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

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11678 11679 11680 11681 11682 11683 11684 11685 11686 11687 11688 11689 11690 11691 11692 11693 11694 11695 11696 11697 11698 11699 11700 11701 11702 11703 11704 11705 11706 11707 11708 11709 11710 11711 11712 11713 11714 11715 11716 11717 11718 11719 11720 11721 11722 11723 11724 11725 11726 11727 11728 11729 11730 11731 11732 11733 11734 11735 11736 11737 11738 11739 11740 11741 11742 11743 11744 11745 11746 11747 11748 11749 11750 11751 11752 11753 11754 11755 11756 11757 11758 11759 11760 11761 11762 11763 11764 11765 11766 11767 11768 11769 11770 11771 11772 11773 11774 11775 11776 11777 11778 11779 11780 11781 11782 11783 11784 11785 11786 11787 11788 11789 11790 11791 11792 11793 11794 11795 11796 11797 11798 11799 11800 11801 11802 11803 11804 11805 11806 11807 11808 11809 11810 11811 11812 11813 11814 11815 11816 11817 11818 11819 11820 11821 11822 11823 11824 11825 11826 11827 11828 11829 11830 11831 11832 11833 11834 11835 11836 11837 11838 11839 11840 11841 11842 11843 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 .|.|.
 \|\|SYM
 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
 C1|c1|NN
 C2|c2|NN
 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
 F1|f1|NN
 F2|f2|NN
 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
 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
 NA|NA|NNP
 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
 NC|nc|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
 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|JJ
 WT|WT|NNP
 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