .|.|. Bioinformatics|bioinformatic|NNS 19|19|CD -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- :|:|: 185|185|CD -RRB-|-rrb-|-RRB- ,|,|, and|and|CC background|background|NN correction|correction|NN as|as|IN implemented|implement|VBN in|in|IN the|the|DT NimbleScan|NimbleScan|NNP software|software|NN package|package|NN ,|,|, version|version|NN 2.4.27|2.4.27|CD -LRB-|-lrb-|-LRB- Roche|Roche|NNP NimbleGen|NimbleGen|NNP ,|,|, Inc.|Inc.|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT raw|raw|JJ data|datum|NNS were|be|VBD normalized|normalize|VBN using|use|VBG a|a|DT space|space|NN and|and|CC intensity-dependant|intensity-dependant|JJ LOWESS|lowess|NN program|program|NN .|.|. Data|datum|NNS from|from|IN faint|faint|JJ spots|spot|NNS were|be|VBD removed|remove|VBN ,|,|, in|in|IN which|which|WDT the|the|DT intensity|intensity|NN was|be|VBD lower|lower|JJR than|than|IN the|the|DT average|average|JJ intensity|intensity|NN plus|plus|CC 2|2|CD standard|standard|JJ deviations|deviation|NNS of|of|IN the|the|DT negative|negative|JJ controls|control|NNS on|on|IN the|the|DT array|array|NN .|.|. For|for|IN each|each|DT experimental|experimental|JJ and|and|CC control|control|JJ sample|sample|NN ,|,|, amplification|amplification|NN and|and|CC hybridization|hybridization|NN were|be|VBD performed|perform|VBN by|by|IN a|a|DT dye-swap|dye-swap|JJ strategy|strategy|NN in|in|IN two|two|CD independent|independent|JJ experiments|experiment|NNS .|.|. Differentially|differentially|RB expressed|express|VBN genes|gene|NNS were|be|VBD identified|identify|VBN with|with|IN at|at|IN least|least|JJS 2|2|CD fold|fold|JJ changes|change|NNS and|and|CC q|q|VB <|<|JJR 0.001|0.001|CD criteria|criterion|NNS using|use|VBG SAM|SAM|NNP software|software|NN .|.|.
The|the|DT raw|raw|JJ pair|pair|NN data|datum|NNS -LRB-|-lrb-|-LRB- .|.|. txt|txt|NN file|file|NN -RRB-|-rrb-|-RRB- was|be|VBD subjected|subject|VBN to|to|TO per|per|IN channel|channel|NN quantile|quantile|NN normalization|normalization|NN -LRB-|-lrb-|-LRB- Bolstad|Bolstad|NNP et|et|FW al.|al.|FW .|.|. Bioinformatics|bioinformatic|NNS 19|19|CD -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- :|:|: 185|185|CD -RRB-|-rrb-|-RRB- ,|,|, IP/mock-IP|ip/mock-ip|JJ ratio|ratio|NN computation|computation|NN and|and|CC enriched|enriched|JJ region|region|NN identification|identification|NN as|as|IN implemented|implement|VBN in|in|IN the|the|DT NimbleScan|NimbleScan|NNP software|software|NN package|package|NN ,|,|, version|version|NN 2.4.27|2.4.27|CD -LRB-|-lrb-|-LRB- www.nimblegen.com|www.nimblegen.com|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT raw|raw|JJ reads|read|VBZ were|be|VBD filtered|filtered|VBN for|for|IN removing|remove|VBG dirty|dirty|JJ raw|raw|JJ reads|read|VBZ which|which|WDT contain|contain|VBP adapters|adapter|NNS ,|,|, unknown|unknown|JJ or|or|CC low|low|JJ quality|quality|NN bases|basis|NNS .|.|.
The|the|DT reads|read|VBZ were|be|VBD processed|process|VBN using|use|VBG BWA|BWA|NNP software|software|NN .|.|.
The|the|DT remaining|remain|VBG reads|read|VBZ were|be|VBD aligned|align|VBN to|to|TO genome|genome|NN using|use|VBG Bowtie|Bowtie|NNP v.|v.|CC 0.12.0|0.12.0|CD allowing|allow|VBG for|for|IN one|one|CD mismatch|mismatch|NN and|and|CC reads|read|VBZ aligning|align|VBG in|in|IN more|more|JJR than|than|IN one|one|CD position|position|NN in|in|IN the|the|DT genome|genome|NN were|be|VBD discarded|discard|VBN
The|the|DT remaining|remain|VBG reads|read|VBZ were|be|VBD aligned|align|VBN using|use|VBG Bowtie|Bowtie|NNP v0|v0|NN .12.7|.12.7|CD against|against|IN E.|e.|FW coli|coli|FW MG1655|mg1655|NN genome|genome|NN using|use|VBG parameters|parameter|NNS -|-|: v1|v1|SYM -|-|: m2|m2|SYM -|-|: k1|k1|NN .|.|.
The|the|DT resulting|result|VBG reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO the|the|DT reference|reference|NN genome|genome|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW str|str|FW .|.|. K-12|k-12|NN substr|substr|NN .|.|. MG1655|mg1655|NN using|use|VBG Tophat2|tophat2|NN using|use|VBG the|the|DT following|follow|VBG parameters|parameter|NNS ,|,|, --|--|: GTF|gtf|NN --|--|: library|library|NN type|type|NN fr-secondstrand|fr-secondstrand|JJ
The|the|DT ribosome|ribosome|NN footprints|footprint|NNS and|and|CC fragmented|fragmented|JJ mRNA|mrna|NN were|be|VBD ligated|ligate|VBN to|to|TO miRNA|miRNA|NNP cloning|clone|VBG linker-1|linker-1|NN -LRB-|-lrb-|-LRB- IDT|idt|NN -RRB-|-rrb-|-RRB- using|use|VBG truncated|truncate|VBN T4|t4|NN RNA|rna|NN ligase|ligase|NN 2|2|CD K227Q|k227q|NN .|.|. The|the|DT ligated|ligate|VBN RNA|rna|NN fragments|fragment|NNS were|be|VBD reverse|reverse|JJ transribed|transribe|VBN using|use|VBG the|the|DT primer|primer|NN 5Phos/GATCGTCGGACTGTAGAACTCTGAACCTGTCGGTGGTCGCC|5phos/gatcgtcggactgtagaactctgaacctgtcggtggtcgcc|NN GTATCATT/iSp18/CACTCA|gtatcatt/isp18/cactca|NN /|/|: iSp18/CAAGCAGAAGACGGCATACGAATTGATG|isp18/caagcagaagacggcatacgaattgatg|NN GTGCCTACAG|gtgcctacag|NN .|.|. The|the|DT resulting|result|VBG cDNA|cdna|NN was|be|VBD circularized|circularize|VBN with|with|IN CircLigase|circligase|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- and|and|CC PCR|pcr|NN amplification|amplification|NN was|be|VBD done|do|VBN as|as|IN described|describe|VBN previously|previously|RB -LRB-|-lrb-|-LRB- Ingolia|Ingolia|NNP et|et|FW al.|al.|FW ,|,|, 2009|2009|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT RNA|rna|NN extraction|extraction|NN from|from|IN the|the|DT samples|sample|NNS was|be|VBD performed|perform|VBN by|by|IN Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN with|with|IN DNAse|dnase|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- Cat.No|cat.no|NN .|.|. 74004|74004|CD -RRB-|-rrb-|-RRB- as|as|IN per|per|IN manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
The|the|DT RNA-Seq|rna-seq|JJ library|library|NN was|be|VBD constructed|construct|VBN with|with|IN TruSeq|truseq|NN RNA|rna|NN Preparation|preparation|NN Kit|kit|NN .|.|.
The|the|DT RNAs|rna|NNS were|be|VBD chemically|chemically|RB fragmented|fragment|VBN using|use|VBG RNA|rna|NN Fragmentation|fragmentation|NN Reagents|reagent|NNS -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- to|to|TO the|the|DT size|size|NN range|range|NN of|of|IN 200-250|200-250|CD bp|bp|NN using|use|VBG 1x|1x|NN fragmentation|fragmentation|NN solution|solution|NN for|for|IN 5|5|CD minutes|minute|NNS at|at|IN 70|70|CD °C|°c|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|. Double|double|JJ stranded|strand|VBN cDNA|cdna|NN was|be|VBD generated|generate|VBN using|use|VBG the|the|DT SuperScript|SuperScript|NNP Double-Stranded|Double-Stranded|NNP cDNA|cdna|NN Synthesis|synthesis|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. The|the|DT Illumina|Illumina|NNP Paired|Paired|NNP End|End|NNP Sample|Sample|NNP Prep|Prep|NNP kit|kit|NN was|be|VBD used|use|VBN for|for|IN Illumina|Illumina|NNP RNA-seq|RNA-seq|NNP library|library|NN creation|creation|NN using|use|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Briefly|briefly|RB ,|,|, the|the|DT fragmented|fragmented|JJ cDNA|cdna|NN was|be|VBD end|end|NN repaired|repair|VBN ,|,|, ligated|ligate|VBN to|to|TO Illumina|Illumina|NNP specific|specific|JJ adapters|adapter|NNS and|and|CC amplified|amplify|VBN with|with|IN 10|10|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN using|use|VBG the|the|DT TruSeq|TruSeq|NNP SR|sr|JJ Cluster|Cluster|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- v2|v2|NN -RRB-|-rrb-|-RRB- .|.|. Single-end|single-end|JJ 36|36|CD bp|bp|NN reads|read|VBZ were|be|VBD generated|generate|VBN by|by|IN sequencing|sequencing|NN on|on|IN the|the|DT Illumina|Illumina|NNP Genome|Genome|NNP Analyzer|Analyzer|NNP IIx|IIx|NNP ,|,|, using|use|VBG the|the|DT TruSeq|TruSeq|NNP SBS|SBS|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- v5|v5|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
The|the|DT RNA|rna|NN was|be|VBD fragmented|fragmented|JJ using|use|VBG Ambion|Ambion|NNP 's|'s|POS Fragmentation|fragmentation|NN Reagent|reagent|NN at|at|IN 70|70|CD °C|°c|NN for|for|IN 5|5|CD min|min|NN ,|,|, and|and|CC collected|collect|VBN by|by|IN Zymo|Zymo|NNP 's|'s|POS RNA|rna|NN columns|column|NNS .|.|. RNA|rna|NN seq|seq|NN libraries|library|NNS were|be|VBD prepared|prepare|VBN according|accord|VBG to|to|TO Illumna|Illumna|NNP 's|'s|POS protocol|protocol|NN ,|,|, using|use|VBG NEB|neb|NN enzymes|enzyme|NNS and|and|CC barcoded|barcoded|JJ adapters|adapter|NNS -LRB-|-lrb-|-LRB- Integrated|Integrated|NNP DNA|DNA|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- .|.|. The|the|DT libraries|library|NNS were|be|VBD pooled|pool|VBN and|and|CC sequenced|sequence|VBN with|with|IN an|a|DT Illumina|Illumina|NNP GA|GA|NNP II|II|NNP machine|machine|NN -LRB-|-lrb-|-LRB- Center|center|NN for|for|IN Systems|Systems|NNP Biology|Biology|NNP ,|,|, Harvard|Harvard|NNP University|University|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT RNeasy|rneasy|NN Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|qiagen|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO extract|extract|NN RNA|rna|NN .|.|. Quantity|quantity|NN and|and|CC quality|quality|NN of|of|IN the|the|DT samples|sample|NNS were|be|VBD determined|determine|VBN by|by|IN NanoDrop|NanoDrop|NNP -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP -RRB-|-rrb-|-RRB- and|and|CC Bioanalyzer|bioanalyzer|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- ,|,|, respectively|respectively|RB
The|the|DT RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN ,|,|, with|with|IN on|on|IN column|column|NN RNase-Free|rnase-free|NN DNase|dnase|NN I|i|CD treatment|treatment|NN ,|,|, -LRB-|-lrb-|-LRB- both|both|CC Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN total|total|JJ RNA|rna|NN isolation|isolation|NN -LRB-|-lrb-|-LRB- RNA|rna|NN ≥|≥|NN 200|200|CD bases|basis|NNS -RRB-|-rrb-|-RRB- ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. RNA|rna|NN quality|quality|NN was|be|VBD determined|determine|VBN by|by|IN a|a|DT Lab-on-a-Chip-System|Lab-on-a-Chip-System|NNP Bioanalyzer|Bioanalyzer|NNP 2100|2100|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP ,|,|, Boeblingen|Boeblingen|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT RNeasy|rneasy|NN Mini|Mini|NNP Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN ;|;|: Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO extract|extract|VB total|total|JJ RNA|rna|NN from|from|IN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN cultures|culture|NNS .|.|. RNAlater|rnalater|NN Stabilization|stabilization|NN Reagent|reagent|NN -LRB-|-lrb-|-LRB- 1.2|1.2|CD ml|ml|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ;|;|: Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- was|be|VBD combined|combine|VBN with|with|IN 0.6|0.6|CD ml|ml|NN E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H7|h7|NN .|.|. After|after|IN 10|10|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN ,|,|, the|the|DT mixture|mixture|NN was|be|VBD centrifuged|centrifuge|VBN at|at|IN 8000|8000|CD x|x|CC g|g|NN for|for|IN 10|10|CD min|min|NN under|under|IN refrigeration|refrigeration|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD decanted|decant|VBN and|and|CC the|the|DT bacterial|bacterial|JJ pellet|pellet|NN was|be|VBD stored|store|VBN at|at|IN -70|-70|CD °C|°c|NN until|until|IN further|further|JJ processed|process|VBN -LRB-|-lrb-|-LRB- 2-10|2-10|CD h|h|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT R|r|NN package|package|NN `|`|`` DESeq2|deseq2|NN '|'|'' -LRB-|-lrb-|-LRB- Version|Version|NNP 1.12.4|1.12.4|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO calculate|calculate|VB differential|differential|JJ gene|gene|NN expression|expression|NN between|between|IN the|the|DT LP|lp|NN group|group|NN and|and|CC the|the|DT HP|HP|NNP group|group|NN .|.|.
The|the|DT R|r|NN package|package|NN ,|,|, Ringo|Ringo|NNP ,|,|, was|be|VBD used|use|VBN to|to|TO read|read|VB the|the|DT pair|pair|NN files|file|NNS and|and|CC the|the|DT limma|limma|NN package|package|NN for|for|IN within|within|IN -|-|: and|and|CC between-array|between-array|JJ normalization|normalization|NN .|.|. ChIP-chip|ChIP-chip|NNP data|datum|NNS were|be|VBD bi-weighted|bi-weighted|JJ scaled|scale|VBN within|within|IN each|each|DT array|array|NN and|and|CC aquantile|aquantile|NN normalized|normalize|VBD between|between|IN arrays|array|NNS .|.|.
The|the|DT sample|sample|NN sources|source|NNS of|of|IN individual|individual|JJ reads|read|VBZ were|be|VBD determined|determine|VBN by|by|IN the|the|DT barcoding|barcoding|NN .|.|. The|the|DT barcodes|barcode|NNS for|for|IN the|the|DT minus|minus|NN and|and|CC plus|plus|CC TAP|tap|NN treatments|treatment|NNS were|be|VBD ACTTGA|ACTTGA|NNP and|and|CC CGATGT|CGATGT|NNP ,|,|, respectively|respectively|RB ,|,|, for|for|IN the|the|DT E.|e.|FW coli|coli|FW RNA|rna|NN ,|,|, and|and|CC CAGATC|CAGATC|NNP and|and|CC ATCACG|ATCACG|NNP ,|,|, respectively|respectively|RB ,|,|, for|for|IN the|the|DT S.|S.|NNP coelicolor|coelicolor|NN RNA|rna|NN .|.|.
The|the|DT samples|sample|NNS were|be|VBD sonicated|sonicate|VBN for|for|IN a|a|DT total|total|NN of|of|IN 16|16|CD minutes|minute|NNS and|and|CC 50|50|CD uL|ul|NN protein|protein|NN A/G|a/g|NN sepharose|sepharose|NN .|.|. All|all|DT reactions|reaction|NNS are|be|VBP performed|perform|VBN in|in|IN an|a|DT Eppendorf|eppendorf|NN ThermalMixerR|thermalmixerr|NN while|while|IN being|be|VBG mixed|mix|VBN at|at|IN 1.4|1.4|CD k|k|NN x|x|NN rpm|rpm|NN .|.|. After|after|IN each|each|DT reaction|reaction|NN ,|,|, the|the|DT sepharose|sepharose|NN was|be|VBD washed|wash|VBN with|with|IN 1|1|CD mL|ml|NN of|of|IN each|each|DT of|of|IN the|the|DT following|follow|VBG buffers|buffer|NNS ,|,|, leaving|leave|VBG 50-100|50-100|CD uL|ul|NN buffer|buffer|NN above|above|IN the|the|DT sepharose|sepharose|NN in-between|in-between|JJ each|each|DT wash|wash|NN :|:|: 1x|1x|VB TE|TE|NNP :|:|: 10mM|10mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 8.0|8.0|CD +|+|CC 1|1|CD mM|mm|NN EDTA|edta|NN ;|;|: 1|1|CD x|x|CC High|high|JJ Salt|Salt|NNP -|-|: 1M|1m|NN NaCl|nacl|NN -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 50|50|CD mM|mm|NN HEPES|hepes|NN ,|,|, pH|ph|NN 8.0|8.0|CD ,|,|, 2|2|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.1|0.1|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN and|and|CC 1M|1m|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- ;|;|: 1x|1x|CD Wash|Wash|NNP Buffer|Buffer|NNP 2|2|CD -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 50|50|CD mM|mm|NN HEPES|hepes|NN ,|,|, pH|ph|NN 8.0|8.0|CD ,|,|, 2|2|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.1|0.1|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN and|and|CC 0.5|0.5|CD M|m|NN NaCl|nacl|NN -RRB-|-rrb-|-RRB- ;|;|: 1x|1x|CD Wash|Wash|NNP Buffer|Buffer|NNP 3|3|CD -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN Triton|Triton|NNP X-100|x-100|NN ,|,|, 50|50|CD mM|mm|NN HEPES|hepes|NN ,|,|, pH|ph|NN 8.0|8.0|CD ,|,|, 2|2|CD mM|mm|NN EDTA|edta|NN ,|,|, 1.0|1.0|CD %|%|NN sodium|sodium|NN deoxycholate|deoxycholate|NN ,|,|, 0.25|0.25|CD M|m|NN LiCl|licl|NN ,|,|, 1|1|CD %|%|NN NP-40|np-40|NN ,|,|, and|and|CC 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 8.0|8.0|CD -RRB-|-rrb-|-RRB- ;|;|: 1x|1x|CD TE|TE|NNP :|:|: 10mM|10mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 8.0|8.0|CD +|+|CC 1mM|1mm|NN EDTA|edta|NN .|.|.
The|the|DT scanned|scan|VBN images|image|NNS were|be|VBD analyzed|analyze|VBN using|use|VBG the|the|DT Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- with|with|IN default|default|NN parameters|parameter|NNS to|to|TO obtain|obtain|VB background|background|NN subtracted|subtract|VBN and|and|CC spatially|spatially|RB detrended|detrend|VBD Processed|processed|JJ Signal|signal|NN intensities|intensity|NNS .|.|.
The|the|DT scanned|scan|VBN images|image|NNS were|be|VBD analyzed|analyze|VBN with|with|IN Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP 10.5|10.5|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- using|use|VBG default|default|NN parameters|parameter|NNS -LRB-|-lrb-|-LRB- protocol|protocol|NN GE1|ge1|NN _|_|NN 105|105|CD _|_|SYM Dec08|dec08|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT scanned|scan|VBN images|image|NNS were|be|VBD analyzed|analyze|VBN with|with|IN Feature|Feature|NNP Extraction|Extraction|NNP Software|Software|NNP version|version|NN 9.5.3.1|9.5.3.1|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- using|use|VBG default|default|NN parameters|parameter|NNS -LRB-|-lrb-|-LRB- protocol|protocol|NN GE1-v5|ge1-v5|NN _|_|CD 95|95|CD and|and|CC Grid|Grid|NNP :|:|: 020097|020097|CD _|_|NN D|d|NN _|_|CD F|f|NN _|_|SYM 20080627|20080627|CD -RRB-|-rrb-|-RRB- to|to|TO obtain|obtain|VB background|background|NN subtracted|subtract|VBN and|and|CC spatially|spatially|RB detrended|detrend|VBD Processed|processed|JJ Signal|signal|NN intensities|intensity|NNS but|but|CC not|not|RB included|include|VBD the|the|DT normalization|normalization|NN process|process|NN .|.|. Features|feature|NNS flagged|flag|VBD in|in|IN Feature|Feature|NNP Extraction|Extraction|NNP as|as|IN Feature|Feature|NNP Non-uniform|non-uniform|JJ outliers|outlier|NNS were|be|VBD excluded|exclude|VBN .|.|.
The|the|DT scanning|scanning|NN process|process|NN of|of|IN the|the|DT hybridized|hybridize|VBN chips|chip|NNS included|include|VBD a|a|DT fourteen-fold|fourteen-fold|JJ scan|scan|VB of|of|IN each|each|DT chip|chip|NN at|at|IN different|different|JJ settings|setting|NNS ,|,|, altering|alter|VBG both|both|CC PMT|PMT|NNP and|and|CC laser|laser|NN power|power|NN settings|setting|NNS .|.|. The|the|DT following|follow|VBG primary|primary|JJ analysis|analysis|NN served|serve|VBD as|as|IN a|a|DT quantification|quantification|NN method|method|NN and|and|CC is|be|VBZ performed|perform|VBN with|with|IN the|the|DT Gene|Gene|NNP Pix|Pix|NNP Pro|pro|FW 6.0|6.0|CD ™|™|NN -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Devices|Devices|NNPS ,|,|, Sunnyvale|Sunnyvale|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- software|software|NN tool|tool|NN .|.|.
The|the|DT secondary|secondary|JJ analysis|analysis|NN is|be|VBZ subsequently|subsequently|RB conducted|conduct|VBN using|use|VBG the|the|DT data|datum|NNS from|from|IN the|the|DT primary|primary|JJ analysis|analysis|NN .|.|. Therefore|therefore|RB ,|,|, data|datum|NNS from|from|IN different|different|JJ scans|scan|NNS is|be|VBZ first|first|JJ searched|search|VBD for|for|IN saturation|saturation|NN effects|effect|NNS ,|,|, which|which|WDT are|be|VBP eliminated|eliminate|VBN .|.|. A|a|DT locally|locally|RB weighted|weighted|JJ linear|linear|JJ regression|regression|NN -LRB-|-lrb-|-LRB- Lowess|lowess|NN -RRB-|-rrb-|-RRB- has|have|VBZ been|be|VBN employed|employ|VBN as|as|IN a|a|DT normalization|normalization|NN method|method|NN in|in|IN order|order|NN to|to|TO account|account|VB for|for|IN intensity-dependent|intensity-dependent|JJ effects|effect|NNS .|.|. Due|due|JJ to|to|TO the|the|DT lacking|lack|VBG gene|gene|NN replicates|replicate|VBZ on|on|IN the|the|DT commercial|commercial|JJ whole|whole|JJ genome|genome|NN array|array|NN ,|,|, a|a|DT t-test|t-test|NN could|could|MD not|not|RB be|be|VB applied|apply|VBN .|.|. Instead|instead|RB ,|,|, the|the|DT quotients|quotient|NNS of|of|IN respectively|respectively|RB two|two|CD states|state|NNS have|have|VBP been|be|VBN calculated|calculate|VBN for|for|IN the|the|DT assessment|assessment|NN of|of|IN the|the|DT regulation|regulation|NN .|.|. A|a|DT absolute|absolute|JJ value|value|NN of|of|IN log-ratio|log-ratio|NN -LRB-|-lrb-|-LRB- to|to|TO base2|base2|NN -RRB-|-rrb-|-RRB- higher|higher|JJR than|than|IN 1|1|CD is|be|VBZ used|use|VBN as|as|IN criteria|criterion|NNS for|for|IN a|a|DT regulated|regulate|VBN gene|gene|NN .|.|.
These|these|DT counts|count|NNS were|be|VBD fed|feed|VBN into|into|IN the|the|DT DESeq|deseq|NN package|package|NN in|in|IN Bioconductor|Bioconductor|NNP to|to|TO estimate|estimate|VB differential|differential|JJ expression|expression|NN between|between|IN the|the|DT mutants|mutant|NNS and|and|CC the|the|DT wildtype|wildtype|JJ .|.|.
The|the|DT sequence|sequence|NN data|datum|NNS were|be|VBD mapped|map|VBN against|against|IN the|the|DT genome|genome|NN sequence|sequence|NN of|of|IN E.|e.|FW coli|coli|FW K12|k12|NN substr|substr|NN .|.|. MG1655|mg1655|NN -LRB-|-lrb-|-LRB- NCBI|ncbi|NN accession|accession|NN number|number|NN NC|nc|NN _|_|CD 000913.3|000913.3|CD -RRB-|-rrb-|-RRB- using|use|VBG Bowtie2|bowtie2|NN -LRB-|-lrb-|-LRB- Langmead|langmead|NN and|and|CC Salzberg|Salzberg|NNP ,|,|, 2012|2012|CD ,|,|, doi|doi|FW :|:|: 10.1038|10.1038|CD /|/|: nmeth|nmeth|JJ .1923|.1923|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT sequencing|sequencing|NN libraries|library|NNS were|be|VBD constructed|construct|VBN using|use|VBG the|the|DT TruSeq|TruSeq|NNP RNA|rna|NN Sample|sample|NN Preparation|preparation|NN kit|kit|NN -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP Inc.|Inc.|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. Each|each|DT library|library|NN was|be|VBD prepared|prepare|VBN with|with|IN RNA|rna|NN isolated|isolate|VBN from|from|IN seven|seven|CD E.|e.|FW coli|coli|FW cultures|culture|NNS grown|grow|VBN in|in|IN triplicate|triplicate|NN to|to|TO an|a|DT exponential|exponential|JJ phase|phase|NN under|under|IN aerobic|aerobic|JJ and|and|CC anaerobic|anaerobic|JJ conditions|condition|NNS .|.|. RT-PCR|rt-pcr|NN was|be|VBD performed|perform|VBN with|with|IN SuperScript|SuperScript|NNP ®|®|NNP II|II|NNP One-step|one-step|JJ RT-PCR|rt-pcr|NN reagents|reagent|NNS -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT libraries|library|NNS were|be|VBD sequenced|sequence|VBN using|use|VBG the|the|DT Illumina|Illumina|NNP HiSeq2000|hiseq2000|NN platform|platform|NN with|with|IN a|a|DT paired-end|paired-end|NN protocol|protocol|NN and|and|CC read|read|VB lengths|length|NNS of|of|IN 50|50|CD nt|nt|NNS .|.|. The|the|DT final|final|JJ concentration|concentration|NN of|of|IN DNA|dna|NN and|and|CC RNA|rna|NN was|be|VBD measured|measure|VBN using|use|VBG a|a|DT Qubit|Qubit|NNP 2.0|2.0|CD Fluorometer|Fluorometer|NNP -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT integrity|integrity|NN of|of|IN total|total|JJ RNA|rna|NN ,|,|, DNA|dna|NN contamination|contamination|NN ,|,|, removal|removal|NN of|of|IN rRNAs|rrna|NNS and|and|CC cDNA|cdna|NN library|library|NN validation|validation|NN were|be|VBD assessed|assess|VBN with|with|IN Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT signal/noise|signal/noise|NN ratio|ratio|NN for|for|IN each|each|DT array|array|NN was|be|VBD calculated|calculate|VBN ,|,|, for|for|IN each|each|DT spot|spot|NN and|and|CC each|each|DT channel|channel|NN ,|,|, as|as|IN -LRB-|-lrb-|-LRB- foreground|foreground|NN intensity|intensity|NN minus|minus|CC background|background|NN intensity|intensity|NN -RRB-|-rrb-|-RRB- /|/|: -LRB-|-lrb-|-LRB- standard|standard|JJ deviation|deviation|NN of|of|IN the|the|DT background|background|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT raw|raw|JJ data|datum|NNS were|be|VBD normalized|normalize|VBN using|use|VBG a|a|DT space|space|NN and|and|CC intensity-dependant|intensity-dependant|JJ LOWESS|lowess|NN program|program|NN .|.|. Faint|faint|JJ spots|spot|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT data|datum|NNS if|if|IN the|the|DT intensities|intensity|NNS were|be|VBD lower|lower|JJR than|than|IN the|the|DT average|average|JJ intensity|intensity|NN plus|plus|CC 2|2|CD standard|standard|JJ deviations|deviation|NNS of|of|IN the|the|DT negative|negative|JJ controls|control|NNS .|.|. The|the|DT significant|significant|JJ genes|gene|NNS differentiating|differentiate|VBG wild-type|wild-type|JJ and|and|CC deleting|delete|VBG dnaK|dnak|NN were|be|VBD selected|select|VBN based|base|VBN on|on|IN q|q|NN <|<|JJR 0.05|0.05|CD and|and|CC greater|greater|JJR than|than|IN twofold|twofold|RB as|as|IN criteria|criterion|NNS .|.|.
The|the|DT sigPep.csv|sigpep.csv|NN file|file|NN contains|contain|VBZ the|the|DT counts|count|NNS for|for|IN each|each|DT specific|specific|JJ signal|signal|NN peptide|peptide|NN fusion|fusion|NN to|to|TO each|each|DT specific|specific|JJ test|test|NN gene|gene|NN .|.|. Entries|entry|NNS with|with|IN SP|sp|NN _|_|CD spkA/D/G|spka/d/g|NN /|/|: K|K|NNP represent|represent|VBP spike|spike|NN in|in|IN control|control|NN molecules|molecule|NNS used|use|VBN for|for|IN normalization|normalization|NN .|.|.
The|the|DT Sphingomonas|sphingomonas|JJ sp.|sp.|NN strain|strain|NN NM-05|nm-05|NN used|use|VBN in|in|IN the|the|DT study|study|NN is|be|VBZ a|a|DT known|known|JJ degrader|degrader|NN of|of|IN γ-hexachlorocyclohexane|γ-hexachlorocyclohexane|NN -LRB-|-lrb-|-LRB- γ-HCH|γ-hch|NN -RRB-|-rrb-|-RRB- and|and|CC has|have|VBZ been|be|VBN isolated|isolate|VBN from|from|IN the|the|DT vicinity|vicinity|NN of|of|IN an|a|DT industry|industry|NN India|India|NNP Pesticide|Pesticide|NNP Limited|Limited|NNP ,|,|, Chinhat|Chinhat|NNP industrial|industrial|JJ area|area|NN ,|,|, Lucknow|Lucknow|NNP which|which|WDT is|be|VBZ involved|involve|VBN in|in|IN manufacturing|manufacture|VBG chlorinated|chlorinate|VBN pesticides|pesticide|NNS for|for|IN last|last|JJ 25|25|CD years|year|NNS .|.|. The|the|DT strain|strain|NN was|be|VBD harvested|harvest|VBN in|in|IN mineral|mineral|NN salt|salt|NN medium|medium|NN with|with|IN 0.34|0.34|CD mM|mm|NN γ-HCH|γ-hch|NN as|as|IN sole|sole|JJ source|source|NN of|of|IN carbon|carbon|NN and|and|CC energy|energy|NN .|.|. The|the|DT strain|strain|NN Bordetella|bordetella|NN sp.|sp.|NN strain|strain|NN IITR-02|iitr-02|NN used|use|VBN in|in|IN this|this|DT study|study|NN has|have|VBZ been|be|VBN isolated|isolate|VBN from|from|IN the|the|DT vicinity|vicinity|NN of|of|IN the|the|DT industry|industry|NN India|India|NNP Pesticide|Pesticide|NNP Limited|Limited|NNP ,|,|, Chinhat|Chinhat|NNP ,|,|, Lucknow|Lucknow|NNP and|and|CC is|be|VBZ found|find|VBN to|to|TO be|be|VB a|a|DT degrader|degrader|NN of|of|IN 1,2|1,2|CD -|-|: ,|,|, 1,4-dichloro|1,4-dichloro|NN and|and|CC 1,2,3|1,2,3|SYM -|-|: and|and|CC 1,2,4-trichlorobenzene|1,2,4-trichlorobenzene|NN .|.|. The|the|DT strain|strain|NN was|be|VBD harvested|harvest|VBN in|in|IN mineral|mineral|NN salt|salt|NN medium|medium|NN with|with|IN 3.2|3.2|CD mM|mm|NN of|of|IN 1,2,4-trichlorobenzene|1,2,4-trichlorobenzene|NN as|as|IN sole|sole|JJ source|source|NN of|of|IN carbon|carbon|NN and|and|CC energy|energy|NN .|.|. The|the|DT bacterium|bacterium|NN Rhodococcus|rhodococcus|NN sp.|sp.|NN strain|strain|NN RHA1|rha1|NN which|which|WDT is|be|VBZ a|a|DT known|known|JJ degrader|degrader|NN of|of|IN polychlorinated|polychlorinate|VBN biphenyls|biphenyl|NNS ,|,|, substituted|substitute|VBN phenols|phenol|NNS ,|,|, benzoates|benzoate|NNS and|and|CC phthalates|phthalate|NNS was|be|VBD grown|grow|VBN on|on|IN 0.2|0.2|CD %|%|NN biphenyl|biphenyl|NN and|and|CC 20mM|20mm|NN of|of|IN benzoate|benzoate|NN as|as|IN carbon|carbon|NN sources|source|NNS .|.|. The|the|DT strain|strain|NN Escherichia|escherichia|FW coli|coli|FW DH5α|dh5α|NN and|and|CC Escherichia|escherichia|FW coli|coli|FW BL21|bl21|NN were|be|VBD grown|grow|VBN in|in|IN Luria-Bertani|luria-bertani|JJ medium|medium|NN and|and|CC strain|strain|NN Escherichia|escherichia|FW coli|coli|FW K12|k12|NN was|be|VBD grown|grow|VBN in|in|IN nutrient|nutrient|NN broth|broth|NN to|to|TO an|a|DT OD560nm|od560nm|NN of|of|IN 0.4|0.4|CD at|at|IN 37|37|CD degree|degree|NN centigrade|centigrade|NN with|with|IN continuous|continuous|JJ shaking|shake|VBG .|.|.
The|the|DT Sphingomonas|sphingomonas|JJ sp.|sp.|NN strain|strain|NN NM-05|nm-05|NN used|use|VBN in|in|IN the|the|DT study|study|NN is|be|VBZ a|a|DT known|known|JJ degrader|degrader|NN of|of|IN γ-hexachlorocyclohexane|γ-hexachlorocyclohexane|NN -LRB-|-lrb-|-LRB- γ-HCH|γ-hch|NN -RRB-|-rrb-|-RRB- and|and|CC has|have|VBZ been|be|VBN isolated|isolate|VBN from|from|IN the|the|DT vicinity|vicinity|NN of|of|IN an|a|DT industry|industry|NN India|India|NNP Pesticide|Pesticide|NNP Limited|Limited|NNP ,|,|, Chinhat|Chinhat|NNP industrial|industrial|JJ area|area|NN ,|,|, Lucknow|Lucknow|NNP which|which|WDT is|be|VBZ involved|involve|VBN in|in|IN manufacturing|manufacture|VBG chlorinated|chlorinate|VBN pesticides|pesticide|NNS for|for|IN last|last|JJ 25|25|CD years|year|NNS .|.|. The|the|DT strain|strain|NN was|be|VBD harvested|harvest|VBN in|in|IN mineral|mineral|NN salt|salt|NN medium|medium|NN with|with|IN 0.34|0.34|CD mM|mm|NN γ-HCH|γ-hch|NN as|as|IN sole|sole|JJ source|source|NN of|of|IN carbon|carbon|NN and|and|CC energy|energy|NN .|.|. The|the|DT strain|strain|NN Escherichia|escherichia|FW coli|coli|FW DH-5α|dh-5α|NN was|be|VBD grown|grow|VBN in|in|IN Luria-Bertani|luria-bertani|JJ medium|medium|NN to|to|TO an|a|DT O.D.|o.d.|NN of|of|IN 0.4|0.4|CD at|at|IN 37|37|CD degree|degree|NN centigrade|centigrade|NN with|with|IN continuous|continuous|JJ shaking|shake|VBG .|.|. The|the|DT soil/sludge|soil/sludge|NN samples|sample|NNS were|be|VBD collected|collect|VBN in|in|IN air|air|NN tight|tight|JJ vessels|vessel|NNS ,|,|, transported|transport|VBN on|on|IN ice|ice|NN -LRB-|-lrb-|-LRB- 4|4|CD ○|○|NN C|c|NN -RRB-|-rrb-|-RRB- to|to|TO the|the|DT laboratory|laboratory|NN and|and|CC processed|process|VBN immediately|immediately|RB for|for|IN DNA|dna|NN isolation|isolation|NN .|.|. At|at|IN each|each|DT sampling|sampling|NN location|location|NN multiple|multiple|JJ samples|sample|NNS were|be|VBD collected|collect|VBN from|from|IN close|close|NN -LRB-|-lrb-|-LRB- 100m|100m|NN -RRB-|-rrb-|-RRB- to|to|TO far|far|RB -LRB-|-lrb-|-LRB- 500m|500m|CD -RRB-|-rrb-|-RRB- from|from|IN the|the|DT industry|industry|NN ,|,|, along|along|IN the|the|DT effluent|effluent|JJ channel|channel|NN and|and|CC at|at|IN the|the|DT place|place|NN where|where|WRB effluent|effluent|JJ channel|channel|NN from|from|IN the|the|DT industrial|industrial|JJ area|area|NN falls|fall|VBZ into|into|IN the|the|DT river|river|NN .|.|.
The|the|DT strain|strain|NN E.|e.|FW coli|coli|FW CMCC|cmcc|NN -LRB-|-lrb-|-LRB- B|b|NN -RRB-|-rrb-|-RRB- 44102|44102|CD ,|,|, was|be|VBD provided|provide|VBN by|by|IN Institute|Institute|NNP of|of|IN Microbiology|Microbiology|NNP ,|,|, Chinese|Chinese|NNP Academy|Academy|NNP of|of|IN Sciences|Sciences|NNPS and|and|CC preserved|preserve|VBN at|at|IN the|the|DT Department|Department|NNP of|of|IN Food|Food|NNP Science|Science|NNP and|and|CC Nutrition|Nutrition|NNP ,|,|, Zhejiang|Zhejiang|NNP University|University|NNP .|.|. The|the|DT strain|strain|NN was|be|VBD maintained|maintain|VBN in|in|IN nutrient|nutrient|NN agar|agar|NN medium|medium|NN -LRB-|-lrb-|-LRB- NA|na|NN ,|,|, Hangzhou|Hangzhou|NNP Microbiological|Microbiological|NNP Agents|Agents|NNPS Co.|Co.|NNP ,|,|, Ltd.|Ltd.|NNP ,|,|, China|China|NNP -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN ,|,|, and|and|CC cultured|culture|VBN in|in|IN tryptic|tryptic|JJ soy|soy|NN broth|broth|NN -LRB-|-lrb-|-LRB- TSB|tsb|NN ,|,|, Qingdao|Qingdao|NNP Hope|Hope|NNP Biotechnology|Biotechnology|NNP Co.|Co.|NNP ,|,|, Ltd.|Ltd.|NNP ,|,|, China|China|NNP -RRB-|-rrb-|-RRB- at|at|IN pH|ph|NN 7.0|7.0|CD and|and|CC transferred|transfer|VBN every|every|DT 20-24|20-24|CD h|h|NN with|with|IN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN .|.|.
The|the|DT strain|strain|NN Escherichia|escherichia|FW coli|coli|FW MG1655|mg1655|NN -LSB-|-lsb-|-LRB- pPROEx-CAT|pproex-cat|NN -RSB-|-rsb-|-RRB- was|be|VBD cultured|culture|VBN in|in|IN a|a|DT fed-batch|fed-batch|JJ fermenter|fermenter|NN in|in|IN LB|LB|NNP media|media|NNS w|w|NN /|/|: glucose|glucose|NN and|and|CC a|a|DT glucose/MgS04|glucose/mgs04|NN feed|feed|NN at|at|IN 37|37|CD degrees|degree|NNS .|.|. Cultures|culture|NNS were|be|VBD synchronized|synchronize|VBN to|to|TO the|the|DT late|late|JJ log|log|NN phase|phase|NN ,|,|, approximately|approximately|RB 4.5|4.5|CD hours|hour|NNS of|of|IN fermentation|fermentation|NN time|time|NN .|.|. Serine|serine|NN hydrxamate|hydrxamate|NN -LRB-|-lrb-|-LRB- 100mg/L|100mg/l|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT cultures|culture|NNS .|.|. Samples|sample|NNS were|be|VBD taken|take|VBN 1|1|CD hour|hour|NN after|after|IN the|the|DT beginning|begin|VBG the|the|DT serine|serine|NN hydrxamate|hydrxamate|NN addition|addition|NN .|.|.
The|the|DT strain|strain|NN MG1655|mg1655|NN -LSB-|-lsb-|-LRB- pPROEx-CAT|pproex-cat|NN -RSB-|-rsb-|-RRB- was|be|VBD cultured|culture|VBN in|in|IN a|a|DT fed-batch|fed-batch|JJ fermenter|fermenter|NN in|in|IN LB|LB|NNP media|media|NNS w|w|NN /|/|: glucose|glucose|NN and|and|CC a|a|DT glucose/MgS04|glucose/mgs04|NN feed|feed|NN at|at|IN 37|37|CD degrees|degree|NNS .|.|. Cultures|culture|NNS were|be|VBD synchronized|synchronize|VBN to|to|TO the|the|DT late|late|JJ log|log|NN phase|phase|NN ,|,|, approximately|approximately|RB 4.5|4.5|CD hours|hour|NNS of|of|IN fermentation|fermentation|NN time|time|NN .|.|. One|one|CD set|set|NN of|of|IN fermentations|fermentation|NNS were|be|VBD exposed|expose|VBN to|to|TO IPTG|iptg|NN and|and|CC one|one|CD set|set|NN was|be|VBD not|not|RB exposed|expose|VBN to|to|TO IPTG|IPTG|NNP .|.|. Samples|sample|NNS were|be|VBD taken|take|VBN 0|0|CD ,|,|, 1|1|CD ,|,|, and|and|CC 4|4|CD hours|hour|NNS post-synchronization|post-synchronization|JJ -LRB-|-lrb-|-LRB- Time|time|NN S0|s0|NN ,|,|, S1|s1|NN ,|,|, and|and|CC S4|s4|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT strains|strain|NNS were|be|VBD grown|grow|VBN exponentially|exponentially|RB -LRB-|-lrb-|-LRB- after|after|IN initiation|initiation|NN by|by|IN a|a|DT 1,000-fold|1,000-fold|JJ dilution|dilution|NN from|from|IN overnight|overnight|JJ cultures|culture|NNS -RRB-|-rrb-|-RRB- for|for|IN ~|~|NN 5|5|CD generations|generation|NNS at|at|IN 37|37|CD °C|°c|NN in|in|IN Vogel-Bonner|Vogel-Bonner|NNP -LRB-|-lrb-|-LRB- VB|VB|NNP -RRB-|-rrb-|-RRB- minimal|minimal|JJ medium|medium|NN supplemented|supplement|VBN with|with|IN glucose|glucose|NN -LRB-|-lrb-|-LRB- 0.4|0.4|CD %|%|NN -RRB-|-rrb-|-RRB- ,|,|, pantothenic|pantothenic|JJ acid|acid|NN -LRB-|-lrb-|-LRB- 5|5|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- ,|,|, casamino|casamino|NN acids|acid|NNS -LRB-|-lrb-|-LRB- Becton-Dickenson|becton-dickenson|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- 1|1|CD %|%|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC hypoxanthine|hypoxanthine|NN -LRB-|-lrb-|-LRB- 50|50|CD µg/ml|µg/ml|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT strain|strain|NN was|be|VBD cultivated|cultivate|VBN in|in|IN 5L|5l|NN defined|define|VBN medium|medium|NN with|with|IN glycerol|glycerol|NN as|as|IN carbon|carbon|NN source|source|NN in|in|IN a|a|DT 7L|7l|NN -LRB-|-lrb-|-LRB- total|total|NN -RRB-|-rrb-|-RRB- MBR-bioreactor|mbr-bioreactor|NN .|.|. When|when|WRB the|the|DT OD|od|NN at|at|IN 600|600|CD nm|nm|NN reached|reach|VBD a|a|DT value|value|NN of|of|IN around|around|IN 5|5|CD ,|,|, the|the|DT BAD|BAD|NNP --|--|: promoter|promoter|NN was|be|VBD induced|induce|VBN by|by|IN adding|add|VBG 1g|1g|NN per|per|IN litre|litre|NN and|and|CC OD|od|NN arabinose|arabinose|NN to|to|TO the|the|DT medium|medium|NN .|.|. Samples|sample|NNS were|be|VBD taken|take|VBN at|at|IN --|--|: 10|10|CD ,|,|, 0|0|CD ,|,|, 2|2|CD ,|,|, 5|5|CD ,|,|, 10|10|CD ,|,|, 20|20|CD ,|,|, 30|30|CD ,|,|, 45|45|CD and|and|CC 60|60|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN induction|induction|NN .|.|.
The|the|DT strain|strain|NN was|be|VBD stocked|stock|VBN in|in|IN tryptic|tryptic|JJ soy|soy|NN broth|broth|NN -LRB-|-lrb-|-LRB- TSB|tsb|NN -RRB-|-rrb-|-RRB- with|with|IN 25|25|CD %|%|NN glycerol|glycerol|NN at|at|IN -80|-80|CD ℃|℃|NN ,|,|, and|and|CC was|be|VBD activated|activate|VBN by|by|IN streaking|streak|VBG onto|onto|IN TSA|TSA|NNP plate|plate|NN and|and|CC incubating|incubate|VBG at|at|IN 37|37|CD ℃|℃|NN for|for|IN 24|24|CD h.|h.|NN And|and|CC then|then|RB ,|,|, a|a|DT single|single|JJ colony|colony|NN was|be|VBD picked|pick|VBN and|and|CC used|use|VBN to|to|TO inoculate|inoculate|VB TSB|TSB|NNP and|and|CC incubated|incubate|VBN at|at|IN 37|37|CD ℃|℃|NN for|for|IN 12|12|CD h|h|NN with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN .|.|. This|this|DT overnight|overnight|JJ culture|culture|NN was|be|VBD transferred|transfer|VBN to|to|TO TSB|tsb|NN at|at|IN a|a|DT dilution|dilution|NN of|of|IN 1:100|1:100|CD and|and|CC grew|grow|VBD to|to|TO the|the|DT exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD550|od550|NN =|=|JJ 0.93|0.93|CD -RRB-|-rrb-|-RRB- .|.|.
The|the|DT subculture|subculture|NN was|be|VBD split|split|VBN into|into|IN two|two|CD 10|10|CD ml|ml|NN portions|portion|NNS ,|,|, one|one|CD of|of|IN which|which|WDT was|be|VBD treated|treat|VBN with|with|IN 6ug/ml|6ug/ml|JJ triclosan|triclosan|NN and|and|CC the|the|DT other|other|JJ retained|retain|VBN as|as|IN an|a|DT untreated|untreated|JJ control|control|NN .|.|. Treated|treat|VBN and|and|CC untreated|untreated|JJ samples|sample|NNS were|be|VBD incubated|incubate|VBN at|at|IN 37c|37c|CD for|for|IN 30|30|CD min|min|NN .|.|.
The|the|DT TAS|tas|NN software|software|NN provides|provide|VBZ analysis|analysis|NN capabilities|capability|NNS specifically|specifically|RB for|for|IN the|the|DT GeneChip|GeneChip|NNP ®|®|NNP Tiling|Tiling|NNP Arrays|Arrays|NNPS .|.|. TAS|tas|NN analyzes|analyze|VBZ feature|feature|NN intensity|intensity|NN data|datum|NNS stored|store|VBN in|in|IN GCOS|gcos|NN output|output|NN .|.|. CEL|CEL|NNP files|file|NNS and|and|CC produces|produce|VBZ :|:|:
The|the|DT total|total|JJ DNA|dna|NN to|to|TO be|be|VB used|use|VBN as|as|IN target|target|NN for|for|IN microarray|microarray|NN hybridization|hybridization|NN was|be|VBD isolated|isolate|VBN from|from|IN soil|soil|NN /|/|: sediment|sediment|NN samples|sample|NNS using|use|VBG the|the|DT Mo|mo|NN Bio|Bio|NNP Power|Power|NNP soil|soil|NN DNA|dna|NN kit|kit|NN -LRB-|-lrb-|-LRB- Mo|mo|NN Bio|Bio|NNP Inc.|Inc.|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- as|as|IN per|per|IN manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Before|before|IN processing|processing|NN for|for|IN DNA|dna|NN isolation|isolation|NN ,|,|, the|the|DT soil|soil|NN /|/|: sediments|sediment|NNS were|be|VBD mixed|mixed|JJ thoroughly|thoroughly|RB using|use|VBG a|a|DT mortar-pestle|mortar-pestle|NN .|.|. One|one|CD gm|gm|NN of|of|IN soil/sediment|soil/sediment|NN was|be|VBD taken|take|VBN for|for|IN DNA|dna|NN isolation|isolation|NN ,|,|, and|and|CC during|during|IN processing|processing|NN with|with|IN the|the|DT kit|kit|NN ,|,|, lysozyme|lysozyme|NN was|be|VBD added|add|VBN to|to|TO facilitate|facilitate|VB the|the|DT lysis|lysis|NN of|of|IN bacteria|bacterium|NNS .|.|. The|the|DT genomic|genomic|JJ DNA|dna|NN from|from|IN pure|pure|JJ bacterial|bacterial|JJ cultures|culture|NNS was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT Wizard|Wizard|NNP genomic|genomic|JJ DNA|dna|NN isolation|isolation|NN kit|kit|NN -LRB-|-lrb-|-LRB- Promega|Promega|NNP corporation|corporation|NN ,|,|, Madison|Madison|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- as|as|IN per|per|IN manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. The|the|DT concentration|concentration|NN of|of|IN DNA|dna|NN was|be|VBD analyzed|analyze|VBN by|by|IN Nanodrop|Nanodrop|NNP spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Nanodrop|Nanodrop|NNP Technologies|Technologies|NNPS Inc|Inc|NNP ,|,|, Rockland|Rockland|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC quality|quality|NN was|be|VBD determined|determine|VBN by|by|IN analysis|analysis|NN on|on|IN DNA|dna|NN 12000|12000|CD kit|kit|NN -LRB-|-lrb-|-LRB- Caliper|Caliper|NNP Sciences|Sciences|NNPS ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- using|use|VBG the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Palo|Palo|NNP Alto|Alto|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
The|the|DT total|total|JJ RNA|rna|NN extracted|extract|VBN from|from|IN Xuzhou21|xuzhou21|NN and|and|CC Xuzhou21m|xuzhou21m|NN were|be|VBD first|first|JJ treated|treat|VBN with|with|IN Ribo-Zero|ribo-zero|NN ™|™|CD rRNA|rrna|NN Removal|removal|NN kit|kit|NN to|to|TO remove|remove|VB rRNA|rrna|NN .|.|. The|the|DT mRNA|mrna|NN was|be|VBD fragmented|fragmented|JJ and|and|CC produced|produce|VBD cDNA|cdna|NN libraries|library|NNS primed|prime|VBN with|with|IN random|random|JJ hexamers|hexamer|NNS .|.|. cDNA|cdna|NN was|be|VBD selected|select|VBN by|by|IN size|size|NN ,|,|, amplificated|amplificate|VBN using|use|VBG PCR|pcr|NN and|and|CC and|and|CC then|then|RB sent|send|VBD to|to|TO sequencing|sequencing|NN using|use|VBG Illumina|Illumina|NNP HiseqTM|HiseqTM|NNP 2000|2000|CD commercially|commercially|RB .|.|.
The|the|DT total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG an|a|DT RNeasy|rneasy|JJ kit|kit|NN ,|,|, Qiagen|Qiagen|NNP ,|,|, in|in|IN accordance|accordance|NN with|with|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
The|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG an|a|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
The|the|DT total|total|JJ sequencing|sequencing|NN base|base|NN pair|pair|NN coverage|coverage|NN for|for|IN all|all|DT annotated|annotated|JJ genes|gene|NNS was|be|VBD summed|sum|VBN for|for|IN each|each|DT sample|sample|NN and|and|CC normalized|normalize|VBD to|to|TO total|total|JJ coverage|coverage|NN using|use|VBG bedtools|bedtool|NNS and|and|CC custom|custom|NN R|r|NN scripts|script|NNS as|as|IN described|describe|VBN in|in|IN Wu|Wu|NNP et|et|FW al.|al.|FW 2015|2015|CD PLoS|PLoS|NNP Genetics|Genetics|NNP Nov|Nov|NNP 6|6|CD ;|;|: 11|11|CD -LRB-|-lrb-|-LRB- 11|11|CD -RRB-|-rrb-|-RRB- :|:|: e1005655|e1005655|NN .|.|.
The|the|DT treatment|treatment|NN condition|condition|NN includes|include|VBZ adding|add|VBG 10|10|CD mM|mm|NN octanoic|octanoic|JJ acid|acid|NN during|during|IN logarithmic|logarithmic|JJ growth|growth|NN .|.|.
The|the|DT trimmed|trimmed|RBR reads|read|VBZ were|be|VBD aligned|align|VBN against|against|IN E.|E.|NNP 149|149|CD coli|coli|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- GenBank|genbank|NN :|:|: U00096|u00096|NN .3|.3|NN -RRB-|-rrb-|-RRB- using|use|VBG bowtie2|bowtie2|NN -LRB-|-lrb-|-LRB- Version|version|NN 2.2.4|2.2.4|CD -RRB-|-rrb-|-RRB-
The|the|DT VALUE|VALUE|NNP data|datum|NNS are|be|VBP normalized|normalize|VBN log2|log2|NN -LRB-|-lrb-|-LRB- test/ref|test/ref|NN -RRB-|-rrb-|-RRB- ratios|ratio|NNS which|which|WDT were|be|VBD normalized|normalize|VBN `|`|`` print-tip-loess|print-tip-loess|NN '|'|'' using|use|VBG the|the|DT software|software|NN R|r|NN -LRB-|-lrb-|-LRB- R|r|NN ,|,|, 2005|2005|CD -RRB-|-rrb-|-RRB- and|and|CC the|the|DT Limma|Limma|NNP package|package|NN included|include|VBD -LRB-|-lrb-|-LRB- Smyth|Smyth|NNP ,|,|, 2005|2005|CD -RRB-|-rrb-|-RRB- .|.|. Additionally|additionally|RB ,|,|, spots|spot|NNS ,|,|, which|which|WDT were|be|VBD classified|classify|VBN as|as|IN not|not|RB found|find|VBN by|by|IN the|the|DT image|image|NN analysis|analysis|NN software|software|NN ,|,|, were|be|VBD down|down|RB weighted|weight|VBN to|to|TO 10|10|CD %|%|NN .|.|.
The|the|DT value|value|NN is|be|VBZ the|the|DT simple|simple|JJ linear|linear|JJ ratio|ratio|NN of|of|IN the|the|DT processed|process|VBN Cy3|cy3|NN and|and|CC Cy5|cy5|NN signals|signal|NNS .|.|.
The|the|DT value|value|NN is|be|VBZ the|the|DT simple|simple|JJ linear|linear|JJ ratio|ratio|NN of|of|IN the|the|DT processed|process|VBN Cy5|cy5|NN and|and|CC Cy3|cy3|NN signals|signal|NNS .|.|.
The|the|DT values|value|NNS below|below|IN 0.01|0.01|CD were|be|VBD set|set|VBN to|to|TO 0.01|0.01|CD .|.|. The|the|DT log2|log2|NN ratio|ratio|NN of|of|IN the|the|DT intensity|intensity|NN of|of|IN signal|signal|NN channel|channel|NN to|to|TO that|that|DT of|of|IN control|control|NN channel|channel|NN was|be|VBD calculated|calculate|VBN and|and|CC was|be|VBD then|then|RB normalized|normalize|VBN to|to|TO each|each|DT slide|slide|NN 's|'s|POS median|median|JJ intensity|intensity|NN ratio|ratio|NN .|.|. The|the|DT default|default|NN interpretation|interpretation|NN mode|mode|NN was|be|VBD set|set|VBN to|to|TO `|`|`` log|log|NN of|of|IN ratio|ratio|NN '|'|'' .|.|. Each|each|DT time|time|NN point|point|NN was|be|VBD then|then|RB tested|test|VBN separately|separately|RB for|for|IN statistical|statistical|JJ differences|difference|NNS using|use|VBG ANOVA|ANOVA|NNP at|at|IN 5|5|CD %|%|NN confidence|confidence|NN level|level|NN ,|,|, in|in|IN conjunction|conjunction|NN with|with|IN Benjamini-Hochberg|Benjamini-Hochberg|NNP multiple|multiple|JJ testing|testing|NN correction|correction|NN .|.|.
The|the|DT web-based|web-based|JJ tool|tool|NN ,|,|, DAVID|DAVID|NNP -LRB-|-lrb-|-LRB- the|the|DT Database|database|NN for|for|IN Annotation|Annotation|NNP ,|,|, Visualization|visualization|NN ,|,|, and|and|CC Integrated|Integrated|NNP Discovery|Discovery|NNP -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN to|to|TO perform|perform|VB the|the|DT biological|biological|JJ interpretation|interpretation|NN of|of|IN differentially|differentially|RB expressed|express|VBN genes|gene|NNS .|.|. Then|then|RB ,|,|, these|these|DT genes|gene|NNS were|be|VBD classified|classify|VBN based|base|VBN on|on|IN the|the|DT information|information|NN of|of|IN gene|gene|NN function|function|NN in|in|IN Gene|Gene|NNP ontology|ontology|NN database|database|NN .|.|.
The|the|DT wildtype|wildtype|JJ and|and|CC mutant|mutant|JJ E.|e.|FW coli|coli|FW O157|o157|NN :|:|: H19|h19|NN strains|strain|NNS were|be|VBD grown|grow|VBN on|on|IN LB|LB|NNP agar|agar|NN incubated|incubate|VBN at|at|IN 37c|37c|CD x|x|CC 24h|24h|CD .|.|. A|a|DT single|single|JJ isolated|isolate|VBN colony|colony|NN for|for|IN each|each|DT strain|strain|NN was|be|VBD selected|select|VBN and|and|CC inoculated|inoculate|VBN into|into|IN 20|20|CD ml|ml|NN LB|lb|NN broth|broth|NN and|and|CC incubated|incubate|VBN at|at|IN 37c|37c|CD until|until|IN growth|growth|NN reached|reach|VBD an|a|DT optical|optical|JJ density|density|NN of|of|IN 0.6|0.6|CD at|at|IN 600nm|600nm|CD .|.|.
The|the|DT Zymo|zymo|NN Fungal/Bacterial|fungal/bacterial|JJ RNA|rna|NN extraction|extraction|NN kit|kit|NN was|be|VBD used|use|VBN to|to|TO extract|extract|NN RNA|rna|NN from|from|IN all|all|DT samples|sample|NNS .|.|. In-column|in-column|JJ DNaseI|dnasei|NN treatment|treatment|NN was|be|VBD used|use|VBN to|to|TO eliminate|eliminate|VB genomic|genomic|JJ DNA|dna|NN carryover|carryover|NN as|as|IN described|describe|VBN by|by|IN the|the|DT manufacturer|manufacturer|NN .|.|.
The|the|DT ΔbolA|δbola|NN and|and|CC wt|wt|JJ 3xflag|3xflag|NN strains|strain|NNS were|be|VBD used|use|VBN to|to|TO perform|perform|VB ChIP-seq|chip-seq|JJ experiments|experiment|NNS .|.|. Overnight|overnight|JJ cultures|culture|NNS were|be|VBD diluted|dilute|VBN 1/100|1/100|CD in|in|IN fresh|fresh|JJ LB|lb|NN medium|medium|NN and|and|CC grown|grow|VBN until|until|IN OD600|od600|NN 0.6|0.6|CD
Third|Third|NNP biological|biological|JJ repeat|repeat|NN 37|37|CD °C|°c|NN
Third|third|JJ biological|biological|JJ repeat|repeat|NN 50|50|CD °C|°c|NN
Thirty-six|thirty-six|CD dye-swap|dye-swap|JJ hybridizations|hybridization|NNS were|be|VBD performed|perform|VBN between|between|IN four|four|CD groups|group|NNS with|with|IN six|six|CD strains|strain|NNS per|per|IN group|group|NN ,|,|, according|accord|VBG to|to|TO a|a|DT balanced|balanced|JJ double|double|JJ loop|loop|NN design|design|NN .|.|. Strains|strain|NNS were|be|VBD grouped|group|VBN based|base|VBN on|on|IN cladestx|cladestx|NN profiles|profile|NNS and|and|CC each|each|DT strain|strain|NN was|be|VBD considered|consider|VBN an|a|DT independent|independent|JJ biological|biological|JJ replicate|replicate|VB of|of|IN its|its|PRP$ group|group|NN -LRB-|-lrb-|-LRB- n|n|NN =|=|JJ 6|6|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT six|six|CD strains|strain|NNS from|from|IN each|each|DT group|group|NN were|be|VBD randomly|randomly|RB hybridized|hybridize|VBN with|with|IN six|six|CD strains|strain|NNS from|from|IN every|every|DT other|other|JJ group|group|NN ;|;|: each|each|DT hybridization|hybridization|NN compared|compare|VBN a|a|DT pair|pair|NN of|of|IN strains|strain|NNS that|that|WDT differed|differ|VBD in|in|IN either|either|CC clade|clade|NN or|or|CC stx|stx|NN profile|profile|NN ,|,|, or|or|CC both|both|DT .|.|. Subsequent|subsequent|JJ to|to|TO local|local|JJ Lowess|Lowess|NNP normalization|normalization|NN ,|,|, averaging|averaging|NN of|of|IN replicate|replicate|VB probes|probe|NNS and|and|CC log2|log2|NN transformation|transformation|NN ,|,|, the|the|DT microarray|microarray|NN data|datum|NNS were|be|VBD fitted|fit|VBN to|to|TO a|a|DT 2-factor|2-factor|NN mixed|mixed|JJ ANOVA|ANOVA|NNP model|model|NN -LRB-|-lrb-|-LRB- intensity|intensity|NN =|=|JJ Array|array|NN +|+|CC Dye|dye|NN +|+|CC Clade|clade|NN +|+|CC Stx|stx|NN +|+|CC Clade|clade|NN :|:|: Stx|stx|NN +|+|CC Sample|sample|NN ;|;|: where|where|WRB the|the|DT biological|biological|JJ replicate|replicate|VB -LRB-|-lrb-|-LRB- Sample|sample|NN -RRB-|-rrb-|-RRB- and|and|CC array|array|NN effects|effect|NNS were|be|VBD considered|consider|VBN random|random|JJ effects|effect|NNS ,|,|, while|while|IN all|all|DT other|other|JJ effects|effect|NNS were|be|VBD considered|consider|VBN fixed|fixed|JJ effects|effect|NNS -RRB-|-rrb-|-RRB- ,|,|, using|use|VBG the|the|DT MAANOVA|MAANOVA|NNP package|package|NN -LRB-|-lrb-|-LRB- version|version|NN 0.98-8|0.98-8|CD -RRB-|-rrb-|-RRB- in|in|IN R|r|NN software|software|NN -LRB-|-lrb-|-LRB- version|version|NN 2.2.1|2.2.1|CD -RRB-|-rrb-|-RRB- .|.|. This|this|DT model|model|NN allows|allow|VBZ independent|independent|JJ consideration|consideration|NN of|of|IN the|the|DT effect|effect|NN of|of|IN `|`|`` Clade|Clade|NNP '|'|'' -LRB-|-lrb-|-LRB- clade|clade|NN divergence|divergence|NN -RRB-|-rrb-|-RRB- and|and|CC `|`|`` Stx|stx|FW '|'|'' -LRB-|-lrb-|-LRB- stx|stx|NN type|type|NN variation|variation|NN -RRB-|-rrb-|-RRB- parameters|parameter|NNS on|on|IN differences|difference|NNS in|in|IN gene|gene|NN expression|expression|NN among|among|IN O157|o157|NN :|:|: H7|h7|NN strains|strain|NNS ,|,|, as|as|RB well|well|RB as|as|IN their|they|PRP$ interaction|interaction|NN -LRB-|-lrb-|-LRB- combined|combine|VBN -RRB-|-rrb-|-RRB- effect|effect|NN -LRB-|-lrb-|-LRB- Clade|clade|NN :|:|: Stx|stx|NN -RRB-|-rrb-|-RRB- .|.|. Overall|overall|JJ differences|difference|NNS in|in|IN gene|gene|NN expression|expression|NN between|between|IN groups|group|NNS were|be|VBD determined|determine|VBN using|use|VBG the|the|DT Fs|f|NNS test|test|NN ,|,|, followed|follow|VBN by|by|IN pair-wise|pair-wise|JJ contrasts|contrast|VBZ to|to|TO determine|determine|VB significant|significant|JJ differential|differential|JJ expression|expression|NN between|between|IN each|each|DT pair|pair|NN of|of|IN groups|group|NNS .|.|. Subsequently|subsequently|RB ,|,|, the|the|DT Fs|f|NNS statistic|statistic|NN was|be|VBD estimated|estimate|VBN for|for|IN the|the|DT `|`|`` Clade|clade|NN '|'|'' effect|effect|NN to|to|TO determine|determine|VB significant|significant|JJ differences|difference|NNS in|in|IN gene|gene|NN expression|expression|NN between|between|IN clades|clade|NNS 8|8|CD -LRB-|-lrb-|-LRB- n|n|NN =|=|JJ 12|12|CD -RRB-|-rrb-|-RRB- and|and|CC 2|2|CD -LRB-|-lrb-|-LRB- n|n|NN =|=|JJ 12|12|CD -RRB-|-rrb-|-RRB- ,|,|, regardless|regardless|RB of|of|IN stx|stx|NN profile|profile|NN .|.|. Similarly|similarly|RB ,|,|, the|the|DT Fs|f|NNS statistic|statistic|NN was|be|VBD estimated|estimate|VBN for|for|IN the|the|DT `|`|`` Stx|stx|NN '|'|'' effect|effect|NN as|as|RB well|well|RB as|as|IN the|the|DT `|`|`` Clade|Clade|NNP :|:|: Stx|stx|NN '|'|'' interaction|interaction|NN effect|effect|NN to|to|TO examine|examine|VB the|the|DT combined|combined|JJ effect|effect|NN of|of|IN clade|clade|NN and|and|CC stx|stx|NN type|type|NN on|on|IN differences|difference|NNS in|in|IN gene|gene|NN expression|expression|NN among|among|IN O157|o157|NN :|:|: H7|h7|NN strains|strain|NNS .|.|. In|in|IN other|other|JJ words|word|NNS ,|,|, this|this|DT analysis|analysis|NN will|will|MD determine|determine|VB whether|whether|IN the|the|DT expression|expression|NN of|of|IN any|any|DT given|give|VBN gene|gene|NN among|among|IN groups|group|NNS with|with|IN different|different|JJ stx|stx|NN types|type|NNS is|be|VBZ also|also|RB dependent|dependent|JJ on|on|IN clade|clade|NN .|.|. An|a|DT interaction|interaction|NN effect|effect|NN would|would|MD be|be|VB observed|observe|VBN if|if|IN expression|expression|NN estimates|estimate|NNS between|between|IN strain|strain|NN groups|group|NNS clade8stx2|clade8stx2|NN and|and|CC clade2stx2|clade2stx2|NN are|be|VBP different|different|JJ from|from|IN expression|expression|NN estimates|estimate|NNS between|between|IN strain|strain|NN groups|group|NNS clade8stx2|clade8stx2|VBP ,2|,2|CD c|c|NN and|and|CC clade2stx1|clade2stx1|NN ,2|,2|CD .|.|. For|for|IN every|every|DT analysis|analysis|NN ,|,|, 1000|1000|CD permutations|permutation|NNS of|of|IN the|the|DT data|datum|NNS were|be|VBD performed|perform|VBN to|to|TO generate|generate|VB P|p|NN values|value|NNS ;|;|: estimates|estimate|NNS were|be|VBD considered|consider|VBN significant|significant|JJ if|if|IN the|the|DT P|p|NN value|value|NN was|be|VBD <|<|JJR 0.05|0.05|CD after|after|IN adjusting|adjust|VBG for|for|IN multiple|multiple|JJ comparisons|comparison|NNS .|.|.
three|three|CD different|different|JJ concentrations|concentration|NNS ,|,|, without|without|IN H2O2|h2o2|NN ,|,|, 10|10|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- or|or|CC 30|30|CD %|%|NN H2O2|h2o2|NN were|be|VBD added|add|VBN directly|directly|RB to|to|TO the|the|DT cell|cell|NN cultures|culture|NNS of|of|IN wild|wild|JJ type|type|NN or|or|CC luxS|luxs|NN mutants|mutant|NNS ,|,|, OD|od|NN of|of|IN which|which|WDT is|be|VBZ 1.0|1.0|CD .|.|. Treated|treat|VBN samples|sample|NNS were|be|VBD continuously|continuously|RB incubated|incubate|VBN at|at|IN 30|30|CD degree|degree|NN Celcius|Celcius|NNP for|for|IN 30|30|CD min|min|NN
Threonine|threonine|NN addition|addition|NN
Thymidine|Thymidine|NNP addition|addition|NN
time|time|NN :|:|: 0-15h|0-15h|JJ
time|time|NN :|:|: 0-16h|0-16h|JJ
time|time|NN :|:|: 0-2h|0-2h|JJ
time|time|NN :|:|: 0.5|0.5|CD min|min|NN
time|time|NN :|:|: 0|0|CD min|min|NN
time|time|NN :|:|: 0|0|CD mins|min|NNS
time|time|NN :|:|: 10|10|CD min|min|NN
time|time|NN :|:|: 10|10|CD min|min|NN
time|time|NN :|:|: 10|10|CD mins|min|NNS
time|time|NN 10|10|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 4.7|4.7|CD -RRB-|-rrb-|-RRB-
time|time|NN 11|11|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 4.8|4.8|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 120|120|CD min|min|NN
time|time|NN :|:|: 120|120|CD minutes|minute|NNS
time|time|NN :|:|: 12|12|CD h|h|NN
time|time|NN :|:|: 180|180|CD minutes|minute|NNS
time|time|NN :|:|: 195|195|CD min|min|NN
time|time|NN :|:|: 1|1|CD h|h|NN with|with|IN 20|20|CD μg/mL|μg/ml|NN ampicillin|ampicillin|NN
time|time|NN :|:|: 1|1|CD min|min|NN
time|time|NN :|:|: 1|1|CD min|min|NN post-infection|post-infection|JJ
time|time|NN 1|1|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.1|0.1|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 20|20|CD min|min|NN
time|time|NN :|:|: 20|20|CD min|min|NN
time|time|NN :|:|: 20|20|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN
time|time|NN :|:|: 210|210|CD min|min|NN
time|time|NN :|:|: 24|24|CD h|h|NN
time|time|NN :|:|: 25h|25h|JJ
time|time|NN :|:|: 25|25|CD min|min|NN
time|time|NN :|:|: 2.5|2.5|CD min|min|NN
time|time|NN :|:|: 2.5|2.5|CD min|min|NN
time|time|NN :|:|: 2.5|2.5|CD mins|min|NNS
time|time|NN :|:|: 26h|26h|JJ
time|time|NN :|:|: 28h|28h|JJ
time|time|NN :|:|: 2|2|CD min|min|NN
time|time|NN 2|2|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.3|0.3|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 300|300|CD minutes|minute|NNS
time|time|NN :|:|: 30|30|CD min|min|NN
time|time|NN :|:|: 30|30|CD mins|min|NNS
time|time|NN :|:|: 330|330|CD min|min|NN
time|time|NN 3|3|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.4|0.4|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 40|40|CD min|min|NN
time|time|NN :|:|: 40|40|CD min|min|NN
time|time|NN :|:|: 40|40|CD minutes|minute|NNS -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB- after|after|IN treatment|treatment|NN
time|time|NN :|:|: 420|420|CD minutes|minute|NNS
time|time|NN :|:|: 45|45|CD min|min|NN
time|time|NN 4|4|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.6|0.6|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 5|5|CD min|min|NN
time|time|NN :|:|: 5|5|CD min|min|NN
time|time|NN :|:|: 5|5|CD min|min|NN post-infection|post-infection|JJ
time|time|NN 5|5|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 1.0|1.0|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 60|60|CD min|min|NN
time|time|NN :|:|: 60|60|CD minutes|minute|NNS
time|time|NN :|:|: 6|6|CD h|h|NN
time|time|NN 6|6|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 1.3|1.3|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 75|75|CD min|min|NN
time|time|NN :|:|: 7|7|CD hours|hour|NNS
time|time|NN :|:|: 7|7|CD mins|min|NNS
time|time|NN 7|7|CD -LRB-|-lrb-|-LRB- OD|od|NN =|=|JJ 1.7|1.7|CD -RRB-|-rrb-|-RRB-
time|time|NN 7|7|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 1.7|1.7|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 80|80|CD min|min|NN
time|time|NN :|:|: 80|80|CD min|min|NN
time|time|NN 8|8|CD -LRB-|-lrb-|-LRB- OD|od|NN =|=|JJ 2.7|2.7|CD -RRB-|-rrb-|-RRB-
time|time|NN 8|8|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 2.7|2.7|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: 9|9|CD min|min|NN post-infection|post-infection|JJ
time|time|NN 9|9|CD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 4.5|4.5|CD -RRB-|-rrb-|-RRB-
time|time|NN :|:|: at|at|IN time|time|NN of|of|IN treatment|treatment|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB-
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 15|15|CD min|min|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 1|1|CD hour|hour|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 2|2|CD hour|hour|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 30|30|CD min|min|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 3|3|CD hour|hour|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 4|4|CD hour|hour|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 5|5|CD hour|hour|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 5|5|CD min|min|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN course|course|NN sample|sample|NN harvested|harvest|VBN after|after|IN 6|6|CD hour|hour|NN of|of|IN glucose|glucose|NN to|to|TO acetate|acetate|NN shift|shift|NN
time|time|NN induction|induction|NN :|:|: 30|30|CD minutes|minute|NNS
time|time|NN induction|induction|NN :|:|: 5|5|CD minutes|minute|NNS
time|time|NN induction|induction|NN :|:|: 60|60|CD minutes|minute|NNS
time|time|NN point|point|NN 0|0|CD
time|time|NN point|point|NN :|:|: 0|0|CD
time|time|NN point|point|NN :|:|: 0|0|CD min|min|NN
time|time|NN point|point|NN :|:|: 0|0|CD min|min|NN
time|time|NN point|point|NN :|:|: 0|0|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 10|10|CD min|min|NN
time|time|NN point|point|NN :|:|: -10|-10|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 10|10|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 135|135|CD min|min|NN
time|time|NN point|point|NN :|:|: 15|15|CD min|min|NN
time|time|NN point|point|NN :|:|: 168|168|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 180|180|CD min|min|NN
time|time|NN point|point|NN :|:|: 1|1|CD min|min|NN
time|time|NN point|point|NN 2|2|CD
time|time|NN point|point|NN :|:|: 20|20|CD min|min|NN
time|time|NN point|point|NN :|:|: 20|20|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 24|24|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 2|2|CD min|min|NN
time|time|NN point|point|NN :|:|: 2|2|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 30|30|CD min|min|NN
time|time|NN point|point|NN :|:|: 30|30|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 336|336|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 3|3|CD hours|hour|NNS
time|time|NN point|point|NN 4|4|CD
time|time|NN point|point|NN :|:|: 4.5|4.5|CD hrs|hr|NNS after|after|IN induction|induction|NN
time|time|NN point|point|NN :|:|: 45|45|CD min|min|NN
time|time|NN point|point|NN :|:|: 45|45|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 48|48|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 4|4|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 4|4|CD min|min|NN
time|time|NN point|point|NN :|:|: 5|5|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 5|5|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN 6|6|CD
time|time|NN point|point|NN :|:|: 60|60|CD minutes|minute|NNS related|related|JJ to|to|TO point|point|NN of|of|IN BRP|brp|NN induction|induction|NN
time|time|NN point|point|NN :|:|: 6|6|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 6|6|CD hrs|hr|NNS after|after|IN induction|induction|NN
time|time|NN point|point|NN :|:|: 6|6|CD min|min|NN
time|time|NN point|point|NN 8|8|CD
time|time|NN point|point|NN :|:|: 8|8|CD hours|hour|NNS
time|time|NN point|point|NN :|:|: 8|8|CD min|min|NN
time|time|NN point|point|NN :|:|: 90|90|CD min|min|NN
time|time|NN point|point|NN :|:|: 90|90|CD min|min|NN
time|time|NN point|point|NN :|:|: 9|9|CD hrs|hr|NNS after|after|IN induction|induction|NN
time|time|NN point|point|NN -LRB-|-lrb-|-LRB- minutes|minute|NNS -RRB-|-rrb-|-RRB- :|:|: 0|0|CD
time|time|NN point|point|NN -LRB-|-lrb-|-LRB- minutes|minute|NNS -RRB-|-rrb-|-RRB- :|:|: 15|15|CD
time|time|NN point|point|NN -LRB-|-lrb-|-LRB- minutes|minute|NNS -RRB-|-rrb-|-RRB- :|:|: 30|30|CD
time|time|NN point|point|NN -LRB-|-lrb-|-LRB- minutes|minute|NNS -RRB-|-rrb-|-RRB- :|:|: 5|5|CD
Time-point|time-point|NN samples|sample|NNS were|be|VBD taken|take|VBN every|every|DT 15-30|15-30|CD minutes|minute|NNS from|from|IN 15|15|CD minutes|minute|NNS to|to|TO 2|2|CD hours|hour|NNS post|post|NN treatment|treatment|NN .|.|.
time|time|NN point|point|NN :|:|: time0|time0|CD
time|time|NN point|point|NN :|:|: time10|time10|JJ
time|time|NN point|point|NN :|:|: time20|time20|JJ
time|time|NN point|point|NN :|:|: time2|time2|CD .5|.5|CD
time|time|NN point|point|NN :|:|: time5|time5|CD
time|time|NN point|point|NN :|:|: time7|time7|CD .5|.5|CD
time|time|NN post-induction|post-induction|JJ :|:|: 0h|0h|NN
time|time|NN post-induction|post-induction|JJ :|:|: 10h|10h|CD
time|time|NN post-induction|post-induction|JJ :|:|: 16h|16h|JJ
time|time|NN post-induction|post-induction|JJ :|:|: 20h|20h|JJ
time|time|NN post-induction|post-induction|JJ :|:|: 5h|5h|JJ
time|time|NN post-induction|post-induction|JJ :|:|: 6h|6h|JJ
time|time|NN post-induction|post-induction|JJ :|:|: 8h|8h|NN
time|time|NN post|post|NN release|release|NN :|:|: E.|e.|FW coli|coli|FW cells|cell|NNS 1|1|CD hour|hour|NN following|follow|VBG release|release|NN from|from|IN Stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- t|t|NN =|=|JJ 1|1|CD -RRB-|-rrb-|-RRB-
time|time|NN post|post|NN release|release|NN :|:|: E.|e.|FW coli|coli|FW cells|cell|NNS 2|2|CD hour2|hour2|NN following|follow|VBG release|release|NN from|from|IN Stationary|stationary|JJ phase|phase|NN -LRB-|-lrb-|-LRB- t|t|NN =|=|JJ 2|2|CD -RRB-|-rrb-|-RRB-
time|time|NN post|post|NN release|release|NN :|:|: E.|e.|FW coli|coli|FW cells|cell|NNS immediately|immediately|RB following|follow|VBG release|release|NN from|from|IN Stationary|stationary|JJ phase|phase|NN t|t|NN =|=|JJ 0|0|CD
time|time|NN :|:|: Sample|sample|NN was|be|VBD taken|take|VBN after|after|IN mouse|mouse|NN was|be|VBD on|on|IN the|the|DT diet|diet|NN for|for|IN 14|14|CD days|day|NNS .|.|.
time|time|NN :|:|: Sample|sample|NN was|be|VBD taken|take|VBN after|after|IN mouse|mouse|NN was|be|VBD on|on|IN the|the|DT diet|diet|NN for|for|IN 1|1|CD days|day|NNS .|.|.
time|time|NN :|:|: Sample|sample|NN was|be|VBD taken|take|VBN after|after|IN mouse|mouse|NN was|be|VBD on|on|IN the|the|DT diet|diet|NN for|for|IN 2|2|CD days|day|NNS .|.|.
time|time|NN :|:|: Sample|sample|NN was|be|VBD taken|take|VBN after|after|IN mouse|mouse|NN was|be|VBD on|on|IN the|the|DT diet|diet|NN for|for|IN 4|4|CD days|day|NNS .|.|.
time|time|NN :|:|: Sample|sample|NN was|be|VBD taken|take|VBN after|after|IN mouse|mouse|NN was|be|VBD on|on|IN the|the|DT diet|diet|NN for|for|IN 6|6|CD days|day|NNS .|.|.
time|time|NN :|:|: Sample|sample|NN was|be|VBD taken|take|VBN after|after|IN mouse|mouse|NN was|be|VBD on|on|IN the|the|DT diet|diet|NN for|for|IN 7|7|CD days|day|NNS .|.|.
tissue|tissue|NN :|:|: bacterial|bacterial|JJ cells|cell|NNS
tissue|tissue|NN :|:|: entire|entire|JJ bacterial|bacterial|JJ cell|cell|NN
tissue|tissue|NN source|source|NN :|:|: kidney|kidney|NN from|from|IN CD-1|cd-1|JJ mice|mouse|NNS
TLD-15-rep1|tld-15-rep1|NN
TLD-15-rep2|tld-15-rep2|NN
TLD-30-rep1|tld-30-rep1|NN
TLD-30-rep2|tld-30-rep2|NN
TLD-45-rep1|tld-45-rep1|NN
TLD-45-rep2|tld-45-rep2|NN
TLD-60-rep1|tld-60-rep1|NN
TLD-60-rep2|tld-60-rep2|NN
TLD-90-rep1|tld-90-rep1|NN
TLD-90-rep2|tld-90-rep2|NN
TLM-15|tlm-15|NN
TLM-30|tlm-30|NN
TLM-45|tlm-45|NN
TLM-60|tlm-60|NN
TLM-90|tlm-90|NN
tnaA2trpA46PR9|tnaa2trpa46pr9|NN vs.|vs.|CC tnaA2|tnaa2|NN ,|,|, W3110|w3110|NN min|min|NN
tnaA2trpA46PR9|tnaa2trpa46pr9|NN ,|,|, W3110|w3110|NN min|min|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ
tnaA2trpR2|tnaa2trpr2|NN vs.|vs.|CC tnaA2|tnaa2|NN ,|,|, W3110|w3110|NN min|min|NN +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|JJ
tnaA2trpR2|tnaa2trpr2|NN ,|,|, W3110|w3110|NN min|min|NN +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ
tnaA2|tnaa2|NN ,|,|, W3110|w3110|NN min|min|NN ,30|,30|CD ug|ug|NN total|total|JJ
tnaA2|tnaa2|NN ,|,|, W3110|w3110|NN minimal|minimal|JJ +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
tnaA2|tnaa2|NN ,|,|, W3110|w3110|NN minimal|minimal|JJ +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|CD vs.|vs.|CC dnaC|dnaC|NNP genomic|genomic|JJ DNA|dna|NN
tnaA2|tnaa2|NN ,|,|, W3110|w3110|NN min|min|NN +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ
To|to|TO analyze|analyze|VB RNAP|rnap|NN pausing|pause|VBG on|on|IN the|the|DT E.|e.|FW coli|coli|FW chromosome|chromosome|NN ,|,|, we|we|PRP counted|count|VBD the|the|DT number|number|NN of|of|IN reads|read|VBZ at|at|IN every|every|DT genomic|genomic|JJ nucleotide|nucleotide|NN position|position|NN using|use|VBG the|the|DT mpileup|mpileup|NN command|command|NN of|of|IN SAM|SAM|NNP tools|tool|NNS v0|v0|VBP .1.18|.1.18|CD with|with|IN --|--|: A|a|DT --|--|: B|b|NN parameters|parameter|NNS .|.|. Pausing|pause|VBG sites|site|NNS were|be|VBD defined|define|VBN P|p|NN -LRB-|-lrb-|-LRB- φ|φ|NN ,|,|, δ|δ|NN -RRB-|-rrb-|-RRB- ,|,|, where|where|WRB φ|φ|NN is|be|VBZ the|the|DT minimal|minimal|JJ fraction|fraction|NN of|of|IN having|have|VBG 3|3|CD '|'|'' RNA|rna|NN ends|end|VBZ in|in|IN the|the|DT mapped|map|VBN reads|read|VBZ and|and|CC δ|δ|NN is|be|VBZ the|the|DT minimal|minimal|JJ read|read|NN depth|depth|NN for|for|IN any|any|DT genomic|genomic|JJ position|position|NN .|.|. We|we|PRP chose|choose|VBD δ|δ|NN to|to|TO be|be|VB 100|100|CD for|for|IN WT|WT|NNP and|and|CC 160|160|CD for|for|IN ΔgreAB|δgreab|NN ,|,|, which|which|WDT normalized|normalize|VBD these|these|DT respective|respective|JJ numbers|number|NNS for|for|IN each|each|DT strain|strain|NN since|since|IN there|there|EX were|be|VBD 1.6-fold|1.6-fold|RB more|more|RBR total|total|JJ reads|read|VBZ in|in|IN the|the|DT ΔgreAB|δgreab|NN strain|strain|NN .|.|. The|the|DT high|high|JJ φ|φ|NN parameter|parameter|NN allowed|allow|VBD us|we|PRP to|to|TO define|define|VB a|a|DT reliable|reliable|JJ pause-inducing|pause-inducing|JJ element|element|NN for|for|IN WT|WT|NNP or|or|CC ΔgreAB|δgreab|NN cells|cell|NNS .|.|.
To|to|TO apply|apply|VB the|the|DT second|second|JJ approach|approach|NN variable|variable|NN in|in|IN length|length|NN reads|read|VBZ from|from|IN Illumina|Illumina|NNP MiSeq|MiSeq|NNP were|be|VBD first|first|JJ trimmed|trim|VBN from|from|IN both|both|DT sides|side|NNS to|to|TO obtain|obtain|VB a|a|DT set|set|NN of|of|IN standard|standard|JJ 50|50|CD nt|nt|NNS sequences|sequence|NNS taken|take|VBN from|from|IN the|the|DT middle|middle|NN of|of|IN longer|longer|JJR reads|read|VBZ .|.|. Reads|read|NNS shorter|shorter|JJR than|than|IN 50|50|CD nt|nt|NNS were|be|VBD discarded|discard|VBN .|.|. Then|then|RB ,|,|, all|all|DT four|four|CD sets|set|NNS from|from|IN both|both|DT experiments|experiment|NNS were|be|VBD aligned|align|VBN to|to|TO the|the|DT genome|genome|NN using|use|VBG the|the|DT Matcher|Matcher|NNP program|program|NN -LRB-|-lrb-|-LRB- available|available|JJ at|at|IN :|:|: http://www.mathcell.ru/DnaRnaTools/Matcher.zip|http://www.mathcell.ru/dnarnatools/matcher.zip|NN -RRB-|-rrb-|-RRB- .|.|. This|this|DT software|software|NN maps|map|VBZ only|only|RB 5|5|CD '|'|'' -|-|: ends|end|VBZ if|if|IN the|the|DT reads|read|VBZ correspond|correspond|VBP to|to|TO the|the|DT top|top|JJ strand|strand|NN of|of|IN genomic|genomic|JJ DNA|dna|NN ,|,|, or|or|CC only|only|RB 3|3|CD '|'|'' -|-|: ends|end|NNS ,|,|, if|if|IN they|they|PRP are|be|VBP aligned|align|VBN to|to|TO the|the|DT bottom|bottom|JJ strand|strand|NN .|.|. As|as|IN such|such|JJ ,|,|, the|the|DT signals|signal|NNS from|from|IN fully|fully|RB complementary|complementary|JJ reads|read|VBZ will|will|MD match|match|VB the|the|DT same|same|JJ -LRB-|-lrb-|-LRB- left|left|JJ -RRB-|-rrb-|-RRB- position|position|NN .|.|. Reporting|Reporting|NNP the|the|DT distribution|distribution|NN of|of|IN matching|match|VBG reads|read|VBZ across|across|IN the|the|DT genome|genome|NN the|the|DT program|program|NN also|also|RB evaluates|evaluate|VBZ reads|read|VBZ with|with|IN multiple|multiple|JJ occurrence|occurrence|NN and|and|CC their|they|PRP$ positions|position|NNS .|.|.
To|to|TO capture|capture|VB target|target|NN protein|protein|NN binding|binding|NN sites|site|NNS corresponding|correspond|VBG genomic|genomic|JJ position|position|NN of|of|IN mapped|map|VBN reads|read|VBZ start|start|NN position|position|NN -LRB-|-lrb-|-LRB- MRSP|mrsp|NN -RRB-|-rrb-|-RRB- was|be|VBD counted|count|VBN and|and|CC stored|store|VBN for|for|IN visual|visual|JJ inspection|inspection|NN using|use|VBG in-house|in-house|JJ scripts|script|NNS .|.|.
To|to|TO enrich|enrich|VB mRNAs|mrna|NNS and|and|CC other|other|JJ transcripts|transcript|NNS ,|,|, majority|majority|NN of|of|IN rRNAs|rrna|NNS were|be|VBD removed|remove|VBN from|from|IN the|the|DT DNase-treated|dnase-treated|JJ total|total|JJ RNA|rna|NN using|use|VBG a|a|DT MICROBExpress|microbexpress|NN kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
To|to|TO generate|generate|VB Illumina-compatible|illumina-compatible|JJ sequencing|sequencing|NN libraries|library|NNS for|for|IN each|each|DT sample|sample|NN ,|,|, molecular|molecular|JJ indexes|index|NNS were|be|VBD added|add|VBN to|to|TO each|each|DT library|library|NN ,|,|, allowing|allow|VBG samples|sample|NNS to|to|TO be|be|VB pooled|pool|VBN and|and|CC sequenced|sequence|VBN on|on|IN the|the|DT Illumina|Illumina|NNP HiSeq|HiSeq|NNP 2500|2500|CD with|with|IN a|a|DT 1|1|CD x|x|CC 50|50|CD bp|bp|NN single-end|single-end|JJ configuration|configuration|NN .|.|. More|more|JJR than|than|IN 250|250|CD million|million|CD reads|read|VBZ were|be|VBD generated|generate|VBN per|per|IN sample|sample|NN ,|,|, and|and|CC at|at|IN least|least|JJS 80|80|CD %|%|NN bases|basis|NNS had|have|VBD quality|quality|NN scores|score|NNS above|above|IN Q30|q30|NN .|.|.
To|to|TO harvest|harvest|VB total|total|JJ RNA|rna|NN samples|sample|NNS ,|,|, overnight|overnight|JJ cultures|culture|NNS of|of|IN wild|wild|JJ type|type|NN MG1655|mg1655|NN grown|grow|VBN in|in|IN LB|lb|NN at|at|IN 37|37|CD ˚C|˚c|NN were|be|VBD diluted|dilute|VBN back|back|RB 1:500|1:500|CD in|in|IN either|either|CC fresh|fresh|JJ LB|lb|NN or|or|CC M63|m63|NN minimal|minimal|JJ glucose|glucose|NN medium|medium|NN and|and|CC allowed|allow|VBN to|to|TO grow|grow|VB until|until|IN the|the|DT cultures|culture|NNS reached|reach|VBD an|a|DT OD600|od600|NN of|of|IN ~|~|NN 0.4|0.4|CD and|and|CC 2.0|2.0|CD for|for|IN cultures|culture|NNS grown|grow|VBN in|in|IN LB|lb|NN and|and|CC an|a|DT OD600|od600|NN of|of|IN ~|~|NN 0.4|0.4|CD for|for|IN cultures|culture|NNS grown|grow|VBN in|in|IN M63|m63|NN .|.|. For|for|IN samples|sample|NNS grown|grow|VBN to|to|TO OD600|od600|NN of|of|IN ~|~|NN 0.4|0.4|CD a|a|DT total|total|JJ volume|volume|NN of|of|IN 25|25|CD ml|ml|NN of|of|IN cells|cell|NNS were|be|VBD harvested|harvest|VBN and|and|CC combined|combine|VBN with|with|IN 5|5|CD ml|ml|NN of|of|IN stop|stop|NN solution|solution|NN -LRB-|-lrb-|-LRB- 95|95|CD %|%|NN Ethanol|ethanol|NN ,|,|, 5|5|CD %|%|NN acid|acid|NN phenol|phenol|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN samples|sample|NNS grown|grow|VBN to|to|TO OD600|od600|NN of|of|IN 2.0|2.0|CD a|a|DT total|total|JJ volume|volume|NN of|of|IN 5|5|CD ml|ml|NN of|of|IN cells|cell|NNS were|be|VBD harvested|harvest|VBN and|and|CC combined|combine|VBN with|with|IN 1|1|CD ml|ml|NN of|of|IN stop|stop|NN solution|solution|NN .|.|.
To|to|TO infer|infer|VB the|the|DT tag|tag|NN copy|copy|NN numbers|number|NNS in|in|IN each|each|DT Tag-Seq|Tag-Seq|NNP library|library|NN ,|,|, all|all|DT sequence|sequence|NN reads|read|VBZ were|be|VBD examined|examine|VBN ,|,|, regardless|regardless|RB of|of|IN their|they|PRP$ quality|quality|NN scores|score|NNS .|.|. If|if|IN the|the|DT first|first|JJ ten|ten|CD nucleotides|nucleotide|NNS of|of|IN a|a|DT read|read|NN perfectly|perfectly|RB matched|match|VBD one|one|CD of|of|IN the|the|DT 13,000|13,000|CD or|or|CC 27,000|27,000|CD designed|design|VBN tags|tag|NNS and|and|CC the|the|DT remaining|remain|VBG nucleotides|nucleotide|NNS matched|match|VBD the|the|DT expected|expect|VBN upstream|upstream|JJ MPRA|MPRA|NNP construct|construct|NN sequence|sequence|NN ,|,|, this|this|DT was|be|VBD counted|count|VBN as|as|IN one|one|CD occurrence|occurrence|NN of|of|IN that|that|DT tag|tag|NN .|.|. All|all|DT reads|read|VBZ that|that|IN did|do|VBD not|not|RB meet|meet|VB this|this|DT criterion|criterion|NN were|be|VBD discarded|discard|VBN .|.|.
To|to|TO lyse|lyse|VB the|the|DT cells|cell|NNS ,|,|, 1.0|1.0|CD mL|ml|NN RLT|rlt|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Inc.|Inc.|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- and|and|CC 0.2|0.2|CD mL|ml|NN 0.1|0.1|CD mm|mm|NN zirconia/silica|zirconia/silica|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Biospec|biospec|NN -RRB-|-rrb-|-RRB- were|be|VBD added|add|VBN to|to|TO the|the|DT frozen|frozen|JJ bead|bead|NN beater|beater|NN tubes|tube|NNS containing|contain|VBG the|the|DT cell|cell|NN pellets|pellet|NNS .|.|. The|the|DT tubes|tube|NNS were|be|VBD closed|close|VBN tightly|tightly|RB and|and|CC beat|beat|VB for|for|IN 50|50|CD seconds|seconds|NNS at|at|IN the|the|DT maximum|maximum|NN speed|speed|NN in|in|IN a|a|DT mini|mini|JJ bead|bead|NN beater|beater|NN -LRB-|-lrb-|-LRB- cat|cat|NN .|.|. no.|no.|RB 3110BX|3110BX|NNP ,|,|, Biospec|Biospec|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN by|by|IN following|follow|VBG the|the|DT protocol|protocol|NN of|of|IN the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- including|include|VBG an|a|DT on-column|on-column|JJ DNase|dnase|NN digestion|digestion|NN with|with|IN RNase-free|rnase-free|JJ DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
To|to|TO obtain|obtain|VB the|the|DT absolute|absolute|JJ expression|expression|NN levels|level|NNS of|of|IN genes|gene|NNS from|from|IN microarray|microarray|NN raw|raw|JJ data|datum|NNS ,|,|, we|we|PRP used|use|VBD the|the|DT Finite|Finite|NNP Hybridization|hybridization|NN model|model|NN -LRB-|-lrb-|-LRB- Furusawa|furusawa|NN et|et|FW al|al|FW ,|,|, 2009|2009|CD ;|;|: Ono|Ono|NNP et|et|FW al|al|FW ,|,|, 2008|2008|CD -RRB-|-rrb-|-RRB- .|.|.
To|to|TO prepare|prepare|VB the|the|DT in|in|FW vitro|vitro|FW samples|sample|NNS ,|,|, APEC|APEC|NNP strain|strain|NN E058|e058|NN was|be|VBD grown|grow|VBN statically|statically|RB at|at|IN 37|37|CD °C|°c|NN in|in|IN 10|10|CD mL|ml|NN of|of|IN LB|lb|NN broth|broth|NN until|until|IN the|the|DT absorbance|absorbance|NN at|at|IN 600|600|CD nm|nm|NN -LRB-|-lrb-|-LRB- A600|a600|NN -RRB-|-rrb-|-RRB- reached|reach|VBD 0.4|0.4|CD .|.|. To|to|TO prepare|prepare|VB the|the|DT in|in|FW vivo|vivo|FW samples|sample|NNS ,|,|, the|the|DT bacteria|bacterium|NNS was|be|VBD harvested|harvest|VBN from|from|IN cardiac|cardiac|JJ blood|blood|NN in|in|IN 1-day-old|1-day-old|JJ chickens|chicken|NNS at|at|IN 5|5|CD hours|hour|NNS post|post|NN infection|infection|NN .|.|.
To|to|TO prepare|prepare|VB the|the|DT in|in|FW vivo|vivo|FW samples|sample|NNS ,|,|, the|the|DT bacteria|bacterium|NNS was|be|VBD harvested|harvest|VBN from|from|IN cardiac|cardiac|JJ blood|blood|NN in|in|IN 1-day-old|1-day-old|JJ chickens|chicken|NNS at|at|IN 5|5|CD hours|hour|NNS post|post|NN infection|infection|NN .|.|.
To|to|TO remove|remove|VB contaminating|contaminate|VBG sequences|sequence|NNS ,|,|, the|the|DT reads|read|VBZ were|be|VBD split|split|VBN according|accord|VBG to|to|TO the|the|DT HinfI|hinfi|NN consensus|consensus|NN motif|motif|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: G|g|NN ^|^|SYM ANTC-3|antc-3|NN '|'|'' -RRB-|-rrb-|-RRB- considered|consider|VBN as|as|IN a|a|DT barcode|barcode|NN sequence|sequence|NN using|use|VBG fastx|fastx|NN _|_|NN toolkit|toolkit|NN -LRB-|-lrb-|-LRB- http://hannonlab.cshl.edu/fastx_toolkit/|http://hannonlab.cshl.edu/fastx_toolkit/|NN -RRB-|-rrb-|-RRB- -LRB-|-lrb-|-LRB- fastx_barcode_splitter.pl|fastx_barcode_splitter.pl|NN --|--|: bcfile|bcfile|JJ barcodelist.txt|barcodelist.txt|NN --|--|: bol|bol|NN --|--|: exact|exact|JJ -RRB-|-rrb-|-RRB- .|.|. Most|most|JJS of|of|IN the|the|DT reads|read|VBZ -LRB-|-lrb-|-LRB- more|more|JJR than|than|IN 90|90|CD %|%|NN -RRB-|-rrb-|-RRB- were|be|VBD rejected|reject|VBN ,|,|, and|and|CC the|the|DT reads|read|VBZ kept|keep|VBN were|be|VBD remapped|remap|VBN to|to|TO the|the|DT reference|reference|NN genomes|genome|NNS with|with|IN bwa|bwa|NN mem|mem|NN and|and|CC samtools|samtool|NNS to|to|TO generate|generate|VB a|a|DT sorted|sort|VBN bam|bam|NN file|file|NN .|.|. The|the|DT bam|bam|NN file|file|NN was|be|VBD further|further|JJ filtered|filter|VBN to|to|TO remove|remove|VB low|low|JJ mapping|mapping|NN quality|quality|NN reads|read|VBZ -LRB-|-lrb-|-LRB- keeping|keep|VBG AS|as|JJ >|>|JJR =|=|JJ 45|45|CD -RRB-|-rrb-|-RRB- and|and|CC split|split|VBN by|by|IN orientation|orientation|NN -LRB-|-lrb-|-LRB- alignmentFlag|alignmentflag|NN 0|0|CD or|or|CC 16|16|CD -RRB-|-rrb-|-RRB- with|with|IN bamtools|bamtool|NNS .|.|. The|the|DT reads|read|VBZ were|be|VBD counted|count|VBN at|at|IN 5|5|CD '|'|'' positions|position|NNS using|use|VBG Bedtools|bedtool|NNS -LRB-|-lrb-|-LRB- bedtools|bedtool|NNS genomecov|genomecov|NN -|-|: d|d|NN -5|-5|CD -RRB-|-rrb-|-RRB- .|.|. Both|both|DT orientation|orientation|NN count|count|NN files|file|NNS were|be|VBD combined|combine|VBN into|into|IN a|a|DT bed|bed|NN file|file|NN at|at|IN each|each|DT identified|identify|VBN 5|5|CD '|'|'' -|-|: GANTC-3|gantc-3|NN '|'|'' motif|motif|NN -LRB-|-lrb-|-LRB- where|where|WRB reverse|reverse|JJ counts|count|NNS >|>|JJR =|=|JJ 1|1|CD at|at|IN position|position|NN N|n|NN +1|+1|CD and|and|CC forward|forward|RB counts|count|VBZ >|>|JJR =|=|JJ 1|1|CD at|at|IN position|position|NN N-1|n-1|NN -RRB-|-rrb-|-RRB- using|use|VBG a|a|DT home-made|home-made|JJ PERL|perl|NN script|script|NN .|.|. The|the|DT HinfI|hinfi|NN positions|position|NNS in|in|IN the|the|DT bed|bed|NN file|file|NN were|be|VBD associated|associate|VBN with|with|IN the|the|DT closest|closest|JJS gene|gene|NN using|use|VBG Bedtools|Bedtools|NNP closest|closest|JJS and|and|CC the|the|DT gff3|gff3|NN file|file|NN of|of|IN the|the|DT reference|reference|NN genomes|genome|NNS .|.|. The|the|DT final|final|JJ bed|bed|NN file|file|NN was|be|VBD converted|convert|VBN to|to|TO an|a|DT MS|ms|NN Excel|Excel|NNP sheet|sheet|NN -LRB-|-lrb-|-LRB- S1|s1|NN and|and|CC S2|s2|NN Tables|table|NNS -RRB-|-rrb-|-RRB- with|with|IN a|a|DT homemade|homemade|NN script|script|NN .|.|. For|for|IN the|the|DT MboI-based|mboi-based|JJ REC-Seq|rec-seq|NN ,|,|, the|the|DT strategy|strategy|NN was|be|VBD identical|identical|JJ except|except|IN that|that|IN a|a|DT different|different|JJ adaptor|adaptor|NN was|be|VBD used|use|VBN for|for|IN ligation|ligation|NN after|after|IN cleavage|cleavage|NN and|and|CC the|the|DT MboI|mboi|NN consensus|consensus|NN motif|motif|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: ^|^|SYM GATC-3|gatc-3|NN '|'|'' -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN as|as|IN barcode|barcode|NN for|for|IN filtering|filter|VBG of|of|IN V.|V.|NNP cholerae|cholerae|VBP O1|o1|NN biovar|biovar|JJ El|El|NNP Tor|Tor|NNP and|and|CC E.|e.|FW coli|coli|FW K12|k12|NN Ec100D|ec100d|NN gDNA|gdna|NN mapped|map|VBD onto|onto|IN the|the|DT MG1655|mg1655|NN genome|genome|NN .|.|.
To|to|TO study|study|VB gene|gene|NN expression|expression|NN ,|,|, 28|28|CD days|day|NNS old|old|JJ E.coli|e.coli|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN the|the|DT presence|presence|NN of|of|IN LB|lb|NN broth|broth|NN and|and|CC LB|lb|NN broth|broth|NN supplemented|supplement|VBN with|with|IN 10|10|CD %|%|NN v/v|v/v|NN glycerol|glycerol|NN .|.|.
To|to|TO study|study|VB gene|gene|NN expression|expression|NN in|in|IN the|the|DT presence|presence|NN and|and|CC absence|absence|NN of|of|IN glycerol|glycerol|NN ,|,|, LB|lb|NN was|be|VBD supplemented|supplement|VBN with|with|IN 10|10|CD %|%|NN -LRB-|-lrb-|-LRB- v/v|v/v|NN -RRB-|-rrb-|-RRB- glycerol|glycerol|NN .|.|. Medium|medium|NN without|without|IN glycerol|glycerol|NN served|serve|VBD as|as|IN a|a|DT control|control|NN .|.|.
Total|Total|NNP cellular|cellular|JJ RNAs|rna|NNS were|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturers|manufacturer|NNS protocol|protocol|NN .|.|. Residual|residual|JJ DNA|dna|NN in|in|IN the|the|DT fractions|fraction|NNS was|be|VBD digested|digest|VBN by|by|IN addition|addition|NN of|of|IN 27|27|CD Kunitz|Kunitz|NNP units|unit|NNS Dnase|Dnase|NNP I|i|CD -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC absence|absence|NN of|of|IN DNA|dna|NN verified|verify|VBN by|by|IN Polymerase|polymerase|NN chain|chain|NN reaction|reaction|NN -LRB-|-lrb-|-LRB- PCR|pcr|NN -RRB-|-rrb-|-RRB- .|.|. mRNA|mrna|NN enrichment|enrichment|NN was|be|VBD conducted|conduct|VBN using|use|VBG the|the|DT Ribo-Zero|Ribo-Zero|NNP kit|kit|NN for|for|IN Gram-negative|gram-negative|JJ bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- epicentre|epicentre|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN quality|quality|NN control|control|NN of|of|IN the|the|DT RNA|rna|NN extracts|extract|NNS ,|,|, as|as|RB well|well|RB as|as|IN the|the|DT successful|successful|JJ mRNA|mrna|NN enrichment|enrichment|NN ,|,|, was|be|VBD conducted|conduct|VBN by|by|IN using|use|VBG an|a|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP .|.|.
total|total|VBP DNaseI|dnasei|NN treated|treated|JJ RNA|rna|NN was|be|VBD depleted|deplete|VBN of|of|IN ribosomal|ribosomal|JJ RNA|rna|NN using|use|VBG the|the|DT Ribo-Zero|Ribo-Zero|NNP ™|™|NN RNA|rna|NN removal|removal|NN kit|kit|NN for|for|IN Gram-negative|gram-negative|JJ bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|. A|a|DT 3|3|CD '|'|'' RNA|rna|NN adapter|adapter|NN ,|,|, based|base|VBN on|on|IN the|the|DT Illumina|Illumina|NNP multiplexing|multiplex|VBG adapter|adapter|NN sequence|sequence|NN -LRB-|-lrb-|-LRB- Oligonucleotide|oligonucleotide|NN sequences|sequence|NNS ©|©|SYM 2007-2014|2007-2014|CD Illumina|Illumina|NNP ,|,|, Inc.|Inc.|NNP .|.|. All|all|DT rights|rights|NNS reserved|reserve|VBN -RRB-|-rrb-|-RRB- blocked|block|VBD at|at|IN the|the|DT 3|3|CD '|'|'' end|end|NN with|with|IN an|a|DT inverted|inverted|JJ dT|dt|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: GAUCGGAAGAGCACACGUCU|gaucggaagagcacacgucu|NN -LSB-|-lsb-|-LRB- idT|idt|NN -RSB-|-rsb-|-RRB- -3|-3|CD '|'|'' -RRB-|-rrb-|-RRB- ,|,|, was|be|VBD phosphorylated|phosphorylate|VBN at|at|IN the|the|DT 5|5|CD '|'|'' end|end|NN using|use|VBG T4|t4|NN PNK|pnk|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. The|the|DT 3|3|CD '|'|'' RNA|rna|NN adapter|adapter|NN was|be|VBD ligated|ligate|VBN to|to|TO the|the|DT 3|3|CD '|'|'' ends|end|NNS of|of|IN the|the|DT rRNA|rrna|NN depleted|deplete|VBN RNA|rna|NN using|use|VBG T4|t4|NN RNA|rna|NN ligase|ligase|NN I|i|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- .|.|. 1.5|1.5|CD mg|mg|NN of|of|IN RNA|rna|NN was|be|VBD incubated|incubate|VBN at|at|IN 20|20|CD °C|°c|NN for|for|IN 6|6|CD hours|hour|NNS in|in|IN 1X|1x|NN T4|t4|NN RNA|rna|NN ligase|ligase|NN reaction|reaction|NN buffer|buffer|NN with|with|IN 1|1|CD mM|mm|NN ATP|atp|NN ,|,|, 30|30|CD µM|µm|NN 3|3|CD '|'|'' RNA|rna|NN adapter|adapter|NN ,|,|, 10|10|CD %|%|NN DMSO|dmso|NN ,|,|, 10|10|CD U|u|NN of|of|IN T4|t4|NN RNA|rna|NN ligase|ligase|NN I|I|PRP ,|,|, and|and|CC 40|40|CD U|u|NN of|of|IN RNasin|rnasin|NN -LRB-|-lrb-|-LRB- Promega|promega|NN -RRB-|-rrb-|-RRB- in|in|IN a|a|DT 20|20|CD ml|ml|NN reaction|reaction|NN .|.|. RNA|rna|NN was|be|VBD then|then|RB fragmented|fragmented|JJ in|in|IN equivalents|equivalent|NNS of|of|IN 100|100|CD ng|ng|NN using|use|VBG the|the|DT RNA|rna|NN fragmentation|fragmentation|NN reagents|reagent|NNS -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ®|®|NNP -RRB-|-rrb-|-RRB- per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN at|at|IN 70|70|CD °C|°c|NN for|for|IN 3|3|CD min|min|NN and|and|CC subsequently|subsequently|RB phosphorylated|phosphorylate|VBN at|at|IN the|the|DT 5|5|CD '|'|'' ends|end|VBZ using|use|VBG T4|t4|NN PNK|pnk|NN -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN to|to|TO allow|allow|VB for|for|IN ligation|ligation|NN of|of|IN the|the|DT 5|5|CD '|'|'' adapter|adapter|NN .|.|. RNA|rna|NN was|be|VBD size-selected|size-selected|JJ -LRB-|-lrb-|-LRB- ≈|≈|JJ 150-300|150-300|CD nt|nt|NNS -RRB-|-rrb-|-RRB- and|and|CC purified|purify|VBN over|over|IN a|a|DT denaturing|denature|VBG 8|8|CD %|%|NN polyacrylamide/8|polyacrylamide/8|CD M|m|NN urea/TBE|urea/tbe|NN gel|gel|NN .|.|. Gel|gel|NN slices|slice|NNS were|be|VBD incubated|incubate|VBN in|in|IN RNA|rna|NN elution|elution|NN buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-HCl|tris-hcl|NN ,|,|, pH|ph|NN 7.5|7.5|CD ,|,|, 2|2|CD mM|mm|NN EDTA|edta|NN ,|,|, 0.1|0.1|CD %|%|NN SDS|sds|NN ,|,|, 0.3|0.3|CD M|m|NN NaOAc|naoac|NN -RRB-|-rrb-|-RRB- with|with|IN vigorous|vigorous|JJ shaking|shake|VBG at|at|IN 4|4|CD °C|°c|NN overnight|overnight|JJ .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD subsequently|subsequently|RB ethanol|ethanol|NN precipitated|precipitate|VBD using|use|VBG glycogen|glycogen|NN as|as|IN a|a|DT carrier|carrier|NN molecule|molecule|NN .|.|. The|the|DT Illumina|Illumina|NNP small|small|JJ RNA|rna|NN 5|5|CD '|'|'' adapter|adapter|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: GUUCAGAGUUCUACAGUCCGACGAUC-3|guucagaguucuacaguccgacgauc-3|NN '|'|'' -RRB-|-rrb-|-RRB- was|be|VBD ligated|ligate|VBN to|to|TO the|the|DT RNA|rna|NN as|as|IN described|describe|VBN before|before|IN except|except|IN the|the|DT concentration|concentration|NN of|of|IN the|the|DT adapter|adapter|NN was|be|VBD 52|52|CD mM|mm|NN and|and|CC 20|20|CD U|u|NN of|of|IN T4|t4|NN RNA|rna|NN ligase|ligase|NN I|I|PRP was|be|VBD used|use|VBN in|in|IN total|total|JJ volume|volume|NN of|of|IN 25|25|CD µl|µl|NN .|.|. The|the|DT ligated|ligate|VBN RNAs|rna|NNS were|be|VBD size-selected|size-selected|JJ -LRB-|-lrb-|-LRB- ≈|≈|JJ 200-300|200-300|CD nt|nt|NNS -RRB-|-rrb-|-RRB- and|and|CC gel-purified|gel-purified|JJ over|over|IN a|a|DT denaturing|denature|VBG 8|8|CD %|%|NN polyacrylamide/8|polyacrylamide/8|CD M|m|NN urea/TBE|urea/tbe|NN gel|gel|NN -LRB-|-lrb-|-LRB- as|as|IN described|describe|VBN above|above|IN -RRB-|-rrb-|-RRB- .|.|. The|the|DT di-tagged|di-tagged|JJ RNA|rna|NN libraries|library|NNS were|be|VBD reverse-transcribed|reverse-transcribed|JJ with|with|IN SuperScript|SuperScript|NNP ®|®|NNP II|II|NNP reverse|reverse|JJ transcriptase|transcriptase|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- using|use|VBG random|random|JJ nonamers|nonamer|NNS per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. RNA|rna|NN was|be|VBD removed|remove|VBN using|use|VBG RNase|rnase|NN H|h|NN -LRB-|-lrb-|-LRB- Promega|promega|NN -RRB-|-rrb-|-RRB- per|per|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN and|and|CC cDNA|cdna|NN was|be|VBD amplified|amplify|VBN in|in|IN PCR|pcr|NN carried|carry|VBD out|out|RP using|use|VBG Phusion|Phusion|NNP ®|®|SYM High-Fidelity|High-Fidelity|NNP Polymerase|Polymerase|NNP -LRB-|-lrb-|-LRB- New|New|NNP England|England|NNP Biolabs|Biolabs|NNP -RRB-|-rrb-|-RRB- .|.|. cDNA|cdna|NN was|be|VBD amplified|amplify|VBN with|with|IN modified|modify|VBN designed|design|VBN Illumina-compatible|illumina-compatible|JJ PCR|pcr|NN primers|primer|NNS -LRB-|-lrb-|-LRB- 3|3|CD '|'|'' library|library|NN Forward|forward|RB 5|5|CD '|'|'' -|-|: CAAGCAGAAGACGGCATACGACAGGTTCAGAGTTCTACAGTCCGA-3|caagcagaagacggcatacgacaggttcagagttctacagtccga-3|NN '|'|'' ;|;|: Reverse|reverse|JJ 5|5|CD '|'|'' -|-|: AATGATACGGCGACCACCGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3|aatgatacggcgaccaccgagatgtgactggagttcagacgtgtgctcttccgatc-3|NN '|'|'' -RRB-|-rrb-|-RRB- by|by|IN 18|18|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN .|.|. The|the|DT products|product|NNS were|be|VBD purified|purify|VBN using|use|VBG Agencourt|Agencourt|NNP AMPure|AMPure|NNP XP|xp|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Beckman|Beckman|NNP -RRB-|-rrb-|-RRB- and|and|CC analyzed|analyze|VBN on|on|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP .|.|. 3|3|CD '|'|'' end|end|NN enriched|enriched|JJ cDNA|cdna|NN libraries|library|NNS were|be|VBD sequenced|sequence|VBN on|on|IN individual|individual|JJ Genome|Genome|NNP Analyzer|Analyzer|NNP IIx|IIx|NNP lanes|lane|NNS -LRB-|-lrb-|-LRB- 36|36|CD bp|bp|NN ,|,|, single-end|single-end|NN -RRB-|-rrb-|-RRB- or|or|CC on|on|IN HiSeq|HiSeq|NNP 2000|2000|CD lanes|lane|NNS -LRB-|-lrb-|-LRB- 50|50|CD bp|bp|NN ,|,|, single-end|single-end|NN -RRB-|-rrb-|-RRB- using|use|VBG primer|primer|NN based|base|VBN on|on|IN Illumina|Illumina|NNP Multiplexing|Multiplexing|NNP Read|Read|NNP 2|2|CD Sequencing|sequencing|NN Primer|primer|NN -LRB-|-lrb-|-LRB- 5|5|CD '|'|'' -|-|: GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3|gtgactggagttcagacgtgtgctcttccgatc-3|NN '|'|'' -RRB-|-rrb-|-RRB- at|at|IN the|the|DT CSF|csf|NN NGS|ngs|NN unit|unit|NN http://csf.ac.at/|http://csf.ac.at/|NN .|.|.
Total|Total|NNP DNA|dna|NN was|be|VBD extracted|extract|VBN from|from|IN three|three|CD human|human|JJ faecal|faecal|JJ samples|sample|NNS using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS DNA|dna|NN Stool|Stool|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, West|West|NNP Sussex|Sussex|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- .|.|. Total|total|JJ genomic|genomic|JJ DNA|dna|NN was|be|VBD extracted|extract|VBN from|from|IN pure|pure|JJ bacterial|bacterial|JJ cultures|culture|NNS using|use|VBG DNeasy|dneasy|JJ Blood|blood|NN and|and|CC Tissue|tissue|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, West|West|NNP Sussex|Sussex|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- .|.|. 10ng|10ng|NN of|of|IN sample|sample|NN was|be|VBD then|then|RB used|use|VBN for|for|IN PCR|pcr|NN amplification|amplification|NN .|.|. 16S|16s|CD rRNA|rrna|NN genes|gene|NNS were|be|VBD amplified|amplify|VBN using|use|VBG universal|universal|JJ primers|primer|NNS 27F|27f|NN -LRB-|-lrb-|-LRB- AGAGTTTGATCMTGGCTCAG|agagtttgatcmtggctcag|NN -RRB-|-rrb-|-RRB- and|and|CC 1492R|1492r|NN -LRB-|-lrb-|-LRB- TACGGYTACCTTGTTACGACT|tacggytaccttgttacgact|NN -RRB-|-rrb-|-RRB- .|.|. PCR|pcr|NN reactions|reaction|NNS were|be|VBD performed|perform|VBN in|in|IN a|a|DT 50µl|50µl|JJ volume|volume|NN ,|,|, using|use|VBG DreamTaq|DreamTaq|NNP DNA|DNA|NNP polymerase|polymerase|NN -LRB-|-lrb-|-LRB- Fermentas|Fermentas|NNP ,|,|, St.|St.|NNP Leon-Rot|Leon-Rot|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT PCR|pcr|NN reaction|reaction|NN consisted|consist|VBD of|of|IN an|a|DT initial|initial|JJ denaturation|denaturation|NN step|step|NN at|at|IN 95|95|CD °C|°c|NN for|for|IN 5|5|CD min|min|NN followed|follow|VBN by|by|IN 35|35|CD cycles|cycle|NNS of|of|IN denaturation|denaturation|NN at|at|IN 95|95|CD °C|°c|NN for|for|IN 30|30|CD s|s|NNS ,|,|, annealing|annealing|NN at|at|IN 58|58|CD °C|°c|NN for|for|IN 40|40|CD s|s|NNS and|and|CC elongation|elongation|NN at|at|IN 72|72|CD °C|°c|NN for|for|IN 2|2|CD min|min|NN .|.|. A|a|DT final|final|JJ extension|extension|NN step|step|NN was|be|VBD performed|perform|VBN at|at|IN 72|72|CD °C|°c|NN for|for|IN 5|5|CD min|min|NN .|.|. PCR|pcr|NN product|product|NN size|size|NN was|be|VBD verified|verify|VBN by|by|IN electrophoresis|electrophoresis|NN with|with|IN 1|1|CD %|%|NN -LRB-|-lrb-|-LRB- w/v|w/v|NN -RRB-|-rrb-|-RRB- agarose|agarose|NN gel|gel|NN and|and|CC were|be|VBD purified|purify|VBN using|use|VBG the|the|DT MinElute|MinElute|NNP PCR|pcr|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Ltd.|Ltd.|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN .|.|.
Total|Total|NNP mRNA|mrna|NN isolated|isolate|VBN from|from|IN each|each|DT cell|cell|NN culture|culture|NN was|be|VBD treated|treat|VBN with|with|IN Terminator|Terminator|NNP 5|5|CD '|'|'' Phosphate|Phosphate|NNP Dependent|Dependent|NNP Exonuclease|Exonuclease|NNP -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- to|to|TO enrich|enrich|VB 5|5|CD '|'|'' tri-phosphorylated|tri-phosphorylated|JJ mRNAs|mrna|NNS .|.|. Intact|intact|JJ tri-phosphorylated|tri-phosphorylated|JJ RNAs|rna|NNS were|be|VBD then|then|RB treated|treat|VBN with|with|IN RNA|rna|NN 5|5|CD '|'|'' -|-|: Polyphosphatase|polyphosphatase|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- to|to|TO generate|generate|VB 5|5|CD '|'|'' -|-|: end|end|VB monophosphorylated|monophosphorylate|VBN RNA|rna|NN for|for|IN ligation|ligation|NN to|to|TO RNA|rna|NN adaptors|adaptor|NNS .|.|. cDNAs|cdna|NNS were|be|VBD synthesized|synthesize|VBN using|use|VBG the|the|DT adaptor-ligated|adaptor-ligated|JJ mRNAs|mrna|NNS as|as|IN template|template|NN using|use|VBG a|a|DT modified|modify|VBN small|small|JJ RNA|rna|NN RT|rt|NN primer|primer|NN from|from|IN Illumina|Illumina|NNP and|and|CC Superscript|Superscript|NNP II|II|NNP Reverse|reverse|JJ Transcriptase|transcriptase|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT cDNA|cdna|NN samples|sample|NNS were|be|VBD amplified|amplify|VBN ,|,|, and|and|CC size|size|NN fractionated|fractionate|VBN from|from|IN 100|100|CD to|to|TO 300|300|CD bp|bp|NN .|.|.
Total|Total|NNP RNA|rna|NN -LRB-|-lrb-|-LRB- 2ug|2ug|JJ -RRB-|-rrb-|-RRB- was|be|VBD subjected|subject|VBN to|to|TO rRNA|rrna|NN depletion|depletion|NN using|use|VBG Ribozero|Ribozero|NNP rRNA|rrna|NN removal|removal|NN kit|kit|NN --|--|: Bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- Epicenter|epicenter|NN ,|,|, illumina|illumina|NN -RRB-|-rrb-|-RRB- .|.|. rRNA-depleted|rrna-depleted|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG Ampure|Ampure|NNP XP|xp|NN beads|bead|NNS .|.|. Purified|purify|VBN RNA|rna|NN was|be|VBD then|then|RB fragmented|fragmented|JJ using|use|VBG RNA|rna|NN Fragmentation|fragmentation|NN Reagents|reagent|NNS -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- at|at|IN 70C|70C|NNP for|for|IN 2|2|CD mins|min|NNS ,|,|, targeting|target|VBG fragments|fragment|NNS ranging|range|VBG from|from|IN 200-300bp|200-300bp|JJ .|.|. Fragmented|fragmented|JJ RNA|rna|NN was|be|VBD then|then|RB purified|purify|VBN using|use|VBG Ampure|Ampure|NNP XP|xp|NN beads|bead|NNS -LRB-|-lrb-|-LRB- Agencourt|agencourt|NN -RRB-|-rrb-|-RRB- .|.|. Reverse|reverse|JJ transcription|transcription|NN was|be|VBD performed|perform|VBN using|use|VBG SuperScript|SuperScript|NNP II|II|NNP Reverse|reverse|JJ Transcription|transcription|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- with|with|IN an|a|DT initial|initial|JJ annealing|annealing|NN of|of|IN random|random|JJ hexamers|hexamer|NNS -LRB-|-lrb-|-LRB- Fermentas|fermenta|NNS -RRB-|-rrb-|-RRB- at|at|IN 65C|65c|NN for|for|IN 5|5|CD mins|min|NNS ,|,|, follow|follow|VBP by|by|IN an|a|DT incubation|incubation|NN of|of|IN 42C|42c|NN for|for|IN 50|50|CD mins|min|NNS and|and|CC an|a|DT inactivation|inactivation|NN step|step|NN at|at|IN 70C|70C|NNP for|for|IN 10|10|CD mins|min|NNS .|.|. cDNA|cdna|NN was|be|VBD then|then|RB purified|purify|VBN with|with|IN Ampure|Ampure|NNP XP|xp|NN beads|bead|NNS .|.|. This|this|DT was|be|VBD followed|follow|VBN by|by|IN second|second|JJ strand|strand|NN synthesis|synthesis|NN using|use|VBG dNTP|dntp|NN mix|mix|NN where|where|WRB dTTP|dttp|NN is|be|VBZ replaced|replace|VBN by|by|IN dUTP|dutp|NN .|.|. Reaction|reaction|NN was|be|VBD performed|perform|VBN at|at|IN 16C|16c|NN for|for|IN 1h|1h|NN .|.|. Double|double|JJ stranded|strand|VBN cDNA|cdna|NN fragments|fragment|NNS were|be|VBD purified|purify|VBN and|and|CC selected|select|VBN for|for|IN targeted|target|VBN fragments|fragment|NNS -LRB-|-lrb-|-LRB- 200-300bp|200-300bp|JJ -RRB-|-rrb-|-RRB- using|use|VBG Ampure|Ampure|NNP XP|xp|NN beads|bead|NNS .|.|. The|the|DT dscDNA|dscdna|NN were|be|VBD then|then|RB blunt-ended|blunt-ended|JJ ,|,|, the|the|DT 3|3|CD '|'|'' ends|end|NNS were|be|VBD adenylated|adenylate|VBN with|with|IN a|a|DT single|single|JJ A|a|NN ,|,|, and|and|CC ligated|ligate|VBN with|with|IN library|library|NN adapters|adapter|NNS using|use|VBG Kapa|Kapa|NNP Library|Library|NNP Amplification|Amplification|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Kapa|Kapa|NNP Biosystems|Biosystems|NNP -RRB-|-rrb-|-RRB- .|.|. Adapter-ligated|adapter-ligated|JJ DNA|dna|NN was|be|VBD purified|purify|VBN using|use|VBG Ampure|Ampure|NNP XP|xp|NN beads|bead|NNS .|.|. Digestion|digestion|NN of|of|IN dUTP|dutp|NN was|be|VBD then|then|RB performed|perform|VBN using|use|VBG AmpErase|AmpErase|NNP UNG|UNG|NNP -LRB-|-lrb-|-LRB- Applied|Applied|NNP Biosystems|Biosystems|NNPS -RRB-|-rrb-|-RRB- to|to|TO remove|remove|VB second|second|JJ strand|strand|NN cDNA|cdna|NN .|.|. Digested|digest|VBN cDNA|cdna|NN was|be|VBD again|again|RB cleaned|clean|VBN up|up|RP with|with|IN Ampure|Ampure|NNP SPRI|SPRI|NNP beads|bead|NNS .|.|. This|this|DT was|be|VBD followed|follow|VBN by|by|IN amplification|amplification|NN by|by|IN 10|10|CD cycles|cycle|NNS of|of|IN PCR|pcr|NN using|use|VBG Kapa|Kapa|NNP Library|Library|NNP Amplification|Amplification|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Kapa|Kapa|NNP Biosystems|Biosystems|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT final|final|JJ library|library|NN was|be|VBD cleaned|clean|VBN up|up|RP with|with|IN Ampure|Ampure|NNP SPRI|SPRI|NNP beads|bead|NNS .|.|. Sequencing|sequencing|NN was|be|VBD done|do|VBN on|on|IN the|the|DT Illumina|Illumina|NNP HiSeq|HiSeq|NNP platform|platform|NN generating|generate|VBG paired|paired|JJ end|end|NN reads|read|VBZ of|of|IN 100bp|100bp|JJ each|each|DT .|.|. Note|note|VB :|:|: Target|target|NN fragments|fragment|NNS here|here|RB refers|refer|VBZ to|to|TO the|the|DT insert|insert|NN only|only|RB ,|,|, that|that|DT is|be|VBZ the|the|DT cDNA|cdna|NN .|.|. The|the|DT actual|actual|JJ size|size|NN we|we|PRP use|use|VBP in|in|IN selection|selection|NN will|will|MD be|be|VB larger|larger|JJR ,|,|, typically|typically|RB the|the|DT target|target|NN fragment|fragment|NN size|size|NN +|+|CC 125bp|125bp|NN adaptors|adaptor|NNS -LRB-|-lrb-|-LRB- ~|~|CD 300-450bp|300-450bp|JJ -RRB-|-rrb-|-RRB- .|.|.
Total|total|JJ RNA|rna|NN extracted|extract|VBN from|from|IN Rho|rho|NN prion-containing|prion-containing|JJ cells|cell|NNS
Total|total|JJ RNA|rna|NN extracted|extract|VBN from|from|IN Rho|rho|NN prion-lacking|prion-lacking|JJ cells|cell|NNS
Total|total|JJ RNA|rna|NN extracted|extract|VBN using|use|VBG Qiagen|Qiagen|NNP RNEASY|RNEASY|NNP kit|kit|NN according|accord|VBG to|to|TO directions|direction|NNS
Total|Total|NNP RNA|RNA|NNP extracted|extract|VBN using|use|VBG QIAGEN|QIAGEN|NNP RNeasy|RNeasy|NNP kit|kit|NN according|accord|VBG to|to|TO manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS
Total|Total|NNP RNA|RNA|NNP extracted|extract|VBN using|use|VBG RiboEX|RiboEX|NNP reagent|reagent|NN -LRB-|-lrb-|-LRB- GeneAll|GeneAll|NNP ,|,|, Korea|Korea|NNP -RRB-|-rrb-|-RRB- ,|,|, treated|treat|VBN with|with|IN Dnase|Dnase|NNP ,|,|, and|and|CC purified|purify|VBN using|use|VBG the|the|DT Rneasy|Rneasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
Total|total|JJ RNA|rna|NN extracted|extract|VBN using|use|VBG RNAprotect|rnaprotect|NN Bacterial|bacterial|JJ Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC an|a|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
total|total|JJ RNA|rna|NN extracted|extract|VBN using|use|VBG Trizol|Trizol|NNP Extraction|Extraction|NNP Protocol|Protocol|NNP
Total|Total|NNP RNA|RNA|NNP extracted|extract|VBN using|use|VBG Trizol|Trizol|NNP following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS
Total|Total|NNP RNA|rna|NN extraction|extraction|NN using|use|VBG Vantage|Vantage|NNP ™|™|CD RNA|rna|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Origene|Origene|NNP ,|,|, Rockville|Rockville|NNP ,|,|, MD|MD|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- was|be|VBD performed|perform|VBN according|accord|VBG with|with|IN the|the|DT manufacter|manufacter|NN instructions|instruction|NNS .|.|. Purity|purity|NN and|and|CC concentration|concentration|NN of|of|IN isolated|isolate|VBN RNA|rna|NN were|be|VBD assessed|assess|VBN in|in|IN a|a|DT NanoDrop|NanoDrop|NNP One|one|CD spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP Incorporated|Incorporated|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. Quality|Quality|NNP was|be|VBD evaluated|evaluate|VBN by|by|IN microfluidic|microfluidic|JJ capillary|capillary|JJ electrophoresis|electrophoresis|NN on|on|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Inc|Inc|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN extraction|extraction|NN was|be|VBD carried|carry|VBN out|out|RP based|base|VBN on|on|IN the|the|DT protocols|protocol|NNS given|give|VBN in|in|IN the|the|DT manual|manual|NN of|of|IN QIAGEN|QIAGEN|NNP -|-|: RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|Reagent|NNP Handbook|Handbook|NNP ,|,|, QIAGEN|QIAGEN|NNP -|-|: RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN and|and|CC QIAGEN|QIAGEN|NNP -|-|: RNase-free|rnase-free|JJ DNase|dnase|NN set|set|NN .|.|. The|the|DT concentration|concentration|NN of|of|IN each|each|DT RNA|rna|NN sample|sample|NN was|be|VBD measured|measure|VBN by|by|IN Qubit|Qubit|NNP ®|®|NNP RNA|rna|NN BR|br|NN Assay|assay|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN extraction|extraction|NN was|be|VBD done|do|VBN using|use|VBG TRIzol|trizol|NN reagent|reagent|NN and|and|CC DNAse|dnase|NN digested|digest|VBN .|.|. RNA|rna|NN purfication|purfication|NN was|be|VBD carried|carry|VBN out|out|RP using|use|VBG Rneasy|Rneasy|NNP spin|spin|VB columns|column|NNS
Total|Total|NNP RNA|rna|NN from|from|IN 8.1|8.1|CD *|*|SYM 10exp9|10exp9|CD cells|cell|NNS was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. On-column|on-column|JJ DNase|dnase|NN digestion|digestion|NN was|be|VBD performed|perform|VBN -LRB-|-lrb-|-LRB- RNase|rnase|NN free|free|JJ DNase|dnase|NN set|set|NN ,|,|, Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN concentration|concentration|NN and|and|CC quality|quality|NN were|be|VBD assessed|assess|VBN photometrically|photometrically|RB -LRB-|-lrb-|-LRB- Nanodrop|nanodrop|JJ ND|nd|NN 1000|1000|CD ,|,|, NanoDrop|NanoDrop|NNP Technologies|Technologies|NNPS ,|,|, Inc.|Inc.|NNP ,|,|, Delaware|Delaware|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- ,|,|, by|by|IN formaldehyde|formaldehyde|NN gel|gel|NN electrophoresis|electrophoresis|NN and|and|CC bioanalyzer|bioanalyzer|NN analysis|analysis|NN -LRB-|-lrb-|-LRB- RNA|rna|NN 6000|6000|CD Nano|Nano|NNP LabChip|LabChip|NNP Kit|kit|NN ,|,|, Agilent|Agilent|NNP Bioanalyzer|Bioanalyzer|NNP 2100|2100|CD ,|,|, Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, California|California|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. Only|only|RB RNA|rna|NN with|with|IN 260|260|CD nm|nm|NN /|/|: 280|280|CD nm|nm|NN ratio|ratio|NN of|of|IN 1.8|1.8|CD -|-|: 2|2|CD as|as|RB well|well|RB as|as|IN 260|260|CD nm|nm|NN /|/|: 230|230|CD nm|nm|NN ratio|ratio|NN >|>|JJR 1.8|1.8|CD was|be|VBD used|use|VBN for|for|IN precipitation|precipitation|NN .|.|. The|the|DT RNA|rna|NN was|be|VBD precipitated|precipitated|JJ and|and|CC resolved|resolve|VBN at|at|IN the|the|DT final|final|JJ concentration|concentration|NN of|of|IN 6|6|CD µg|µg|NN /|/|: µl|µl|NN required|require|VBN for|for|IN reverse|reverse|JJ transcription|transcription|NN and|and|CC labeling|labeling|NN with|with|IN fluorescent|fluorescent|JJ dyes|dye|NNS .|.|. Total|total|JJ RNA|rna|NN isolate|isolate|NN was|be|VBD mixed|mix|VBN with|with|IN 1/10|1/10|CD volume|volume|NN of|of|IN NaCl|nacl|NN solution|solution|NN -LRB-|-lrb-|-LRB- 3|3|CD M|m|NN -RRB-|-rrb-|-RRB- and|and|CC 2|2|CD volumes|volume|NNS of|of|IN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- 100|100|CD %|%|NN -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN at|at|IN -20|-20|CD °C|°c|NN overnight|overnight|JJ .|.|. The|the|DT samples|sample|NNS were|be|VBD subsequently|subsequently|RB centrifuged|centrifuge|VBN -LRB-|-lrb-|-LRB- 14000|14000|CD rpm|rpm|NN ;|;|: 20800|20800|CD g|g|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD discarded|discard|VBN .|.|. The|the|DT RNA|rna|NN was|be|VBD washed|wash|VBN with|with|IN ethanol|ethanol|NN -LRB-|-lrb-|-LRB- 70|70|CD %|%|NN -RRB-|-rrb-|-RRB- and|and|CC vacuum|vacuum|NN dried|dry|VBD .|.|. 100|100|CD µg|µg|NN of|of|IN RNA|rna|NN were|be|VBD used|use|VBN for|for|IN reverse|reverse|JJ transcription|transcription|NN .|.|.
Total|Total|NNP RNA|rna|NN from|from|IN bacterial|bacterial|JJ culture|culture|NN
Total|Total|NNP RNA|rna|NN from|from|IN both|both|CC the|the|DT in|in|FW vitro|vitro|FW and|and|CC in|in|FW vivo|vivo|FW samples|sample|NNS of|of|IN APEC|APEC|NNP E058|e058|NN was|be|VBD extracted|extract|VBN with|with|IN the|the|DT RNAiso|rnaiso|NN Plus|plus|NN kit|kit|NN -LRB-|-lrb-|-LRB- Takara|Takara|NNP ,|,|, Dalian|Dalian|NNP ,|,|, China|China|NNP -RRB-|-rrb-|-RRB- and|and|CC further|further|JJ purified|purify|VBN with|with|IN NucleoSpin|nucleospin|NN RNA|rna|NN Clean-up|clean-up|NN -LRB-|-lrb-|-LRB- Macherey-Nagel|Macherey-Nagel|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturers|manufacturer|NNS '|'|POS instructions|instruction|NNS .|.|.
Total|Total|NNP RNA|rna|NN from|from|IN cells|cell|NNS of|of|IN the|the|DT microemulsion-treated|microemulsion-treated|JJ E.|e.|FW coli|coli|FW was|be|VBD extracted|extract|VBN in|in|IN duplicate|duplicate|VB using|use|VBG an|a|DT RNAiso|rnaiso|NN Plus|plus|NN -LRB-|-lrb-|-LRB- Cat|cat|NN .|.|. #|#|# 908|908|CD ,|,|, Takara|Takara|NNP ,|,|, Japan|Japan|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS ,|,|,
Total|Total|NNP RNA|rna|NN from|from|IN in|in|FW vivo|vivo|FW samples|sample|NNS of|of|IN APEC|APEC|NNP E058|e058|NN and|and|CC E058ΔrstAB|e058δrstab|NN was|be|VBD extracted|extract|VBN and|and|CC purified|purify|VBN using|use|VBG RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #|#|# 74106|74106|CD ,|,|, QIAGEN|QIAGEN|NNP ,|,|, GmBH|GmBH|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
Total|Total|NNP RNA|rna|NN is|be|VBZ extracted|extract|VBN from|from|IN 10|10|CD ^|^|CD 9|9|CD cells|cell|NNS by|by|IN phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN according|accord|VBG to|to|TO Sambrook|Sambrook|NNP et|et|FW al.|al.|FW and|and|CC ethanol|ethanol|NN precipitation|precipitation|NN with|with|IN 5M|5m|NN NaCl|nacl|NN .|.|. Subsequently|subsequently|RB a|a|DT DNAse|dnase|NN I|I|PRP digest|digest|VBP at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS and|and|CC an|a|DT additional|additional|JJ phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN step|step|NN is|be|VBZ performed|perform|VBN .|.|. Integrity|integrity|NN of|of|IN the|the|DT total|total|JJ RNA|rna|NN is|be|VBZ electrophoretically|electrophoretically|RB confirmed|confirm|VBN using|use|VBG the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP .|.|.
Total|Total|NNP RNA|rna|NN is|be|VBZ extracted|extract|VBN from|from|IN 10|10|CD ^|^|CD 9|9|CD cells|cell|NNS by|by|IN phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN and|and|CC ethanol|ethanol|NN precipitation|precipitation|NN with|with|IN 5M|5m|NN NaCl|nacl|NN .|.|. Subsequently|subsequently|RB a|a|DT DNAse|dnase|NN I|I|PRP digest|digest|VBP at|at|IN 37|37|CD °C|°c|NN for|for|IN 30|30|CD minutes|minute|NNS and|and|CC an|a|DT additional|additional|JJ phenol-chloroform|phenol-chloroform|JJ extraction|extraction|NN step|step|NN is|be|VBZ performed|perform|VBN .|.|. Integrity|integrity|NN of|of|IN the|the|DT total|total|JJ RNA|rna|NN is|be|VBZ electrophoretically|electrophoretically|RB confirmed|confirm|VBN using|use|VBG the|the|DT Agilent|Agilent|NNP 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP .|.|.
Total|Total|NNP RNA|rna|NN isolated|isolate|VBN from|from|IN E.|e.|FW coli|coli|FW
Total|total|JJ RNA|rna|NN isolation|isolation|NN was|be|VBD performed|perform|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Protect|Protect|NNP Bacteria|bacterium|NNS system|system|NN from|from|IN Qiagen|Qiagen|NNP .|.|.
Total|Total|NNP RNA|rna|NN samples|sample|NNS were|be|VBD isolated|isolate|VBN using|use|VBG RNAzol|rnazol|NN RT|rt|NN -LRB-|-lrb-|-LRB- Molecular|molecular|JJ Research|Research|NNP Center|Center|NNP -RRB-|-rrb-|-RRB- by|by|IN following|follow|VBG manufature|manufature|NN 's|'s|POS instructions|instruction|NNS .|.|. Contaminating|contaminate|VBG DNA|dna|NN was|be|VBD removed|remove|VBN from|from|IN RNA|rna|NN samples|sample|NNS by|by|IN DNase|dnase|NN I|i|CD digestion|digestion|NN using|use|VBG the|the|DT TURBO|TURBO|NNP DNA-free|dna-free|JJ kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN samples|sample|NNS were|be|VBD purified|purify|VBN using|use|VBG the|the|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Chatsworth|Chatsworth|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
Total|Total|NNP RNA-seq|RNA-seq|NNP 20|20|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD rnr|rnr|NN cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN 20|20|CD min|min|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN 4|4|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD rnr|rnr|NN cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN 4|4|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD rnr|rnr|NN cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN 8|8|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN after|after|IN rifampicin|rifampicin|NN treatment|treatment|NN --|--|: 4|4|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD rnr|rnr|NN cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN after|after|IN rifampicin|rifampicin|NN treatment|treatment|NN --|--|: 4|4|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN before|before|IN rifampicin|rifampicin|NN treatment|treatment|NN --|--|: 2|2|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN ∆|∆|CD rnr|rnr|NN cells|cell|NNS
Total|total|JJ RNA-seq|rna-seq|NN before|before|IN rifampicin|rifampicin|NN treatment|treatment|NN --|--|: 2|2|CD hr|hr|NN after|after|IN shift|shift|NN to|to|TO 10|10|CD °C|°c|NN in|in|IN WT|wt|JJ cells|cell|NNS
Total|total|JJ RNAs|rna|NNS from|from|IN two|two|CD biological|biological|JJ replicate|replicate|VB ,|,|, each|each|DT with|with|IN two|two|CD technical|technical|JJ replicates|replicate|VBZ were|be|VBD extracted|extract|VBN using|use|VBG the|the|DT Total|total|JJ RNA|rna|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Norgen|Norgen|NNP Biotek|Biotek|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN with|with|IN the|the|DT addition|addition|NN of|of|IN 1|1|CD mg/ml|mg/ml|NN lysozyme|lysozyme|NN for|for|IN cell|cell|NN lysis|lysis|NN .|.|.
Total|Total|NNP RNAs|rna|NNS were|be|VBD extracted|extract|VBN from|from|IN the|the|DT bacterial|bacterial|JJ isolates|isolate|NNS using|use|VBG TRIzol|trizol|NN
Total|total|JJ RNAs|rna|NNS were|be|VBD extracted|extract|VBN using|use|VBG an|a|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- in|in|IN accordance|accordance|NN with|with|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
Total|Total|NNP RNAs|rna|NNS were|be|VBD extracted|extract|VBN using|use|VBG RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, #|#|# 74104|74104|CD -RRB-|-rrb-|-RRB- following|follow|VBG manufacture|manufacture|NN 's|'s|POS instruction|instruction|NN
Total|total|JJ RNAs|rna|NNS were|be|VBD isolated|isolate|VBN using|use|VBG TRIzol|trizol|NN reagent|reagent|NN ,|,|, followed|follow|VBN by|by|IN clean-up|clean-up|JJ and|and|CC DNase|dnase|NN I|i|CD treatment|treatment|NN with|with|IN QIAGEN|QIAGEN|NNP RNeasy|RNeasy|NNP mini|minus|NNS kit|kit|NN .|.|. Illumina|Illumina|NNP TruSeq|TruSeq|NNP RNA|rna|NN Sample|sample|NN Prep|Prep|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Cat|cat|NN #FC|#fc|NN -122-1001|-122-1001|CD -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN the|the|DT construction|construction|NN of|of|IN sequencing|sequencing|NN libraries|library|NNS .|.|.
Total|Total|NNP RNA|rna|NN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP kit|kit|NN
Total|Total|NNP RNA|rna|NN was|be|VBD depleted|deplete|VBN of|of|IN ribosomal|ribosomal|JJ RNAs|rna|NNS using|use|VBG Epicentre|Epicentre|NNP 's|'s|POS RiboZero|RiboZero|NNP rRNA|rrna|NN removal|removal|NN kit|kit|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN and|and|CC DNase-treated|dnase-treated|JJ according|accord|VBG to|to|TO published|publish|VBN protocols|protocol|NNS -LRB-|-lrb-|-LRB- Khodurksy|khodurksy|NN A|a|NN ,|,|, Bernstein|Bernstein|NNP J|J|NNP ,|,|, Peter|Peter|NNP B|B|NNP ,|,|, Rhodius|Rhodius|NNP V|V|NNP ,|,|, Wendisch|Wendisch|NNP V|V|NNP ,|,|, Zimmer|Zimmer|NNP D.|D.|NNP Escherichia|escherichia|FW coli|coli|FW Spotted|spot|VBN Double-Strand|Double-Strand|NNP DNA|DNA|NNP Microarrays|Microarrays|NNPS -RRB-|-rrb-|-RRB-
Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN by|by|IN the|the|DT hot|hot|JJ phenol|phenol|NN --|--|: chloroform|chloroform|NN method|method|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN 1|1|CD ml|ml|NN cells|cell|NNS using|use|VBG the|the|DT RNeasy|RNeasy|NNP Protect|Protect|NNP Bacteria|bacterium|NNS Mini|Mini|NNP Prep|Prep|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- as|as|IN recommended|recommend|VBN by|by|IN the|the|DT manufacturer|manufacturer|NN including|include|VBG the|the|DT ``|``|`` on-column|on-column|JJ ''|''|'' DNase|dnase|NN treatment|treatment|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN 5|5|CD ml|ml|NN cell|cell|NN culture|culture|NN after|after|IN 30|30|CD min|min|NN incubation|incubation|NN with|with|IN or|or|CC without|without|IN H2O2|h2o2|NN treatment|treatment|NN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Inc.|Inc.|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN
Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN 5|5|CD ml|ml|NN cell|cell|NN culture|culture|NN at|at|IN 0|0|CD ,|,|, 10|10|CD ,|,|, 30|30|CD and|and|CC 60|60|CD min|min|NN incubation|incubation|NN after|after|IN addition|addition|NN of|of|IN 5|5|CD %|%|NN isooctane|isooctane|NN using|use|VBG RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Inc.|Inc.|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN
Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN 5|5|CD ml|ml|NN cell|cell|NN culture|culture|NN at|at|IN 10|10|CD min|min|NN incubation|incubation|NN with|with|IN or|or|CC without|without|IN 1|1|CD %|%|NN Hydrogen|hydrogen|NN peroxide|peroxide|NN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Inc.|Inc.|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN
Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN cell|cell|NN pellets|pellet|NNS by|by|IN hot|hot|JJ phenol|phenol|NN extraction|extraction|NN .|.|. The|the|DT integrity|integrity|NN of|of|IN total|total|JJ RNA|rna|NN was|be|VBD determined|determine|VBN from|from|IN agarose|agarose|NN gel|gel|NN or|or|CC microchannel|microchannel|NN electrophoretograms|electrophoretogram|NNS .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN cell|cell|NN pellets|pellet|NNS by|by|IN hot|hot|JJ phenol|phenol|NN extraction|extraction|NN .|.|. The|the|DT integrity|integrity|NN of|of|IN total|total|JJ RNA|rna|NN was|be|VBD determined|determine|VBN from|from|IN agarose|agarose|NN gel|gel|NN or|or|CC microchannel|microchannel|NN electrophoretograms|electrophoretogram|NNS .|.|. 16S|16s|NN and|and|CC 23S|23s|NN Ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD depleted|deplete|VBN prior|prior|RB to|to|TO construction|construction|NN of|of|IN RNAseq|rnaseq|NN libraries|library|NNS using|use|VBG MICROBExpress|microbexpress|NN reagents|reagent|NNS .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN cell|cell|NN pellets|pellet|NNS with|with|IN TRI|TRI|NNP Reagent|Reagent|NNP -LRB-|-lrb-|-LRB- MRC|MRC|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD precipitated|precipitated|JJ ,|,|, resuspended|resuspended|JJ in|in|IN DNase|dnase|NN Reaction|reaction|NN Buffer|buffer|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- for|for|IN 30|30|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN .|.|. DNase-treated|dnase-treated|JJ samples|sample|NNS were|be|VBD subsequently|subsequently|RB purified|purify|VBN with|with|IN an|a|DT Rneasy|Rneasy|NNP Plus|Plus|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN cells|cell|NNS with|with|IN the|the|DT UltraClean|UltraClean|NNP Microbial|Microbial|NNP RNA|rna|NN isolation|isolation|NN kit|kit|NN -LRB-|-lrb-|-LRB- MO|MO|NNP BIO|BIO|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|. After|after|IN extraction|extraction|NN ,|,|, contaminating|contaminate|VBG DNA|dna|NN was|be|VBD digested|digest|VBN with|with|IN DNAse|dnase|NN I|i|NN -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP -RRB-|-rrb-|-RRB- and|and|CC total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN by|by|IN phenol/chloroform|phenol/chloroform|NN extraction|extraction|NN and|and|CC ethanol|ethanol|NN precipitation|precipitation|NN .|.|. RNA|rna|NN purity|purity|NN and|and|CC quantity|quantity|NN was|be|VBD assess|assess|VB by|by|IN optical|optical|JJ density|density|NN measurements|measurement|NNS -LRB-|-lrb-|-LRB- OD|od|NN 260/280|260/280|CD and|and|CC OD|od|NN 260/230|260/230|CD -RRB-|-rrb-|-RRB- and|and|CC RNA|rna|NN integrity|integrity|NN was|be|VBD checked|check|VBN with|with|IN the|the|DT Bioanalyseur|Bioanalyseur|NNP 2100|2100|CD -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP Rna|Rna|NNP was|be|VBD extracted|extract|VBN from|from|IN cultures|culture|NNS using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Protect|protect|VB Bacteria|bacterium|NNS Mini|Mini|NNP Kit|kit|NN .|.|. For|for|IN rRNA|rrna|NN depletion|depletion|NN ,|,|, samples|sample|NNS were|be|VBD treated|treat|VBN with|with|IN the|the|DT MICROBExpressTM|MICROBExpressTM|NNP Bacterial|bacterial|JJ mRNA|mrna|NN Enrichment|Enrichment|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Samples|sample|NNS were|be|VBD cleaned|clean|VBN with|with|IN the|the|DT Zymo|Zymo|NNP RNA|rna|NN Clean|clean|JJ and|and|CC ConcentratorTM|concentratortm|NN -LRB-|-lrb-|-LRB- Zymo|Zymo|NNP Research|Research|NNP -RRB-|-rrb-|-RRB- and|and|CC then|then|RB subjected|subject|VBN to|to|TO a|a|DT second|second|JJ cycle|cycle|NN of|of|IN rRNA|rrna|NN depletion|depletion|NN .|.|. RNA|rna|NN was|be|VBD recovered|recover|VBN by|by|IN ethanol|ethanol|NN precipitation|precipitation|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG a|a|DT hot|hot|JJ phenol|phenol|NN method|method|NN -LRB-|-lrb-|-LRB- Khodursky|Khodursky|NNP et|et|FW al|al|FW ,|,|, Methods|method|NNS in|in|IN Molecular|molecular|JJ Biology|Biology|NNP 2003|2003|CD -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG a|a|DT Thermo|Thermo|NNP Scientific|Scientific|NNP GeneJET|GeneJET|NNP RNA|rna|NN isolation|isolation|NN kit|kit|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG MasterPure|masterpure|NN RNA|rna|NN purification|purification|NN kits|kit|NNS -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN
Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP kit|kit|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Hilden|hilden|NN ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- following|follow|VBG manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS and|and|CC checked|check|VBD for|for|IN a|a|DT RIN|rin|NN number|number|NN to|to|TO inspect|inspect|VB RNA|rna|NN integration|integration|NN by|by|IN an|a|DT Agilent|Agilent|NNP Bioanalyzer|Bioanalyzer|NNP 2100|2100|CD -LRB-|-lrb-|-LRB- Agilent|agilent|JJ technologies|technology|NNS ,|,|, Santa|Santa|NNP Clara|Clara|NNP ,|,|, CA|CA|NNP ,|,|, US|US|NNP -RRB-|-rrb-|-RRB- .|.|. Qualified|qualify|VBN total|total|JJ RNA|rna|NN was|be|VBD further|further|JJ purified|purify|VBN by|by|IN RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP ,|,|, GmBH|GmBH|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- and|and|CC RNase‐Free|rnase‐free|NN DNase|dnase|NN Set|set|VB -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP ,|,|, GmBH|GmBH|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN .|.|. DNA|dna|NN was|be|VBD removed|remove|VBN using|use|VBG Ambion|Ambion|NNP DNA-free|dna-free|JJ kit|kit|NN .|.|. RNA|rna|NN quality|quality|NN was|be|VBD assessed|assess|VBN using|use|VBG 2|2|CD %|%|NN agarose|agarose|NN gels|gel|NNS and|and|CC OD260/OD280|od260/od280|NN ratio|ratio|NN .|.|. Amino-allyl|amino-allyl|JJ dUTP|dutp|NN was|be|VBD used|use|VBN to|to|TO label|label|VB 5µg|5µg|NN of|of|IN RNA|rna|NN during|during|IN reverse|reverse|JJ transcription|transcription|NN .|.|. The|the|DT reverse|reverse|JJ transcription|transcription|NN was|be|VBD performed|perform|VBN at|at|IN 42|42|CD °C|°c|NN during|during|IN 50|50|CD min|min|NN using|use|VBG 600|600|CD units|unit|NNS of|of|IN superscript|superscript|JJ RT|rt|NN II|ii|CD -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- ,|,|, 3|3|CD µg|µg|NN of|of|IN random|random|JJ hexamers|hexamer|NNS ,|,|, 0.6|0.6|CD mM|mm|NN dATP|datp|NN ,|,|, dCTP|dctp|NN and|and|CC dGTP|dgtp|NN ,|,|, 0.2|0.2|CD mM|mm|NN dTTP|dttp|NN ,|,|, and|and|CC 0.4|0.4|CD mM|mm|NN amino-allyl|amino-allyl|NN dUTP|dutp|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN was|be|VBD then|then|RB degraded|degrade|VBN by|by|IN incubation|incubation|NN at|at|IN 65|65|CD °C|°c|NN ,|,|, for|for|IN 15|15|CD min|min|NN ,|,|, after|after|IN adding|add|VBG 10µL|10µl|NN of|of|IN 0.5|0.5|CD M|m|NN EDTA|edta|NN and|and|CC 10µL|10µl|NN of|of|IN 1M|1m|NN NaOH|naoh|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO instructions|instruction|NNS in|in|IN the|the|DT kit|kit|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT genomic|genomic|JJ DNA|dna|NN was|be|VBD removed|remove|VBN using|use|VBG RNase-Free|rnase-free|JJ DNase|dnase|NN Set|set|VB -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT commercial|commercial|JJ product|product|NN TRIzol|trizol|NN Reagent|reagent|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP -RRB-|-rrb-|-RRB- .|.|. Disrupt|disrupt|VB about|about|IN 107cells|107cell|NNS with|with|IN a|a|DT homogenizer|homogenizer|NN with|with|IN 1|1|CD ml|ml|NN TRIzol|trizol|NN Reafent|reafent|NN on|on|IN ice|ice|NN .|.|. Store|Store|NNP the|the|DT homogenate|homogenate|NN for|for|IN 5|5|CD minutes|minute|NNS at|at|IN room|room|NN temperature|temperature|NN to|to|TO permit|permit|VB the|the|DT complete|complete|JJ dissociation|dissociation|NN of|of|IN nucleoprotein|nucleoprotein|NN complexes|complex|NNS .|.|. Next|next|RB ,|,|, supplement|supplement|VBP the|the|DT homogenate|homogenate|NN with|with|IN 0.2|0.2|CD ml|ml|NN chloroform|chloroform|NN per|per|IN 1|1|CD ml|ml|NN of|of|IN TRI|TRI|NNP Reagent|Reagent|NNP ,|,|, cover|cover|VBP the|the|DT samples|sample|NNS tightly|tightly|RB and|and|CC shake|shake|VB vigorously|vigorously|RB for|for|IN 15|15|CD seconds|seconds|NNS .|.|. Store|Store|NNP the|the|DT resulting|result|VBG mixture|mixture|NN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 2-15|2-15|CD minutes|minute|NNS and|and|CC centrifuge|centrifuge|NN at|at|IN 12,000|12,000|CD g|g|NN for|for|IN 15|15|CD minutes|minute|NNS at|at|IN 4|4|CD C.|C.|NNP Following|follow|VBG centrifugation|centrifugation|NN ,|,|, the|the|DT mixture|mixture|NN separates|separate|VBZ into|into|IN a|a|DT lower|lower|JJR red|red|JJ phenol-chloroform|phenol-chloroform|NN phase|phase|NN ,|,|, interphase|interphase|NN and|and|CC the|the|DT colorless|colorless|JJ upper|upper|JJ aqueous|aqueous|JJ phase|phase|NN .|.|. Transfer|transfer|NN the|the|DT aqueous|aqueous|JJ phase|phase|NN to|to|TO a|a|DT fresh|fresh|JJ tube|tube|NN .|.|. Precipitate|precipitate|VB RNA|rna|NN from|from|IN the|the|DT aqueous|aqueous|JJ phase|phase|NN by|by|IN mixing|mix|VBG with|with|IN isopropanol|isopropanol|NN .|.|. Use|Use|NNP 0.5|0.5|CD ml|ml|NN of|of|IN isopropanol|isopropanol|NN per|per|IN 1|1|CD ml|ml|NN of|of|IN TRI|TRI|NNP Reagent|Reagent|NNP used|use|VBD for|for|IN the|the|DT initial|initial|JJ homogenization|homogenization|NN .|.|. Store|Store|NNP samples|sample|NNS at|at|IN room|room|NN temperature|temperature|NN for|for|IN 5-10|5-10|CD minutes|minute|NNS and|and|CC centrifuge|centrifuge|NN at|at|IN 12,000|12,000|CD g|g|NN for|for|IN 8|8|CD minutes|minute|NNS at|at|IN 4|4|CD -|-|: 25|25|CD C.|C.|NNP Remove|remove|VB the|the|DT supernatant|supernatant|NN and|and|CC wash|wash|VB the|the|DT RNA|rna|NN pellet|pellet|NN -LRB-|-lrb-|-LRB- by|by|IN vortexing|vortex|VBG -RRB-|-rrb-|-RRB- with|with|IN 75|75|CD %|%|NN ethanol|ethanol|NN and|and|CC subsequent|subsequent|JJ centrifugation|centrifugation|NN at|at|IN 7,500|7,500|CD g|g|NN for|for|IN 5|5|CD minutes|minute|NNS at|at|IN 4|4|CD -|-|: 25|25|CD C.|C.|NNP Add|add|VB at|at|IN least|least|JJS 1|1|CD ml|ml|NN of|of|IN 75|75|CD %|%|NN ethanol|ethanol|NN per|per|IN 1|1|CD ml|ml|NN TRI|TRI|NNP Reagent|Reagent|NNP used|use|VBD for|for|IN the|the|DT initial|initial|JJ homogenization|homogenization|NN .|.|. Remove|remove|VB the|the|DT ethanol|ethanol|NN wash|wash|NN and|and|CC briefly|briefly|NN air-dry|air-dry|VB the|the|DT RNA|rna|NN pellet|pellet|NN for|for|IN 3|3|LS -|-|: 5|5|CD min|min|NN .|.|. Dissolve|dissolve|VB RNA|rna|NN in|in|IN DEPC-treated|depc-treated|JJ water|water|NN by|by|IN passing|pass|VBG solution|solution|NN a|a|DT few|few|JJ times|time|NNS through|through|IN a|a|DT pipette|pipette|NN tip|tip|NN .|.|. Using|use|VBG an|a|DT on-column|on-column|JJ DNase|dnase|NN digestion|digestion|NN with|with|IN RNase-free|rnase-free|JJ DNase|dnase|NN I|i|CD -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- to|to|TO purify|purify|VB the|the|DT total|total|JJ RNA|rna|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT frozen|frozen|JJ acid-phenol|acid-phenol|NN method|method|NN described|describe|VBN by|by|IN Maes|mae|NNS and|and|CC Messens|messen|NNS -LRB-|-lrb-|-LRB- Maes|mae|NNS and|and|CC Messens|messen|NNS ,|,|, 1992|1992|CD -RRB-|-rrb-|-RRB- and|and|CC then|then|RB treated|treat|VBN with|with|IN RNase-free|rnase-free|JJ DNaseI|dnasei|NN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS recommendations|recommendation|NNS -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC DNA|dna|NN was|be|VBD removed|remove|VBN by|by|IN on-column|on-column|JJ DNase|dnase|NN digestion|digestion|NN with|with|IN the|the|DT RNase-Free|rnase-free|JJ DNase|dnase|NN set|set|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN concentration|concentration|NN was|be|VBD measured|measure|VBN by|by|IN SpectorPhotometer|spectorphotometer|NN -LRB-|-lrb-|-LRB- NonoDrop|nonodrop|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufactures|manufacture|VBZ recommendations|recommendation|NNS .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Inc.|Inc.|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT RNAprotect|rnaprotect|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC DNA|dna|NN was|be|VBD removed|remove|VBN by|by|IN on-column|on-column|JJ DNase|dnase|NN digestion|digestion|NN with|with|IN the|the|DT RNase-Free|rnase-free|JJ DNase|dnase|NN set|set|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN concentration|concentration|NN was|be|VBD determined|determine|VBN on|on|IN a|a|DT Nanodrop|Nanodrop|NNP ND-1000|nd-1000|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- and|and|CC RNA|rna|NN quality|quality|NN was|be|VBD determined|determine|VBN by|by|IN analysis|analysis|NN with|with|IN an|a|DT Agilent|Agilent|NNP 2100|2100|CD bioanalyzer|bioanalyzer|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT RNeasy|RNeasy|NNP Plus|Plus|NNP Mini|Mini|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP Inc.|Inc.|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC genomic|genomic|JJ DNA|dna|NN was|be|VBD removed|remove|VBN by|by|IN gDNA|gdna|NN Eliminator|eliminator|NN spin|spin|NN column|column|NN in|in|IN the|the|DT RNeasy|RNeasy|NNP Plus|Plus|NNP Mini|Mini|NNP Kit|kit|NN .|.|. RNA|rna|NN quality|quality|NN and|and|CC concentration|concentration|NN was|be|VBD determined|determine|VBN by|by|IN analysis|analysis|NN with|with|IN a|a|DT NanoDrop|NanoDrop|NNP 1000|1000|CD -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP Inc.|Inc.|NNP ,|,|, Wilmington|Wilmington|NNP ,|,|, DE|de|NN ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG the|the|DT Trizol|Trizol|NNP reagent|reagent|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- and|and|CC the|the|DT concentration|concentration|NN and|and|CC purity|purity|NN of|of|IN the|the|DT samples|sample|NNS were|be|VBD determined|determine|VBN using|use|VBG Nano|Nano|NNP Drop|Drop|NNP .|.|. RNA|rna|NN integrity|integrity|NN was|be|VBD monitored|monitor|VBN using|use|VBG the|the|DT R6K|r6k|NN ScreenTape|screentape|NN system|system|NN on|on|IN the|the|DT Agilent|Agilent|NNP 2200|2200|CD TapeStation|TapeStation|NNP .|.|. gDNA|gdna|NN was|be|VBD removed|remove|VBN by|by|IN Turbo|Turbo|NNP DNase|dnase|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- in|in|IN the|the|DT presence|presence|NN of|of|IN 1U|1u|NN /|/|: L|l|NN RiboLock|ribolock|NN RNase|rnase|NN Inhibitor|inhibitor|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Fisher|Fisher|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- for|for|IN 60|60|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN .|.|. Following|follow|VBG organic|organic|JJ extraction|extraction|NN -LRB-|-lrb-|-LRB- 1x|1x|NN 25:24:1|25:24:1|CD v/v|v/v|NN phenol/chloroform|phenol/chloroform|NN /|/|: isoamyalcohol|isoamyalcohol|NN ,|,|, 1x|1x|NN chloroform|chloroform|NN -RRB-|-rrb-|-RRB- ,|,|, RNA|rna|NN was|be|VBD recovered|recover|VBN by|by|IN overnight|overnight|JJ precipitation|precipitation|NN with|with|IN 3|3|CD volumes|volume|NNS of|of|IN 30:1|30:1|CD 100|100|CD %|%|NN ethanol/3|ethanol/3|CD M|m|NN sodium|sodium|NN acetate|acetate|NN -LRB-|-lrb-|-LRB- pH|ph|NN 5.2|5.2|CD -RRB-|-rrb-|-RRB- .|.|. Next|next|RB ,|,|, the|the|DT sample|sample|NN -LRB-|-lrb-|-LRB- TEX|tex|NN +|+|CC -RRB-|-rrb-|-RRB- was|be|VBD depleted|deplete|VBN of|of|IN processed|process|VBN RNAs|rna|NNS using|use|VBG 1U|1u|NN per|per|IN 1μg|1μg|NN of|of|IN RNA|rna|NN Terminator|Terminator|NNP 5|5|CD '|'|'' -|-|: Phosphate-Dependent|phosphate-dependent|JJ Exonuclease|exonuclease|NN -LRB-|-lrb-|-LRB- TEX|tex|NN ,|,|, Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- in|in|IN the|the|DT presence|presence|NN of|of|IN 1U/μL|1u/μl|NN RNase|rnase|NN Inhibitor|inhibitor|NN for|for|IN 60|60|CD min|min|NN at|at|IN 30|30|CD °|°|CD C|c|NN .|.|. A|a|DT control|control|NN reaction|reaction|NN without|without|IN TEX|TEX|NNP -LRB-|-lrb-|-LRB- TEX|TEX|NNP -|-|: -RRB-|-rrb-|-RRB- was|be|VBD run|run|VBN in|in|IN parallel|parallel|NN .|.|. Following|follow|VBG organic|organic|JJ extraction|extraction|NN ,|,|, RNA|rna|NN was|be|VBD recovered|recover|VBN by|by|IN overnight|overnight|JJ precipitation|precipitation|NN and|and|CC resuspended|resuspend|VBN in|in|IN RNase-free|rnase-free|JJ water|water|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG TRI|TRI|NNP Reagent|Reagent|NNP -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP Aldrich|Aldrich|NNP -RRB-|-rrb-|-RRB- ,|,|, enriched|enrich|VBN by|by|IN depleting|deplete|VBG small|small|JJ RNAs|rna|NNS with|with|IN GeneJET|GeneJET|NNP Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Fermentas|fermentas|NN -RRB-|-rrb-|-RRB- and|and|CC rRNA|rrna|NN with|with|IN MICROBExpres|microbexpre|NNS Bacterial|bacterial|JJ mRNA|mrna|NN Enrichment|Enrichment|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- and|and|CC fragmented|fragmented|JJ in|in|IN alkaline|alkaline|NN solution|solution|NN -LRB-|-lrb-|-LRB- 2|2|CD mM|mm|NN EDTA|edta|NN and|and|CC 100|100|CD mM|mm|NN Na2CO3|na2co3|NN pH|ph|NN 9.2|9.2|CD for|for|IN 40|40|CD min|min|NN at|at|IN 95|95|CD °C|°c|NN -RRB-|-rrb-|-RRB- to|to|TO fragments|fragment|NNS with|with|IN size|size|NN of|of|IN 24-35|24-35|CD nts|nt|NNS .|.|. For|for|IN RPFS|rpf|NNS ,|,|, cells|cell|NNS were|be|VBD lysed|lyse|VBN by|by|IN freeze-rupturing|freeze-rupturing|NN -LRB-|-lrb-|-LRB- Retch|Retch|NNP Mill|Mill|NNP -RRB-|-rrb-|-RRB- and|and|CC 100|100|CD A260|a260|NN units|unit|NNS of|of|IN ribosome-bound|ribosome-bound|JJ mRNA|mrna|NN fraction|fraction|NN were|be|VBD directly|directly|RB used|use|VBN for|for|IN polysomal|polysomal|JJ analysis|analysis|NN or|or|CC subjected|subject|VBN to|to|TO nucleolytic|nucleolytic|JJ digestion|digestion|NN with|with|IN 10|10|CD units/µl|units/µl|NN micrococcal|micrococcal|JJ nuclease|nuclease|NN -LRB-|-lrb-|-LRB- Fermentas|fermentas|NN -RRB-|-rrb-|-RRB- for|for|IN 10|10|CD min|min|NN at|at|IN room|room|NN temperature|temperature|NN in|in|IN buffer|buffer|NN with|with|IN pH|ph|NN 9.2|9.2|CD -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris|Tris|NNP pH|ph|NN 11|11|CD containing|contain|VBG 50|50|CD mM|mm|NN NH4Cl|nh4cl|NN ,|,|, 10|10|CD mM|mm|NN MgCl2|mgcl2|NN ,|,|, 0.2|0.2|CD %|%|NN triton|triton|NN X-100|x-100|NN ,|,|, 100|100|CD µg/ml|µg/ml|JJ chloramphenicol|chloramphenicol|NN and|and|CC 20|20|CD mM|mm|NN CaCl2|cacl2|NN -RRB-|-rrb-|-RRB- to|to|TO obtain|obtain|VB the|the|DT monosomal|monosomal|JJ fraction|fraction|NN .|.|. Separation|separation|NN was|be|VBD obtained|obtain|VBN by|by|IN sucrose|sucrose|NN density|density|NN gradient|gradient|NN -LRB-|-lrb-|-LRB- 15-50|15-50|CD %|%|NN w/v|w/v|NN -RRB-|-rrb-|-RRB- .|.|. Subsequently|subsequently|RB ,|,|, 20-35-nt|20-35-nt|JJ RNA|rna|NN fragments|fragment|NNS from|from|IN the|the|DT monosomal|monosomal|JJ fraction|fraction|NN were|be|VBD size|size|NN selected|select|VBN on|on|IN a|a|DT denaturing|denature|VBG 15|15|CD %|%|NN polyacrylamide|polyacrylamide|NN gel|gel|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG TRIzol|trizol|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB-
Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN using|use|VBG TRIzol|trizol|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT sample|sample|NN was|be|VBD enriched|enrich|VBN in|in|IN mRNA|mrna|NN ,|,|, depleting|deplete|VBG small|small|JJ RNAs|rna|NNS with|with|IN GeneJET|genejet|NN ™|™|NN RNA|rna|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Fermentas|fermentas|NN -RRB-|-rrb-|-RRB- and|and|CC ribosomal|ribosomal|JJ RNA|rna|NN with|with|IN two|two|CD cycle|cycle|NN of|of|IN MICROBExpress|microbexpress|NN ™|™|CD Bacterial|bacterial|JJ mRNA|mrna|NN Enrichment|Enrichment|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|. To|to|TO probe|probe|VB the|the|DT RNA|rna|NN structure|structure|NN two|two|CD µg|µg|NN of|of|IN enriched|enriched|JJ mRNA|mrna|NN were|be|VBD resuspended|resuspend|VBN in|in|IN 45|45|CD µl|µl|NN of|of|IN DEPC|depc|NN water|water|NN and|and|CC denatured|denature|VBN for|for|IN 3|3|CD min|min|NN at|at|IN 95|95|CD °C|°c|NN ,|,|, refolded|refold|VBN at|at|IN 37|37|CD °C|°c|NN ,|,|, after|after|IN addition|addition|NN of|of|IN 10x|10x|CD RNA-structure|rna-structure|NN buffer|buffer|NN with|with|IN pH|ph|NN 7.0|7.0|CD -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Tris|Tris|NNP ,|,|, 1|1|CD M|m|NN KCl|kcl|NN ,|,|, 100|100|CD mM|mm|NN MgCl2|mgcl2|NN -RRB-|-rrb-|-RRB- and|and|CC digested|digest|VBN for|for|IN 1|1|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN either|either|CC 0.05|0.05|CD U|U|NNP RNase|rnase|NN V1|v1|NN -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS -RRB-|-rrb-|-RRB- or|or|CC a|a|DT combination|combination|NN of|of|IN 2|2|CD µg|µg|NN RNase|rnase|NN A|a|NN and|and|CC 5|5|CD U|U|NNP RNase|rnase|NN T1|t1|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT reaction|reaction|NN was|be|VBD stopped|stop|VBN by|by|IN extracting|extract|VBG the|the|DT RNA|rna|NN with|with|IN phenol-chlorophorm|phenol-chlorophorm|NN .|.|. The|the|DT RNase|rnase|NN A/T1-digested|a/t1-digested|JJ sample|sample|NN was|be|VBD phosphorylated|phosphorylate|VBN with|with|IN T4|t4|NN PNK|pnk|NN -LRB-|-lrb-|-LRB- NEB|neb|NN -RRB-|-rrb-|-RRB- and|and|CC purified|purify|VBN with|with|IN RNA|rna|NN Clean|Clean|NNP &|&|CC Concentrator|Concentrator|NNP ™|™|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Zymo|Zymo|NNP Research|Research|NNP -RRB-|-rrb-|-RRB- .|.|. Both|both|CC the|the|DT V1|v1|NN and|and|CC A/T1|a/t1|NN digested|digest|VBD samples|sample|NNS were|be|VBD randomly|randomly|RB fragmented|fragmented|JJ in|in|IN buffer|buffer|NN with|with|IN pH|ph|NN 9.2|9.2|CD -LRB-|-lrb-|-LRB- 100|100|CD mM|mm|NN Na2CO3|na2co3|NN ,|,|, 2|2|CD mM|mm|NN EDTA|edta|NN -RRB-|-rrb-|-RRB- for|for|IN 12|12|CD min|min|NN at|at|IN 95|95|CD °C|°c|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN with|with|IN phenol|phenol|NN chloroform|chloroform|NN and|and|CC alkaline|alkaline|NN fragmented|fragmented|JJ ,|,|, then|then|RB fragments|fragment|NNS -LRB-|-lrb-|-LRB- 20-40|20-40|CD nt|nt|NNS -RRB-|-rrb-|-RRB- were|be|VBD gel-purified|gel-purified|JJ .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD extracted|extract|VBN with|with|IN Qiagen|Qiagen|NNP 's|'s|POS Rneasy|Rneasy|NNP Mini|Mini|NNP Kit|kit|NN
total|total|JJ RNA|rna|NN was|be|VBD extreacted|extreact|VBN using|use|VBG Quagen|quagen|JJ RNA|rna|NN mini|minus|NNS kit|kit|NN .|.|. DNA|dna|NN was|be|VBD removed|remove|VBN by|by|IN DNase|dnase|NN digestion|digestion|NN .|.|. RNA|rna|NN quality|quality|NN and|and|CC concentration|concentration|NN was|be|VBD determined|determine|VBN by|by|IN analysis|analysis|NN with|with|IN an|a|DT Thermo|Thermo|NNP NanoDrop|NanoDrop|NNP 1000|1000|CD .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD harvested|harvest|VBN from|from|IN C.|C.|NNP glutamicum|glutamicum|NN cells|cell|NNS using|use|VBG TRIzol|trizol|NN ®|®|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC NucleoSpin|NucleoSpin|NNP ®|®|NNP -LRB-|-lrb-|-LRB- Macherey-Nagel|Macherey-Nagel|NNP ,|,|, Düren|Düren|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS with|with|IN the|the|DT following|follow|VBG modifications|modification|NNS .|.|. Cells|cell|NNS were|be|VBD harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN ,|,|, resuspended|resuspend|VBN in|in|IN TRIzol|trizol|NN ®|®|NN reagent|reagent|NN ,|,|, and|and|CC transferred|transfer|VBN to|to|TO a|a|DT vial|vial|NN containing|contain|VBG Lysing|lyse|VBG Matrix|Matrix|NNP B|B|NNP ®|®|NN -LRB-|-lrb-|-LRB- MP|mp|NN Biomedicals|biomedical|NNS ,|,|, Solon|Solon|NNP ,|,|, OH|oh|NN ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- for|for|IN lysis|lysis|NN .|.|. The|the|DT suspension|suspension|NN was|be|VBD centrifuged|centrifuge|VBN ,|,|, and|and|CC the|the|DT supernatant|supernatant|NN was|be|VBD applied|apply|VBN to|to|TO a|a|DT NucleoSpin|NucleoSpin|NNP ®|®|NN RNA|rna|NN II|ii|CD kit|kit|NN for|for|IN purification|purification|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN according|accord|VBG to|to|TO the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- QIAGEN|qiagen|NN -RRB-|-rrb-|-RRB- manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN and|and|CC purified|purify|VBN from|from|IN cells|cell|NNS using|use|VBG an|a|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN with|with|IN on-column|on-column|JJ DNA|dna|NN digestion|digestion|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN as|as|IN described|describe|VBN -LRB-|-lrb-|-LRB- Sambrook|Sambrook|NNP et|et|FW al.|al.|FW ,|,|, 1989|1989|CD -RRB-|-rrb-|-RRB- .|.|. The|the|DT extracted|extract|VBN RNA|rna|NN was|be|VBD checked|check|VBN for|for|IN purity|purity|NN by|by|IN gel|gel|NN electrophoresis|electrophoresis|NN and|and|CC was|be|VBD quantified|quantify|VBN by|by|IN measuring|measure|VBG extinction|extinction|NN spectrophotometrically|spectrophotometrically|RB at|at|IN 260|260|CD nm|nm|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN as|as|IN desribed|desribe|VBN in|in|IN Kime|Kime|NNP et|et|FW al.|al.|FW ,|,|, 2008|2008|CD
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN by|by|IN the|the|DT Trizol-Phenol-Chloroform|trizol-phenol-chloroform|NN method|method|NN .|.|. An|a|DT additional|additional|JJ clean-up|clean-up|JJ including|include|VBG the|the|DT on-column|on-column|JJ DNase|dnase|NN I|i|CD treatment|treatment|NN was|be|VBD performed|perform|VBN by|by|IN using|use|VBG the|the|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN cell|cell|NN lysates|lysate|NNS using|use|VBG RNeasy|RNeasy|NNP kits|kit|NNS -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- .|.|. mRNA|mrna|NN was|be|VBD extracted|extract|VBN from|from|IN total|total|JJ RNA|rna|NN using|use|VBG MicroPoly|MicroPoly|NNP -LRB-|-lrb-|-LRB- A|A|NNP -RRB-|-rrb-|-RRB- Puristâ|Puristâ|NNP ``|``|`` ¢|¢|$ kits|kit|NNS -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP -RRB-|-rrb-|-RRB- and|and|CC treated|treat|VBN with|with|IN DNase|dnase|NN I|i|CD using|use|VBG the|the|DT Turbo|Turbo|NNP DNA-freeâ|DNA-freeâ|NNP ``|``|`` ¢|¢|$ kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|. First-strand|first-strand|JJ cDNA|cdna|NN was|be|VBD synthesized|synthesize|VBN from|from|IN 400-700|400-700|CD ng|ng|NN mRNA|mrna|NN using|use|VBG High|high|JJ Capacity|capacity|NN RNA-to-cDNA|rna-to-cdna|NN kits|kit|NNS -LRB-|-lrb-|-LRB- Applied|Applied|NNP Biosystems|Biosystems|NNPS -RRB-|-rrb-|-RRB- .|.|. Tag-Seq|tag-seq|JJ sequencing|sequencing|NN libraries|library|NNS were|be|VBD generated|generate|VBN directly|directly|RB from|from|IN 12|12|CD %|%|NN of|of|IN a|a|DT cDNA|cdna|NN reaction|reaction|NN or|or|CC 50|50|CD ng|ng|NN plasmid|plasmid|NN DNA|dna|NN by|by|IN 26|26|CD cycle|cycle|NN PCR|pcr|NN using|use|VBG Pfu|pfu|NN Ultra|Ultra|NNP HS|hs|NN DNA|dna|NN polymerase|polymerase|NN 2x|2x|NN master|master|NN mix|mix|NN -LRB-|-lrb-|-LRB- Agilent|agilent|NN -RRB-|-rrb-|-RRB- and|and|CC primers|primer|NNS AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT|AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT|NNP and|and|CC CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG|CAAGCAGAAGACGGCATACGAGATXXXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCGAGGTGCCTAAAGG|NNP -LRB-|-lrb-|-LRB- where|where|WRB XXXXXXXX|XXXXXXXX|NNP is|be|VBZ a|a|DT library-specific|library-specific|JJ index|index|NN sequence|sequence|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT resultant|resultant|JJ PCR|pcr|NN products|product|NNS were|be|VBD size-selected|size-selected|JJ using|use|VBG 2|2|CD %|%|NN agarose|agarose|NN E-Gel|e-gel|NN EX|ex|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN cell|cell|NN pellets|pellet|NNS using|use|VBG Aurum|Aurum|NNP total|total|JJ RNA|rna|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Bio-Rad|Bio-Rad|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS ,|,|, and|and|CC RNA|rna|NN quality|quality|NN was|be|VBD controlled|control|VBN using|use|VBG the|the|DT RNA|rna|NN 6000|6000|CD nano|nano|NN kit|kit|NN and|and|CC 2100|2100|CD Bioanalyzer|Bioanalyzer|NNP -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP -RRB-|-rrb-|-RRB- .|.|. Ribosomal|ribosomal|JJ RNA|rna|NN was|be|VBD removed|remove|VBN using|use|VBG Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN for|for|IN Gram-Negative|gram-negative|JJ Bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN cells|cell|NNS grown|grow|VBN in|in|IN LB|lb|NN medium|medium|NN using|use|VBG the|the|DT Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP column|column|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN E.coli|e.coli|JJ cells|cell|NNS using|use|VBG NucleoSpin|NucleoSpin|NNP ®|®|SYM RNA|rna|NN II|ii|CD kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturers|manufacturer|NNS '|'|POS instructions|instruction|NNS -LRB-|-lrb-|-LRB- Macherey|Macherey|NNP Nagel|Nagel|NNP ,|,|, Duren|Duren|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD examined|examine|VBN in|in|IN a|a|DT 1.5|1.5|CD %|%|NN denaturing|denature|VBG agarose|agarose|NN gel|gel|NN ,|,|, quantitated|quantitate|VBN by|by|IN absorbance|absorbance|NN at|at|IN 260|260|CD nm|nm|NN and|and|CC stored|store|VBN until|until|IN further|further|JJ use|use|NN for|for|IN microarray|microarray|NN and|and|CC RT-PCR|rt-pcr|NN verification|verification|NN
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN E.coli|e.coli|JJ cells|cell|NNS using|use|VBG NucleoSpin|NucleoSpin|NNP ®|®|SYM RNA|rna|NN II|ii|CD kit|kit|NN according|accord|VBG to|to|TO the|the|DT manufacturers|manufacturer|NNS '|'|POS instructions|instruction|NNS -LRB-|-lrb-|-LRB- Macherey|Macherey|NNP Nagel|Nagel|NNP ,|,|, Duren|Duren|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD examined|examine|VBN in|in|IN a|a|DT 1.5|1.5|CD %|%|NN denaturing|denature|VBG agarose|agarose|NN gel|gel|NN ,|,|, quantitated|quantitate|VBN by|by|IN absorbance|absorbance|NN at|at|IN 260|260|CD nm|nm|NN and|and|CC stored|store|VBN until|until|IN further|further|JJ use|use|NN for|for|IN microarray|microarray|NN and|and|CC RT-PCR|rt-pcr|NN verification|verification|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN strains|strain|NNS using|use|VBG NucleoSpin|NucleoSpin|NNP RNAII|RNAII|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Macherey-Nagel|Macherey-Nagel|NNP Corporation|Corporation|NNP -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT instruction|instruction|NN .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD examined|examine|VBN in|in|IN a|a|DT 1.5|1.5|CD %|%|NN denaturing|denature|VBG agarose|agarose|NN gel|gel|NN ,|,|, quantitated|quantitate|VBN by|by|IN absorbance|absorbance|NN at|at|IN 260|260|CD nm|nm|NN and|and|CC stored|store|VBN until|until|IN further|further|JJ use|use|NN for|for|IN microarray|microarray|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN the|the|DT cell|cell|NN pellets|pellet|NNS using|use|VBG a|a|DT bead|bead|NN mill|mill|NN and|and|CC the|the|DT mirVana|mirvana|NN RNA|rna|NN isolation|isolation|NN kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- including|include|VBG DNase|dnase|NN treatment|treatment|NN .|.|. From|from|IN the|the|DT total|total|JJ RNA|rna|NN samples|sample|NNS ,|,|, ribosomal|ribosomal|JJ RNA|rna|NN molecules|molecule|NNS were|be|VBD depleted|deplete|VBN using|use|VBG the|the|DT Ribo-Zero|Ribo-Zero|NNP rRNA|rrna|NN Removal|removal|NN Kit|kit|NN for|for|IN bacteria|bacterium|NNS -LRB-|-lrb-|-LRB- Illumina|Illumina|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN the|the|DT cells|cell|NNS stored|store|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN using|use|VBG TRIzol|trizol|NN Reagent|reagent|NN -LRB-|-lrb-|-LRB- Invitrogen|Invitrogen|NNP Life|Life|NNP Technologies|Technologies|NNPS ,|,|, Carlsbad|Carlsbad|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- and|and|CC RNeasy|rneasy|NN MinElute|MinElute|NNP Cleanup|Cleanup|NNP Kits|kit|NNS -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Valencia|Valencia|NNP ,|,|, CA|CA|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB-
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN from|from|IN the|the|DT VBNC|vbnc|NN cells|cell|NNS and|and|CC the|the|DT exponential-phase|exponential-phase|NN cells|cell|NNS using|use|VBG TRIzol|trizol|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. The|the|DT RNA|rna|NN samples|sample|NNS were|be|VBD treated|treat|VBN with|with|IN DNase|dnase|NN Ⅰ|ⅰ|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- to|to|TO remove|remove|VB residual|residual|JJ genomic|genomic|JJ DNA|dna|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG a|a|DT RiboPureTM|ribopuretm|NN -|-|: Bacteria|bacterium|NNS Kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|. Once|once|RB isolated|isolate|VBN ,|,|, ~|~|SYM 10μg|10μg|CD total|total|JJ RNA|rna|NN was|be|VBD treated|treat|VBN with|with|IN 8|8|CD units|unit|NNS DNase|dnase|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- twice|twice|RB to|to|TO remove|remove|VB genomic|genomic|JJ DNA|dna|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG a|a|DT RNeasy|rneasy|NN ®|®|NN RNA|rna|NN isolation|isolation|NN kit|kit|NN ,|,|, according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS specifications|specification|NNS -LRB-|-lrb-|-LRB- QIAGEN|QIAGEN|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- and|and|CC stored|store|VBN in|in|IN RNase-free|rnase-free|JJ water|water|NN at|at|IN --|--|: 80|80|CD °C|°c|NN .|.|. RNA|rna|NN concentration|concentration|NN was|be|VBD determined|determine|VBN by|by|IN UV-spectrometry|uv-spectrometry|NN and|and|CC its|its|PRP$ quality|quality|NN controlled|control|VBN by|by|IN agarose|agarose|NN gel|gel|NN electrophoresis|electrophoresis|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Qiagen|Qiagen|NNP RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN and|and|CC treated|treat|VBN with|with|IN DNase|dnase|NN I|i|CD
Total|total|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG Ribopure|Ribopure|NNP Bacteria|bacterium|NNS Kit|kit|NN as|as|IN described|describe|VBN by|by|IN the|the|DT manufacturer|manufacturer|NN -LRB-|-lrb-|-LRB- Ambion|Ambion|NNP ,|,|, Huntingdon|Huntingdon|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN quality|quality|NN was|be|VBD assessed|assess|VBN by|by|IN Agilent|Agilent|NNP 2100|2100|CD bioanalyser|bioanalyser|NN using|use|VBG the|the|DT RNA|rna|NN 6000|6000|CD Nano|Nano|NNP Chip|chip|NN -LRB-|-lrb-|-LRB- Agilent|Agilent|NNP Technologies|Technologies|NNPS ,|,|, Amstelveen|Amstelveen|NNP ,|,|, The|the|DT Netherlands|Netherlands|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC quantity|quantity|NN was|be|VBD determined|determine|VBN by|by|IN ND-1000|nd-1000|NN Spectrophotometer|spectrophotometer|NN -LRB-|-lrb-|-LRB- NanoDrop|NanoDrop|NNP Technologies|Technologies|NNPS ,|,|, Inc.|Inc.|NNP ,|,|, DE|de|NN ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT hot|hot|JJ phenol|phenol|NN method|method|NN as|as|IN described|describe|VBN in|in|IN -LRB-|-lrb-|-LRB- Lybecker|Lybecker|NNP et|et|FW al.|al.|FW ,|,|, 2014|2014|CD -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT Rneasy|Rneasy|NNP Mini|Mini|NNP Kit|kit|NN procedure|procedure|NN with|with|IN on|on|IN column|column|NN Dnase|dnase|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT RNeasy|rneasy|NN Mini-Kit|mini-kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN `|`|`` s|be|VBZ instruction|instruction|NN and|and|CC DNA|dna|NN was|be|VBD removed|remove|VBN by|by|IN using|use|VBG RNAse-Free|rnase-free|JJ DNAse|dnase|NN Set|set|VB -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN the|the|DT MasterPure|masterpure|NN RNA|rna|NN Isolation|isolation|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- ,|,|, enriched|enriched|JJ for|for|IN mRNA|mrna|NN using|use|VBG the|the|DT mRNA|mrna|NN Prokaryotic|prokaryotic|JJ mRNA|mrna|NN Isolation|isolation|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Epicentre|Epicentre|NNP -RRB-|-rrb-|-RRB- ,|,|, and|and|CC polyadenylated|polyadenylated|JJ with|with|IN kit|kit|NN all|all|DT based|base|VBN on|on|IN the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS
Total|Total|NNP RNA|rna|NN was|be|VBD isolated|isolate|VBN with|with|IN the|the|DT RNeasy|RNeasy|NNP Protect|Protect|NNP Bacteria|bacterium|NNS Mini|Mini|NNP Kit|kit|NN from|from|IN Qiagen|Qiagen|NNP -LRB-|-lrb-|-LRB- Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. The|the|DT isolated|isolate|VBN RNA|rna|NN was|be|VBD further|further|JJ purified|purify|VBN from|from|IN genomic|genomic|JJ DNA|dna|NN contaminations|contamination|NNS using|use|VBG Ambion|Ambion|NNP DNase|dnase|NN I|i|CD treatment|treatment|NN following|follow|VBG the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS -LRB-|-lrb-|-LRB- DNA-free|dna-free|NN ,|,|, Ambion|Ambion|NNP by|by|IN Life|Life|NNP Technologies|Technologies|NNPS ,|,|, Darmstadt|Darmstadt|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN samples|sample|NNS were|be|VBD further|further|JJ subjected|subject|VBN to|to|TO an|a|DT mRNA|mrna|NN enrichment|enrichment|NN step|step|NN using|use|VBG the|the|DT MICROBExpress|MICROBExpress|NNP Kit|kit|NN from|from|IN Ambion|Ambion|NNP according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN `|`|`` s|be|VBZ instructions|instruction|NNS -LRB-|-lrb-|-LRB- Life|Life|NNP Technologies|Technologies|NNPS ,|,|, Darmstadt|Darmstadt|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD purified|purify|VBN on|on|IN a|a|DT RNeasy|rneasy|NN columns|column|NNS -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- ;|;|: ribosomal|ribosomal|JJ RNAs|rna|NNS were|be|VBD removed|remove|VBN with|with|IN the|the|DT MicroExpress|MicroExpress|NNP kit|kit|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT resulting|result|VBG RNA|rna|NN was|be|VBD reverse|reverse|JJ transcribed|transcribe|VBN with|with|IN SuperScript|SuperScript|NNP II|II|NNP reverse|reverse|JJ transcriptase|transcriptase|NN -LRB-|-lrb-|-LRB- Invitrogen|invitrogen|NN -RRB-|-rrb-|-RRB- +|+|CC random|random|JJ hexamers|hexamer|NNS +|+|CC dNTP|dntp|NN mix|mix|NN containing|contain|VBG aminoallyl-dUTP|aminoallyl-dutp|NN .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG the|the|DT RNAeasy|rnaeasy|NN kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD purified|purify|VBN with|with|IN an|a|DT RNeasy|rneasy|NN micro|micro|JJ kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP K.K.|K.K.|NNP ,|,|, Tokyo|Tokyo|NNP ,|,|, Japan|Japan|NNP -RRB-|-rrb-|-RRB- .|.|.
Total|Total|NNP RNA|rna|NN was|be|VBD stabilised|stabilise|VBN and|and|CC subsequently|subsequently|RB purified|purify|VBN from|from|IN a|a|DT 500|500|CD ul|ul|NN portion|portion|NN of|of|IN each|each|DT bacterial|bacterial|JJ culture|culture|NN using|use|VBG a|a|DT RNAprotect|rnaprotect|NN Bacterial|bacterial|JJ Reagent|reagent|NN Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP ,|,|, Crawley|Crawley|NNP ,|,|, UK|UK|NNP -RRB-|-rrb-|-RRB-
Total|Total|NNP RNA|rna|NN were|be|VBD then|then|RB isolated|isolate|VBN according|accord|VBG to|to|TO the|the|DT standard|standard|JJ protocol|protocol|NN using|use|VBG an|a|DT RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. Genomic|genomic|JJ DNA|dna|NN were|be|VBD extracted|extract|VBN from|from|IN both|both|DT Xuzhou21|xuzhou21|NN and|and|CC Xuzhou21m|xuzhou21m|NN using|use|VBG Wizard|Wizard|NNP Genomic|genomic|JJ DNA|dna|NN purification|purification|NN kit|kit|NN -LRB-|-lrb-|-LRB- Promega|Promega|NNP ,|,|, Madison|Madison|NNP ,|,|, WI|WI|NNP ,|,|, USA|USA|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS protocols|protocol|NNS .|.|.
toxin|toxin|NN :|:|: deoxynivalenol|deoxynivalenol|NN
toxin|toxin|NN :|:|: nivalenol|nivalenol|NN
TPM|tpm|NN -LRB-|-lrb-|-LRB- transcripts|transcript|NNS per|per|IN million|million|CD -RRB-|-rrb-|-RRB- was|be|VBD calculated|calculate|VBN by|by|IN RSEM|rsem|NN -LRB-|-lrb-|-LRB- version|version|NN 1.2.19|1.2.19|CD -RRB-|-rrb-|-RRB-
Transcript|Transcript|NNP Abundance|Abundance|NNP in|in|IN LB|LB|NNP at|at|IN 30|30|CD degrees|degree|NNS OD600|od600|NN =|=|JJ 0.8|0.8|CD Trial|trial|NN A|a|DT
Transcript|Transcript|NNP Abundance|Abundance|NNP in|in|IN LB|LB|NNP at|at|IN 30|30|CD degrees|degree|NNS OD600|od600|NN =|=|JJ 0.8|0.8|CD Trial|trial|NN B|b|NN
Transcript|transcript|NN Abundance|abundance|NN in|in|IN M9|m9|NN at|at|IN 30|30|CD degrees|degree|NNS OD600|od600|NN =|=|JJ 0.8|0.8|CD Trial|trial|NN A|a|NN
Transcript|transcript|NN Abundance|abundance|NN in|in|IN M9|m9|NN at|at|IN 30|30|CD degrees|degree|NNS OD600|od600|NN =|=|JJ 0.8|0.8|CD Trial|trial|NN B|b|NN
transcript|transcript|NN abundance|abundance|NN was|be|VBD quantified|quantify|VBN using|use|VBG rockhopper|rockhopper|NN
Transcript|transcript|NN assembly|assembly|NN an|a|DT quantification|quantification|NN was|be|VBD performed|perform|VBN using|use|VBG a|a|DT protocols|protocol|NNS from|from|IN Trapnell|Trapnell|NNP et|et|FW al.|al.|FW ,|,|, and|and|CC Li|Li|NNP et|et|FW al.|al.|FW .|.|. Fragments|fragment|NNS Per|per|IN Kilobases|kilobase|NNS of|of|IN exon|exon|NN per|per|IN million|million|CD -LRB-|-lrb-|-LRB- FPKM|fpkm|NN -RRB-|-rrb-|-RRB- were|be|VBD calculated|calculate|VBN .|.|.
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW cultured|culture|VBN under|under|IN severe|severe|JJ zinc|zinc|NN limitation|limitation|NN Chemostat|Chemostat|NNP 1A|1a|NN
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW cultured|culture|VBN under|under|IN severe|severe|JJ zinc|zinc|NN limitation|limitation|NN Chemostat|chemostat|NN 1B|1b|NN
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW cultured|culture|VBN under|under|IN severe|severe|JJ zinc|zinc|NN limitation|limitation|NN Chemostat|Chemostat|NNP 2A|2a|NN
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW cultured|culture|VBN under|under|IN severe|severe|JJ zinc|zinc|NN limitation|limitation|NN Chemostat|Chemostat|NNP 2B|2b|NN
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW cultured|culture|VBN under|under|IN severe|severe|JJ zinc|zinc|NN limitation|limitation|NN Chemostat|Chemostat|NNP 3A|3a|NN
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW cultured|culture|VBN under|under|IN severe|severe|JJ zinc|zinc|NN limitation|limitation|NN Chemostat|Chemostat|NNP 3B|3b|NN
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- 0A1|0a1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 0A2|0a2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 0B1|0b1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 0B2|0b2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 10A1|10a1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 10A2|10a2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 10A3|10a3|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 10B1|10b1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 10B2|10b2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 2.5|2.5|CD A1|a1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 2.5|2.5|CD A2|a2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 2.5|2.5|CD B1|b1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 2.5|2.5|CD B2|b2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 30A1|30a1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 30A2|30a2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 30B1|30b1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 30B2|30b2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 7A1|7a1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 7A2|7a2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 7B1|7b1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ profiling|profiling|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW during|during|IN a|a|DT transition|transition|NN from|from|IN zinc|zinc|NN starvation|starvation|NN to|to|TO surfeit|surfeit|NN -LRB-|-lrb-|-LRB- slide|slide|NN 7B2|7b2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ response|response|NN of|of|IN E.|e.|FW coli|coli|FW to|to|TO TPEN|tpen|NN -LRB-|-lrb-|-LRB- m1|m1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ response|response|NN of|of|IN E.|e.|FW coli|coli|FW to|to|TO TPEN|tpen|NN -LRB-|-lrb-|-LRB- m2|m2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ response|response|NN of|of|IN E.|e.|FW coli|coli|FW to|to|TO TPEN|tpen|NN -LRB-|-lrb-|-LRB- m3|m3|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ response|response|NN of|of|IN E.|e.|FW coli|coli|FW to|to|TO TPEN|tpen|NN -LRB-|-lrb-|-LRB- t1|t1|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ response|response|NN of|of|IN E.|e.|FW coli|coli|FW to|to|TO TPEN|tpen|NN -LRB-|-lrb-|-LRB- t2|t2|NN -RRB-|-rrb-|-RRB-
Transcriptional|transcriptional|JJ response|response|NN of|of|IN E.|e.|FW coli|coli|FW to|to|TO TPEN|tpen|NN -LRB-|-lrb-|-LRB- t3|t3|NN -RRB-|-rrb-|-RRB-
transcription|transcription|NN factor|factor|NN :|:|: CsiR|csir|NN
transcription|transcription|NN factor|factor|NN :|:|: Nac|Nac|NNP
transcription|transcription|NN factor|factor|NN :|:|: NtrC|ntrc|NN
transcription|transcription|NN factor|factor|NN :|:|: OmpR|ompr|NN
Transcription|transcription|NN profiles|profile|NNS of|of|IN NTG-treated|ntg-treated|JJ E.|e.|FW coli|coli|FW imp|imp|FW fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- and|and|CC its|its|PRP$ control|control|NN strain|strain|NN in|in|IN the|the|DT absence|absence|NN of|of|IN triclosan|triclosan|NN
Transcription|transcription|NN profiles|profile|NNS of|of|IN NTG-treated|ntg-treated|JJ E.|e.|FW coli|coli|FW imp|imp|FW fabI|fabi|NN -LRB-|-lrb-|-LRB- G93V|g93v|NN -RRB-|-rrb-|-RRB- and|and|CC its|its|PRP$ control|control|NN strain|strain|NN in|in|IN the|the|DT presence|presence|NN of|of|IN triclosan|triclosan|NN
Transcriptome|transcriptome|NN of|of|IN cells|cell|NNS was|be|VBD prepared|prepare|VBN using|use|VBG a|a|DT RNA|rna|NN extraction|extraction|NN kit|kit|NN -LRB-|-lrb-|-LRB- RNeasy|rneasy|NN mini|minus|NNS kit|kit|NN ;|;|: Qiagen|Qiagen|NNP ,|,|, Hilden|Hilden|NNP ,|,|, Germany|Germany|NNP -RRB-|-rrb-|-RRB-
Transcriptomic|transcriptomic|JJ analyses|analysis|NNS were|be|VBD carried|carry|VBN out|out|RP after|after|IN growing|grow|VBG bacteria|bacterium|NNS in|in|IN minimal|minimal|JJ media|media|NNS supplemented|supplement|VBN with|with|IN glucose|glucose|NN .|.|. Several|several|JJ Ni|ni|NN concentrations|concentration|NNS and|and|CC exposure|exposure|NN times|time|NNS were|be|VBD assayed|assay|VBN .|.|. rcnA|rcna|NN gene|gene|NN expression|expression|NN was|be|VBD taken|take|VBN as|as|IN an|a|DT internal|internal|JJ control|control|NN to|to|TO arbitrate|arbitrate|VB between|between|IN the|the|DT different|different|JJ conditions|condition|NNS .|.|. rcnA|rcna|NN is|be|VBZ induced|induce|VBN by|by|IN Ni|ni|NN when|when|WRB cells|cell|NNS are|be|VBP overloaded|overload|VBN with|with|IN this|this|DT ion|ion|NN and|and|CC must|must|MD detoxify|detoxify|VB the|the|DT cytoplasm|cytoplasm|NN by|by|IN extruding|extrude|VBG excess|excess|JJ metal|metal|NN via|via|IN the|the|DT RcnAB|rcnab|NN efflux|efflux|NN system|system|NN .|.|. rcnA|rcna|NN induction|induction|NN was|be|VBD maximised|maximise|VBN after|after|IN culture|culture|NN incubation|incubation|NN for|for|IN 10|10|CD min|min|NN ,|,|, and|and|CC longer|longer|RBR periods|period|NNS of|of|IN incubation|incubation|NN lead|lead|NN to|to|TO a|a|DT decline|decline|NN in|in|IN rcnA|rcna|NN expression|expression|NN -LRB-|-lrb-|-LRB- Fig|fig|NN .|.|. S1|s1|NN -RRB-|-rrb-|-RRB- .|.|. For|for|IN the|the|DT RNA-Seq|rna-seq|NN experiments|experiment|NNS ,|,|, bacteria|bacterium|NNS were|be|VBD grown|grow|VBN until|until|IN O.D600nm|o.d600nm|NN =|=|JJ 0.3|0.3|CD ,|,|, were|be|VBD treated|treat|VBN with|with|IN 50|50|CD µM|µm|NN NiCl2|nicl2|NN for|for|IN 10|10|CD min|min|NN and|and|CC were|be|VBD frozen|freeze|VBN prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN .|.|.
Transcripts|transcript|NNS evaluation|evaluation|NN of|of|IN differential|differential|JJ expression|expression|NN were|be|VBD accomplished|accomplish|VBN using|use|VBG MARS|mars|NN -LRB-|-lrb-|-LRB- MA-plot-based|ma-plot-based|JJ method|method|NN with|with|IN Random|Random|NNP sampling|sampling|NN model|model|NN -RRB-|-rrb-|-RRB- in|in|IN DEGseq|degseq|NN package|package|NN .|.|. -LRB-|-lrb-|-LRB- Bioinformatics|bioinformatic|NNS 2010|2010|CD ,|,|, 26|26|CD :|:|: 136-138|136-138|CD -RRB-|-rrb-|-RRB-
Transfer|transfer|NN 700|700|CD μl|μl|NN lysate|lysate|NN into|into|IN RNeasy|RNeasy|NNP Mini|Mini|NNP column|column|NN place|place|NN in|in|IN a|a|DT 2|2|CD ml|ml|NN collection|collection|NN tube|tube|NN and|and|CC centrifuge|centrifuge|NN for|for|IN 30|30|CD s|s|NNS at|at|IN highest|highest|JJS speed|speed|NN .|.|. Add|add|VB 350|350|CD μl|μl|NN Buffer|buffer|NN RW1|rw1|NN to|to|TO the|the|DT column|column|NN and|and|CC centrifuge|centrifuge|NN for|for|IN 30|30|CD s.|s.|NN Discard|Discard|NNP flow-through|flow-through|JJ and|and|CC reuse|reuse|VB the|the|DT collection|collection|NN tube|tube|NN .|.|. Add|add|VB 10|10|CD μl|μl|NN DNase|dnase|NN stock|stock|NN solution|solution|NN to|to|TO 70|70|CD μ|μ|NN l|l|NN RDD|RDD|NNP Buffer|Buffer|NNP .|.|. Add|add|VB the|the|DT DNase|dnase|NN I|i|CD solution|solution|NN into|into|IN the|the|DT column|column|NN and|and|CC incubate|incubate|VB at|at|IN RT|rt|NN for|for|IN 15|15|CD min|min|NN .|.|. Add|add|VB 350|350|CD μl|μl|NN Buffer|buffer|NN RW1|rw1|NN to|to|TO the|the|DT column|column|NN and|and|CC wait|wait|VB for|for|IN 5|5|CD min|min|NN ,|,|, centrifuge|centrifuge|NN for|for|IN 30|30|CD s.|s.|NN Discard|Discard|NNP the|the|DT flow-through|flow-through|JJ and|and|CC collection|collection|NN tubes|tube|NNS .|.|. Place|place|VB the|the|DT RNeasy|RNeasy|NNP Mini|Mini|NNP spin|spin|VB column|column|NN in|in|IN a|a|DT new|new|JJ 2|2|CD ml|ml|NN collection|collection|NN tube|tube|NN .|.|. Add|add|VB 500|500|CD μl|μl|NN Buffer|buffer|NN RPE|rpe|NN to|to|TO the|the|DT column|column|NN .|.|. Centrifuge|Centrifuge|NNP for|for|IN 30|30|CD s.|s.|NN Place|place|NN the|the|DT column|column|NN in|in|IN a|a|DT new|new|JJ 1.5|1.5|CD ml|ml|NN tube|tube|NN ,|,|, and|and|CC centrifuge|centrifuge|NN for|for|IN 1|1|CD min|min|NN to|to|TO eliminate|eliminate|VB any|any|DT residue|residue|NN ethanol|ethanol|NN .|.|. Place|place|VB the|the|DT column|column|NN in|in|IN a|a|DT new|new|JJ collection|collection|NN tube|tube|NN .|.|. Add|add|VB 50|50|CD μl|μl|NN RNase|rnase|NN free|free|JJ water|water|NN ,|,|, centrifuge|centrifuge|NN for|for|IN 1|1|CD min|min|NN .|.|. Store|store|NN RNA|rna|NN samples|sample|NNS at|at|IN -20|-20|CD °C|°c|NN .|.|.
transformation|transformation|NN :|:|: empty|empty|JJ vector|vector|NN
transformation|transformation|NN :|:|: pSigma70-LB|psigma70-lb|NN
transformation|transformation|NN :|:|: pSigma70-LP|psigma70-lp|NN
Transform|transform|VB the|the|DT mapped|map|VBN file|file|NN format|format|NN from|from|IN sam|sam|NN to|to|TO sorted|sort|VBN bam|bam|NN which|which|WDT are|be|VBP later|later|RB tranfered|tranfer|VBN to|to|TO bigWig|bigwig|NN ,|,|, and|and|CC separated|separate|VBN by|by|IN the|the|DT strand|strand|NN -LRB-|-lrb-|-LRB- plus|plus|NN and|and|CC minus|minus|NN -RRB-|-rrb-|-RRB- .|.|.
transition|transition|NN phase|phase|NN
Transition|transition|NN phase|phase|NN sample|sample|NN 1|1|CD
Transition|transition|NN phase|phase|NN sample|sample|NN 2|2|CD
Transition|transition|NN phase|phase|NN sample|sample|NN 3|3|CD
Transition|transition|NN phase|phase|NN sample|sample|NN 4|4|CD
Treated|treat|VBN experimental|experimental|JJ sets|set|NNS transformed|transform|VBN with|with|IN plasmids|plasmid|NNS containing|contain|VBG BCM/WT|bcm/wt|NN rho|rho|NN .|.|. Rho|rho|NN treated|treated|JJ cells|cell|NNS subjected|subject|VBN to|to|TO P1|p1|NN transduction|transduction|NN to|to|TO delete|delete|VB the|the|DT genomic|genomic|JJ counterparts|counterpart|NNS of|of|IN the|the|DT gene|gene|NN .|.|.
Treated|treat|VBN experimental|experimental|JJ sets|set|NNS transformed|transform|VBN with|with|IN plasmids|plasmid|NNS containing|contain|VBG Rho|rho|NN -LRB-|-lrb-|-LRB- WT/N340S/G324D|wt/n340s/g324d|NN -RRB-|-rrb-|-RRB- .|.|. Cells|cell|NNS subjected|subject|VBN to|to|TO P1|p1|NN transduction|transduction|NN to|to|TO delete|delete|VB the|the|DT genomic|genomic|JJ counterparts|counterpart|NNS of|of|IN the|the|DT gene|gene|NN .|.|.
Treated|treat|VBN experimental|experimental|JJ sets|set|NNS transformed|transform|VBN with|with|IN plasmids|plasmid|NNS containing|contain|VBG WT/G181D/R258C|wt/g181d/r258c|NN NusA|nusa|NN .|.|. Cells|cell|NNS subjected|subject|VBN to|to|TO P1|p1|NN transduction|transduction|NN to|to|TO delete|delete|VB the|the|DT genomic|genomic|JJ counterparts|counterpart|NNS of|of|IN the|the|DT respective|respective|JJ gene|gene|NN .|.|.
treated|treat|VBN sample|sample|NN at|at|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep1|rep1|NN
treated|treat|VBN sample|sample|NN at|at|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep2|rep2|NN
treated|treat|VBN sample|sample|NN at|at|IN 60|60|CD min|min|NN ,|,|, biological|biological|JJ rep1|rep1|NN
treated|treat|VBN sample|sample|NN at|at|IN 60|60|CD min|min|NN ,|,|, biological|biological|JJ rep2|rep2|NN
treated|treat|VBN with|with|IN :|:|: 0.5|0.5|CD μg/ml|μg/ml|NN trimethoprim|trimethoprim|NN
treated|treat|VBN with|with|IN :|:|: 100|100|CD µg/ml|µg/ml|JJ BSA|bsa|NN for|for|IN 30|30|CD min|min|NN -LRB-|-lrb-|-LRB- control|control|NN -RRB-|-rrb-|-RRB-
treated|treat|VBN with|with|IN :|:|: 100|100|CD µg/ml|µg/ml|JJ PGRP|pgrp|NN for|for|IN 30|30|CD min|min|NN
Treated|treat|VBN with|with|IN 100|100|CD uM|um|NN KCN|kcn|NN for|for|IN 5|5|CD minutes|minute|NNS before|before|IN harvesting|harvest|VBG
treated|treat|VBN with|with|IN :|:|: 172mM|172mm|NN NaCl|nacl|NN
treated|treat|VBN with|with|IN :|:|: 172mM|172mm|NN short|short|JJ chain|chain|NN fatty|fatty|JJ acid|acid|NN mix|mix|NN
Treated|treat|VBN with|with|IN 1|1|CD %|%|NN vol/vol|vol/vol|NN butanol|butanol|NN 10|10|CD minutes|minute|NNS prior|prior|RB to|to|TO harvest|harvest|NN
Treated|treat|VBN with|with|IN 1|1|CD %|%|NN vol/vol|vol/vol|NN isobutanol|isobutanol|NN 10|10|CD minutes|minute|NNS prior|prior|RB to|to|TO harvest|harvest|VB
treated|treat|VBN with|with|IN :|:|: 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN
treated|treat|VBN with|with|IN :|:|: 250|250|CD uM|um|NN of|of|IN paraquat|paraquat|NN at|at|IN mid-log|mid-log|JJ pahse|pahse|NN for|for|IN 20|20|CD min|min|NN
treated|treat|VBN with|with|IN :|:|: 250|250|CD uM|um|NN of|of|IN paraquat|paraquat|NN at|at|IN mid-log|mid-log|JJ phase|phase|NN for|for|IN 20|20|CD min|min|NN
treated|treat|VBN with|with|IN :|:|: 30mM|30mm|NN NaCl|nacl|NN
treated|treat|VBN with|with|IN :|:|: 30mM|30mm|NN short|short|JJ chain|chain|NN fatty|fatty|JJ acid|acid|NN mix|mix|NN
Treated|treat|VBN with|with|IN 3|3|CD %|%|NN vol/vol|vol/vol|NN ethanol|ethanol|NN 10|10|CD minutes|minute|NNS prior|prior|RB to|to|TO harvest|harvest|VB
treated|treat|VBN with|with|IN :|:|: 5|5|CD µg/ml|µg/ml|NN gentamicin|gentamicin|NN for|for|IN 30|30|CD min|min|NN
treated|treat|VBN with|with|IN :|:|: 800|800|CD µM|µm|NN CCCP|cccp|NN for|for|IN 15|15|CD min|min|NN
treated|treat|VBN with|with|IN :|:|: none|none|NN
treated|treat|VBN with|with|IN :|:|: none|none|NN -LRB-|-lrb-|-LRB- untreated|untreated|JJ control|control|NN -RRB-|-rrb-|-RRB-
treated|treat|VBN with|with|IN :|:|: Rifampicin|Rifampicin|NNP for|for|IN 20|20|CD minutes|minute|NNS
treatment|treatment|NN :|:|: 0.025|0.025|CD mM|mm|NN CspA|cspa|NN protein|protein|NN
treatment|treatment|NN :|:|: 0.05|0.05|CD mM|mm|NN CspA|cspa|NN protein|protein|NN
treatment|treatment|NN :|:|: 0.1|0.1|CD mM|mm|NN CspA|cspa|NN protein|protein|NN
treatment|treatment|NN :|:|: 0.3|0.3|CD %|%|NN glucose|glucose|NN
treatment|treatment|NN :|:|: 0.4|0.4|CD %|%|NN glucose|glucose|NN
treatment|treatment|NN :|:|: 0.5|0.5|CD µg/ml|µg/ml|NN Carolacton|carolacton|NN
treatment|treatment|NN :|:|: 0.5|0.5|CD mg/ml|mg/ml|NN menadione|menadione|NN
treatment|treatment|NN :|:|: 0.5|0.5|CD mg/ml|mg/ml|NN serine|serine|NN hydroxamate|hydroxamate|NN for|for|IN 20|20|CD min|min|NN
treatment|treatment|NN :|:|: 0.5|0.5|CD mg/ml|mg/ml|NN SHX|shx|NN for|for|IN 40|40|CD min|min|NN
treatment|treatment|NN :|:|: 0.8|0.8|CD %|%|NN n-butanol|n-butanol|NN was|be|VBD added|add|VBN at|at|IN time|time|NN 0|0|CD
treatment|treatment|NN :|:|: 0|0|CD μg/ml|μg/ml|NN nalidixic|nalidixic|JJ acid|acid|NN
treatment|treatment|NN :|:|: 100|100|CD μg/ml|μg/ml|NN nalidixic|nalidixic|JJ acid|acid|NN
treatment|treatment|NN :|:|: 10|10|CD %|%|NN H202|h202|NN
treatment|treatment|NN :|:|: 10|10|CD μg/ml|μg/ml|NN nalidixic|nalidixic|JJ acid|acid|NN
treatment|treatment|NN :|:|: 15|15|CD min|min|NN
treatment|treatment|NN :|:|: 15|15|CD min|min|NN after|after|IN induction|induction|NN with|with|IN arabinose|arabinose|NN
treatment|treatment|NN :|:|: 15|15|CD min|min|NN after|after|IN induction|induction|NN with|with|IN rhamnose|rhamnose|NN
treatment|treatment|NN :|:|: 1|1|CD %|%|NN H202|h202|NN ,|,|, anaerobic|anaerobic|JJ
treatment|treatment|NN :|:|: 1|1|CD %|%|NN H2O2|h2o2|NN ,|,|, anaerobic|anaerobic|JJ
treatment|treatment|NN :|:|: 1mM|1mm|NN IPTG|iptg|NN
Treatment|treatment|NN 1|1|CD :|:|: UA30|ua30|NN -LRB-|-lrb-|-LRB- EHEC|ehec|NN 86-24|86-24|CD exposed|expose|VBN to|to|TO pH|ph|NN 3|3|CD for|for|IN 30|30|CD min|min|NN -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: 200|200|CD mM|mm|NN glyphosate|glyphosate|NN shock|shock|NN for|for|IN 1|1|CD h|h|NN
Treatment|treatment|NN 2|2|CD :|:|: AA30|aa30|NN -LRB-|-lrb-|-LRB- EHEC|ehec|NN 86-24|86-24|CD pH|ph|NN 5.0|5.0|CD ,|,|, followed|follow|VBN by|by|IN 30|30|CD min|min|NN pH|ph|NN 3.0|3.0|CD -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: 2|2|CD mM|mm|NN NaN3|nan3|NN for|for|IN 10|10|CD minutes|minute|NNS
treatment|treatment|NN :|:|: 2ug/ml|2ug/ml|NN of|of|IN ciprofloxacin|ciprofloxacin|NN
treatment|treatment|NN :|:|: 30|30|CD C|c|NN
treatment|treatment|NN :|:|: 30|30|CD %|%|NN H202|h202|NN
treatment|treatment|NN :|:|: 37|37|CD °C|°c|NN
Treatment|treatment|NN 3|3|CD :|:|: UA15|ua15|NN -LRB-|-lrb-|-LRB- EHEC|ehec|NN 86-24|86-24|CD exposed|expose|VBN to|to|TO pH|ph|NN 3|3|CD for|for|IN 15|15|CD min|min|NN -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: 42|42|CD C|c|NN
treatment|treatment|NN :|:|: 4ug/ml|4ug/ml|NN of|of|IN ciprofloxacin|ciprofloxacin|NN
treatment|treatment|NN :|:|: 50|50|CD °C|°c|NN heatshock|heatshock|NN
treatment|treatment|NN :|:|: 5|5|CD percent|percent|NN isooctane|isooctane|NN
treatment|treatment|NN :|:|: 60|60|CD min|min|NN after|after|IN induction|induction|NN with|with|IN arabinose|arabinose|NN
treatment|treatment|NN :|:|: 60|60|CD min|min|NN after|after|IN induction|induction|NN with|with|IN rhamnose|rhamnose|NN
treatment|treatment|NN :|:|: After|after|IN 10|10|CD mg/mL|mg/ml|NN kasugamycin|kasugamycin|NN treatment|treatment|NN for|for|IN 40|40|CD min|min|NN
treatment|treatment|NN :|:|: After|after|IN 250|250|CD µg/mL|µg/ml|NN rifampicin|rifampicin|NN treatment|treatment|NN for|for|IN 2|2|CD hr|hr|NN
treatment|treatment|NN :|:|: ampicillin|ampicillin|NN -LRB-|-lrb-|-LRB- 50|50|CD µg/mL|µg/ml|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB-
Treatment|treatment|NN A|a|NN Population|Population|NNP 1|1|CD Colony|Colony|NNP a|a|DT replica|replica|NN 1|1|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 1|1|CD Colony|Colony|NNP a|a|DT replica|replica|NN 2|2|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 1|1|CD Colony|Colony|NNP b|b|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 1|1|CD Colony|Colony|NNP b|b|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 1|1|CD Colony|Colony|NNP c|c|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 1|1|CD Colony|Colony|NNP c|c|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 2|2|CD Colony|Colony|NNP a|a|DT replica|replica|NN 1|1|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 2|2|CD Colony|Colony|NNP a|a|DT replica|replica|NN 2|2|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 2|2|CD Colony|Colony|NNP b|b|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 2|2|CD Colony|Colony|NNP b|b|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 2|2|CD Colony|Colony|NNP c|c|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN A|a|DT Population|Population|NNP 2|2|CD Colony|Colony|NNP c|c|NN replica|replica|NN 2|2|CD
treatment|treatment|NN :|:|: Bacillus|bacillus|NN volatile|volatile|JJ organic|organic|JJ compounds|compound|NNS -LRB-|-lrb-|-LRB- VOCs|voc|NNS -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: batch|batch|NN growth|growth|NN
treatment|treatment|NN :|:|: BCM|BCM|NNP
treatment|treatment|NN :|:|: Before|before|IN rifampicin|rifampicin|NN treatment|treatment|NN
treatment|treatment|NN :|:|: bicontinious|bicontinious|JJ microemulsion|microemulsion|NN
Treatment|treatment|NN B|b|NN Population|Population|NNP 3|3|CD Colony|Colony|NNP a|a|DT replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 3|3|CD Colony|Colony|NNP a|a|DT replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 3|3|CD Colony|Colony|NNP b|b|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 3|3|CD Colony|Colony|NNP b|b|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 3|3|CD Colony|Colony|NNP c|c|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 3|3|CD Colony|Colony|NNP c|c|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 4|4|CD Colony|Colony|NNP a|a|DT replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 4|4|CD Colony|Colony|NNP a|a|DT replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 4|4|CD Colony|Colony|NNP b|b|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 4|4|CD Colony|Colony|NNP b|b|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 4|4|CD Colony|Colony|NNP c|c|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 4|4|CD Colony|Colony|NNP c|c|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 5|5|CD Colony|Colony|NNP a|a|DT replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 5|5|CD Colony|Colony|NNP a|a|DT replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 5|5|CD Colony|Colony|NNP b|b|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 5|5|CD Colony|Colony|NNP b|b|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 5|5|CD Colony|Colony|NNP c|c|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN B|b|NN Population|Population|NNP 5|5|CD Colony|Colony|NNP c|c|NN replica|replica|NN 2|2|CD
treatment|treatment|NN :|:|: Carbon|Carbon|NNP starvation|starvation|NN
treatment|treatment|NN :|:|: chemostat|chemostat|NN growth|growth|NN
treatment|treatment|NN :|:|: ciprofloxacin|ciprofloxacin|NN
treatment|treatment|NN :|:|: clindamycin|clindamycin|NN
treatment|treatment|NN :|:|: Cold|Cold|NNP Shock|shock|NN
treatment|treatment|NN :|:|: Con1|con1|NN
treatment|treatment|NN :|:|: Con2|con2|NN
treatment|treatment|NN :|:|: Con3|con3|NN
treatment|treatment|NN :|:|: Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 0.1|0.1|CD L/min|l/min|NN CO|co|NN gas|gas|NN
treatment|treatment|NN :|:|: Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN
treatment|treatment|NN :|:|: Continuous|continuous|JJ aerobically|aerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN iCORM-3|icorm-3|NN
treatment|treatment|NN :|:|: Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO 40uM|40um|NN CORM-3|corm-3|NN
treatment|treatment|NN :|:|: Continuous|continuous|JJ anaerobically|anaerobically|RB grown|grow|VBN cultures|culture|NNS in|in|IN Evans|Evans|NNP medium|medium|NN ,|,|, exposed|expose|VBN to|to|TO CO|CO|NNP gas|gas|NN at|at|IN 0.1|0.1|CD L/min|l/min|NN
treatment|treatment|NN :|:|: control|control|NN
treatment|treatment|NN :|:|: control|control|NN ,|,|, anaerobic|anaerobic|JJ
Treatment|treatment|NN C|c|NN Population|Population|NNP 6|6|CD Colony|Colony|NNP b|b|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN C|c|NN Population|Population|NNP 6|6|CD Colony|Colony|NNP b|b|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN C|c|NN Population|Population|NNP 6|6|CD Colony|Colony|NNP c|c|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN C|c|NN Population|Population|NNP 6|6|CD Colony|Colony|NNP c|c|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN C|c|NN Population|Population|NNP 7|7|CD Colony|Colony|NNP b|b|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN C|c|NN Population|Population|NNP 7|7|CD Colony|Colony|NNP b|b|NN replica|replica|NN 2|2|CD
Treatment|treatment|NN C|c|NN Population|Population|NNP 7|7|CD Colony|Colony|NNP c|c|NN replica|replica|NN 1|1|CD
Treatment|treatment|NN C|c|NN Population|Population|NNP 7|7|CD Colony|Colony|NNP c|c|NN replica|replica|NN 2|2|CD
treatment|treatment|NN :|:|: DpnI|dpni|NN digested|digest|VBD DNA|dna|NN
treatment|treatment|NN duration|duration|NN :|:|: 10|10|CD min|min|NN
treatment|treatment|NN duration|duration|NN :|:|: 15|15|CD h|h|NN
treatment|treatment|NN duration|duration|NN :|:|: 2.5|2.5|CD h|h|NN
treatment|treatment|NN duration|duration|NN :|:|: 8|8|CD min|min|NN
treatment|treatment|NN duration|duration|NN :|:|: none|none|NN
treatment|treatment|NN :|:|: erythromycin|erythromycin|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 10|10|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 120|120|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 20|20|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 40|40|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB CORM-3|corm-3|NN for|for|IN 60|60|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 10|10|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 120|120|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 20|20|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 40|40|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO 100uM|100um|VB iCORM-3|icorm-3|NN for|for|IN 60|60|CD min|min|NN
treatment|treatment|NN :|:|: exposed|expose|VBN to|to|TO the|the|DT lettuce|lettuce|NN rhizosphere|rhizosphere|NN for|for|IN 3|3|CD days|day|NNS
treatment|treatment|NN :|:|: florfenicol|florfenicol|NN -LRB-|-lrb-|-LRB- 30|30|CD µg/mL|µg/ml|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 10|10|CD mM|mm|NN leucine|leucine|NN .|.|.
treatment|treatment|NN :|:|: glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 20|20|CD mg/L|mg/l|NN tryptophan|tryptophan|NN .|.|.
treatment|treatment|NN :|:|: glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN without|without|IN 10|10|CD mM|mm|NN leucine|leucine|NN .|.|.
treatment|treatment|NN :|:|: glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ M9|m9|NN medium|medium|NN supplemented|supplement|VBN without|without|IN 20|20|CD mg/L|mg/l|NN tryptophan|tryptophan|NN .|.|.
treatment|treatment|NN :|:|: glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ W2|w2|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 1g/L|1g/l|NN arginine|arginine|NN .|.|.
treatment|treatment|NN :|:|: glucose|glucose|NN -LRB-|-lrb-|-LRB- 2|2|CD g/L|g/l|NN -RRB-|-rrb-|-RRB- minimal|minimal|JJ W2|w2|NN medium|medium|NN supplemented|supplement|VBN with|with|IN 2g/L|2g/l|NN glutamine|glutamine|NN .|.|.
treatment|treatment|NN :|:|: glutamine|glutamine|NN
treatment|treatment|NN group|group|NN :|:|: cold|cold|JJ stress|stress|NN
treatment|treatment|NN group|group|NN :|:|: control|control|NN
treatment|treatment|NN group|group|NN :|:|: heat|heat|NN stress|stress|NN
treatment|treatment|NN group|group|NN :|:|: indole|indole|NN treated|treat|VBN
treatment|treatment|NN group|group|NN :|:|: lactose|lactose|NN shift|shift|NN
treatment|treatment|NN group|group|NN :|:|: oxidative|oxidative|JJ stress|stress|NN
treatment|treatment|NN group|group|NN :|:|: rifampicin|rifampicin|NN time|time|NN point|point|NN 0|0|CD
treatment|treatment|NN group|group|NN :|:|: rifampicin|rifampicin|NN time|time|NN point|point|NN 2|2|CD
treatment|treatment|NN group|group|NN :|:|: rifampicin|rifampicin|NN time|time|NN point|point|NN 4|4|CD
treatment|treatment|NN group|group|NN :|:|: rifampicin|rifampicin|NN time|time|NN point|point|NN 6|6|CD
treatment|treatment|NN group|group|NN :|:|: rifampicin|rifampicin|NN time|time|NN point|point|NN 8|8|CD
treatment|treatment|NN :|:|: grown|grow|VBN in|in|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN
treatment|treatment|NN :|:|: grown|grow|VBN without|without|IN lettuce|lettuce|NN rhizosphere|rhizosphere|NN
treatment|treatment|NN :|:|: heat|heat|NN shock|shock|NN
treatment|treatment|NN :|:|: Heat|Heat|NNP Shock|shock|NN
treatment|treatment|NN :|:|: induced|induce|VBN DNA|dna|NN double|double|JJ strand|strand|NN break|break|NN
treatment|treatment|NN :|:|: log|log|NN phase|phase|NN sample|sample|NN
treatment|treatment|NN :|:|: Low|low|JJ pH|ph|NN
treatment|treatment|NN :|:|: MG1655|mg1655|NN +|+|CC 3µM|3µm|NN HgCl2|hgcl2|NN at|at|IN t10|t10|NN
treatment|treatment|NN :|:|: MG1655|mg1655|NN +|+|CC 3µM|3µm|NN HgCl2|hgcl2|NN at|at|IN t30|t30|NN
treatment|treatment|NN :|:|: MG1655|mg1655|NN +|+|CC 3µM|3µm|NN HgCl2|hgcl2|NN at|at|IN t60|t60|NN
treatment|treatment|NN :|:|: MG1655|mg1655|NN +|+|CC 3µM|3µm|NN PMA|pma|NN at|at|IN t10|t10|NN
treatment|treatment|NN :|:|: MG1655|mg1655|NN +|+|CC 3µM|3µm|NN PMA|pma|NN at|at|IN t30|t30|NN
treatment|treatment|NN :|:|: MG1655|mg1655|NN +|+|CC 3µM|3µm|NN PMA|pma|NN at|at|IN t60|t60|NN
treatment|treatment|NN :|:|: MG1655|mg1655|SYM -|-|: unexposed|unexposed|JJ at|at|IN t0|t0|NN
treatment|treatment|NN :|:|: MG1655|mg1655|SYM -|-|: unexposed|unexposed|JJ at|at|IN t10|t10|NN
treatment|treatment|NN :|:|: MG1655|mg1655|SYM -|-|: unexposed|unexposed|JJ at|at|IN t30|t30|CD
treatment|treatment|NN :|:|: MG1655|mg1655|SYM -|-|: unexposed|unexposed|JJ at|at|IN t60|t60|NN
treatment|treatment|NN :|:|: minimal|minimal|JJ C&N|c&n|NN source|source|NN
treatment|treatment|NN :|:|: minimal|minimal|JJ C|c|NN source|source|NN
treatment|treatment|NN :|:|: minimal|minimal|JJ N|n|NN source|source|NN
treatment|treatment|NN :|:|: NA|NA|NNP
treatment|treatment|NN :|:|: N/A|n/a|NN
treatment|treatment|NN :|:|: Nitrogen|nitrogen|NN starvation|starvation|NN
treatment|treatment|NN :|:|: none|none|NN
treatment|treatment|NN :|:|: None|none|NN
treatment|treatment|NN :|:|: non-sorted|non-sorted|JJ
treatment|treatment|NN :|:|: No|no|DT treatment|treatment|NN
Treatment|treatment|NN of|of|IN sub-lethal|sub-lethal|JJ triclosan|triclosan|NN ;|;|: 50|50|CD mg/L|mg/l|NN triclosan|triclosan|NN
treatment|treatment|NN :|:|: oil|oil|NN in|in|IN water|water|NN
treatment|treatment|NN :|:|: Osmotic|osmotic|JJ stress|stress|NN
treatment|treatment|NN :|:|: Oxidative|oxidative|JJ stress|stress|NN
treatment|treatment|NN :|:|: PA1|pa1|NN
treatment|treatment|NN :|:|: PA2|pa2|NN
treatment|treatment|NN :|:|: PA3|pa3|NN
treatment|treatment|NN :|:|: Pooled|pool|VBN RNA|rna|NN from|from|IN mixture|mixture|NN of|of|IN the|the|DT same|same|JJ amount|amount|NN of|of|IN wt|wt|JJ ,|,|, wt|wt|JJ +|+|CC SHX|shx|NN ,|,|, dksA|dksa|NN ,|,|, dksA|dksa|NN +|+|CC SHX|shx|NN RNA|rna|NN samples|sample|NNS
treatment|treatment|NN :|:|: prior|prior|RB to|to|TO CORM-3|corm-3|NN addition|addition|NN -LRB-|-lrb-|-LRB- t|t|NN =|=|JJ 0|0|CD -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: prior|prior|RB to|to|TO iCORM-3|icorm-3|NN addition|addition|NN -LRB-|-lrb-|-LRB- t|t|NN =|=|JJ 0|0|CD -RRB-|-rrb-|-RRB-
Treatment|treatment|NN protocol|protocol|NN -|-|: E.coli|e.coli|NN cells|cell|NNS grown|grow|VBN in|in|IN LB|LB|NNP media|media|NNS with|with|IN at|at|IN 37C|37c|NN until|until|IN early|early|JJ log|log|NN phase|phase|NN -LRB-|-lrb-|-LRB- 0.4|0.4|CD -RRB-|-rrb-|-RRB- ,|,|, then|then|RB were|be|VBD treated|treat|VBN with|with|IN 200|200|CD mM|mm|NN glyphosate|glyphosate|NN for|for|IN 1|1|CD h|h|NN ,|,|, after|after|IN that|that|IN the|the|DT cells|cell|NNS were|be|VBD harvested|harvest|VBN to|to|TO extract|extract|NN RNA|rna|NN .|.|.
treatment|treatment|NN :|:|: PS-60min|ps-60min|JJ
treatment|treatment|NN :|:|: Ribosome-protected|ribosome-protected|JJ mRNA|mrna|NN ,|,|, Ribosome|ribosome|NN footprint|footprint|NN sample|sample|NN digested|digest|VBN with|with|IN 60|60|CD units|unit|NNS of|of|IN micrococcal|micrococcal|JJ nuclease|nuclease|NN per|per|IN A260|a260|NN absorbance|absorbance|NN
treatment|treatment|NN :|:|: rifampicin|rifampicin|NN
treatment|treatment|NN :|:|: saline|saline|NN
treatment|treatment|NN :|:|: sham-treated|sham-treated|JJ power|power|NN line|line|NN intermittent|intermittent|JJ -LRB-|-lrb-|-LRB- 2|2|CD min|min|NN on|on|IN ,|,|, 4|4|CD min|min|NN off|off|IN -RRB-|-rrb-|-RRB- magnetic|magnetic|JJ field|field|NN
treatment|treatment|NN :|:|: sham-treated|sham-treated|JJ sinusoidal|sinusoidal|JJ continous|continous|JJ magnetic|magnetic|JJ field|field|NN
treatment|treatment|NN :|:|: sham-treated|sham-treated|JJ sinusoidal|sinusoidal|JJ intermittent|intermittent|JJ -LRB-|-lrb-|-LRB- 2|2|CD min|min|NN on|on|IN ,|,|, 4|4|CD min|min|NN off|off|IN -RRB-|-rrb-|-RRB- magnetic|magnetic|JJ field|field|NN
treatment|treatment|NN :|:|: sorted|sort|VBN
treatment|treatment|NN :|:|: Standard|Standard|NNP
treatment|treatment|NN :|:|: starvation|starvation|NN growth|growth|NN
treatment|treatment|NN :|:|: stationary|stationary|JJ phase|phase|NN
treatment|treatment|NN :|:|: streptomycin|streptomycin|NN -LRB-|-lrb-|-LRB- 50|50|CD µg/mL|µg/ml|NN final|final|JJ concentration|concentration|NN -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: Supernatant|supernatant|NN
treatment|treatment|NN temperature|temperature|NN :|:|: 30C|30c|CD
treatment|treatment|NN temperature|temperature|NN :|:|: 42C|42c|NN
treatment|treatment|NN time|time|NN :|:|: T10|t10|NN :|:|: 210|210|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T11|t11|NN :|:|: 235|235|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T12|t12|NN :|:|: 260|260|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T1|t1|NN :|:|: OD|od|NN 0.3|0.3|CD
treatment|treatment|NN time|time|NN :|:|: T1|t1|NN :|:|: OD|od|NN 0.5|0.5|CD
treatment|treatment|NN time|time|NN :|:|: T2|t2|NN :|:|: OD|od|NN 0.5|0.5|CD
treatment|treatment|NN time|time|NN :|:|: T2|t2|NN :|:|: OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T3|t3|NN :|:|: 10|10|CD min|min|NN after|after|IN reaching|reach|VBG OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T3|t3|NN :|:|: 10|10|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T3|t3|NN :|:|: OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T3|t3|NN :|:|: OD|od|NN 0.7|0.7|CD
treatment|treatment|NN time|time|NN :|:|: T4|t4|NN :|:|: 10|10|CD min|min|NN after|after|IN growth|growth|NN lag|lag|NN
treatment|treatment|NN time|time|NN :|:|: T4|t4|NN :|:|: 10|10|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T4|t4|NN :|:|: 20|20|CD min|min|NN after|after|IN reaching|reach|VBG OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T4|t4|NN :|:|: 20|20|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T5|t5|NN :|:|: 20|20|CD min|min|NN after|after|IN growth|growth|NN lag|lag|NN
treatment|treatment|NN time|time|NN :|:|: T5|t5|NN :|:|: 20|20|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T5|t5|NN :|:|: 30|30|CD min|min|NN after|after|IN reaching|reach|VBG OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T5|t5|NN :|:|: 30|30|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T6|t6|NN :|:|: 30|30|CD min|min|NN after|after|IN growth|growth|NN lag|lag|NN
treatment|treatment|NN time|time|NN :|:|: T6|t6|NN :|:|: 30|30|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T6|t6|NN :|:|: 40|40|CD min|min|NN after|after|IN reaching|reach|VBG OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T6|t6|NN :|:|: 40|40|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T7|t7|NN :|:|: 40|40|CD min|min|NN after|after|IN growth|growth|NN lag|lag|NN
treatment|treatment|NN time|time|NN :|:|: T7|t7|NN :|:|: 40|40|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T7|t7|NN :|:|: 50|50|CD min|min|NN after|after|IN reaching|reach|VBG OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T7|t7|NN :|:|: 50|50|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T8|t8|NN :|:|: 90|90|CD min|min|NN after|after|IN reaching|reach|VBG OD|od|NN 0.6|0.6|CD
treatment|treatment|NN time|time|NN :|:|: T8|t8|NN :|:|: 90|90|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN time|time|NN :|:|: T9|t9|NN :|:|: 150|150|CD min|min|NN after|after|IN stress|stress|NN
treatment|treatment|NN :|:|: tobacco|tobacco|NN acid|acid|NN pyrophosphatase|pyrophosphatase|NN -LRB-|-lrb-|-LRB- TAP|tap|NN -RRB-|-rrb-|-RRB-
treatment|treatment|NN :|:|: Treated|treat|VBN by|by|IN HPCD|hpcd|NN at|at|IN 5|5|CD MPa|mpa|NN and|and|CC 25|25|CD ℃|℃|NN for|for|IN 40|40|CD min|min|NN
treatment|treatment|NN :|:|: treated|treated|JJ culture|culture|NN
treatment|treatment|NN :|:|: treated|treat|VBN power|power|NN line|line|NN intermittent|intermittent|JJ -LRB-|-lrb-|-LRB- 2|2|CD min|min|NN on|on|IN ,|,|, 4|4|CD min|min|NN off|off|IN -RRB-|-rrb-|-RRB- magnetic|magnetic|JJ field|field|NN
treatment|treatment|NN :|:|: treated|treat|VBN sinusoidal|sinusoidal|JJ continous|continous|JJ magnetic|magnetic|JJ field|field|NN
treatment|treatment|NN :|:|: treated|treat|VBN sinusoidal|sinusoidal|JJ intermittent|intermittent|JJ -LRB-|-lrb-|-LRB- 2|2|CD min|min|NN on|on|IN ,|,|, 4|4|CD min|min|NN off|off|IN -RRB-|-rrb-|-RRB- magnetic|magnetic|JJ field|field|NN
treatment|treatment|NN :|:|: triclosan|triclosan|NN
treatment|treatment|NN :|:|: unexposed|unexposed|JJ ,|,|, left|left|JJ chamber/bioreacator|chamber/bioreacator|NN
treatment|treatment|NN :|:|: unexposed|unexposed|JJ ,|,|, right|right|JJ chamber/bioreacator|chamber/bioreacator|NN
treatment|treatment|NN :|:|: unexposed|unexposed|JJ ,|,|, treated|treat|VBN with|with|IN 1mM|1mm|NN H2O2|h2o2|NN
treatment|treatment|NN :|:|: unexposed|unexposed|JJ ,|,|, treated|treat|VBN with|with|IN water|water|NN
treatment|treatment|NN :|:|: untreated|untreated|JJ
treatment|treatment|NN :|:|: untreated|untreated|JJ culture|culture|NN
treatment|treatment|NN :|:|: UV|uv|NN
treatment|treatment|NN :|:|: vector|vector|NN control|control|NN
treatment|treatment|NN :|:|: water|water|NN in|in|IN oil|oil|NN
treatment|treatment|NN :|:|: with|with|IN homogenization|homogenization|NN and|and|CC separation|separation|NN
treatment|treatment|NN :|:|: without|without|IN salt|salt|NN shock|shock|NN
treatment|treatment|NN :|:|: WT|WT|NNP Rho|rho|NN plasmid|plasmid|NN
Triclosan|Triclosan|NNP tolerant|tolerant|JJ mutant|mutant|JJ triclosan|triclosan|NN treated|treat|VBN biological|biological|JJ rep|rep|NN 1|1|CD
Triclosan|Triclosan|NNP tolerant|tolerant|JJ mutant|mutant|JJ triclosan|triclosan|NN treated|treat|VBN biological|biological|JJ rep|rep|NN 2|2|CD
Triclosan|Triclosan|NNP tolerant|tolerant|JJ mutant|mutant|JJ triclosan|triclosan|NN treated|treat|VBN biological|biological|JJ rep|rep|NN 3|3|CD
Triclosan|triclosan|NN tolerant|tolerant|JJ mutant|mutant|JJ untreated|untreated|JJ biological|biological|JJ rep|rep|NN 1|1|CD
Triclosan|Triclosan|NNP tolerant|tolerant|JJ mutant|mutant|JJ untreated|untreated|JJ biological|biological|JJ rep|rep|NN 2|2|CD
Triclosan|Triclosan|NNP tolerant|tolerant|JJ mutant|mutant|JJ untreated|untreated|JJ biological|biological|JJ rep|rep|NN 3|3|CD
trim|trim|JJ adaptors|adaptor|NNS on|on|IN raw|raw|JJ reads|read|VBZ and|and|CC moved|move|VBD trimmed|trimmed|RBR reads|read|VBZ to|to|TO trimmed|trimmed|RBR _|_|SYM reads|read|VBZ with|with|IN flexbar|flexbar|JJ
Trimethoprim-treated|trimethoprim-treated|JJ E.|e.|FW coli|coli|FW cells|cell|NNS
Trimmed|trimmed|JJ adaptor|adaptor|NN sequences|sequence|NNS from|from|IN reads|read|VBZ using|use|VBG Flexbar|Flexbar|NNP 2.31|2.31|CD
Trimmed|trim|VBD reads|read|VBZ were|be|VBD aligned|align|VBN on|on|IN most|most|JJS recent|recent|JJ reference|reference|NN genome|genome|NN of|of|IN Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- GenBank|genbank|NN U00096|u00096|NN .3|.3|NN -RRB-|-rrb-|-RRB- by|by|IN using|use|VBG TopHat|TopHat|NNP -LRB-|-lrb-|-LRB- v2|v2|NN .0.10|.0.10|CD -RRB-|-rrb-|-RRB- coupled|couple|VBN with|with|IN bowtie|bowtie|NN -LRB-|-lrb-|-LRB- v1|v1|NN .0.0|.0.0|CD -RRB-|-rrb-|-RRB- .|.|.
Trimmed|trim|VBD reads|read|VBZ were|be|VBD aligned|align|VBN using|use|VBG Bowtie|Bowtie|NNP v0|v0|NN .12.7|.12.7|CD against|against|IN the|the|DT reference|reference|NN genome|genome|NN using|use|VBG parameters|parameter|NNS -|-|: a|a|SYM -|-|: v|v|LS 3|3|LS -|-|: m|m|NN 1|1|CD
Trimmed|trim|VBD reads|read|VBZ were|be|VBD sequentially|sequentially|RB aligned|align|VBN using|use|VBG Bowtie|Bowtie|NNP v0|v0|NN .12.7|.12.7|CD to|to|TO E|E|NNP coli|coli|NN genome|genome|NN using|use|VBG parameters|parameter|NNS -|-|: v|v|LS 1|1|LS -|-|: m|m|NN 1|1|CD --|--|: best|best|JJS .|.|. This|this|DT allows|allow|VBZ one|one|CD mismatch|mismatch|NN and|and|CC reports|report|NNS only|only|RB reads|read|VBZ that|that|IN align|align|NN 1|1|CD or|or|CC fewer|fewer|JJR times|time|NNS to|to|TO the|the|DT genome|genome|NN
Trimmed|trim|VBD reads|read|VBZ were|be|VBD sequentially|sequentially|RB aligned|align|VBN using|use|VBG Bowtie|Bowtie|NNP v0|v0|NN .12.7|.12.7|CD to|to|TO E|E|NNP coli|coli|NN rRNA|rrna|NN and|and|CC noncoding|noncoding|JJ RNA|rna|NN allowing|allow|VBG one|one|CD mismatch|mismatch|NN .|.|. Reads|read|VBZ aligning|align|VBG to|to|TO any|any|DT of|of|IN these|these|DT indices|index|NNS were|be|VBD discarded|discard|VBN .|.|.
Trimmed|trim|VBD reads|read|VBZ were|be|VBD sequentially|sequentially|RB aligned|align|VBN using|use|VBG Bowtie|Bowtie|NNP v0|v0|NN .12.7|.12.7|CD to|to|TO E.|e.|FW coli|coli|FW rRNA|rrna|NN and|and|CC noncoding|noncoding|JJ RNA|rna|NN allowing|allow|VBG one|one|CD mismatch|mismatch|NN .|.|. Reads|read|VBZ aligning|align|VBG to|to|TO any|any|DT of|of|IN these|these|DT indices|index|NNS were|be|VBD discarded|discard|VBN .|.|.
triplicate|triplicate|NN samples|sample|NNS were|be|VBD prepared|prepare|VBN by|by|IN combining|combine|VBG cells|cell|NNS from|from|IN 5|5|CD tubes|tube|NNS each|each|DT .|.|. Each|each|DT pellet|pellet|NN was|be|VBD
TRI|TRI|NNP Reagent|Reagent|NNP -LRB-|-lrb-|-LRB- Sigma|Sigma|NNP -RRB-|-rrb-|-RRB- or|or|CC Rneasy|rneasy|NN -LRB-|-lrb-|-LRB- QIAGEN|qiagen|NN -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO manufacturer|manufacturer|NN 's|'s|POS protocol|protocol|NN .|.|. No|no|DT Rnase|rnase|NN treatment|treatment|NN .|.|.
Trizol|trizol|NN extraction|extraction|NN of|of|IN total|total|JJ RNA|rna|NN was|be|VBD performed|perform|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS
Trizol|Trizol|NNP extraction|extraction|NN of|of|IN total|total|JJ RNA|rna|NN was|be|VBD performed|perform|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
Trizol|trizol|NN for|for|IN RNAseq|rnaseq|NN ,|,|, gradient|gradient|NN centrifugation|centrifugation|NN =|=|JJ >|>|JJR RNase|rnase|NN digestions|digestion|NNS =|=|JJ >|>|JJR Trizol|trizol|NN =|=|JJ >|>|JJR gel|gel|NN extraction|extraction|NN for|for|IN RIBOseq|riboseq|NN
TRIzol|trizol|NN reagent|reagent|NN -LRB-|-lrb-|-LRB- Gibco|Gibco|NNP BRL|brl|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN instruction|instruction|NN .|.|. RNA|rna|NN was|be|VBD treated|treat|VBN with|with|IN DNase|dnase|NN -LRB-|-lrb-|-LRB- Ambion|ambion|NN -RRB-|-rrb-|-RRB- .|.|. RNA|rna|NN sample|sample|NN was|be|VBD converted|convert|VBN to|to|TO cDNA|cdna|NN in|in|IN 5|5|CD independent|independent|JJ reverse-transcription|reverse-transcription|JJ reactions|reaction|NNS as|as|IN described|describe|VBN previously|previously|RB -LRB-|-lrb-|-LRB- Graham|Graham|NNP ,|,|, J.|J.|NNP 1999|1999|CD .|.|. PNAS|PNAS|NNP 96:11554-559|96:11554-559|CD -RRB-|-rrb-|-RRB- .|.|. Bacterial|bacterial|JJ transcript|transcript|NN were|be|VBD purified|purify|VBN from|from|IN host|host|NN transcript|transcript|NN by|by|IN using|use|VBG 3|3|CD round|round|NN of|of|IN the|the|DT SCOTS|SCOTS|NNP procedure|procedure|NN -LRB-|-lrb-|-LRB- Daigle|daigle|NN ,|,|, F.|F.|NNP 2002|2002|CD .|.|. Methods|method|NNS Enzymol|Enzymol|NNP .|.|. 358:108-122|358:108-122|CD -RRB-|-rrb-|-RRB- .|.|.
trpD|trpd|NN KO|ko|NN rep1|rep1|NN
trpD|trpd|NN KO|ko|NN rep2|rep2|NN
trpD|trpd|NN KO|ko|NN rep3|rep3|NN
trpEA2trpR2|trpea2trpr2|NN vs.|vs.|CC trpEA2|trpea2|NN ,|,|, W3110|w3110|NN min|min|NN +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|JJ
trpEA2trpR2|trpea2trpr2|NN ,|,|, W3110|w3110|NN min|min|NN +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ
trpEA2|trpea2|NN ,|,|, W3110|w3110|NN min|min|NN +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ
trpR2|trpr2|NN +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ RNA|rna|NN
trpR2|trpr2|NN +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN vs.|vs.|CC wt|wt|JJ +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN
trpR2tnaA2|trpr2tnaa2|NN ,|,|, W3110|w3110|NN minimal|minimal|JJ +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|CD vs.|vs.|CC dnaC|dnaC|NNP genomic|genomic|JJ DNA|dna|NN
trpR2tnaA2|trpr2tnaa2|NN ,|,|, W3110|w3110|NN min|min|NN +|+|CC Trp|trp|NN 50ug/ml|50ug/ml|NN ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
trpR2|trpr2|NN +|+|CC trp|trp|NN vs.|vs.|NN -|-|: trp|trp|NN ,|,|, min|min|NN +.2|+.2|CD %|%|NN glucose|glucose|NN ,|,|, W3110|w3110|NN
trpR2|trpr2|NN vs.|vs.|CC wt|wt|JJ ,|,|, min|min|NN +.2|+.2|CD %|%|NN glucose|glucose|NN ,|,|, W3110|w3110|NN
TrpR|trpr|NN _|_|NN glucose|glucose|NN
TrpR|trpr|NN _|_|CD Trp|Trp|NNP
TruSeq|TruSeq|NNP
Truseq|Truseq|NNP ChIP|ChIP|NNP kit|kit|NN was|be|VBD used|use|VBN for|for|IN the|the|DT library|library|NN preparation|preparation|NN .|.|. DNA|dna|NN was|be|VBD end|end|NN repaired|repair|VBN and|and|CC adapters|adapter|NNS were|be|VBD ligated|ligate|VBN .|.|. After|after|IN ligation|ligation|NN ,|,|, purify|purify|VB ligation|ligation|NN products|product|NNS and|and|CC then|then|RB amplify|amplify|VB .|.|.
Truseq|truseq|NN Small|small|JJ RNA|rna|NN
Tryptophan|tryptophan|NN addition|addition|NN
TTAGGC-D3|ttaggc-d3|NN
Tube|Tube|NNP state|state|NN 1|1|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Tube|Tube|NNP state|state|NN 2|2|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Tube|Tube|NNP state|state|NN 3|3|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Tube|Tube|NNP state|state|NN 4|4|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP -|-|: -RRB-|-rrb-|-RRB-
Tube|Tube|NNP state|state|NN 5|5|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
Tube|Tube|NNP state|state|NN 6|6|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|SYM -|-|: /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
Tube|Tube|NNP state|state|NN 7|7|CD -LRB-|-lrb-|-LRB- IPTG|iptg|SYM -|-|: /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
Tube|Tube|NNP state|state|NN 8|8|CD -LRB-|-lrb-|-LRB- IPTG|iptg|NN +|+|CC /|/|: aTc|atc|NN +|+|CC /|/|: Ara|Ara|NNP +|+|CC -RRB-|-rrb-|-RRB-
TW09308|tw09308|NN batch|batch|NN
TW09308|tw09308|NN chemostat|chemostat|NN
TW09308|tw09308|NN starvation|starvation|NN
TW09308|tw09308|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 1|1|CD
TW09308|tw09308|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 2|2|CD
TW09308|tw09308|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 1|1|CD
TW09308|tw09308|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 2|2|CD
TW09308|tw09308|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 1|1|CD
TW09308|tw09308|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 2|2|CD
TW10915|tw10915|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW10916|tw10916|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW10917|tw10917|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW10938|tw10938|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW10948|tw10948|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW10950|tw10950|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW10957|tw10957|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW10967|tw10967|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN DMEM|DMEM|NNP medium|medium|NN upto|upto|NN exponential|exponential|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.5|0.5|CD ,|,|, 2.5|2.5|CD h|h|NN after|after|IN inoclulation|inoclulation|NN -RRB-|-rrb-|-RRB- at|at|IN 37C|37c|NN .|.|.
TW11588|tw11588|NN batch|batch|NN
TW11588|tw11588|NN chemostat|chemostat|NN
TW11588|tw11588|NN starvation|starvation|NN
TW11588|tw11588|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 1|1|CD
TW11588|tw11588|NN transcriptome|transcriptome|NN from|from|IN batch|batch|NN growth|growth|NN _|_|NN 2|2|CD
TW11588|tw11588|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 1|1|CD
TW11588|tw11588|NN transcriptome|transcriptome|NN from|from|IN chemostat|chemostat|NN growth|growth|NN _|_|NN 2|2|CD
TW11588|tw11588|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 1|1|CD
TW11588|tw11588|NN transcriptome|transcriptome|NN from|from|IN starvation|starvation|NN growth|growth|NN _|_|NN 2|2|CD
Two|two|CD Avian|avian|JJ Pathogenic|pathogenic|JJ Escherichia|escherichia|FW coli|coli|FW strains|strain|NNS -LRB-|-lrb-|-LRB- APEC|apec|NNS -RRB-|-rrb-|-RRB- were|be|VBD grown|grow|VBN at|at|IN 37|37|CD °C|°c|NN in|in|IN Dulbecco|Dulbecco|NNP 's|'s|POS Modified|modify|VBN Eagle|Eagle|NNP 's|'s|POS Media|Media|NNP -LRB-|-lrb-|-LRB- DMEM|DMEM|NNP -RRB-|-rrb-|-RRB- media|media|NNS until|until|IN reach|reach|NN O.D|o.d|NN 600|600|CD =|=|JJ 0.8|0.8|CD .|.|.
Two|two|CD biological|biological|JJ replicates|replicate|VBZ were|be|VBD performed|perform|VBN for|for|IN samples|sample|NNS with|with|IN and|and|CC without|without|IN treatment|treatment|NN with|with|IN bicyclomycin|bicyclomycin|NN .|.|. For|for|IN samples|sample|NNS without|without|IN BCM|bcm|NN treatment|treatment|NN ,|,|, cells|cell|NNS were|be|VBD grown|grow|VBN OD600|od600|NN ≈|≈|NN 0.8|0.8|CD at|at|IN 370|370|CD with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN .|.|. For|for|IN samples|sample|NNS with|with|IN BCM|bcm|NN treatment|treatment|NN ,|,|, cells|cell|NNS were|be|VBD grown|grow|VBN to|to|TO early|early|JJ log|log|NN phase|phase|NN -LRB-|-lrb-|-LRB- O.D.|o.d.|NN 600|600|CD =|=|JJ 0.1|0.1|CD -RRB-|-rrb-|-RRB- ≈|≈|SYM 1h|1h|VBP at|at|IN 370|370|CD with|with|IN shaking|shake|VBG at|at|IN 200|200|CD rpm|rpm|NN .|.|. BCM|BCM|NNP was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 25ug|25ug|JJ mL-1|ml-1|NN
Two|two|CD biological|biological|JJ replicates|replicate|VBZ were|be|VBD processed|process|VBN seperatedly|seperatedly|RB ,|,|, and|and|CC only|only|RB sequence|sequence|NN reads|read|VBZ presented|present|VBN in|in|IN both|both|CC biological|biological|JJ replciates|replciate|NNS were|be|VBD considered|consider|VBN for|for|IN further|further|JJ process|process|NN .|.|. The|the|DT genomic|genomic|JJ coordinates|coordinate|VBZ of|of|IN the|the|DT 5|5|CD '|'|'' -|-|: end|end|NN of|of|IN these|these|DT uniquely|uniquely|RB aligned|align|VBN reads|read|VBZ were|be|VBD defined|define|VBN as|as|IN potential|potential|JJ TSSs|tsss|NNS .|.|.
Two|two|CD color|color|NN cDNA|cdna|NN microarray|microarray|NN data|datum|NNS are|be|VBP never|never|RB devoid|devoid|JJ of|of|IN spurious|spurious|JJ technical|technical|JJ contributions|contribution|NNS that|that|WDT
Two|two|CD color|color|NN cDNA|cdna|NN microarray|microarray|NN data|datum|NNS are|be|VBP never|never|RB devoid|devoid|JJ of|of|IN spurious|spurious|JJ technical|technical|JJ contributions|contribution|NNS that|that|WDT originate|originate|VBP during|during|IN array|array|NN printing|printing|NN ,|,|, as|as|RB well|well|RB as|as|IN during|during|IN the|the|DT collection|collection|NN and|and|CC processing|processing|NN of|of|IN samples|sample|NNS ,|,|, fluorescent|fluorescent|JJ labeling|labeling|NN and|and|CC hybridization|hybridization|NN and|and|CC scanning|scanning|NN of|of|IN the|the|DT microarray|microarray|NN images|image|NNS -LRB-|-lrb-|-LRB- Balazsi|balazsus|NNS et|et|FW al.|al.|FW 2003|2003|CD ,|,|, PNAS|PNAS|NNP -RRB-|-rrb-|-RRB- .|.|. To|to|TO minimize|minimize|VB the|the|DT effect|effect|NN of|of|IN such|such|JJ contributions|contribution|NNS ,|,|, microarray|microarray|NN data|datum|NNS were|be|VBD normalized|normalize|VBN as|as|IN described|describe|VBN before|before|IN -LRB-|-lrb-|-LRB- Tong|Tong|NNP et|et|FW al.|al.|FW 2004|2004|CD BBRC|BBRC|NNP -RRB-|-rrb-|-RRB- .|.|. Briefly|briefly|RB ,|,|, spots|spot|NNS were|be|VBD excluded|exclude|VBN from|from|IN further|further|JJ analysis|analysis|NN if|if|IN the|the|DT foreground|foreground|NN intensity|intensity|NN of|of|IN less|less|JJR than|than|IN 50|50|CD %|%|NN of|of|IN the|the|DT pixels|pixel|NNS within|within|IN the|the|DT spot|spot|NN were|be|VBD above|above|IN 2|2|CD standard|standard|JJ deviations|deviation|NNS of|of|IN the|the|DT background|background|NN .|.|. We|we|PRP generated|generate|VBD expression|expression|NN data|datum|NNS tables|table|NNS in|in|IN Microsoft|Microsoft|NNP Excel|Excel|NNP ,|,|, containing|contain|VBG the|the|DT following|follow|VBG information|information|NN for|for|IN each|each|DT of|of|IN the|the|DT 14,352|14,352|CD entries|entry|NNS :|:|: block|block|NN -LRB-|-lrb-|-LRB- B|b|NN -RRB-|-rrb-|-RRB- ,|,|, column|column|NN -LRB-|-lrb-|-LRB- X|x|NN -RRB-|-rrb-|-RRB- ,|,|, and|and|CC row|row|NN -LRB-|-lrb-|-LRB- Y|y|NN -RRB-|-rrb-|-RRB- number|number|NN ,|,|, red|red|JJ foreground|foreground|NN -LRB-|-lrb-|-LRB- f|f|FW _|_|FW r|r|NN -RRB-|-rrb-|-RRB- and|and|CC background|background|NN -LRB-|-lrb-|-LRB- b|b|NN _|_|CD r|r|NN -RRB-|-rrb-|-RRB- ,|,|, green|green|JJ foreground|foreground|NN -LRB-|-lrb-|-LRB- f|f|FW _|_|FW g|g|NN -RRB-|-rrb-|-RRB- and|and|CC background|background|NN -LRB-|-lrb-|-LRB- b|b|NN _|_|CD g|g|NN -RRB-|-rrb-|-RRB- intensity|intensity|NN .|.|. The|the|DT position|position|NN of|of|IN each|each|DT probe|probe|NN within|within|IN a|a|DT block|block|NN ,|,|, P|p|NN is|be|VBZ defined|define|VBN by|by|IN the|the|DT pair|pair|NN of|of|IN integers|integer|NNS -LRB-|-lrb-|-LRB- X|x|NN ,|,|, Y|y|NN -RRB-|-rrb-|-RRB- .|.|. Log|log|VB ratios|ratio|NNS were|be|VBD defined|define|VBN as|as|IN the|the|DT base|base|NN 10|10|CD logarithm|logarithm|NN of|of|IN -LRB-|-lrb-|-LRB- F|f|NN _|_|CD r-B|r-b|NN _|_|NN r|r|NN -RRB-|-rrb-|-RRB- /|/|: -LRB-|-lrb-|-LRB- F|f|NN _|_|CD g-B|g-b|NN _|_|CD g|g|NN -RRB-|-rrb-|-RRB- ,|,|, where|where|WRB F|f|NN _|_|NN r|r|NN ,|,|, B|b|NN _|_|NN r|r|NN ,|,|, F|f|NN _|_|CD g|g|NN and|and|CC B|b|NN _|_|CD g|g|NN represent|represent|VBP the|the|DT median|median|JJ Cy5|cy5|NN -LRB-|-lrb-|-LRB- red|red|NN -RRB-|-rrb-|-RRB- foreground|foreground|NN and|and|CC background|background|NN ,|,|, and|and|CC the|the|DT median|median|JJ Cy3|cy3|NN -LRB-|-lrb-|-LRB- green|green|JJ -RRB-|-rrb-|-RRB- foreground|foreground|NN and|and|CC background|background|NN intensities|intensity|NNS ,|,|, respectively|respectively|RB .|.|. In|in|IN some|some|DT cases|case|NNS ,|,|, when|when|WRB the|the|DT intensity|intensity|NN of|of|IN the|the|DT background|background|NN was|be|VBD higher|higher|JJR than|than|IN or|or|CC equal|equal|JJ to|to|TO the|the|DT intensity|intensity|NN of|of|IN the|the|DT foreground|foreground|NN ,|,|, the|the|DT resulting|result|VBG log|log|NN ratios|ratio|NNS became|become|VBD complex|complex|JJ or|or|CC infinity|infinity|NN .|.|. These|these|DT values|value|NNS were|be|VBD eliminated|eliminate|VBN using|use|VBG the|the|DT find|find|VB ,|,|, imag|imag|NN ,|,|, and|and|CC isfinite|isfinite|NN functions|function|NNS in|in|IN Matlab|Matlab|NNP .|.|. Next|next|RB ,|,|, data|datum|NNS were|be|VBD normalized|normalize|VBN ,|,|, by|by|IN averaging|average|VBG the|the|DT log|log|NN ratios|ratio|NNS resulting|result|VBG from|from|IN all|all|DT spots|spot|NNS printed|print|VBN by|by|IN a|a|DT print|print|NN tip|tip|NN ,|,|, and|and|CC subtracting|subtract|VBG the|the|DT resulting|result|VBG average|average|NN from|from|IN all|all|DT the|the|DT individual|individual|JJ log|log|NN ratios|ratio|NNS corresponding|correspond|VBG to|to|TO the|the|DT same|same|JJ tip|tip|NN .|.|. Finally|finally|RB ,|,|, all|all|PDT the|the|DT log|log|NN ratios|ratio|NNS of|of|IN the|the|DT same|same|JJ gene|gene|NN from|from|IN each|each|DT slide|slide|NN were|be|VBD averaged|average|VBN and|and|CC listed|list|VBN in|in|IN a|a|DT new|new|JJ file|file|NN .|.|.
Two|two|CD different|different|JJ approaches|approach|NNS were|be|VBD used|use|VBN to|to|TO align|align|VB sequence|sequence|NN reads|read|VBZ to|to|TO the|the|DT genome|genome|NN of|of|IN E.|e.|FW coli|coli|FW K-12|k-12|NN MG1655|mg1655|NN -LRB-|-lrb-|-LRB- U00096|u00096|NN .3|.3|NN -RRB-|-rrb-|-RRB- .|.|. First|first|RB ,|,|, quality|quality|NN controlled|controlled|JJ reads|read|VBZ were|be|VBD mapped|map|VBN using|use|VBG the|the|DT CLC|clc|NN Genomics|genomic|NNS Workbench|workbench|JJ version|version|NN 7.5.1|7.5.1|CD -LRB-|-lrb-|-LRB- CLC|clc|NN GW|gw|NN ,|,|, Bio-Qiagen|bio-qiagen|NN ,|,|, Aarhus|Aarhus|NNP ,|,|, Denmark|Denmark|NNP -RRB-|-rrb-|-RRB- with|with|IN either|either|CC default|default|NN settings|setting|NNS for|for|IN the|the|DT length|length|NN and|and|CC similarity|similarity|NN fractions|fraction|NNS -LRB-|-lrb-|-LRB- 0.5|0.5|CD and|and|CC 0.8|0.8|CD ,|,|, respectively|respectively|RB ,|,|, see|see|VB supplemental|supplemental|JJ Table|Table|NNP 2|2|CD of|of|IN the|the|DT paper|paper|NN -RRB-|-rrb-|-RRB- or|or|CC with|with|IN the|the|DT most|most|RBS stringent|stringent|JJ criteria|criterion|NNS -LRB-|-lrb-|-LRB- 1.0|1.0|CD and|and|CC 1.0|1.0|CD ,|,|, respectively|respectively|RB ,|,|, deposited|deposit|VBN -RRB-|-rrb-|-RRB- .|.|. Reads|read|VBZ with|with|IN sequences|sequence|NNS aligned|align|VBN to|to|TO multiple|multiple|JJ genomic|genomic|JJ regions|region|NNS were|be|VBD ignored|ignore|VBN .|.|.
Two|two|CD precultures|preculture|NNS were|be|VBD performed|perform|VBN in|in|IN LB|lb|NN medium|medium|NN and|and|CC mineral|mineral|NN salt|salt|NN medium|medium|NN with|with|IN 10|10|CD g|g|NN L|l|NN 1|1|CD of|of|IN glucose|glucose|NN without|without|IN antifoam|antifoam|JJ agent|agent|NN consecutively|consecutively|RB at|at|IN 37|37|CD °C|°c|NN at|at|IN a|a|DT rotary|rotary|JJ shaker|shaker|NN at|at|IN 180|180|CD rpm|rpm|NN .|.|. Main|Main|NNP cultivations|cultivation|NNS were|be|VBD started|start|VBN as|as|IN batch|batch|NN cultures|culture|NNS at|at|IN a|a|DT temperature|temperature|NN of|of|IN 37|37|CD °C|°c|NN .|.|. The|the|DT pH|ph|NN was|be|VBD kept|keep|VBN at|at|IN 7.0|7.0|CD by|by|IN controlled|controlled|JJ addition|addition|NN of|of|IN 25|25|CD %|%|NN ammonia|ammonia|NN solution|solution|NN .|.|. At|at|IN the|the|DT end|end|NN of|of|IN the|the|DT exponential|exponential|JJ growth|growth|NN phase|phase|NN -LRB-|-lrb-|-LRB- cell|cell|NN dry|dry|JJ weight|weight|NN about|about|IN 16|16|CD g|g|NN L-1|l-1|NN -RRB-|-rrb-|-RRB- the|the|DT stirrer|stirrer|NN rate|rate|NN was|be|VBD lowered|lower|VBN from|from|IN 1000|1000|CD rpm|rpm|NN to|to|TO 500|500|CD rpm|rpm|NN ,|,|, to|to|TO provoke|provoke|VB oxygen|oxygen|NN limitation|limitation|NN by|by|IN decreased|decrease|VBN oxygen|oxygen|NN transfer|transfer|NN .|.|. Constant|constant|JJ glucose|glucose|NN feed|feed|NN of|of|IN 100|100|CD g|g|NN L-1|l-1|NN h-1|h-1|NN was|be|VBD started|start|VBN 15|15|CD min|min|NN after|after|IN the|the|DT oxygen|oxygen|NN drop|drop|NN which|which|WDT was|be|VBD enough|enough|RB to|to|TO ensure|ensure|VB glucose|glucose|NN excess|excess|NN during|during|IN the|the|DT whole|whole|JJ cultivation|cultivation|NN .|.|.
tynA|tyna|SYM -|-|: at|at|IN T0|t0|NN
tynA|tyna|NN -|-|: at|at|IN T1h|t1h|NN
tynA|tyna|NN -|-|: at|at|IN T4h|t4h|NN
ug/ml|ug/ml|JJ smx|smx|NN /|/|: ug/ml|ug/ml|JJ tm|tm|NN :|:|: 20/4|20/4|CD -LRB-|-lrb-|-LRB- 1x|1x|NN -RRB-|-rrb-|-RRB-
ug/ml|ug/ml|NN smx|smx|NN /|/|: ug/ml|ug/ml|JJ tm|tm|NN :|:|: 540/108|540/108|CD -LRB-|-lrb-|-LRB- 27x|27x|NN -RRB-|-rrb-|-RRB-
ugpC|ugpc|NN KO|ko|NN rep1|rep1|NN
ugpC|ugpc|NN KO|ko|NN rep2|rep2|NN
ugpC|ugpc|NN KO|ko|NN rep3|rep3|NN
umuD|umud|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r1|r1|NN
umuD|umud|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r2|r2|NN
umuD|umud|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r3|r3|NN
umuD|umud|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
Un|un|NN _|_|CD IN|in|IN _|_|CD 3|3|CD
Un|un|NN _|_|CD IN|in|IN _|_|CD Mu|mu|NN _|_|NN 1|1|CD
Un|un|NN _|_|CD IN|in|IN _|_|CD Mu|mu|NN _|_|NN 2|2|CD
Un|un|NN _|_|CD IP|IP|NNP _|_|SYM 3|3|CD
Un|un|NN _|_|CD IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 1|1|CD
Un|un|NN _|_|CD IP|IP|NNP _|_|SYM Mu|mu|FW _|_|FW 2|2|CD
untreated|untreated|JJ
Untreated|untreated|JJ
untreated|untreated|JJ cells|cell|NNS ,|,|, 25|25|CD ug|ug|NN total|total|JJ RNA|rna|NN
untreated|untreated|JJ cells|cell|NNS after|after|IN 24|24|CD min|min|NN
untreated|untreated|JJ cells|cell|NNS after|after|IN 60|60|CD min|min|NN
untreated|untreated|JJ control|control|NN
Untreated|untreated|JJ E.|e.|FW coli|coli|FW cells|cell|NNS
Untreated|untreated|JJ Rep|Rep|NNP 1|1|LS -|-|: A-IP|a-ip|NN
Untreated|untreated|JJ Rep|Rep|NNP 1|1|LS -|-|: A+IP|a+ip|NN
Untreated|untreated|JJ Rep|Rep|NNP 2|2|LS -|-|: A-IP|a-ip|NN
Untreated|untreated|JJ Rep|Rep|NNP 2|2|LS -|-|: A+IP|a+ip|NN
Untreated|untreated|JJ Rep|Rep|NNP 3|3|LS -|-|: A-IP|a-ip|NN
Untreated|untreated|JJ Rep|Rep|NNP 3|3|LS -|-|: A+IP|a+ip|NN
Untreated|untreated|JJ _|_|NN replicate|replicate|VB _|_|SYM 1|1|CD
Untreated|untreated|JJ _|_|NN replicate|replicate|VBP _|_|NN 2|2|CD
Untreated|untreated|JJ _|_|NN replicate|replicate|VB _|_|SYM 3|3|CD
Untreated|untreated|JJ wild|wild|JJ type|type|NN versus|versus|CC untreated|untreated|JJ yajL|yajl|NN mutant|mutant|NN .|.|.
Uridine|uridine|NN addition|addition|NN
uropathogenic|uropathogenic|JJ Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- UPEC|upec|NN -RRB-|-rrb-|-RRB-
uropathogenic|uropathogenic|JJ Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- UPEC|upec|NN -RRB-|-rrb-|-RRB- grown|grow|VBN with|with|IN nitrosative|nitrosative|JJ stress|stress|NN
uropathogenic|uropathogenic|JJ Escherichia|escherichia|FW coli|coli|FW -LRB-|-lrb-|-LRB- UPEC|upec|NN -RRB-|-rrb-|-RRB- grown|grow|VBN without|without|IN nitrosative|nitrosative|JJ stress|stress|NN
Used|use|VBD SAMTOOLS|samtools|NN -LRB-|-lrb-|-LRB- Li|Li|NNP ,|,|, et|et|FW al.|al.|FW ,|,|, PMID|pmid|NN 1950593|1950593|CD -RRB-|-rrb-|-RRB- to|to|TO sort|sort|VB and|and|CC index|index|NN the|the|DT SAM|SAM|NNP files|file|NNS obtained|obtain|VBN from|from|IN Bowtie2|bowtie2|NN and|and|CC convert|convert|VB them|they|PRP to|to|TO BAM|BAM|NNP format|format|NN .|.|.
Used|use|VBD SAMTOOLS|samtools|NN -LRB-|-lrb-|-LRB- Li|Li|NNP ,|,|, et|et|FW al.|al.|FW ,|,|, PMID|pmid|NN 1950593|1950593|CD -RRB-|-rrb-|-RRB- to|to|TO sort|sort|VB and|and|CC index|index|NN the|the|DT SAM|SAM|NNP files|file|NNS obtained|obtain|VBN from|from|IN Bowtie|Bowtie|NNP and|and|CC convert|convert|VB them|they|PRP to|to|TO BAM|BAM|NNP format|format|NN .|.|.
Using|use|VBG a|a|DT combination|combination|NN of|of|IN python|python|NN -LRB-|-lrb-|-LRB- 3.2.1|3.2.1|CD -RRB-|-rrb-|-RRB- and|and|CC bowtie|bowtie|NN -LRB-|-lrb-|-LRB- 0.12.7|0.12.7|CD -RRB-|-rrb-|-RRB- ,|,|, from|from|IN the|the|DT raw|raw|JJ sequencing|sequencing|NN data|datum|NNS ,|,|, we|we|PRP isolated|isolate|VBD reads|read|VBZ which|which|WDT contained|contain|VBD barcode|barcode|NN sequences|sequence|NNS that|that|WDT corresponded|correspond|VBD to|to|TO our|we|PRP$ original|original|JJ list|list|NN of|of|IN single|single|JJ molecule|molecule|NN barcodes|barcode|NNS in|in|IN both|both|CC forward|forward|RB and|and|CC reverse|reverse|VB reads|read|VBZ for|for|IN each|each|DT sequence|sequence|NN pair|pair|NN that|that|WDT had|have|VBD at|at|IN most|most|JJS one|one|CD mismatch|mismatch|NN .|.|. We|we|PRP then|then|RB aligned|align|VBD the|the|DT first|first|JJ 28|28|CD bases|basis|NNS -LRB-|-lrb-|-LRB- 26|26|CD bases|basis|NNS for|for|IN the|the|DT second|second|JJ sequencing|sequencing|NN run|run|NN -RRB-|-rrb-|-RRB- of|of|IN the|the|DT targeted|target|VBN sequence|sequence|NN of|of|IN both|both|CC the|the|DT forward|forward|JJ and|and|CC reverse|reverse|JJ reads|read|VBZ of|of|IN each|each|DT cluster|cluster|NN to|to|TO the|the|DT E.|e.|FW coli|coli|FW genome|genome|NN and|and|CC kept|keep|VBD the|the|DT sequences|sequence|NNS that|that|WDT uniquely|uniquely|RB align|align|VB fewer|fewer|JJR than|than|IN three|three|CD mismatches|mismatch|NNS and|and|CC where|where|WRB the|the|DT two|two|CD reads|read|VBZ did|do|VBD not|not|RB map|map|VB to|to|TO the|the|DT same|same|JJ sense|sense|NN or|or|CC antisense|antisense|JJ strand|strand|NN of|of|IN the|the|DT genome|genome|NN .|.|. We|we|PRP used|use|VBD a|a|DT detailed|detailed|JJ filtering|filter|VBG process|process|NN to|to|TO determine|determine|VB the|the|DT identity|identity|NN of|of|IN closely-mapped|closely-mapped|JJ reads|read|VBZ .|.|. Mapped|map|VBN sequence|sequence|NN fragments|fragment|NNS with|with|IN a|a|DT length|length|NN of|of|IN at|at|IN least|least|JJS 1,000|1,000|CD bases|basis|NNS were|be|VBD discarded|discard|VBN .|.|. All|all|DT sequences|sequence|NNS within|within|IN the|the|DT same|same|JJ transcription|transcription|NN unit|unit|NN that|that|WDT had|have|VBD the|the|DT same|same|JJ unique|unique|JJ tag|tag|NN were|be|VBD analyzed|analyze|VBN further|further|RB .|.|. We|we|PRP determined|determine|VBD that|that|IN more|more|JJR than|than|IN one|one|CD sequence|sequence|NN with|with|IN the|the|DT same|same|JJ unique|unique|JJ tag|tag|NN were|be|VBD identical|identical|JJ if|if|IN the|the|DT distance|distance|NN between|between|IN their|they|PRP$ center|center|NN positions|position|NNS was|be|VBD less|less|JJR than|than|IN four|four|CD base-pairs|base-pair|NNS and|and|CC if|if|IN the|the|DT difference|difference|NN in|in|IN length|length|NN was|be|VBD less|less|JJR than|than|IN 9|9|CD base-pairs|base-pair|NNS .|.|. Then|then|RB for|for|IN each|each|DT unique|unique|JJ sequence|sequence|NN ,|,|, we|we|PRP counted|count|VBD the|the|DT number|number|NN of|of|IN unique|unique|JJ barcode|barcode|NN tags|tag|NNS that|that|WDT appeared|appear|VBD to|to|TO determine|determine|VB the|the|DT copy|copy|NN number|number|NN of|of|IN each|each|DT sequence|sequence|NN and|and|CC mapped|map|VBD each|each|DT of|of|IN them|they|PRP to|to|TO genes|gene|NNS .|.|. We|we|PRP include|include|VBP indexed|index|VBN genome|genome|NN viewer|viewer|NN files|file|NNS -LRB-|-lrb-|-LRB- .|.|. sam|sam|NN and|and|CC .|.|. sai|sai|NN -RRB-|-rrb-|-RRB- for|for|IN both|both|DT experiments|experiment|NNS using|use|VBG both|both|CC the|the|DT conventional|conventional|JJ method|method|NN and|and|CC the|the|DT digital|digital|JJ method|method|NN .|.|.
Using|use|VBG blind|blind|JJ and|and|CC fit-only|fit-only|JJ parameter|parameter|NN in|in|IN DE-Seq|de-seq|NN pakage|pakage|NN ,|,|, expressions|expression|NNS of|of|IN genes|gene|NNS in|in|IN all|all|DT samples|sample|NNS were|be|VBD changed|change|VBN to|to|TO count|count|VB per|per|IN gene|gene|NN ,|,|, using|use|VBG RNA-Seq|rna-seq|NN protocol|protocol|NN on|on|IN Illumina|Illumina|NNP HiSeq2500|HiSeq2500|NNP platform|platform|NN
Using|use|VBG Bowtie2|bowtie2|NN -LRB-|-lrb-|-LRB- version|version|NN 2.0.2|2.0.2|CD -RRB-|-rrb-|-RRB- ,|,|, sequenced|sequence|VBN reads|read|VBZ were|be|VBD mapped|map|VBN to|to|TO an|a|DT EPEC|epec|NN O127|o127|NN :|:|: H6|h6|NN reference|reference|NN genome|genome|NN -LRB-|-lrb-|-LRB- EMBL/GenBank|embl/genbank|NN accession|accession|NN codes|code|NNS FM180568|fm180568|NN ,|,|, FM180569|fm180569|NN ,|,|, and|and|CC FM180570|fm180570|NN -RRB-|-rrb-|-RRB- .|.|.
using|use|VBG RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN
uspA|uspa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r1|r1|FW
uspA|uspa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
uspA|uspa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
uspA|uspa|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
UVA|uva|NN irradiated|irradiated|JJ chemostat|chemostat|NN for|for|IN 1|1|CD h|h|NN ,|,|, run|run|VBP 1|1|CD
UVA|uva|NN irradiated|irradiated|JJ chemostat|chemostat|NN for|for|IN 1|1|CD h|h|NN ,|,|, run|run|NN 2|2|CD
UVA|uva|NN irradiated|irradiated|JJ chemostat|chemostat|NN for|for|IN 1|1|CD h|h|NN ,|,|, run|run|NN 2|2|CD dye|dye|VBP swap|swap|NN
UVA|uva|NN irradiated|irradiated|JJ chemostat|chemostat|NN for|for|IN 1|1|CD h|h|NN ,|,|, run|run|VBP 3|3|CD
UVA|uva|NN irradiated|irradiated|JJ chemostat|chemostat|NN for|for|IN 50|50|CD h|h|NN ,|,|, run|run|VBP 1|1|CD
UVA|uva|NN irradiated|irradiated|JJ chemostat|chemostat|NN for|for|IN 50|50|CD h|h|NN ,|,|, run|run|NN 2|2|CD
UVA|uva|NN irradiated|irradiated|JJ chemostat|chemostat|NN for|for|IN 50|50|CD h|h|NN ,|,|, run|run|VBP 3|3|CD
uvrA|uvra|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r1|r1|NN
uvrA|uvra|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|VBD r2|r2|NN
uvrA|uvra|NN ___|___|CD U|U|NNP _|_|NNP N0025|N0025|NNP _|_|SYM r3|r3|FW
uvrA|uvra|NN upregulation|upregulation|NN ,|,|, amp|amp|NN 50ug/ml|50ug/ml|NN ,|,|, 0.0125|0.0125|CD %|%|NN arabinose|arabinose|NN ,|,|, 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN OD|od|NN ~|~|NN 0.3|0.3|CD
UvrY|uvry|NN -|-|: ChIP-exo|ChIP-exo|NNP
UvrY|uvry|NN -LRB-|-lrb-|-LRB- Response|response|NN regulator|regulator|NN of|of|IN the|the|DT BarA/UvrY|bara/uvry|NN two-component|two-component|JJ system|system|NN -RRB-|-rrb-|-RRB-
V1|v1|NN biological|biological|JJ replicate|replicate|VB
Valine|Valine|NNP addition|addition|NN
VALUE|VALUE|NNP is|be|VBZ Log|log|NN -LRB-|-lrb-|-LRB- base|base|NN 2|2|CD -RRB-|-rrb-|-RRB- of|of|IN the|the|DT ratio|ratio|NN of|of|IN the|the|DT mean|mean|NN of|of|IN Channel|Channel|NNP 2|2|CD -LRB-|-lrb-|-LRB- usually|usually|RB 635|635|CD nm|nm|NN -RRB-|-rrb-|-RRB- to|to|TO Channel|Channel|NNP 1|1|CD -LRB-|-lrb-|-LRB- usually|usually|RB 532|532|CD nm|nm|NN -RRB-|-rrb-|-RRB-
VALUE|value|NN is|be|VBZ Log|log|NN -LRB-|-lrb-|-LRB- base|base|NN 2|2|CD -RRB-|-rrb-|-RRB- of|of|IN the|the|DT ratio|ratio|NN of|of|IN the|the|DT median|median|NN of|of|IN Channel|Channel|NNP 2|2|CD -LRB-|-lrb-|-LRB- usually|usually|RB 635|635|CD nm|nm|NN -RRB-|-rrb-|-RRB- to|to|TO Channel|Channel|NNP 1|1|CD -LRB-|-lrb-|-LRB- usually|usually|RB 532|532|CD nm|nm|NN -RRB-|-rrb-|-RRB-
VALUE|value|NN =|=|JJ log2|log2|NN -LRB-|-lrb-|-LRB- Cy3|cy3|NN _|_|CD signal/Cy5|signal/cy5|NN _|_|NN signal|signal|NN -RRB-|-rrb-|-RRB- =|=|JJ log2|log2|NN -LRB-|-lrb-|-LRB- SIGNAL|signal|NN _|_|CD GREEN/SIGNAL|green/signal|NN _|_|CD RED|red|NN -RRB-|-rrb-|-RRB-
VALUE|value|NN =|=|JJ log2|log2|NN -LRB-|-lrb-|-LRB- Cy5|cy5|NN _|_|CD signal/Cy3|signal/cy3|NN _|_|NN signal|signal|NN -RRB-|-rrb-|-RRB- =|=|JJ log2|log2|NN -LRB-|-lrb-|-LRB- SIGNAL|signal|NN _|_|CD RED/SIGNAL|red/signal|NN _|_|CD GREEN|green|NN -RRB-|-rrb-|-RRB-
VALUEs|value|NNS are|be|VBP calculated|calculate|VBN as|as|IN log2-transformed|log2-transformed|JJ -LRB-|-lrb-|-LRB- test/ref|test/ref|NN -RRB-|-rrb-|-RRB- ratios|ratio|NNS after|after|IN background|background|NN correction|correction|NN and|and|CC limma|limma|NN 's|'s|POS LOESS|loess|JJ normalization|normalization|NN
vector|vector|NN :|:|: pET-28a|pet-28a|NN
vector|vector|NN :|:|: pET-28a-BnTR1|pet-28a-bntr1|NN
Vector|Vector|NNP rep1|rep1|NN
Vector|Vector|NNP rep2|rep2|NN
Vector|Vector|NNP rep3|rep3|NN
Veg|veg|NN
verified|verify|VBN with|with|IN in-house|in-house|JJ pipeline|pipeline|NN
Vertis|Vertis|NNP Biotechnologie|Biotechnologie|NNP AG|AG|NNP bioinformatics|bioinformatic|NNS department|department|NN did|do|VBD a|a|DT preliminary|preliminary|JJ analysis|analysis|NN of|of|IN the|the|DT high-throughput|high-throughput|JJ sequencing|sequencing|NN results|result|NNS which|which|WDT included|include|VBD the|the|DT mapping|mapping|NN of|of|IN the|the|DT reads|read|VBZ against|against|IN E.|e.|FW coli|coli|FW genome|genome|NN -LRB-|-lrb-|-LRB- NC|nc|NN _|_|CD 000913|000913|CD downloaded|download|VBN from|from|IN NCBI|NCBI|NNP genome|genome|NN database|database|NN -RRB-|-rrb-|-RRB- .|.|.
Viable|viable|JJ clones|clone|NNS of|of|IN the|the|DT UvsW-expressing|uvsw-expressing|JJ strains|strain|NNS GJ13531|gj13531|NN -LRB-|-lrb-|-LRB- Δrho|δrho|NN -RRB-|-rrb-|-RRB- and|and|CC GJ13507|gj13507|NN -LRB-|-lrb-|-LRB- ΔnusG|δnusg|NN -RRB-|-rrb-|-RRB- were|be|VBD obtained|obtain|VBN as|as|IN white|white|JJ colonies|colony|NNS from|from|IN their|they|PRP$ respective|respective|JJ shelter|shelter|NN plasmid-carrying|plasmid-carrying|JJ derivatives|derivative|NNS GJ13531/pHYD2411|gj13531/phyd2411|NN and|and|CC GJ13507|gj13507|NN /|/|: pHYD2412|phyd2412|NN on|on|IN glucose-minimal|glucose-minimal|NN A|a|NN plates|plate|VBZ supplemented|supplement|VBN with|with|IN Xgal|xgal|NN and|and|CC IPTG|iptg|NN at|at|IN 200|200|CD μM|μm|NN -LRB-|-lrb-|-LRB- for|for|IN Δrho|δrho|NN -RRB-|-rrb-|-RRB- or|or|CC 3|3|CD μM|μm|NN -LRB-|-lrb-|-LRB- for|for|IN ΔnusG|δnusg|NN -RRB-|-rrb-|-RRB- ,|,|, as|as|IN previously|previously|RB described|describe|VBN
Visualizations|visualization|NNS for|for|IN assessing|assess|VBG the|the|DT quality|quality|NN of|of|IN the|the|DT array|array|NN data|datum|NNS
W3110|w3110|NN -LRB-|-lrb-|-LRB- KCTC|kctc|NN 2223|2223|CD -RRB-|-rrb-|-RRB-
W3110|w3110|NN -LRB-|-lrb-|-LRB- lacI-deleted|laci-deleted|JJ -RRB-|-rrb-|-RRB- strain|strain|NN harboring|harbor|VBG pKK223-3|pkk223-3|NN
W3110|w3110|NN lsrK|lsrk|NN mutants|mutant|NNS
W3110|w3110|NN lsrK|lsrk|NN mutants|mutant|NNS
W3110|w3110|NN lsrK|lsrk|NN mutants|mutant|NNS ,|,|, biological|biological|JJ rep1|rep1|NN
W3110|w3110|NN lsrK|lsrk|NN mutants|mutant|NNS ,|,|, biological|biological|JJ rep2|rep2|NN
W3110|w3110|NN lsrR|lsrr|NN mutants|mutant|NNS
W3110|w3110|NN lsrR|lsrr|NN mutants|mutant|NNS ,|,|, biological|biological|JJ rep1|rep1|NN
W3110|w3110|NN lsrR|lsrr|NN mutants|mutant|NNS ,|,|, biological|biological|JJ rep2|rep2|NN
W3110|w3110|NN overexpressing|overexpress|VBG pck|pck|NN
W3110|w3110|NN rpoC-6xHis|rpoc-6xhis|NN :|:|: :|:|: kan|kan|FW gal490|gal490|FW
W3110|w3110|NN rpoC-6xHis|rpoc-6xhis|NN :|:|: :|:|: kan|kan|NN greA|grea|NN :|:|: :|:|: tet|tet|NN ,|,|, greB|greb|NN :|:|: :|:|: amp|amp|NN
W3110|w3110|NN trpR2|trpr2|NN ,|,|, min|min|NN +.2|+.2|CD %|%|NN glucose|glucose|NN ,|,|, 30|30|CD ug|ug|NN RNA|rna|NN
W3110|w3110|NN trpR2|trpr2|NN -|-|: trp|trp|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ RNA|rna|NN
W3110|w3110|NN trpR2|trpr2|NN +|+|CC trp|trp|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ RNA|rna|NN
W3110|w3110|NN wild|wild|JJ type|type|NN
W3110|w3110|NN wild|wild|JJ type|type|NN ,|,|, biological|biological|JJ rep1|rep1|NN
W3110|w3110|NN wild|wild|JJ type|type|NN ,|,|, biological|biological|JJ rep2|rep2|NN
W3110|w3110|NN wt|wt|JJ ,|,|, min|min|NN +.2|+.2|CD %|%|NN glucose|glucose|NN ,|,|, 30|30|CD ug|ug|NN RNA|rna|NN
W3110|w3110|NN wt-trp|wt-trp|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ RNA|rna|NN
W3110|w3110|NN wt|wt|JJ +|+|CC trp|trp|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ RNA|rna|NN
Washed|wash|VBD pellets|pellet|NNS were|be|VBD resuspended|resuspend|VBN in|in|IN 1|1|CD ml|ml|NN of|of|IN TESS|TESS|NNP buffer|buffer|NN -LRB-|-lrb-|-LRB- 10|10|CD mM|mm|NN Tris-Cl|tris-cl|NN pH7|ph7|NN .5|.5|CD ,|,|, 1|1|CD mM|mm|NN EDTA|edta|NN ,|,|, 250|250|CD mM|mm|NN NaCl|nacl|NN ,|,|, 0.02|0.02|CD %|%|NN SDS|sds|NN ,|,|, 0.2|0.2|CD %|%|NN Tween-20|tween-20|NN -RRB-|-rrb-|-RRB- with|with|IN addition|addition|NN of|of|IN proteases|protease|NNS inhibitors|inhibitor|NNS cocktail|cocktail|NN -LRB-|-lrb-|-LRB- cOmplete|complete|JJ ultra|ultra|NNS EDTA|edta|NN free|free|JJ ,|,|, Roche|Roche|NNP -RRB-|-rrb-|-RRB- and|and|CC RNAse|rnase|NN A|a|NN -LRB-|-lrb-|-LRB- Thermo|Thermo|NNP Scientific|Scientific|NNP -RRB-|-rrb-|-RRB- .|.|. Resulting|result|VBG suspensions|suspension|NNS were|be|VBD sonicated|sonicate|VBN with|with|IN parameters|parameter|NNS optimized|optimize|VBN to|to|TO obtain|obtain|VB DNA|dna|NN fragments|fragment|NNS between|between|IN 200|200|CD and|and|CC 700|700|CD bp|bp|NN -LRB-|-lrb-|-LRB- SONOPULS|sonopuls|NN HD|hd|NN 3100|3100|CD -RRB-|-rrb-|-RRB- .|.|. Lysates|lysate|NNS were|be|VBD diluted|dilute|VBN with|with|IN 1|1|CD ml|ml|NN of|of|IN TES|tes|NN buffer|buffer|NN and|and|CC 100|100|CD μl|μl|NN of|of|IN ANTI-FLAG|anti-flag|NN ®|®|CD M2|m2|NN affinity|affinity|NN gel|gel|NN -LRB-|-lrb-|-LRB- Sigma-Aldrich|sigma-aldrich|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN .|.|. Immunoprecipitation|immunoprecipitation|NN was|be|VBD performed|perform|VBN for|for|IN 1.5-2|1.5-2|CD hours|hour|NNS at|at|IN room|room|NN temperature|temperature|NN with|with|IN moderate|moderate|JJ mixing|mix|VBG ,|,|, then|then|RB affinity|affinity|NN gel|gel|NN was|be|VBD washed|wash|VBN 4|4|CD times|time|NNS by|by|IN repeating|repeat|VBG steps|step|NNS of|of|IN centrifugation|centrifugation|NN -LRB-|-lrb-|-LRB- 1.5|1.5|CD minute|minute|NN ,|,|, 1000xg|1000xg|NN at|at|IN room|room|NN temperature|temperature|NN -RRB-|-rrb-|-RRB- and|and|CC resuspention|resuspention|NN -LRB-|-lrb-|-LRB- x2|x2|NN with|with|IN 1|1|CD ml|ml|NN of|of|IN TESS|TESS|NNP buffer|buffer|NN ,|,|, x1|x1|NN with|with|IN 1|1|CD ml|ml|NN of|of|IN TES|tes|NN buffer|buffer|NN ,|,|, x1|x1|NN with|with|IN 1|1|CD ml|ml|NN of|of|IN TE|TE|NNP buffer|buffer|NN -RRB-|-rrb-|-RRB- .|.|.
was|be|VBD washed|wash|VBN with|with|IN 70|70|CD percent|percent|NN ethanol|ethanol|NN ,|,|, resuspended|resuspend|VBN in|in|IN 30|30|CD ul|ul|NN water|water|NN ,|,|, and|and|CC held|hold|VBN at|at|IN 4|4|CD deg|deg|NN .|.|. C|c|NN for|for|IN
We|we|PRP compared|compare|VBD the|the|DT microarray-determined|microarray-determined|JJ mRNA|mrna|NN profiles|profile|NNS -LRB-|-lrb-|-LRB- Affymetrix|Affymetrix|NNP E.|E.|NNP coli|coli|NN Genome|Genome|NNP 2.0|2.0|CD Array|array|NN -RRB-|-rrb-|-RRB- of|of|IN Δfur|δfur|NN and|and|CC WT|wt|JJ genotypes|genotype|NNS in|in|IN response|response|NN to|to|TO ciprofloxacin|ciprofloxacin|NN treatment|treatment|NN -LRB-|-lrb-|-LRB- 100|100|CD ng/ml|ng/ml|NN -RRB-|-rrb-|-RRB- with|with|IN those|those|DT of|of|IN untreated|untreated|JJ cultures|culture|NNS .|.|. We|we|PRP used|use|VBD two|two|CD biological|biological|JJ replicates|replicate|VBZ per|per|IN genotype|genotype|NN .|.|.
We|we|PRP developed|develop|VBD in-house|in-house|JJ computational|computational|JJ and|and|CC statistical|statistical|JJ analysis|analysis|NN tools|tool|NNS for|for|IN use|use|NN with|with|IN the|the|DT E.|e.|FW coli|coli|FW tiling|tiling|NN array|array|NN .|.|. We|we|PRP used|use|VBD a|a|DT previous|previous|JJ study|study|NN -LRB-|-lrb-|-LRB- Choe|Choe|NNP et|et|FW al.|al.|FW ,|,|, 2005|2005|CD -RRB-|-rrb-|-RRB- as|as|IN a|a|DT model|model|NN for|for|IN perfect|perfect|JJ match|match|NN adjustment|adjustment|NN on|on|IN single|single|JJ arrays|array|NNS .|.|. Analysis|analysis|NN scripts|script|NNS were|be|VBD written|write|VBN in|in|IN Perl|Perl|NNP ,|,|, MatLab|MatLab|NNP ,|,|, and|and|CC R|r|NN to|to|TO standardize|standardize|VB the|the|DT statistical|statistical|JJ manipulations|manipulation|NNS across|across|IN all|all|DT data|datum|NNS sets|set|NNS .|.|. The|the|DT output|output|NN file|file|NN from|from|IN the|the|DT scanning|scanning|NN process|process|NN is|be|VBZ a|a|DT CEL|cel|NN file|file|NN .|.|. The|the|DT raw|raw|JJ CEL|cel|NN data|datum|NNS were|be|VBD used|use|VBN as|as|IN the|the|DT basis|basis|NN for|for|IN the|the|DT manuscript|manuscript|NN ;|;|: no|no|DT processed|process|VBN data|datum|NNS are|be|VBP available|available|JJ .|.|.
We|we|PRP established|establish|VBD a|a|DT method|method|NN for|for|IN preparing|prepare|VBG five|five|CD different|different|JJ cDNA|cdna|NN libraries|library|NNS each|each|DT with|with|IN its|its|PRP$ own|own|JJ barcode|barcode|NN for|for|IN Illumina|Illumina|NNP sequencing|sequencing|NN .|.|. Each|each|DT 6-nt|6-nt|JJ barcode|barcode|NN allows|allow|VBZ multiplexing|multiplex|VBG all|all|DT five|five|CD in|in|FW vitro|vitro|FW and|and|CC in|in|FW vivo|vivo|FW preparations|preparation|NNS in|in|IN a|a|DT single|single|JJ sequencing|sequencing|NN analysis|analysis|NN .|.|. our|we|PRP$ method|method|NN introduces|introduce|VBZ internal|internal|JJ control|control|NN sequences|sequence|NNS to|to|TO the|the|DT library|library|NN that|that|WDT are|be|VBP subjected|subject|VBN to|to|TO the|the|DT artifact|artifact|NN errors|error|NNS ,|,|, but|but|CC are|be|VBP not|not|RB for|for|IN RNAP|rnap|NN errors|error|NNS .|.|. The|the|DT 5|5|CD '|'|'' fragment|fragment|NN of|of|IN the|the|DT 5.7|5.7|CD kb|kb|NN RNA|rna|NN transcripts|transcript|NNS was|be|VBD reverse|reverse|JJ transcribed|transcribe|VBN to|to|TO make|make|VB the|the|DT cDNA|cdna|NN .|.|. The|the|DT cDNA|cdna|NN was|be|VBD subjected|subject|VBN to|to|TO PCR|pcr|NN reactions|reaction|NNS that|that|WDT generated|generate|VBD six|six|CD 200|200|CD bp|bp|NN segments|segment|NNS .|.|. The|the|DT primers|primer|NNS contained|contain|VBD a|a|DT specific|specific|JJ barcode|barcode|NN for|for|IN each|each|DT of|of|IN the|the|DT five|five|CD starting|start|VBG preparations|preparation|NNS and|and|CC the|the|DT inner|inner|JJ Illuminasequencing|illuminasequencing|NN adapters|adapter|NNS .|.|. The|the|DT 2nd-step|2nd-step|NN of|of|IN PCR|pcr|NN generated|generate|VBD the|the|DT final|final|JJ cDNA|cdna|NN libraries|library|NNS for|for|IN the|the|DT Illumina|Illumina|NNP sequencing|sequencing|NN by|by|IN using|use|VBG the|the|DT 1st-step|1st-step|JJ PCR|pcr|NN product|product|NN as|as|IN a|a|DT template|template|NN and|and|CC primers|primer|NNS containing|contain|VBG the|the|DT outer|outer|JJ sequencing|sequencing|NN adapters|adapter|NNS in|in|IN the|the|DT 5|5|CD '|'|'' tails|tail|NNS .|.|.
We|we|PRP extracted|extract|VBD RNA|rna|NN using|use|VBG RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- and|and|CC RNeasy|RNeasy|NNP Mini|Mini|NNP Kit|kit|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- combined|combine|VBN with|with|IN RNase-Free|rnase-free|JJ DNase|dnase|NN Set|set|VB -LRB-|-lrb-|-LRB- Qiagen|Qiagen|NNP -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS instructions|instruction|NNS .|.|.
We|we|PRP grew|grow|VBD cells|cell|NNS in|in|IN 10|10|CD ml|ml|NN M9|m9|NN minimal|minimal|JJ medium|medium|NN to|to|TO OD600|od600|NN =|=|JJ 0.5-0.6|0.5-0.6|CD .|.|. Then|then|RB ,|,|, we|we|PRP divided|divide|VBD each|each|DT culture|culture|NN into|into|IN 500µl|500µl|JJ aliquots|aliquot|NNS to|to|TO which|which|WDT we|we|PRP added|add|VBD the|the|DT appropriate|appropriate|JJ concentration|concentration|NN of|of|IN NA|NA|NNP .|.|.
We|we|PRP incubated|incubate|VBD each|each|DT aliquot|aliquot|NN at|at|IN 37ºC|37ºc|NN for|for|IN 4|4|CD hours|hour|NNS with|with|IN NA|na|NN
were|be|VBD above|above|IN 2|2|CD standard|standard|JJ deviations|deviation|NNS of|of|IN the|the|DT background|background|NN .|.|. We|we|PRP generated|generate|VBD expression|expression|NN data|datum|NNS tables|table|NNS
were|be|VBD averaged|average|VBN and|and|CC listed|list|VBN in|in|IN a|a|DT new|new|JJ file|file|NN .|.|.
were|be|VBD immediately|immediately|RB frozen|freeze|VBN in|in|IN liquid|liquid|JJ nitrogen|nitrogen|NN and|and|CC stored|store|VBD at|at|IN -80|-80|CD deg|deg|NN .|.|. C.|c.|NN For|for|IN RNA|rna|NN isolation|isolation|NN ,|,|,
We|we|PRP then|then|RB used|use|VBD the|the|DT mapped|map|VBN files|file|NNS to|to|TO run|run|VB Cufflinks|Cufflinks|NNP -LRB-|-lrb-|-LRB- estimates|estimate|VBZ the|the|DT relative|relative|JJ abundance|abundance|NN of|of|IN the|the|DT transcripts|transcript|NNS -RRB-|-rrb-|-RRB- and|and|CC after|after|IN Cuffdiff|Cuffdiff|NNP to|to|TO find|find|VB significant|significant|JJ changes|change|NNS in|in|IN transcript|transcript|NN expression|expression|NN when|when|WRB comparing|compare|VBG two|two|CD samples|sample|NNS -LRB-|-lrb-|-LRB- Trapnell|Trapnell|NNP ,|,|, Williams|Williams|NNP et|et|FW al.|al.|FW 2010|2010|CD -RRB-|-rrb-|-RRB- .|.|.
We|we|PRP used|use|VBD an|a|DT Illumina|Illumina|NNP NextSeq|NextSeq|NNP 500|500|CD system|system|NN and|and|CC a|a|DT MID|mid|NN 150|150|CD Kit|kit|NN with|with|IN 1x75|1x75|CD bp|bp|NN read|read|VBD length|length|NN .|.|. Base-calling|base-calling|NN was|be|VBD perform|perform|VB online|online|NN during|during|IN the|the|DT sequencing|sequencing|NN procedure|procedure|NN with|with|IN the|the|DT Real-Time|Real-Time|NNP Analysis|analysis|NN -LRB-|-lrb-|-LRB- RTA|rta|NN -RRB-|-rrb-|-RRB- software|software|NN version|version|NN 2.4.11|2.4.11|CD and|and|CC System|System|NNP Suite|Suite|NNP Version|Version|NNP 2.1.2.1|2.1.2.1|CD .|.|.
We|we|PRP use|use|VBP Rockhopper|Rockhopper|NNP for|for|IN alignment|alignment|NN and|and|CC the|the|DT complete|complete|JJ analysis|analysis|NN of|of|IN data|datum|NNS
When|when|WRB cultures|culture|NNS reached|reach|VBD OD595|od595|NN ≈|≈|CD 0.470|0.470|CD -LRB-|-lrb-|-LRB- ~|~|NN 200|200|CD min|min|NN -RRB-|-rrb-|-RRB- ,|,|, two|two|CD cultures|culture|NNS were|be|VBD made|make|VBN 3|3|CD µM|µm|NN mercuric|mercuric|NN chloride|chloride|NN -LRB-|-lrb-|-LRB- HgCl2|hgcl2|NN -RRB-|-rrb-|-RRB- or|or|CC 3|3|CD µM|µm|NN phenylmercuric-acetate|phenylmercuric-acetate|NN -LRB-|-lrb-|-LRB- PMA|pma|NN -RRB-|-rrb-|-RRB- and|and|CC the|the|DT third|third|JJ was|be|VBD left|leave|VBN as|as|IN an|a|DT unexposed|unexposed|JJ control|control|NN .|.|. Duplicate|duplicate|VB 1|1|CD ml|ml|NN aliquots|aliquot|NNS of|of|IN each|each|DT culture|culture|NN were|be|VBD collected|collect|VBN at|at|IN 0|0|CD -LRB-|-lrb-|-LRB- unexposed|unexposed|JJ control|control|NN only|only|RB -RRB-|-rrb-|-RRB- ,|,|, 10|10|CD ,|,|, 30|30|CD ,|,|, 60|60|CD min|min|NN after|after|IN mercurial|mercurial|JJ exposure|exposure|NN and|and|CC immediately|immediately|RB centrifuged|centrifuge|VBN at|at|IN 21|21|CD krpm|krpm|NN ,|,|, for|for|IN 3|3|CD min|min|NN at|at|IN 4|4|CD °C|°c|NN .|.|. Spent|spent|JJ medium|medium|NN was|be|VBD aspirated|aspirate|VBN and|and|CC cell|cell|NN pellets|pellet|NNS were|be|VBD frozen|freeze|VBN at|at|IN -70|-70|CD °C|°c|NN within|within|IN 5|5|CD min|min|NN after|after|IN collection|collection|NN .|.|.
When|when|WRB E.|e.|FW coli|coli|FW cells|cell|NNS were|be|VBD cultivated|cultivate|VBN to|to|TO the|the|DT exponential|exponential|JJ growth|growth|NN phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.5|0.5|CD -RRB-|-rrb-|-RRB- in|in|IN Riesenberg|Riesenberg|NNP medium|medium|NN ,|,|, 3|3|CD or|or|CC 10|10|CD mM|mm|NN heptanoic|heptanoic|JJ acid|acid|NN was|be|VBD treated|treat|VBN to|to|TO BL21|bl21|NN -LRB-|-lrb-|-LRB- DE3|de3|NN -RRB-|-rrb-|-RRB- and|and|CC K-12|k-12|NN MG1655|mg1655|NN ,|,|, respectively|respectively|RB .|.|. After|after|IN 3|3|CD h|h|NN incubation|incubation|NN ,|,|, the|the|DT E.|e.|FW coli|coli|FW cells|cell|NNS were|be|VBD harvested|harvest|VBN for|for|IN transcriptome|transcriptome|NN analysis|analysis|NN
When|when|WRB OD600|od600|NN of|of|IN the|the|DT culture|culture|NN reached|reach|VBD 0.54|0.54|CD ±|±|SYM 0.06|0.06|CD ,|,|, cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN 100|100|CD µg/ml|µg/ml|NN of|of|IN -LRB-|-lrb-|-LRB- -|-|: -RRB-|-rrb-|-RRB- -|-|: Roemerine|roemerine|NN .|.|. Since|since|IN the|the|DT alkaloid|alkaloid|NN was|be|VBD dissolved|dissolve|VBN in|in|IN DMSO|dmso|NN ,|,|, control|control|NN cells|cell|NNS were|be|VBD also|also|RB treated|treat|VBN with|with|IN the|the|DT same|same|JJ amount|amount|NN of|of|IN DMSO|dmso|NN .|.|.
When|when|WRB reaching|reach|VBG the|the|DT optical|optical|JJ density|density|NN indicated|indicate|VBD -LRB-|-lrb-|-LRB- OD600|od600|NN =|=|JJ 0.6-0.8|0.6-0.8|CD -RRB-|-rrb-|-RRB- the|the|DT culture|culture|NN was|be|VBD bisected|bisect|VBN and|and|CC DNA|dna|NN gyrase|gyrase|NN poison|poison|NN -LRB-|-lrb-|-LRB- ciprofloxacin|ciprofloxacin|NN ,|,|, oxolinic|oxolinic|JJ acid|acid|NN or|or|CC microcin|microcin|NN B17|b17|NN -RRB-|-rrb-|-RRB- was|be|VBD added|add|VBN to|to|TO the|the|DT first|first|JJ half|half|NN -LRB-|-lrb-|-LRB- +|+|CC A|a|DT samples|sample|NNS -RRB-|-rrb-|-RRB- ,|,|, while|while|IN second|second|JJ served|serve|VBD as|as|IN a|a|DT control|control|NN -LRB-|-lrb-|-LRB- -|-|: A|a|NN samples|sample|NNS -RRB-|-rrb-|-RRB- .|.|.
When|when|WRB the|the|DT cultures|culture|NNS reached|reach|VBD an|a|DT OD600|od600|NN 0.6|0.6|CD they|they|PRP were|be|VBD split|split|VBN into|into|IN two|two|CD flasks|flask|NNS ,|,|, each|each|DT containing|contain|VBG 20|20|CD ml|ml|NN of|of|IN the|the|DT culture|culture|NN .|.|. One|one|CD was|be|VBD treated|treat|VBN with|with|IN a|a|DT subinhibitory|subinhibitory|JJ concentration|concentration|NN of|of|IN purified|purify|VBN colicin|colicin|NN M|m|NN ,|,|, while|while|IN the|the|DT untreated|untreated|JJ served|serve|VBD as|as|IN a|a|DT control|control|NN .|.|. 2-ml|2-ml|JJ culture|culture|NN aliquotes|aliquote|NNS were|be|VBD harvested|harvest|VBN from|from|IN each|each|DT flask|flask|NN after|after|IN 30|30|CD min|min|NN and|and|CC 60|60|CD min|min|NN incubation|incubation|NN at|at|IN 37|37|CD °C|°c|NN and|and|CC were|be|VBD mixed|mix|VBN with|with|IN 4|4|CD ml|ml|NN RNAProtect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|.
When|when|WRB the|the|DT cultures|culture|NNS reached|reach|VBD the|the|DT desired|desire|VBN density|density|NN ,|,|, 2|2|CD ml|ml|NN of|of|IN culture|culture|NN was|be|VBD added|add|VBN to|to|TO 4|4|CD ml|ml|NN of|of|IN RNAprotect|rnaprotect|NN Bacteria|bacterium|NNS Reagent|reagent|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- .|.|. The|the|DT mixture|mixture|NN was|be|VBD incubated|incubate|VBN at|at|IN room|room|NN temperature|temperature|NN for|for|IN 5|5|CD min|min|NN and|and|CC then|then|RB centrifuged|centrifuge|VBD at|at|IN 5000|5000|CD g|g|NN for|for|IN 10|10|CD min|min|NN .|.|. The|the|DT supernatant|supernatant|NN was|be|VBD removed|remove|VBN and|and|CC the|the|DT pellets|pellet|NNS were|be|VBD stored|store|VBN at|at|IN -80|-80|CD C.|c.|JJ RNA|rna|NN was|be|VBD isolated|isolate|VBN using|use|VBG the|the|DT Norgen|Norgen|NNP Total|Total|NNP RNA|rna|NN Purification|purification|NN Kit|kit|NN -LRB-|-lrb-|-LRB- Product|product|NN #|#|# 17200|17200|CD -RRB-|-rrb-|-RRB- according|accord|VBG to|to|TO the|the|DT manufacturer|manufacturer|NN 's|'s|POS directions|direction|NNS except|except|IN in|in|IN the|the|DT last|last|JJ step|step|NN the|the|DT RNA|rna|NN was|be|VBD eluted|elute|VBN in|in|IN 35|35|CD uL|ul|NN .|.|.
When|when|WRB the|the|DT samples|sample|NNS had|have|VBD reached|reach|VBN an|a|DT OD600|od600|NN of|of|IN 0.4-0.5|0.4-0.5|CD ,|,|, 25|25|CD ml|ml|NN of|of|IN each|each|DT culture|culture|NN was|be|VBD added|add|VBN to|to|TO a|a|DT 2.5|2.5|CD ml|ml|NN mixture|mixture|NN of|of|IN cold|cold|JJ 95|95|CD %|%|NN ethanol|ethanol|NN and|and|CC 5|5|CD %|%|NN phenol|phenol|NN to|to|TO preserve|preserve|VB the|the|DT mRNA|mrna|NN .|.|. The|the|DT cells|cell|NNS were|be|VBD cooled|cool|VBN rapidly|rapidly|RB on|on|IN ice|ice|NN and|and|CC immediately|immediately|RB harvested|harvest|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 4|4|CD °C|°c|NN ,|,|, and|and|CC the|the|DT pellet|pellet|NN was|be|VBD frozen|freeze|VBN on|on|IN dry|dry|JJ ice|ice|NN .|.|.
Whole|whole|JJ bacterial|bacterial|JJ cell|cell|NN RNA|rna|NN transcriptome|transcriptome|NN
Whole|whole|JJ cell|cell|NN ,|,|, aspC|aspc|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, cysA|cysa|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, cysG|cysg|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, cysH|cysh|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, dcd|dcd|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, dcd|dcd|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, entF|entf|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, fadR|fadr|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, fadR|fadr|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, fepA|fepa|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, fepA|fepa|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, fliY|fliy|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, gabT|gabt|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, galE|gale|NN KO|KO|NNP ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, kefB|kefb|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, khc|khc|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, lacA|laca|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, lacA|laca|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, lplA|lpla|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
whole|whole|JJ cell|cell|NN lysate|lysate|NN
Whole|whole|JJ cell|cell|NN lysates|lysate|NNS were|be|VBD clarified|clarify|VBN by|by|IN brief|brief|JJ centrifugation|centrifugation|NN .|.|. Ribosome|ribosome|NN footprints|footprint|NNS were|be|VBD created|create|VBN using|use|VBG Mnase|Mnase|NNP digestion|digestion|NN -LRB-|-lrb-|-LRB- 45|45|CD enzyme|enzyme|NN units|unit|NNS per|per|IN absorbance|absorbance|NN unit|unit|NN of|of|IN lysate|lysate|NN at|at|IN 260nm|260nm|NN -RRB-|-rrb-|-RRB- .|.|. Using|use|VBG sucrose|sucrose|NN gradients|gradient|NNS the|the|DT monosome|monosome|JJ fraction|fraction|NN of|of|IN lysate|lysate|NN was|be|VBD isolated|isolate|VBN and|and|CC footprints|footprint|NNS were|be|VBD size|size|NN selected|select|VBN and|and|CC converted|convert|VBN to|to|TO a|a|DT cDNA|cdna|NN library|library|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD extracted|extract|VBN from|from|IN purified|purify|VBN lysate|lysate|NN for|for|IN a|a|DT simultaneous|simultaneous|JJ RNA-seq|rna-seq|NN library|library|NN production|production|NN for|for|IN total|total|JJ RNA|rna|NN samples|sample|NNS .|.|. Small|small|JJ RNA|rna|NN and|and|CC ribosomal|ribosomal|JJ RNA|rna|NN subtraction|subtraction|NN was|be|VBD performed|perform|VBN in|in|IN total|total|JJ RNA|rna|NN samples|sample|NNS using|use|VBG MEGAClear|megaclear|NN -LRB-|-lrb-|-LRB- ThermoFisher|thermofisher|NN -RRB-|-rrb-|-RRB- and|and|CC MicrobExpress|microbexpress|NN -LRB-|-lrb-|-LRB- ThermoFisher|thermofisher|NN -RRB-|-rrb-|-RRB- kits|kit|NNS .|.|. Subtracted|subtract|VBN total|total|JJ RNA|rna|NN was|be|VBD then|then|RB subjected|subject|VBN to|to|TO alkaline|alkaline|NN fragmentation|fragmentation|NN prior|prior|RB to|to|TO library|library|NN preparation|preparation|NN .|.|.
Whole|whole|JJ cell|cell|NN ,|,|, mgtA|mgta|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, mhpD|mhpd|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, ppk|ppk|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, ppk|ppk|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, putP|putp|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, rfbA|rfba|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, sdhC|sdhc|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, trpD|trpd|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, ugpC|ugpc|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, WT|WT|NNP ,|,|, LB|LB|NNP and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, WT|WT|NNP ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, WT|WT|NNP ,|,|, M9|m9|NN and|and|CC 0.4|0.4|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, wzc|wzc|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, wzc|wzc|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, yghD|yghd|NN KO|ko|NN ,|,|, LB|lb|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
Whole|whole|JJ cell|cell|NN ,|,|, yghD|yghd|NN KO|ko|NN ,|,|, M9|m9|NN and|and|CC 0.3|0.3|CD %|%|NN glucose|glucose|NN
WIG|wig|NN files|file|NNS were|be|VBD normalized|normalize|VBN by|by|IN using|use|VBG an|a|DT in-house|in-house|JJ script|script|NN that|that|WDT reads|read|VBZ in|in|IN the|the|DT raw|raw|JJ WIG|wig|NN files|file|NNS while|while|IN excluding|exclude|VBG counts|count|NNS from|from|IN all|all|DT 22|22|CD rRNA|rrna|NN genes|gene|NNS .|.|. A|a|DT simple|simple|JJ global|global|JJ normalization|normalization|NN approach|approach|NN was|be|VBD utilized|utilize|VBN that|that|IN multiplied|multiply|VBD the|the|DT count|count|NN at|at|IN each|each|DT base|base|NN location|location|NN by|by|IN 1|1|CD billion|billion|CD and|and|CC divides|divide|VBZ that|that|IN value|value|NN by|by|IN the|the|DT sum|sum|NN of|of|IN base|base|NN counts|count|VBZ at|at|IN all|all|DT base|base|NN locations|location|NNS in|in|IN the|the|DT file|file|NN .|.|. This|this|DT normalization|normalization|NN strategy|strategy|NN is|be|VBZ anlogous|anlogous|JJ to|to|TO the|the|DT Total|total|JJ Count|count|NN approach|approach|NN used|use|VBD for|for|IN normalizing|normalize|VBG gene-specific|gene-specific|JJ read|read|NN alignments|alignment|NNS .|.|. In|in|IN this|this|DT way|way|NN ,|,|, the|the|DT base|base|NN counts|count|NNS are|be|VBP expressed|express|VBN as|as|IN parts|part|NNS per|per|IN billion|billion|CD .|.|.
WIG|wig|NN files|file|NNS were|be|VBD viewed|view|VBN and|and|CC annotated|annotated|JJ using|use|VBG Jbrowse|Jbrowse|NNP and|and|CC Integrated|Integrated|NNP Genome|Genome|NNP Viewer|Viewer|NNP .|.|.
Wiggle|Wiggle|NNP files|file|NNS were|be|VBD created|create|VBN by|by|IN center|center|NN mapping|map|VBG the|the|DT reads|read|VBZ between|between|IN 20-40bps|20-40bp|NNS .|.|. Using|use|VBG a|a|DT 10bp|10bp|JJ trim|trim|JJ on|on|IN either|either|DT side|side|NN of|of|IN the|the|DT read|read|NN then|then|RB mapping|map|VBG the|the|DT read|read|NN across|across|IN the|the|DT remaining|remain|VBG location|location|NN using|use|VBG Plastid|Plastid|NNP .|.|.
wild|wild|JJ type|type|NN
wild-type|wild-type|JJ
wild|wild|JJ type|type|NN ,|,|, 10|10|CD %|%|NN H2O2|h2o2|NN
wild-type|wild-type|JJ 1.0|1.0|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
wild-type|wild-type|JJ 15|15|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 15|15|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 15|15|CD min|min|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 15|15|CD min|min|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 1|1|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 2|2|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild|wild|JJ type|type|NN ,|,|, 30|30|CD %|%|NN H2O2|h2o2|NN
wild-type|wild-type|JJ 30|30|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 30|30|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 30|30|CD min|min|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 30|30|CD min|min|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 3|3|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 4|4|CD hour|hour|NN -LRB-|-lrb-|-LRB- 3|3|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 5|5|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 5|5|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 5|5|CD min|min|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 5|5|CD min|min|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 5|5|CD min|min|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 1|1|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
wild-type|wild-type|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 1|1|CD
wild-type|wild-type|JJ 6|6|CD hour|hour|NN -LRB-|-lrb-|-LRB- 2|2|CD -RRB-|-rrb-|-RRB- slide|slide|NN 2|2|CD
Wild-type|wild-type|JJ Aerobic|Aerobic|NNP A|A|NNP
Wild-type|wild-type|JJ Aerobic|aerobic|JJ B|b|NN
Wild-type|wild-type|JJ Anaerobic|anaerobic|JJ A|a|NN
Wild-type|wild-type|JJ Anaerobic|anaerobic|JJ B|b|NN
Wild|Wild|NNP type|type|NN and|and|CC the|the|DT mutant|mutant|NN were|be|VBD grown|grow|VBN on|on|IN minimal|minimal|JJ M9|m9|NN media|media|NNS with|with|IN 4|4|CD g/L|g/l|NN glucose|glucose|NN as|as|IN a|a|DT sole|sole|JJ carbon|carbon|NN source|source|NN at|at|IN 37C|37c|NN with|with|IN aeration|aeration|NN -LRB-|-lrb-|-LRB- +|+|CC O2|o2|CD -RRB-|-rrb-|-RRB- or|or|CC nitrogen|nitrogen|NN sparging|sparging|NN -LRB-|-lrb-|-LRB- -|-|: O2|o2|CD -RRB-|-rrb-|-RRB-
wild|wild|JJ type|type|NN _|_|CD anoxic|anoxic|JJ -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB- _|_|SYM glycerol|glycerol|NN
wild|wild|JJ type|type|NN _|_|CD anoxic|anoxic|JJ -LRB-|-lrb-|-LRB- NO3|no3|NN -RRB-|-rrb-|-RRB- _|_|SYM glycerol|glycerol|NN +|+|CC propionate|propionate|NN
wildtype|wildtype|JJ ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN ,|,|, rep|rep|NN 1|1|CD
wildtype|wildtype|JJ ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN ,|,|, rep|rep|NN 2|2|CD
wildtype|wildtype|JJ ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN ,|,|, rep|rep|NN 3|3|CD
wildtype|wildtype|JJ ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN +|+|CC Sucrose|sucrose|NN +|+|CC MgSO4|mgso4|NN ,|,|, rep|rep|NN 1|1|CD
wildtype|wildtype|JJ ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN +|+|CC Sucrose|sucrose|NN +|+|CC MgSO4|mgso4|NN ,|,|, rep|rep|NN 2|2|CD
wildtype|wildtype|JJ ,|,|, brain|brain|NN heart|heart|NN infusion|infusion|NN agar|agar|NN +|+|CC Sucrose|sucrose|NN +|+|CC MgSO4|mgso4|NN ,|,|, rep|rep|NN 3|3|CD
Wild-type|wild-type|JJ _|_|NN cDNA|cdna|NN _|_|CD Aerobic|aerobic|JJ
Wild-type|wild-type|JJ _|_|NN cDNA|cdna|NN _|_|CD Anaerobic|anaerobic|JJ
Wild-type|wild-type|JJ Cells|cell|NNS
Wild-type|wild-type|JJ Cells|cell|NNS Replicate|replicate|VBP 1|1|CD
Wild-type|wild-type|JJ Cells|cell|NNS Replicate|replicate|VB 2|2|CD
Wild-type|wild-type|JJ Cells|cell|NNS Replicate|replicate|VB 3|3|CD
wild-type|wild-type|JJ cells|cell|NNS with|with|IN 0.025|0.025|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
wild-type|wild-type|JJ cells|cell|NNS with|with|IN 0.050|0.050|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
wild-type|wild-type|JJ cells|cell|NNS with|with|IN 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
wild-type|wild-type|JJ cells|cell|NNS without|without|IN norfloxacin|norfloxacin|JJ
wildtype|wildtype|JJ colony|colony|NN morphology|morphology|NN
Wild|Wild|NNP type|type|NN control|control|NN
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 0|0|CD min|min|NN -RRB-|-rrb-|-RRB-
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 10|10|CD min|min|NN -RRB-|-rrb-|-RRB-
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 15|15|CD min|min|NN -RRB-|-rrb-|-RRB-
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 20|20|CD min|min|NN -RRB-|-rrb-|-RRB-
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 2.5|2.5|CD min|min|NN -RRB-|-rrb-|-RRB-
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 30|30|CD min|min|NN -RRB-|-rrb-|-RRB-
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 5|5|CD min|min|NN -RRB-|-rrb-|-RRB-
Wild|Wild|NNP type|type|NN control|control|NN -LRB-|-lrb-|-LRB- 60|60|CD min|min|NN -RRB-|-rrb-|-RRB-
wild|wild|JJ type|type|NN E0|e0|NN ,|,|, biological|biological|JJ rep1|rep1|NN
wild|wild|JJ type|type|NN E0|e0|NN ,|,|, biological|biological|JJ rep2|rep2|NN
wild|wild|JJ type|type|NN E0|e0|NN ,|,|, biological|biological|JJ rep3|rep3|NN
Wild-type|wild-type|JJ E.|e.|FW coli|coli|FW ATCC|atcc|NN 25922|25922|CD replicate|replicate|VBP 1|1|CD
Wild-type|wild-type|JJ E.|e.|FW coli|coli|FW ATCC|atcc|NN 25922|25922|CD replicate|replicate|VBP 2|2|CD
Wild|Wild|NNP type|type|NN E.|e.|FW coli|coli|FW K-12|k-12|NN -LRB-|-lrb-|-LRB- strain|strain|NN BW38038|bw38038|NN -RRB-|-rrb-|-RRB- and|and|CC BW39452|bw39452|NN -LRB-|-lrb-|-LRB- ΔrpoS|δrpos|NN -RRB-|-rrb-|-RRB- cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN MOPS|mop|NNS glucose|glucose|NN minimal|minimal|JJ medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN as|as|IN sole|sole|JJ carbon|carbon|NN source|source|NN at|at|IN 37|37|CD °C|°c|NN ,|,|, pH|ph|NN was|be|VBD initially|initially|RB 7.4|7.4|CD ,|,|, and|and|CC the|the|DT agitation|agitation|NN speed|speed|NN was|be|VBD 500|500|CD rpm|rpm|NN .|.|. Culture|culture|NN samples|sample|NNS were|be|VBD harvested|harvest|VBN during|during|IN logarithmic|logarithmic|JJ growth|growth|NN and|and|CC following|follow|VBG entry|entry|NN into|into|IN stationary|stationary|JJ phase|phase|NN for|for|IN the|the|DT WT|WT|NNP and|and|CC rpoS|rpos|NN mutant|mutant|NN .|.|. OD600|od600|CD measurements|measurement|NNS were|be|VBD made|make|VBN on|on|IN a|a|DT Beckman|Beckman|NNP Coulter|Coulter|NNP DU|DU|NNP 800|800|CD spectrophotometer|spectrophotometer|NN .|.|. Samples|sample|NNS were|be|VBD harvested|harvest|VBN directly|directly|RB into|into|IN ice-cold|ice-cold|JJ RNAlater|rnalater|NN at|at|IN a|a|DT 1:1|1:1|CD dilution|dilution|NN to|to|TO protect|protect|VB RNA|rna|NN from|from|IN degradation|degradation|NN and|and|CC cells|cell|NNS then|then|RB were|be|VBD pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 8000rpm|8000rpm|CD for|for|IN 10|10|CD minutes|minute|NNS .|.|. Cell|cell|NN pellets|pellet|NNS were|be|VBD stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN in|in|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN RNAlater|rnalater|NN prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN .|.|.
Wild|Wild|NNP type|type|NN E.|e.|FW coli|coli|FW K-12|k-12|NN -LRB-|-lrb-|-LRB- strain|strain|NN BW38038|bw38038|NN -RRB-|-rrb-|-RRB- and|and|CC BW39452|bw39452|NN -LRB-|-lrb-|-LRB- ΔrpoS|δrpos|NN -RRB-|-rrb-|-RRB- cultures|culture|NNS were|be|VBD grown|grow|VBN on|on|IN MOPS|mop|NNS glucose|glucose|NN minimal|minimal|JJ medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN as|as|IN sole|sole|JJ carbon|carbon|NN source|source|NN in|in|IN a|a|DT 2L|2L|NNP B.|B.|NNP Braun|Braun|NNP Biostat|Biostat|NNP ®|®|NN B|b|NN fermenter|fermenter|NN with|with|IN working|work|VBG volume|volume|NN of|of|IN 1|1|CD L|l|NN MOPS|mop|NNS minimal|minimal|JJ medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, at|at|IN 37|37|CD °C|°c|NN ,|,|, pH|ph|NN was|be|VBD kept|keep|VBN constant|constant|JJ at|at|IN 7.4|7.4|CD by|by|IN the|the|DT addition|addition|NN of|of|IN 1|1|CD M|m|NN NaOH|naoh|NN ,|,|, and|and|CC dissolved|dissolve|VBD oxygen|oxygen|NN was|be|VBD maintained|maintain|VBN above|above|IN 40|40|CD %|%|NN of|of|IN saturation|saturation|NN by|by|IN adjusting|adjust|VBG the|the|DT agitation|agitation|NN speeds|speed|NNS in|in|IN the|the|DT range|range|NN of|of|IN 270|270|CD --|--|: 500|500|CD rpm|rpm|NN with|with|IN fixed|fix|VBN 1.5|1.5|CD liter/min|liter/min|JJ air|air|NN flow|flow|NN .|.|. Culture|culture|NN samples|sample|NNS were|be|VBD harvested|harvest|VBN by|by|IN using|use|VBG a|a|DT homemade|homemade|NN sampling|sampling|NN device|device|NN seven|seven|CD times|time|NNS during|during|IN logarithmic|logarithmic|JJ growth|growth|NN and|and|CC three|three|CD times|time|NNS following|follow|VBG entry|entry|NN into|into|IN stationary|stationary|JJ phase|phase|NN for|for|IN the|the|DT WT|WT|NNP and|and|CC two|two|CD times|time|NNS during|during|IN logarithmic|logarithmic|JJ phase|phase|NN and|and|CC three|three|CD times|time|NNS during|during|IN stationary|stationary|JJ phase|phase|NN for|for|IN the|the|DT rpoS|rpos|NN mutant|mutant|NN .|.|. OD600|od600|CD measurements|measurement|NNS were|be|VBD made|make|VBN on|on|IN a|a|DT Beckman|Beckman|NNP Coulter|Coulter|NNP DU|DU|NNP 800|800|CD spectrophotometer|spectrophotometer|NN .|.|. Samples|sample|NNS were|be|VBD harvested|harvest|VBN directly|directly|RB into|into|IN ice-cold|ice-cold|JJ RNAlater|rnalater|NN at|at|IN a|a|DT 1:1|1:1|CD dilution|dilution|NN to|to|TO protect|protect|VB RNA|rna|NN from|from|IN degradation|degradation|NN and|and|CC cells|cell|NNS then|then|RB were|be|VBD pelleted|pellete|VBN by|by|IN centrifugation|centrifugation|NN at|at|IN 8000rpm|8000rpm|CD for|for|IN 10|10|CD minutes|minute|NNS .|.|. Cell|cell|NN pellets|pellet|NNS were|be|VBD stored|store|VBN at|at|IN -80|-80|CD °C|°c|NN in|in|IN an|a|DT equal|equal|JJ volume|volume|NN of|of|IN RNAlater|rnalater|NN prior|prior|RB to|to|TO RNA|rna|NN extraction|extraction|NN .|.|.
Wildtype|wildtype|NN E.|e.|FW coli|coli|FW O157|o157|NN treated|treat|VBN with|with|IN 6|6|CD ug/ml|ug/ml|NN triclosan|triclosan|NN for|for|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Wildtype|wildtype|NN E.|e.|FW coli|coli|FW O157|o157|NN treated|treat|VBN with|with|IN 6|6|CD ug/ml|ug/ml|NN triclosan|triclosan|NN for|for|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Wildtype|wildtype|JJ E.|e.|FW coli|coli|FW O157|o157|NN treated|treat|VBN with|with|IN 6|6|CD ug/ml|ug/ml|NN triclosan|triclosan|NN for|for|IN 30|30|CD min|min|NN ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
Wildtype|wildtype|NN E.|e.|FW coli|coli|FW O157|o157|NN untreated|untreated|JJ ,|,|, biological|biological|JJ rep|rep|NN 1|1|CD
Wildtype|wildtype|NN E.|e.|FW coli|coli|FW O157|o157|NN untreated|untreated|JJ ,|,|, biological|biological|JJ rep|rep|NN 2|2|CD
Wildtype|wildtype|JJ E.|e.|FW coli|coli|FW O157|o157|NN untreated|untreated|JJ ,|,|, biological|biological|JJ rep|rep|NN 3|3|CD
Wild|Wild|NNP type|type|NN E.coli|e.coli|NN SE15|se15|NN vs.|vs.|CC LuxS|luxs|NN mutant|mutant|JJ E.coli|e.coli|NN SE15|se15|NN
wildtype|wildtype|JJ Escherichia|escherichia|FW coli|coli|FW
wild|wild|JJ type|type|NN grown|grow|VBN to|to|TO logarithmic|logarithmic|JJ phase|phase|NN
wild|wild|JJ type|type|NN grown|grow|VBN to|to|TO transition|transition|NN phase|phase|NN
wild-type|wild-type|JJ in|in|IN ala|ala|NN media|media|NNS _|_|NN 1|1|CD
wild-type|wild-type|JJ in|in|IN ala|ala|NN media|media|NNS _|_|NN 2|2|CD
wild-type|wild-type|JJ in|in|IN gln|gln|NN media|media|NNS _|_|NN 1|1|CD
wild-type|wild-type|JJ in|in|IN gln|gln|NN media|media|NNS _|_|NN 2|2|CD
Wild-type|wild-type|JJ IrrE|irre|NN ,|,|, biological|biological|JJ rep1|rep1|NN
Wild-type|wild-type|JJ IrrE|irre|NN ,|,|, biological|biological|JJ rep2|rep2|NN
Wild-type|wild-type|JJ IrrE|irre|NN ,|,|, biological|biological|JJ rep3|rep3|NN
Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD CMid|cmid|NN Log|log|NN
Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
wild|wild|JJ type|type|NN MG1655|mg1655|CD
wild-type|wild-type|JJ MG1655|mg1655|NN
wild-type|wild-type|JJ MG1655|mg1655|NN +|+|CC glycolaldehyde|glycolaldehyde|NN 10|10|CD mM|mm|NN
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- RNA-seq|rna-seq|NN
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T0|t0|NN RNA|rna|NN rep|rep|NN 2|2|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T0|t0|NN RP|rp|NN rep|rep|NN 1|1|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T0|t0|NN RP|rp|NN rep|rep|NN 2|2|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T1|t1|NN RNA|rna|NN rep|rep|NN 1|1|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T1|t1|NN RNA|rna|NN rep|rep|NN 2|2|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T1|t1|NN RP|rp|NN rep|rep|NN 1|1|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T1|t1|NN RP|rp|NN rep|rep|NN 2|2|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T2|t2|NN RNA|rna|NN rep|rep|NN 1|1|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T2|t2|NN RNA|rna|NN rep|rep|NN 2|2|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T2|t2|NN RP|rp|NN rep|rep|NN 1|1|CD
Wild-type|wild-type|JJ -LRB-|-lrb-|-LRB- MG1655|mg1655|NN -RRB-|-rrb-|-RRB- T2|t2|NN RP|rp|NN rep|rep|NN 2|2|CD
Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
Wild|Wild|NNP Type|type|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
wild|wild|JJ type|type|NN _|_|CD oxic|oxic|JJ _|_|NN glycerol|glycerol|NN
wild|wild|JJ type|type|NN _|_|CD oxic|oxic|JJ _|_|NN glycerol|glycerol|NN +|+|CC propionate|propionate|NN
wild-type|wild-type|JJ pBAD-ryhB|pbad-ryhb|NN #|#|# 1|1|CD +|+|CC arabinose|arabinose|NN
wild-type|wild-type|JJ pBAD-ryhB|pbad-ryhb|NN #|#|# 1|1|CD +|+|CC FeSO4|feso4|NN +|+|CC arabinose|arabinose|NN
wild-type|wild-type|JJ pBAD-ryhB|pbad-ryhb|NN #|#|# 2|2|CD +|+|CC arabinose|arabinose|NN
wild-type|wild-type|JJ pBAD-ryhB|pbad-ryhb|NN #|#|# 2|2|CD +|+|CC FeSO4|feso4|NN +|+|CC arabinose|arabinose|NN
wild-type|wild-type|JJ pNM12|pnm12|NN #|#|# 1|1|CD +|+|CC arabinose|arabinose|NN
wild-type|wild-type|JJ pNM12|pnm12|NN #|#|# 1|1|CD +|+|CC FeSO4|feso4|NN +|+|CC arabinose|arabinose|NN
wild-type|wild-type|JJ pNM12|pnm12|NN #|#|# 2|2|CD +|+|CC arabinose|arabinose|NN
wild-type|wild-type|JJ pNM12|pnm12|NN #|#|# 2|2|CD +|+|CC FeSO4|feso4|NN +|+|CC arabinose|arabinose|NN
wild|wild|JJ type|type|NN rep|rep|NN 1|1|CD
wild|wild|JJ type|type|NN rep|rep|NN 2|2|CD
Wild-types|wild-types|JJ cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, leucine|leucine|NN ,|,|, isoleucine|isoleucine|NN ,|,|, valine|valine|NN ,|,|, glycine|glycine|NN ,|,|, phenylalanine|phenylalanine|NN ,|,|, threonine|threonine|NN -LRB-|-lrb-|-LRB- 40|40|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC uracil|uracil|NN -LRB-|-lrb-|-LRB- 50|50|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN and|and|CC treated|treat|VBN with|with|IN 0.5|0.5|CD mg/ml|mg/ml|NN serine|serine|NN hydroxamate|hydroxamate|NN -LRB-|-lrb-|-LRB- SHX|shx|NN -RRB-|-rrb-|-RRB- for|for|IN 20|20|CD min|min|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN vigorous|vigorous|JJ shaking|shake|VBG .|.|.
Wild-types|wild-types|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, leucine|leucine|NN ,|,|, isoleucine|isoleucine|NN ,|,|, valine|valine|NN ,|,|, glycine|glycine|NN ,|,|, phenylalanine|phenylalanine|NN ,|,|, threonine|threonine|NN -LRB-|-lrb-|-LRB- 40|40|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC uracil|uracil|NN -LRB-|-lrb-|-LRB- 50|50|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN at|at|IN 37|37|CD °C|°c|NN with|with|IN vigorous|vigorous|JJ shaking|shake|VBG .|.|.
Wild-types|wild-types|NN cells|cell|NNS were|be|VBD grown|grow|VBN in|in|IN MOPS|MOPS|NNP medium|medium|NN with|with|IN 0.2|0.2|CD %|%|NN glucose|glucose|NN ,|,|, leucine|leucine|NN ,|,|, isoleucine|isoleucine|NN ,|,|, valine|valine|NN ,|,|, glycine|glycine|NN ,|,|, phenylalanine|phenylalanine|NN ,|,|, threonine|threonine|NN -LRB-|-lrb-|-LRB- 40|40|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- and|and|CC uracil|uracil|NN -LRB-|-lrb-|-LRB- 50|50|CD mg/ml|mg/ml|NN -RRB-|-rrb-|-RRB- until|until|IN mid-log|mid-log|JJ phase|phase|NN -LRB-|-lrb-|-LRB- OD600|od600|NN ~|~|NN 0.4|0.4|CD -RRB-|-rrb-|-RRB- at|at|IN 37|37|CD °C|°c|NN with|with|IN vigorous|vigorous|JJ shaking|shake|VBG .|.|.
wild|wild|JJ type|type|NN SdiA|sdia|NN
wildtype|wildtype|JJ strain|strain|NN ;|;|: minimal|minimal|JJ medium|medium|NN
Wildtype|wildtype|NN strain|strain|NN ,|,|, rep1|rep1|NN
wildtype|wildtype|JJ strain|strain|NN ,|,|, rep2|rep2|NN
Wildtype|wildtype|JJ triclosan|triclosan|NN treated|treat|VBN biological|biological|JJ rep|rep|NN 1|1|CD
Wildtype|wildtype|JJ triclosan|triclosan|NN treated|treat|VBN biological|biological|JJ rep|rep|NN 2|2|CD
Wildtype|wildtype|JJ triclosan|triclosan|NN treated|treat|VBN biological|biological|JJ rep|rep|NN 3|3|CD
Wildtype|wildtype|JJ untreated|untreated|JJ biological|biological|JJ rep|rep|NN 1|1|CD
Wildtype|wildtype|JJ untreated|untreated|JJ biological|biological|JJ rep|rep|NN 2|2|CD
Wildtype|wildtype|JJ untreated|untreated|JJ biological|biological|JJ rep|rep|NN 3|3|CD
wild|wild|JJ type|type|NN ,|,|, without|without|IN H2O2|h2o2|NN
with|with|IN D-galactose|d-galactose|JJ
without|without|IN D-galactose|d-galactose|JJ
without|without|IN Symbioflor|Symbioflor|NNP
with/without|with/without|NN 2.5|2.5|CD mM|mm|NN Fumaric|fumaric|JJ acid|acid|NN
write.table|write.table|JJ -LRB-|-lrb-|-LRB- norm.temp|norm.temp|JJ ,|,|, file|file|NN =\|=\|CD
WT|WT|NNP _|_|SYM 01|01|CD _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 02|02|CD _|_|NN rep1|rep1|NN
WT|wt|JJ _|_|NN 03|03|CD _|_|NN rep1|rep1|NN
WT|wt|JJ _|_|NN 04|04|CD _|_|NN rep1|rep1|NN
WT|wt|JJ _|_|NN 04|04|CD _|_|NN rep2|rep2|NN
WT|wt|JJ _|_|NN 04-R|04-r|NN _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 04|04|CD _|_|SYM TEX|TEX|NNP
WT|WT|NNP _|_|SYM 08|08|CD _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 0|0|CD _|_|NN Hx|hx|NN Rep1|rep1|NN
WT|wt|JJ _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep2|rep2|JJ
WT|wt|JJ _|_|NN 0|0|CD _|_|SYM Hx|hx|FW Rep3|rep3|JJ
WT|wt|NN 0|0|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
WT|wt|NN 0|0|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
wt|wt|JJ _|_|NN 1|1|CD
WT|wt|JJ _|_|NN 1|1|CD
WT-1|wt-1|NN
WT|wt|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
WT|wt|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
WT|wt|NN 100|100|CD μg/ml|μg/ml|NN NA|na|NN rep3|rep3|NN
WT1088|wt1088|NN in|in|IN LB|lb|NN at|at|IN 37|37|CD Mid|Mid|NNP Log|Log|NNP Phase|phase|NN
WT1088|wt1088|NN vs.|vs.|CC dpiA|dpia|NN 2x|2x|NN Overexpression|overexpression|NN pHI1429|phi1429|NN in|in|IN LB|lb|NN at|at|IN 37|37|CD Mid|Mid|NNP Log|Log|NNP Phase|phase|NN Trial|trial|NN A|a|NN
WT1088|wt1088|NN vs.|vs.|CC dpiA|dpia|NN 2x|2x|NN Overexpression|overexpression|NN pHI1429|phi1429|NN in|in|IN LB|lb|NN at|at|IN 37|37|CD Mid|Mid|NNP Log|Log|NNP Phase|phase|NN Trial|trial|NN B|b|NN
WT|wt|VBD 10|10|CD μg/ml|μg/ml|NN NA|na|NN rep1|rep1|NN
WT|wt|VBD 10|10|CD μg/ml|μg/ml|NN NA|na|NN rep2|rep2|NN
WT|wt|JJ _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
WT|wt|JJ _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
WT|wt|JJ _|_|NN 120|120|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
Wt|wt|NN --|--|: 120|120|CD min|min|NN
WT|wt|JJ _|_|NN 12h|12h|NN _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 12h|12h|NN _|_|CD rep2|rep2|NN
WT|wt|JJ _|_|NN 14|14|CD _|_|NN rep1|rep1|NN
wt|wt|JJ 150|150|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
wt|wt|JJ 150|150|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
wt|wt|JJ 150|150|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
WT|wt|JJ _|_|NN 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
WT|wt|JJ _|_|NN 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
WT|wt|JJ _|_|NN 15|15|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
WT|wt|JJ _|_|NN 15|15|CD min|min|NN _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 16|16|CD _|_|NN rep1|rep1|NN
WT|wt|JJ _|_|NN 16-R|16-r|NN _|_|CD rep1|rep1|NN
Wt|wt|NN --|--|: 180|180|CD min|min|NN
WT|wt|JJ _|_|NN 180|180|CD min|min|NN _|_|CD rep1|rep1|NN
wt|wt|JJ _|_|NN 1|1|CD _|_|NN input|input|NN
wt|wt|JJ _|_|NN 1|1|CD _|_|CD IP|IP|NNP
WT1|wt1|NN _|_|CD IPTG|iptg|NN
WT|wt|NN 1|1|CD min|min|NN rep7|rep7|NN
wt|wt|JJ _|_|NN 2|2|CD
WT|wt|JJ _|_|NN 2|2|CD
WT-2|wt-2|NN
WT|wt|NN 22|22|CD °C|°c|NN
wt|wt|JJ 240|240|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
wt|wt|JJ 240|240|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
wt|wt|JJ 240|240|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
WT|wt|VBD _|_|CD 24h|24h|JJ _|_|NN rep1|rep1|NN
WT|wt|VBD _|_|CD 24h|24h|JJ _|_|NN rep2|rep2|NN
wt|wt|JJ _|_|NN 2|2|CD _|_|NN input|input|NN
wt|wt|JJ _|_|NN 2|2|CD _|_|CD IP|IP|NNP
WT2|wt2|NN _|_|CD IPTG|iptg|NN
WT|wt|JJ _|_|NN 3|3|CD
WT-3|wt-3|NN
Wt|wt|NN --|--|: 300|300|CD min|min|NN
WT|wt|JJ _|_|NN 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
WT|wt|JJ _|_|NN 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
WT|wt|JJ _|_|NN 30|30|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
WT|wt|JJ _|_|NN 30|30|CD min|min|NN _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 30|30|CD min|min|NN _|_|CD rep2|rep2|NN
WT|wt|JJ _|_|NN 30min-R|30min-r|NN _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 30|30|CD min|min|NN _|_|CD TEX|TEX|NNP
WT3110|WT3110|NNP _|_|SYM 1|1|CD
WT3110|wt3110|NN _|_|NN 2|2|CD
WT3110|wt3110|NN _|_|CD 3|3|CD
wt|wt|JJ 360|360|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
wt|wt|JJ 360|360|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
wt|wt|JJ 360|360|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
WT|wt|NN 37|37|CD °C|°c|NN
WT|wt|JJ _|_|NN 37C|37c|NN
Wt|wt|NN --|--|: 420|420|CD min|min|NN
WT|wt|JJ _|_|NN 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
WT|wt|JJ _|_|NN 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
WT|wt|JJ _|_|NN 45|45|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
WT|wt|JJ _|_|NN 48h|48h|NN _|_|CD rep1|rep1|NN
WT|wt|JJ _|_|NN 48h|48h|NN _|_|CD rep2|rep2|NN
wt|wt|JJ +50|+50|CD ug/ml|ug/ml|JJ Trp|trp|NN ,|,|, 30|30|CD ug|ug|NN total|total|JJ RNA|rna|NN
WT|wt|JJ _|_|NN 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep1|rep1|JJ
WT|wt|JJ _|_|NN 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep2|rep2|JJ
WT|wt|JJ _|_|NN 60|60|CD -LRB-|-lrb-|-LRB- Low|low|JJ Dilution|dilution|NN -RRB-|-rrb-|-RRB- Rep3|rep3|JJ
Wt|wt|NN --|--|: 60|60|CD min|min|NN
WT|wt|VBD _|_|CD 6h|6h|JJ _|_|NN rep1|rep1|NN
WT|wt|VBD _|_|CD 6h|6h|JJ _|_|NN rep2|rep2|NN
wt|wt|JJ 90|90|CD minutes|minute|NNS growth|growth|NN rep1|rep1|NN
wt|wt|JJ 90|90|CD minutes|minute|NNS growth|growth|NN rep2|rep2|NN
wt|wt|JJ 90|90|CD minutes|minute|NNS growth|growth|NN rep3|rep3|NN
WT|wt|VBD 9|9|CD min|min|NN rep7|rep7|NN
WT|wt|VBD 9|9|CD min|min|NN rep8|rep8|NN
WTA1|wta1|NN
WT|wt|JJ _|_|NN acetate|acetate|NN
WT|wt|JJ acetate|acetate|NN 1|1|CD
WT|wt|JJ acetate|acetate|NN 2|2|CD
WT|wt|NN +|+|CC ade|ade|NN
wt|wt|JJ aerobic|aerobic|JJ
wt|wt|JJ aerobic|aerobic|JJ AN|a|DT rep|rep|NN 1|1|CD
wt|wt|JJ aerobic|aerobic|JJ AN|a|DT rep|rep|NN 2|2|CD
wt|wt|JJ aerobic|aerobic|JJ AN|a|DT rep|rep|NN 3|3|CD
wt|wt|JJ aerobic|aerobic|JJ rep|rep|NN 1|1|CD
wt|wt|JJ aerobic|aerobic|JJ rep|rep|NN 2|2|CD
wt|wt|JJ aerobic|aerobic|JJ rep|rep|NN 3|3|CD
wt|wt|JJ anaerobic|anaerobic|JJ
wt|wt|JJ anaerobic|anaerobic|JJ
wt|wt|JJ anaerobic|anaerobic|JJ AN|a|DT rep|rep|NN 1|1|CD
wt|wt|JJ anaerobic|anaerobic|JJ AN|a|DT rep|rep|NN 2|2|CD
wt|wt|JJ anaerobic|anaerobic|JJ AN|a|DT rep|rep|NN 3|3|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN AN|a|DT rep|rep|NN 1|1|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN AN|a|DT rep|rep|NN 2|2|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN AN|a|DT rep|rep|NN 3|3|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN rep|rep|NN 1|1|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN rep|rep|NN 2|2|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO2|no2|NN rep|rep|NN 3|3|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN AN|a|DT rep|rep|NN 1|1|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN AN|a|DT rep|rep|NN 2|2|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN AN|a|DT rep|rep|NN 3|3|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN rep|rep|NN 1|1|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN rep|rep|NN 2|2|CD
wt|wt|JJ anaerobic|anaerobic|NN plus|plus|CC NO3|no3|NN rep|rep|NN 3|3|CD
wt|wt|JJ anaerobic|anaerobic|JJ rep|rep|NN 1|1|CD
wt|wt|JJ anaerobic|anaerobic|JJ rep|rep|NN 2|2|CD
wt|wt|JJ anaerobic|anaerobic|JJ rep|rep|NN 3|3|CD
WT|wt|JJ _|_|CD Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|CD A|a|DT _|_|NN Tag|tag|NN _|_|CD Count.txt|count.txt|NN :|:|: U00096|u00096|NN .2|.2|NN
WT|wt|VBD _|_|CD Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|CD A|a|DT _|_|NN WIG.wig|wig.wig|NN :|:|: U00096|u00096|NN .2|.2|NN
WT|wt|VBD _|_|CD Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|NN B|b|NN _|_|CD Tag|tag|NN _|_|CD Count.txt|count.txt|NN :|:|: U00096|u00096|NN .2|.2|NN
WT|wt|VBD _|_|CD Anaerobic|anaerobic|JJ _|_|NN RNAseq|rnaseq|NN _|_|NN B|b|NN _|_|CD WIG.wig|wig.wig|NN :|:|: U00096|u00096|NN .2|.2|NN
WTA|WTA|NNP _|_|SYM time0|time0|CD
WTA|WTA|NNP _|_|SYM time10|time10|CD
WTA|WTA|NNP _|_|SYM time20|time20|CD
WTA|WTA|NNP _|_|SYM time2|time2|CD .5|.5|CD
WTA|WTA|NNP _|_|SYM time5|time5|CD
WTA|WTA|NNP _|_|SYM time7|time7|CD .5|.5|CD
wt|wt|JJ at|at|IN T0|t0|NN
wt|wt|JJ at|at|IN T1h|t1h|NN
wt|wt|JJ at|at|IN T4h|t4h|NN
WTB1|wtb1|NN
WTB|wtb|NN _|_|CD time0|time0|NN
WTB|wtb|NN _|_|CD time2|time2|NN .5|.5|CD
WTB|wtb|NN _|_|SYM time7|time7|CD .5|.5|CD
WTC3|wtc3|NN
WT|wt|JJ cells|cell|NNS were|be|VBD treated|treat|VBN with|with|IN 10|10|CD mM|mm|NN Glycolaldehyde|glycolaldehyde|NN for|for|IN 30|30|CD min|min|NN whenever|whenever|WRB the|the|DT culture|culture|NN OD600nm|od600nm|NN reached|reach|VBD ~|~|NN 1|1|CD .|.|.
WT|WT|NNP _|_|NNP CPR|CPR|NNP _|_|SYM 1|1|CD
WT|wt|JJ _|_|NN CPR|CPR|NNP _|_|SYM 2|2|CD
WT|wt|JJ _|_|NN D|d|NN _|_|CD N1000|n1000|NN _|_|CD r1|r1|NN
WT|wt|JJ _|_|NN D|d|NN _|_|CD N1000|n1000|NN _|_|CD r2|r2|NN
wt|wt|JJ E.|e.|FW coli|coli|FW ,|,|, after|after|IN butanol|butanol|NN treatment|treatment|NN
wt|wt|JJ E.|e.|FW coli|coli|FW ,|,|, before|before|IN butanol|butanol|NN treatment|treatment|NN
wt|wt|JJ _|_|NN EE|ee|NN _|_|NN 1|1|CD
wt|wt|JJ _|_|NN EE|ee|NN _|_|NN 2|2|CD
WT|wt|JJ _|_|NN exp1|exp1|NN _|_|NN mRNA|mrna|NN
WT|wt|JJ _|_|NN exp1|exp1|NN _|_|NN ribosome|ribosome|NN
WT|wt|JJ _|_|NN exp2|exp2|NN _|_|NN mRNA|mrna|NN
WT|wt|JJ _|_|NN exp2|exp2|NN _|_|NN ribosome|ribosome|NN
WT|wt|JJ _|_|NN exp3|exp3|NN _|_|NN mRNA|mrna|NN
WT|wt|JJ _|_|NN exp3|exp3|NN _|_|NN ribosome|ribosome|NN
WT|wt|JJ _|_|NN exp4|exp4|NN _|_|NN mRNA|mrna|NN
WT|wt|JJ _|_|NN exp4|exp4|NN _|_|CD ribosome|ribosome|NN
WT|WT|NNP exp|exp|NN mRNA|mrna|NN
WT|wt|JJ exp|exp|NN RPF|rpf|NN
WT|wt|JJ _|_|NN fructose|fructose|NN
WT|wt|JJ fructose|fructose|NN 1|1|CD
WT|wt|JJ fructose|fructose|NN 2|2|CD
WT|wt|JJ _|_|NN glucose|glucose|NN
WT|wt|JJ glucose|glucose|NN 1|1|CD
WT|wt|JJ glucose|glucose|NN 2|2|CD
WT|wt|JJ _|_|NN glucose|glucose|NN _|_|CD log|log|NN
WT|wt|JJ _|_|NN glucose|glucose|NN _|_|CD log|log|NN _|_|CD TEX|TEX|NNP
WT-glucose-Rep1|wt-glucose-rep1|NN
WT-glucose-Rep2|wt-glucose-rep2|NN
WT|wt|JJ glucose|glucose|NN _|_|NN replicate1|replicate1|NN
WT|wt|JJ glucose|glucose|NN _|_|NN replicate2|replicate2|NN
WT|wt|JJ glucose|glucose|NN _|_|NN replicate3|replicate3|NN
WT|wt|JJ _|_|NN glucose|glucose|NN _|_|CD stat|stat|NN
WT|wt|JJ _|_|NN glucose|glucose|NN _|_|CD stat|stat|NN _|_|CD TEX|TEX|NNP
WT|WT|NNP _|_|NNP glycerol|glycerol|NN _|_|CD replicate1|replicate1|NN
WT|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD replicate2|replicate2|NN
WT|wt|JJ _|_|NN glycerol|glycerol|NN _|_|CD replicate3|replicate3|NN
WT|wt|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD 0C|0c|NN Mid|Mid|NNP Log|Log|NNP 6.0|6.0|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1.5|1.5|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3|3|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6.0|6.0|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN 40|40|CD mM|mm|NN Succinate|succinate|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- vs|vs|CC Eno|eno|NN -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP A|A|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- vs|vs|CC Eno|eno|NN -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP B|B|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- vs|vs|CC Eno|eno|NN -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP A1|a1|NN
WT|wt|NN -LRB-|-lrb-|-LRB- K10|k10|NN -RRB-|-rrb-|-RRB- vs|vs|CC Eno|eno|NN -|-|: -LRB-|-lrb-|-LRB- DF261|df261|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN ,|,|, 40|40|CD mM|mm|NN Suc|suc|NN .|.|. at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP B1|b1|NN
WTKasRep1|wtkasrep1|NN _|_|NN 0|0|CD min|min|NN
WTKasRep1|wtkasrep1|NN _|_|CD 15|15|CD min|min|NN
WTKasRep1|wtkasrep1|NN _|_|CD 20|20|CD min|min|NN
WTKasRep1|wtkasrep1|NN _|_|NN 2|2|CD min|min|NN
WTKasRep1|wtkasrep1|NN _|_|CD 4|4|CD min|min|NN
WTKasRep1|wtkasrep1|NN _|_|CD 6|6|CD min|min|NN
WTKasRep1|wtkasrep1|NN _|_|CD 8|8|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|NN 0|0|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|CD 10|10|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|CD 15|15|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|CD 20|20|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|NN 2|2|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|CD 4|4|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|CD 6|6|CD min|min|NN
WTKasRep2|wtkasrep2|NN _|_|CD 8|8|CD min|min|NN
WT|wt|SYM -|-|: Keio|Keio|NNP Sample|Sample|NNP 1|1|CD
WT|wt|SYM -|-|: Keio|Keio|NNP Sample|Sample|NNP 20|20|CD
WT|wt|SYM -|-|: Keio|Keio|NNP Sample|Sample|NNP 39|39|CD
wt|wt|JJ +|+|CC Leu|leu|NN vs.|vs.|CC wt|wt|JJ -|-|: Leu|leu|NN
wt|wt|JJ _|_|NN LS|ls|NN _|_|NN 1|1|CD
wt|wt|JJ _|_|NN LS|ls|NN _|_|NN 2|2|CD
WT|wt|NN +|+|CC L-trp|l-trp|JJ
WT-mannose|wt-mannose|NN
wt|wt|JJ _|_|CD ME|me|NN _|_|NN 1|1|CD
wt|wt|JJ _|_|CD ME|me|NN _|_|NN 2|2|CD
WT|wt|JJ _|_|NN minimal|minimal|JJ _|_|NN mRNA|mrna|NN
WT|wt|JJ _|_|NN minimal|minimal|JJ _|_|NN ribosome|ribosome|NN
WT|wt|JJ _|_|NN minus|minus|CC _|_|SYM 2DG|2dg|CD _|_|NN 1|1|CD
WT|wt|JJ _|_|NN minus|minus|CC _|_|SYM 2DG|2dg|CD _|_|NN 2|2|CD
WT|wt|JJ _|_|NN minus|minus|CC _|_|SYM 2DG|2dg|CD _|_|SYM 3|3|CD
WT-mucus-P1|wt-mucus-p1|NN
WT-mucus-P2|wt-mucus-p2|NN
WT|wt|JJ _|_|NN N0000|n0000|NN _|_|CD r1|r1|NN
WT|wt|JJ _|_|NN N0000|n0000|NN _|_|CD r2|r2|NN
WT|wt|JJ _|_|SYM N0025|n0025|CD _|_|SYM r1|r1|FW
WT|wt|FW _|_|SYM N0025|n0025|CD _|_|CD r2|r2|NN
WT|wt|JJ _|_|NN N0050|n0050|NN _|_|CD r1|r1|NN
WT|wt|JJ _|_|NN N0050|n0050|NN _|_|CD r2|r2|NN
WT|wt|JJ _|_|NN N0075|n0075|NN _|_|CD r1|r1|NN
WT|wt|JJ _|_|NN N0075|n0075|NN _|_|CD r2|r2|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1.5|1.5|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3.0|3.0|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3|3|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6|6|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6|6|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP A2|a2|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP B2|b2|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC Pnp|pnp|NN -|-|: -LRB-|-lrb-|-LRB- YHC012|yhc012|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP C2|c2|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP A|A|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP A1|a1|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP B|B|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP B1|b1|NN
WT|wt|NN -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP C|C|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- N3433|n3433|NN -RRB-|-rrb-|-RRB- vs|vs|CC RhlB|rhlb|NN -|-|: -LRB-|-lrb-|-LRB- SU02|su02|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP C1|c1|NN
WT|wt|JJ NaCl|nacl|NN 1|1|CD
WT|wt|JJ NaCl|nacl|NN 2|2|CD
WT|wt|JJ NO3|no3|NN 1|1|CD
WT|wt|JJ NO3|no3|NN 2|2|CD
WT|wt|JJ NO3|no3|NN w/propionate|w/propionate|NN 1|1|CD
WT|wt|JJ NO3|no3|NN w/propionate|w/propionate|NN 2|2|CD
WT|wt|JJ _|_|NN noCPR|nocpr|NN _|_|NN 1|1|CD
WT|wt|JJ _|_|NN noCPR|nocpr|NN _|_|NN 2|2|CD
WT|wt|JJ _|_|NN N|n|NN _|_|CD strv|strv|NN
WT|wt|JJ _|_|NN N|n|NN _|_|CD strv|strv|NN _|_|CD TEX|TEX|NNP
WT|wt|SYM -|-|: O2|o2|CD
WT|wt|SYM -|-|: O2|o2|CD 1|1|CD
WT|wt|NN +|+|CC O2|o2|CD 1|1|CD
WT|wt|NN O2|o2|CD 1|1|CD
WT|wt|SYM -|-|: O2|o2|CD 2|2|CD
WT|wt|NN +|+|CC O2|o2|CD 2|2|CD
WT|WT|NNP O2|o2|CD 2|2|CD
WT|wt|SYM -|-|: O2|o2|CD 3|3|CD
WT|wt|NN +|+|CC O2|o2|CD 3|3|CD
WT|wt|NN O2|o2|CD w/propionate|w/propionate|NN 1|1|CD
WT|wt|NN O2|o2|CD w/propionate|w/propionate|NN 2|2|CD
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: P2-08|p2-08|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: P2-51|p2-51|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: P2-58|p2-58|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: P2-66|p2-66|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: P2-77|p2-77|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: PF2-04|pf2-04|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: PF2-08|pf2-08|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: PF2-12|pf2-12|NN
wt|wt|JJ or|or|CC mutant|mutant|JJ :|:|: WT|WT|NNP @|@|SYM 0.8|0.8|CD %|%|NN But|but|CC
WT|WT|NNP pH5|ph5|NN .5|.5|CD
WT|wt|JJ pH5|ph5|NN .5|.5|CD 1|1|CD
WT|wt|JJ pH5|ph5|NN .5|.5|NN 2|2|CD
WT|WT|NNP pH|ph|NN 5.6|5.6|CD A|a|DT
WT|wt|NN pH|ph|NN 5.6|5.6|CD B|b|NN
WT|wt|NN pH|ph|NN 5.6|5.6|CD C|c|NN
WT|wt|JJ pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN A|a|NN
WT|wt|JJ pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN B|b|NN
WT|wt|JJ pH|ph|NN 7.2|7.2|CD +15|+15|CD %|%|NN sucrose|sucrose|NN C|c|NN
WT|wt|JJ _|_|NN plus|plus|CC _|_|SYM 2DG|2dg|CD _|_|NN 1|1|CD
WT|wt|JJ _|_|NN plus|plus|CC _|_|SYM 2DG|2dg|CD _|_|NN 2|2|CD
WT|wt|JJ _|_|NN plus|plus|CC _|_|SYM 2DG|2dg|CD _|_|SYM 3|3|CD
WT|WT|NNP PQ|PQ|NNP
WT|WT|NNP PQ|PQ|NNP 1|1|CD
WT|WT|NNP PQ|PQ|NNP 2|2|CD
WT|WT|NNP rep1|rep1|NN
WT|wt|JJ rep|rep|NN 1|1|CD
WTRep1|wtrep1|NN _|_|NN 0|0|CD min|min|NN
WTRep1|wtrep1|NN _|_|CD 10|10|CD min|min|NN
WTRep1|wtrep1|NN _|_|CD 15|15|CD min|min|NN
WTRep1|wtrep1|NN _|_|CD 20|20|CD min|min|NN
WTRep1|wtrep1|NN _|_|NN 2|2|CD min|min|NN
WTRep1|wtrep1|NN _|_|CD 4|4|CD min|min|NN
WTRep1|wtrep1|NN _|_|CD 6|6|CD min|min|NN
WTRep1|wtrep1|NN _|_|CD 8|8|CD min|min|NN
wt.rep1.ee|wt.rep1.ee|NN
wt.rep1.me|wt.rep1.me|NN
WT|wt|JJ rep2|rep2|NN
WT|wt|JJ rep|rep|NN 2|2|CD
WTRep2|wtrep2|NN _|_|NN 0|0|CD min|min|NN
WTRep2|wtrep2|NN _|_|CD 10|10|CD min|min|NN
WTRep2|wtrep2|NN _|_|CD 15|15|CD min|min|NN
WTRep2|wtrep2|NN _|_|CD 20|20|CD min|min|NN
WTRep2|wtrep2|NN _|_|NN 2|2|CD min|min|NN
WTRep2|wtrep2|NN _|_|CD 4|4|CD min|min|NN
WTRep2|wtrep2|NN _|_|CD 6|6|CD min|min|NN
WTRep2|wtrep2|NN _|_|CD 8|8|CD min|min|NN
wt.rep2.ee|wt.rep2.ee|NN
wt.rep2.me|wt.rep2.me|NN
WT|wt|JJ rep3|rep3|NN
WT|wt|JJ rep|rep|NN 3|3|CD
WT|wt|JJ _|_|NN RNA-Seq|rna-seq|NN
wt|wt|JJ _|_|NN S|s|NN _|_|NN 1|1|CD
wt|wt|JJ _|_|NN S|s|NN _|_|NN 2|2|CD
WT|wt|NN -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 1.5|1.5|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 3|3|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 4.5|4.5|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP 6|6|CD '|'|'' post|post|JJ rif|rif|NN
WT|wt|NN -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- vs|vs|CC N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- vs|vs|CC N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP A|A|NNP
WT|WT|NNP -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- vs|vs|CC N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|trial|NN B|b|NN
WT|wt|NN -LRB-|-lrb-|-LRB- SH3208|sh3208|NN -RRB-|-rrb-|-RRB- vs|vs|CC N-RNaseE|n-rnasee|NN -LRB-|-lrb-|-LRB- BZ453|bz453|NN -RRB-|-rrb-|-RRB- in|in|IN M9|m9|NN +|+|CC 0.2|0.2|CD %|%|NN Glycerol|glycerol|NN ,|,|, 0.2|0.2|CD %|%|NN Tryptone|tryptone|NN at|at|IN 30|30|CD C|c|NN Mid|Mid|NNP Log|Log|NNP Trial|Trial|NNP C|C|NNP
WT|WT|NNP strain|strain|NN treated|treat|VBN with|with|IN glycolaldehyde|glycolaldehyde|NN first|first|JJ repetition|repetition|NN
WT|wt|JJ strain|strain|NN treated|treat|VBN with|with|IN glycolaldehyde|glycolaldehyde|NN second|second|JJ repetition|repetition|NN
WT|wt|JJ strain|strain|NN treated|treat|VBN with|with|IN glycolaldehyde|glycolaldehyde|NN third|third|JJ repetition|repetition|NN
WT|wt|JJ strain|strain|NN without|without|IN glycolaldehyde|glycolaldehyde|NN first|first|JJ repetition|repetition|NN
WT|wt|JJ strain|strain|NN without|without|IN glycolaldehyde|glycolaldehyde|NN second|second|JJ repetition|repetition|NN
WT|wt|JJ strain|strain|NN without|without|IN glycolaldehyde|glycolaldehyde|NN third|third|JJ repetition|repetition|NN
wt|wt|JJ _|_|NN T|t|NN _|_|NN 1|1|CD
wt|wt|JJ _|_|NN T|t|NN _|_|NN 2|2|CD
wt|wt|JJ _|_|NN T|t|NN _|_|CD 3|3|CD
wt|wt|JJ +|+|CC trp|trp|NN vs.|vs.|NN -|-|: trp|trp|NN ,|,|, min|min|NN +.2|+.2|CD %|%|NN glucose|glucose|NN ,|,|, W3110|w3110|NN
wt|wt|JJ _|_|NN TS|ts|NN _|_|NN 1|1|CD
wt|wt|JJ _|_|NN TS|ts|NN _|_|NN 2|2|CD
wt|wt|JJ _|_|NN un|un|NN _|_|NN 1|1|CD
wt|wt|JJ _|_|NN un|un|NN _|_|NN 2|2|CD
wt|wt|JJ _|_|NN un|un|NN _|_|NN 3|3|CD
WT|wt|JJ UvsW|uvsw|NN _|_|NN replicate1|replicate1|NN
WT|wt|JJ UvsW|uvsw|NN _|_|NN replicate2|replicate2|NN
WT|wt|JJ UvsW|uvsw|NN _|_|NN replicate3|replicate3|NN
WT|wt|VBD _|_|CD vs|vs|CC _|_|CD dcd|dcd|NN
WT|wt|VBD _|_|CD vs|vs|CC _|_|CD ndk|ndk|NN
WT|wt|VBD _|_|CD vs|vs|CC _|_|CD recA730|reca730|NN
WT|wt|NN with|with|IN DPD|dpd|NN 1|1|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
WT|wt|NN with|with|IN DPD|dpd|NN 2|2|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
WT|wt|NN with|with|IN Fe|Fe|NNP 1|1|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
WT|wt|NN with|with|IN Fe|Fe|NNP 2|2|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
wzc|wzc|NN KO|ko|NN LB|lb|NN rep1|rep1|NN
wzc|wzc|NN KO|ko|NN LB|lb|NN rep2|rep2|NN
wzc|wzc|NN KO|ko|NN M9|m9|NN rep1|rep1|NN
wzc|wzc|NN KO|ko|NN M9|m9|NN rep2|rep2|NN
X515|x515|NN _|_|CD V1|v1|NN _|_|CD T4|t4|NN _|_|CD 424287A03|424287a03|NN
X515|x515|NN _|_|CD V1|v1|NN _|_|CD T4|t4|NN _|_|CD 475655A02|475655a02|NN
X515|x515|NN _|_|CD V1|v1|NN _|_|CD T6|t6|NN _|_|CD 475649A04s|475649a04|NNS
X515|x515|NN _|_|CD V1|v1|NN _|_|CD T7|t7|NN _|_|CD 475654A02|475654a02|NN
X515|x515|NN _|_|CD V1|v1|NN _|_|CD T8|t8|NN _|_|CD 475585A04|475585a04|NN
X515|x515|NN _|_|CD V2|v2|NN _|_|CD T4|t4|NN _|_|CD 424219A04|424219a04|NN
X515|x515|NN _|_|CD V2|v2|NN _|_|CD T4|t4|NN _|_|CD 475655A03|475655a03|NN
X515|x515|NN _|_|CD V2|v2|NN _|_|CD T6|t6|NN _|_|CD 475644A04|475644a04|NN
X515|x515|NN _|_|CD V2|v2|NN _|_|CD T7|t7|NN _|_|CD 475649A01|475649a01|NN
X515|x515|NN _|_|CD V2|v2|NN _|_|CD T8|t8|NN _|_|CD 424219A01s|424219a01|NNS
X515|x515|NN _|_|CD V3|v3|NN _|_|CD T4|t4|NN _|_|CD 475585A02s|475585a02|NNS
X515|x515|NN _|_|CD V3|v3|NN _|_|CD T6|t6|NN _|_|CD 424221A04|424221a04|NN
X515|x515|NN _|_|CD V3|v3|NN _|_|CD T7|t7|NN _|_|CD 475649A02|475649a02|NN
X515|x515|NN _|_|CD V3|v3|NN _|_|CD T8|t8|NN _|_|CD 475641A04|475641a04|NN
X515|x515|NN _|_|CD V4|v4|NN _|_|CD T4|t4|NN _|_|CD 475585A03|475585a03|NN
X515|x515|NN _|_|CD V4|v4|NN _|_|CD T4|t4|NN _|_|CD 475644A01|475644a01|NN
X515|x515|NN _|_|CD V4|v4|NN _|_|CD T6|t6|NN _|_|CD 424221A03|424221a03|NN
X515|x515|NN _|_|CD V4|v4|NN _|_|CD T7|t7|NN _|_|CD 424287A04|424287a04|NN
X515|x515|NN _|_|CD V4|v4|NN _|_|CD T8|t8|NN _|_|CD 475655A04|475655a04|NN
X520|x520|NN _|_|CD V1|v1|NN _|_|CD T4|t4|NN _|_|CD 424221A01|424221a01|NN
X520|x520|NN _|_|CD V1|v1|NN _|_|CD T6|t6|NN _|_|CD 475649A03|475649a03|NN
X520|x520|NN _|_|CD V1|v1|NN _|_|CD T7|t7|NN _|_|CD 475655A01|475655a01|NN
X520|x520|NN _|_|CD V1|v1|NN _|_|CD T8|t8|NN _|_|CD 475641A01|475641a01|NN
X520|x520|NN _|_|CD V2|v2|NN _|_|CD T3|t3|NN _|_|CD 424221A02|424221a02|NN
X520|x520|NN _|_|CD V2|v2|NN _|_|CD T4|t4|NN _|_|CD 475641A03|475641a03|NN
X520|x520|NN _|_|CD V2|v2|NN _|_|CD T6|t6|NN _|_|CD 424287A02|424287a02|NN
X520|x520|NN _|_|CD V2|v2|NN _|_|CD T7|t7|NN _|_|CD 475654A01|475654a01|NN
X520|x520|NN _|_|CD V2|v2|NN _|_|CD T8|t8|NN _|_|CD 424219A02|424219a02|NN
X520|x520|NN _|_|CD V3|v3|NN _|_|CD T4|t4|NN _|_|CD 475654A04|475654a04|NN
X520|x520|NN _|_|CD V3|v3|NN _|_|CD T6|t6|NN _|_|CD 475641A02|475641a02|NN
X520|x520|NN _|_|CD V3|v3|NN _|_|CD T7|t7|NN _|_|CD 475644A02s|475644a02|NNS
X520|x520|NN _|_|CD V3|v3|NN _|_|CD T8|t8|NN _|_|CD 424219A03|424219a03|NN
X520|x520|NN _|_|CD V4|v4|NN _|_|CD T4|t4|NN _|_|CD 475654A03|475654a03|NN
X520|x520|NN _|_|CD V4|v4|NN _|_|CD T6|t6|NN _|_|CD 424287A01|424287a01|NN
X520|x520|NN _|_|CD V4|v4|NN _|_|CD T7|t7|NN _|_|CD 475644A03|475644a03|NN
X520|x520|NN _|_|CD V4|v4|NN _|_|CD T8|t8|NN _|_|CD 475585A01|475585a01|NN
Xpression|xpression|NN -LRB-|-lrb-|-LRB- https://depts.washington.edu/cshlab/html/rnaseq.html|https://depts.washington.edu/cshlab/html/rnaseq.html|NN -RRB-|-rrb-|-RRB- was|be|VBD used|use|VBN for|for|IN RNA-Seq|rna-seq|NN data|datum|NNS processing|processing|NN .|.|.
Xpression|xpression|NN was|be|VBD used|use|VBN for|for|IN filtering|filter|VBG and|and|CC trimming|trim|VBG reads|read|VBZ .|.|.
Xuzhou21|xuzhou21|NN cured|cure|VBD of|of|IN the|the|DT pO157|po157|NN _|_|NN Sal|sal|NN plasmid|plasmid|NN
yajL|yajl|NN mutant|mutant|NN -LRB-|-lrb-|-LRB- genetic|genetic|JJ background|background|NN MG1655|mg1655|NN -RRB-|-rrb-|-RRB-
year|year|NN :|:|: 2000|2000|CD
year|year|NN :|:|: 2001|2001|CD
year|year|NN :|:|: 2003|2003|CD
year|year|NN :|:|: 2004|2004|CD
year|year|NN :|:|: 2005|2005|CD
year|year|NN :|:|: 2006|2006|CD
year|year|NN :|:|: 2007|2007|CD
year|year|NN :|:|: 2008|2008|CD
yebF|yebf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
yebF|yebf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
yebF|yebf|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
yebF|yebf|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
yghD|yghd|NN KO|ko|NN LB|lb|NN rep1|rep1|NN
yghD|yghd|NN KO|ko|NN LB|lb|NN rep2|rep2|NN
yghD|yghd|NN KO|ko|NN M9|m9|NN rep1|rep1|NN
yghD|yghd|NN KO|ko|NN M9|m9|NN rep2|rep2|NN
yoeB|yoeb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
yoeB|yoeb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r2|r2|NN
yoeB|yoeb|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
yoeB|yoeb|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD mg/mL|mg/ml|NN norfloxacin|norfloxacin|NN
yPileup|ypileup|NN was|be|VBD used|use|VBN to|to|TO generate|generate|VB count|count|NN data|datum|NNS for|for|IN the|the|DT whole|whole|JJ genome|genome|NN -|-|: Example|example|NN :|:|: pyPileup.py|pypileup.py|NN --|--|: file|file|NN _|_|NN type|type|NN =|=|JJ novo|novo|FW -|-|: f|f|LS DL4184.novo|dl4184.novo|NN --|--|: tab|tab|NN =|=|JJ NC000913|nc000913|NN .3|.3|NN .|.|. tab|tab|NN --|--|: chr|chr|NN =|=|JJ Wholechom.txt|wholechom.txt|NN --|--|: ignorestrand|ignorestrand|JJ
yPileup|ypileup|NN was|be|VBD used|use|VBN to|to|TO generate|generate|VB count|count|NN data|datum|NNS for|for|IN the|the|DT whole|whole|JJ genome|genome|NN -|-|: Example|example|NN :|:|: pyPileup.py|pypileup.py|NN --|--|: file|file|NN _|_|NN type|type|NN =|=|JJ novo|novo|FW -|-|: f|f|LS DL4900.novo|dl4900.novo|NN --|--|: tab|tab|NN =|=|JJ NC000913|nc000913|NN .3|.3|NN .|.|. tab|tab|NN --|--|: chr|chr|NN =|=|JJ Wholechom.txt.gz|wholechom.txt.gz|NN --|--|: ignorestrand|ignorestrand|JJ
zipA|zipa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|VBD r1|r1|NN
zipA|zipa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r2|r2|FW
zipA|zipa|NN __|__|CD U|U|NNP _|_|NNP N0075|N0075|NNP _|_|SYM r3|r3|FW
zipA|zipa|NN upregulation|upregulation|NN ,|,|, 0.075|0.075|CD ug/ml|ug/ml|NN norfloxacin|norfloxacin|NN
zi|zi|NN =|=|JJ -LRB-|-lrb-|-LRB- Ri|Ri|NNP --|--|: mean|mean|NN -LRB-|-lrb-|-LRB- R|r|NN -RRB-|-rrb-|-RRB- -RRB-|-rrb-|-RRB- /|/|: sd|sd|NN -LRB-|-lrb-|-LRB- R|r|NN -RRB-|-rrb-|-RRB- ,|,|, where|where|WRB zi|zi|NN is|be|VBZ the|the|DT z-score|z-score|NN for|for|IN each|each|DT element|element|NN ,|,|, Ri|Ri|NNP is|be|VBZ the|the|DT log-ratio|log-ratio|NN for|for|IN each|each|DT element|element|NN ,|,|, and|and|CC sd|sd|NN -LRB-|-lrb-|-LRB- R|r|NN -RRB-|-rrb-|-RRB- is|be|VBZ the|the|DT standard|standard|JJ deviation|deviation|NN of|of|IN the|the|DT log-ratio|log-ratio|NN .|.|. With|with|IN this|this|DT criterion|criterion|NN ,|,|, the|the|DT elements|element|NNS with|with|IN a|a|DT z-score|z-score|NN >|>|RBR 2|2|CD standard|standard|JJ deviations|deviation|NNS would|would|MD be|be|VB the|the|DT significantly|significantly|RB differentially|differentially|RB expressed|express|VBN genes|gene|NNS .|.|.
Zn-depleted|zn-depleted|JJ custom-built|custom-built|JJ chemostats|chemostat|NNS were|be|VBD grown|grow|VBN for|for|IN 50|50|CD h|h|NN .|.|. At|at|IN this|this|DT point|point|NN ,|,|, ZnSO4|znso4|NN .7|.7|CD H2O|h2o|NN in|in|IN water|water|NN was|be|VBD added|add|VBN to|to|TO a|a|DT final|final|JJ concentration|concentration|NN of|of|IN 0.2|0.2|CD M|m|NN in|in|IN the|the|DT chemostat|chemostat|NN .|.|. A|a|DT 10|10|CD ml|ml|NN sample|sample|NN of|of|IN culture|culture|NN was|be|VBD taken|take|VBN using|use|VBG a|a|DT polypropylene|polypropylene|NN pipette|pipette|NN tip|tip|NN immediately|immediately|RB prior|prior|RB to|to|TO Zn|zn|NN addition|addition|NN and|and|CC 2.5|2.5|CD ,|,|, 7|7|CD ,|,|, 10|10|CD and|and|CC 30|30|CD min|min|NN after|after|IN addition|addition|NN .|.|. The|the|DT culture|culture|NN was|be|VBD pipetted|pipet|VBN directly|directly|RB into|into|IN RNAprotect|rnaprotect|NN -LRB-|-lrb-|-LRB- Qiagen|qiagen|NN -RRB-|-rrb-|-RRB- to|to|TO stabilize|stabilize|VB RNA|rna|NN .|.|. Total|total|JJ RNA|rna|NN was|be|VBD purified|purify|VBN using|use|VBG Qiagen|Qiagen|NNP 's|'s|POS RNeasy|RNeasy|NNP Mini|Mini|NNP kit|kit|NN as|as|IN recommended|recommend|VBN by|by|IN the|the|DT suppliers|supplier|NNS .|.|. RNA|rna|NN was|be|VBD quantified|quantify|VBN using|use|VBG a|a|DT BioPhotometer|biophotometer|NN -LRB-|-lrb-|-LRB- Eppendorf|eppendorf|NN -RRB-|-rrb-|-RRB- .|.|. A|a|DT control|control|NN experiment|experiment|NN was|be|VBD carried|carry|VBN out|out|RP in|in|IN which|which|WDT water|water|NN was|be|VBD added|add|VBN .|.|.
∆|∆|SYM zwf|zwf|FW parent|parent|NN Sample|sample|NN 2|2|CD
∆|∆|CD zwf|zwf|NN parent|parent|NN Sample|sample|NN 21|21|CD
∆|∆|CD zwf|zwf|NN parent|parent|NN Sample|Sample|NNP 40|40|CD
zwf|zwf|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 22|22|CD
zwf|zwf|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 3|3|CD
zwf|zwf|NN suppressor|suppressor|NN 1-1|1-1|CD Sample|sample|NN 41|41|CD
zwf|zwf|NN suppressor|suppressor|NN 1-2|1-2|CD Sample|sample|NN 23|23|CD
zwf|zwf|NN suppressor|suppressor|NN 1-2|1-2|CD Sample|sample|NN 4|4|CD
zwf|zwf|NN suppressor|suppressor|NN 1-2|1-2|CD Sample|sample|NN 42|42|CD
ΔbolA|δbola|NN
Δcra|δcra|NN _|_|NN acetate|acetate|NN
Δcra|δcra|NN acetate|acetate|NN 1|1|CD
Δcra|δcra|NN acetate|acetate|NN 2|2|CD
Δcra|δcra|NN _|_|NN fructose|fructose|NN
Δcra|δcra|NN fructose|fructose|NN 1|1|CD
Δcra|δcra|NN fructose|fructose|NN 2|2|CD
Δcra|δcra|NN _|_|NN glucose|glucose|NN
Δcra|δcra|NN glucose|glucose|NN 1|1|CD
Δcra|δcra|NN glucose|glucose|NN 2|2|CD
Δfur|δfur|NN with|with|IN DPD|dpd|NN 1|1|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
Δfur|δfur|NN with|with|IN DPD|dpd|NN 2|2|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
Δfur|δfur|NN with|with|IN Fe|Fe|NNP 1|1|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
Δfur|δfur|NN with|with|IN Fe|Fe|NNP 2|2|CD -LRB-|-lrb-|-LRB- RNA-seq|rna-seq|NN -RRB-|-rrb-|-RRB-
ΔgadE|δgade|NN pH5|ph5|NN .5|.5|CD
ΔgadE|δgade|NN pH5|ph5|NN .5|.5|CD 1|1|CD
ΔgadE|δgade|NN pH5|ph5|NN .5|.5|CD 2|2|CD
ΔgadW|δgadw|NN pH5|ph5|NN .5|.5|CD
ΔgadW|δgadw|NN pH5|ph5|NN .5|.5|CD 1|1|CD
ΔgadW|δgadw|NN pH5|ph5|NN .5|.5|CD 2|2|CD
ΔgadX|δgadx|NN pH5|ph5|NN .5|.5|CD
ΔgadX|δgadx|NN pH5|ph5|NN .5|.5|CD 1|1|CD
ΔgadX|δgadx|NN pH5|ph5|NN .5|.5|CD 2|2|CD
ΔompR|δompr|NN NaCl|nacl|NN 1|1|CD
ΔompR|δompr|NN NaCl|nacl|NN 2|2|CD
ΔoxyR|δoxyr|NN PQ|pq|NN
ΔoxyR|δoxyr|NN PQ|pq|NN 1|1|CD
ΔoxyR|δoxyr|NN PQ|pq|NN 2|2|CD
Δrac|δrac|JJ
Δrac|δrac|NN 1|1|CD
Δrac|δrac|NN 2|2|CD
Δrac|δrac|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN
Δrac|δrac|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN 1|1|CD
Δrac|δrac|NN +|+|CC 20|20|CD ug/ml|ug/ml|NN bicyclomycin|bicyclomycin|NN 2|2|CD
Δrac|δrac|NN ΔnusG|δnusg|NN
Δrac|δrac|NN ΔnusG|δnusg|NN 1|1|CD
Δrac|δrac|NN ΔnusG|δnusg|NN 2|2|CD
ΔsoxR|δsoxr|NN PQ|pq|NN
ΔsoxR|δsoxr|NN PQ|pq|NN 1|1|CD
ΔsoxR|δsoxr|NN PQ|pq|NN 2|2|CD
ΔsoxS|δsoxs|NN PQ|pq|NN
ΔsoxS|δsoxs|VBZ PQ|pq|NN 1|1|CD
ΔsoxS|δsoxs|NN PQ|pq|NN 2|2|CD
σ32|σ32|NN 30|30|CD °C|°c|NN rep1|rep1|NN
σ32|σ32|NN 30|30|CD °C|°c|NN rep2|rep2|NN
σ32|σ32|NN 30|30|CD °C|°c|NN short|short|JJ RNase|rnase|NN
σ32|σ32|NN 43|43|CD °C|°c|NN rep1|rep1|NN
σ32|σ32|NN 43|43|CD °C|°c|NN rep2|rep2|NN
σ32|σ32|NN 43|43|CD °C|°c|NN short|short|JJ RNase|rnase|NN
σ32|σ32|NN ChIP|chip|NN DNA|dna|NN ,|,|, control|control|NN
σ32|σ32|NN ChIP|chip|NN DNA|dna|NN ,|,|, heat|heat|NN
σ32|σ32|NN ChIP|chip|NN DNA|dna|NN ,|,|, short|short|JJ RNase|rnase|NN digestion|digestion|NN
σ70|σ70|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Aerobic|Aerobic|NNP A|A|NNP
σ70|σ70|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Aerobic|Aerobic|NNP B|B|NNP
σ70|σ70|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Anaerobic|Anaerobic|NNP A|A|NNP
σ70|σ70|NN IP|IP|NNP ChIP-seq|ChIP-seq|NNP Anaerobic|anaerobic|JJ B|b|NN